1
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Hou K, Pan H, Shahpasand-Kroner H, Hu C, Abskharon R, Seidler P, Mekkittikul M, Balbirnie M, Lantz C, Sawaya MR, Dolinsky JL, Jones M, Zuo X, Loo JA, Frautschy S, Cole G, Eisenberg DS. D-peptide-magnetic nanoparticles fragment tau fibrils and rescue behavioral deficits in a mouse model of Alzheimer's disease. Sci Adv 2024; 10:eadl2991. [PMID: 38691615 PMCID: PMC11062580 DOI: 10.1126/sciadv.adl2991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/29/2024] [Indexed: 05/03/2024]
Abstract
Amyloid fibrils of tau are increasingly accepted as a cause of neuronal death and brain atrophy in Alzheimer's disease (AD). Diminishing tau aggregation is a promising strategy in the search for efficacious AD therapeutics. Previously, our laboratory designed a six-residue, nonnatural amino acid inhibitor D-TLKIVW peptide (6-DP), which can prevent tau aggregation in vitro. However, it cannot block cell-to-cell transmission of tau aggregation. Here, we find D-TLKIVWC (7-DP), a d-cysteine extension of 6-DP, not only prevents tau aggregation but also fragments tau fibrils extracted from AD brains to neutralize their seeding ability and protect neuronal cells from tau-induced toxicity. To facilitate the transport of 7-DP across the blood-brain barrier, we conjugated it to magnetic nanoparticles (MNPs). The MNPs-DP complex retains the inhibition and fragmentation properties of 7-DP alone. Ten weeks of MNPs-DP treatment appear to reverse neurological deficits in the PS19 mouse model of AD. This work offers a direction for development of therapies to target tau fibrils.
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Affiliation(s)
- Ke Hou
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Hope Pan
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Hedieh Shahpasand-Kroner
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Carolyn Hu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Romany Abskharon
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Paul Seidler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Marisa Mekkittikul
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Melinda Balbirnie
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Joshua L. Dolinsky
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Mychica Jones
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Xiaohong Zuo
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Sally Frautschy
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Greg Cole
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - David S. Eisenberg
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
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2
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Agdanowski MP, Castells-Graells R, Sawaya MR, Cascio D, Yeates TO, Arbing MA. X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. Acta Crystallogr F Struct Biol Commun 2024; 80:S2053230X2400414X. [PMID: 38767964 DOI: 10.1107/s2053230x2400414x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.
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Affiliation(s)
- Matthew P Agdanowski
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roger Castells-Graells
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mark A Arbing
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
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3
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Miller JE, Agdanowski MP, Dolinsky JL, Sawaya MR, Cascio D, Rodriguez JA, Yeates TO. AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography. Acta Crystallogr D Struct Biol 2024; 80:270-278. [PMID: 38451205 PMCID: PMC10994174 DOI: 10.1107/s205979832400072x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/19/2024] [Indexed: 03/08/2024] Open
Abstract
Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.
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Affiliation(s)
- Justin E. Miller
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew P. Agdanowski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua L. Dolinsky
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
| | - Jose A. Rodriguez
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
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4
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Hou K, Ge P, Sawaya MR, Dolinsky JL, Yang Y, Jiang YX, Lutter L, Boyer DR, Cheng X, Pi J, Zhang J, Lu J, Yang S, Yu Z, Feigon J, Eisenberg DS. How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer's disease brain by a strain-relief mechanism. bioRxiv 2024:2024.03.25.586668. [PMID: 38585812 PMCID: PMC10996594 DOI: 10.1101/2024.03.25.586668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer's disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC disassembles tau fibrils from AD brains (AD-tau) into benign segments with no energy source present beyond ambient thermal agitation. This disassembly by a short peptide was unexpected, given that AD-tau is sufficiently stable to withstand disassembly in boiling SDS detergent. To consider D peptide-mediated disassembly as a potential therapeutic for AD, it is essential to understand the mechanism and energy source of the disassembly action. We find assembly of D-peptides into amyloid-like fibrils is essential for tau fibril disassembly. Cryo-EM and atomic force microscopy reveal that these D-peptide fibrils have a right-handed twist and embrace tau fibrils which have a left-handed twist. In binding to the AD-tau fibril, the oppositely twisted D-peptide fibril produces a strain, which is relieved by disassembly of both fibrils. This strain-relief mechanism appears to operate in other examples of amyloid fibril disassembly and provides a new direction for the development of first-in-class therapeutics for amyloid diseases.
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5
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Meador K, Castells-Graells R, Aguirre R, Sawaya MR, Arbing MA, Sherman T, Senarathne C, Yeates TO. A suite of designed protein cages using machine learning and protein fragment-based protocols. Structure 2024:S0969-2126(24)00056-X. [PMID: 38513658 DOI: 10.1016/j.str.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/22/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational approaches to design a suite of tetrahedrally symmetric, self-assembling protein cages. For the generation of docked conformations, we emphasize a protein fragment-based approach, while for sequence design of the de novo interface, a comparison of knowledge-based and machine learning protocols highlights the power and increased experimental success achieved using ProteinMPNN. An analysis of design outcomes provides insights for improving interface design protocols, including prioritizing fragment-based motifs, balancing interface hydrophobicity and polarity, and identifying preferred polar contact patterns. In all, we report five structures for seven protein cages, along with two structures of intermediate assemblies, with the highest resolution reaching 2.0 Å using cryo-EM. This set of designed cages adds substantially to the body of available protein nanoparticles, and to methodologies for their creation.
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Affiliation(s)
- Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | | | - Roman Aguirre
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Mark A Arbing
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Trent Sherman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Chethaka Senarathne
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA.
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6
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Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska MI, Wydorski PM, Macierzyńska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak LA. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. Structure 2024:S0969-2126(24)00055-8. [PMID: 38508190 DOI: 10.1016/j.str.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/17/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
J-domain protein (JDP) molecular chaperones have emerged as central players that maintain a healthy proteome. The diverse members of the JDP family function as monomers/dimers and a small subset assemble into micron-sized oligomers. The oligomeric JDP members have eluded structural characterization due to their low-complexity, intrinsically disordered middle domains. This in turn, obscures the biological significance of these larger oligomers in protein folding processes. Here, we identified a short, aromatic motif within DNAJB8 that drives self-assembly through π-π stacking and determined its X-ray structure. We show that mutations in the motif disrupt DNAJB8 oligomerization in vitro and in cells. DNAJB8 variants that are unable to assemble bind to misfolded tau seeds more specifically and retain capacity to reduce protein aggregation in vitro and in cells. We propose a new model for DNAJB8 function in which the sequences in the low-complexity domains play distinct roles in assembly and substrate activity.
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Affiliation(s)
- Bryan D Ryder
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizaveta Ustyantseva
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - David R Boyer
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikołaj I Kuska
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paweł M Wydorski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paulina Macierzyńska
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nabil Morgan
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael R Sawaya
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Lu J, Ge P, Sawaya MR, Hughes MP, Boyer DR, Cao Q, Abskharon R, Cascio D, Tayeb-Fligelman E, Eisenberg DS. Cryo-EM structures of the D290V mutant of the hnRNPA2 low-complexity domain suggests how D290V affects phase separation and aggregation. J Biol Chem 2024; 300:105531. [PMID: 38072051 PMCID: PMC10844680 DOI: 10.1016/j.jbc.2023.105531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 02/02/2024] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2) is a human ribonucleoprotein that transports RNA to designated locations for translation via its ability to phase separate. Its mutated form, D290V, is implicated in multisystem proteinopathy known to afflict two families, mainly with myopathy and Paget's disease of bone. Here, we investigate this mutant form of hnRNPA2 by determining cryo-EM structures of the recombinant D290V low complexity domain. We find that the mutant form of hnRNPA2 differs from the WT fibrils in four ways. In contrast to the WT fibrils, the PY-nuclear localization signals in the fibril cores of all three mutant polymorphs are less accessible to chaperones. Also, the mutant fibrils are more stable than WT fibrils as judged by phase separation, thermal stability, and energetic calculations. Similar to other pathogenic amyloids, the mutant fibrils are polymorphic. Thus, these structures offer evidence to explain how a D-to-V missense mutation diverts the assembly of reversible, functional amyloid-like fibrils into the assembly of pathogenic amyloid, and may shed light on analogous conversions occurring in other ribonucleoproteins that lead to neurological diseases such as amyotrophic lateral sclerosis and frontotemporal dementia.
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Affiliation(s)
- Jiahui Lu
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Peng Ge
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David R Boyer
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Duilio Cascio
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Einav Tayeb-Fligelman
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA.
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8
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Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska M, Wydorski PM, Macierzynska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak L. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. bioRxiv 2024:2023.03.06.531355. [PMID: 36945632 PMCID: PMC10028812 DOI: 10.1101/2023.03.06.531355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
J-domain protein (JDP) molecular chaperones have emerged as central players that maintain a healthy proteome. The diverse members of the JDP family function as monomers/dimers and a small subset assemble into micron-sized oligomers. The oligomeric JDP members have eluded structural characterization due to their low-complexity, intrinsically disordered middle domains. This in turn, obscures the biological significance of these larger oligomers in protein folding processes. Here, we identified a short, aromatic motif within DNAJB8, that drives self-assembly through pi-pi stacking and determined its X-ray structure. We show that mutations in the motif disrupt DNAJB8 oligomerization in vitro and in cells. DNAJB8 variants that are unable to assemble bind to misfolded tau seeds more specifically and retain capacity to reduce protein aggregation in vitro and in cells. We propose a new model for DNAJB8 function in which the sequences in the low-complexity domains play distinct roles in assembly and substrate activity.
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9
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Nguyen BA, Singh V, Afrin S, Yakubovska A, Wang L, Ahmed Y, Pedretti R, Fernandez-Ramirez MDC, Singh P, Pękała M, Cabrera Hernandez LO, Kumar S, Lemoff A, Gonzalez-Prieto R, Sawaya MR, Eisenberg DS, Benson MD, Saelices L. Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy. Nat Commun 2024; 15:581. [PMID: 38233397 PMCID: PMC10794703 DOI: 10.1038/s41467-024-44820-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024] Open
Abstract
ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies.
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Affiliation(s)
- Binh An Nguyen
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Virender Singh
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Shumaila Afrin
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Anna Yakubovska
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Lanie Wang
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Yasmin Ahmed
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Rose Pedretti
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maria Del Carmen Fernandez-Ramirez
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Preeti Singh
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maja Pękała
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Luis O Cabrera Hernandez
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Siddharth Kumar
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roman Gonzalez-Prieto
- Andalusian Center for Molecular Biology and regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Departmento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Michael R Sawaya
- Department of Biological Chemistry, University of California, Los Angeles, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David S Eisenberg
- Department of Biological Chemistry, University of California, Los Angeles, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Merrill Douglas Benson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lorena Saelices
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
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10
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Rosenberg GM, Abskharon R, Boyer DR, Ge P, Sawaya MR, Eisenberg DS. Fibril structures of TFG protein mutants validate the identification of TFG as a disease-related amyloid protein by the IMPAcT method. PNAS Nexus 2023; 2:pgad402. [PMID: 38077690 PMCID: PMC10703350 DOI: 10.1093/pnasnexus/pgad402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
We previously presented a bioinformatic method for identifying diseases that arise from a mutation in a protein's low-complexity domain that drives the protein into pathogenic amyloid fibrils. One protein so identified was the tropomyosin-receptor kinase-fused gene protein (TRK-fused gene protein or TFG). Mutations in TFG are associated with degenerative neurological conditions. Here, we present experimental evidence that confirms our prediction that these conditions are amyloid-related. We find that the low-complexity domain of TFG containing the disease-related mutations G269V or P285L forms amyloid fibrils, and we determine their structures using cryo-electron microscopy (cryo-EM). These structures are unmistakably amyloid in nature and confirm the propensity of the mutant TFG low-complexity domain to form amyloid fibrils. Also, despite resulting from a pathogenic mutation, the fibril structures bear some similarities to other amyloid structures that are thought to be nonpathogenic and even functional, but there are other factors that support these structures' relevance to disease, including an increased propensity to form amyloid compared with the wild-type sequence, structure-stabilizing influence from the mutant residues themselves, and double-protofilament amyloid cores. Our findings elucidate two potentially disease-relevant structures of a previously unknown amyloid and also show how the structural features of pathogenic amyloid fibrils may not conform to the features commonly associated with pathogenicity.
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Affiliation(s)
- Gregory M Rosenberg
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA
| | - Romany Abskharon
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA
| | - David R Boyer
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA
| | - Peng Ge
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA
| | - David S Eisenberg
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA
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11
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Hazari A, Sawaya MR, Sajimon M, Vlahakis N, Rodriguez J, Eisenberg D, Raskatov JA. Racemic Peptides from Amyloid β and Amylin Form Rippled β-Sheets Rather Than Pleated β-Sheets. J Am Chem Soc 2023; 145:25917-25926. [PMID: 37972334 DOI: 10.1021/jacs.3c11712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The rippled β-sheet was theorized by Pauling and Corey in 1953 as a structural motif in which mirror image peptide strands assemble into hydrogen-bonded periodic arrays with strictly alternating chirality. Structural characterization of the rippled β-sheet was limited to biophysical methods until 2022 when atomic resolution structures of the motif were first obtained. The crystal structural foundation is restricted to four model tripeptides composed exclusively of aromatic residues. Here, we report five new rippled sheet crystal structures derived from amyloid β and amylin, the aggregating toxic peptides of Alzheimer's disease and type II diabetes, respectively. Despite the variation in peptide sequence composition, all five structures form antiparallel rippled β-sheets that extend, like a fibril, along the entire length of the crystalline needle. The long-range packing of the crystals, however, varies. In three of the crystals, the sheets pack face-to-face and exclude water, giving rise to cross-β architectures grossly resembling the steric zipper motif of amyloid fibrils but differing in fundamental details. In the other two crystals, the solvent is encapsulated between the sheets, yielding fibril architectures capable of host-guest chemistry. Our study demonstrates that the formation of rippled β-sheets from aggregating racemic peptide mixtures in three-dimensional (3D) assemblies is a general phenomenon and provides a structural basis for targeting intrinsically disordered proteins.
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Affiliation(s)
- Amaruka Hazari
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Michael R Sawaya
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Maria Sajimon
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Niko Vlahakis
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Jose Rodriguez
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - David Eisenberg
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
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12
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Richards LS, Flores MD, Zink S, Schibrowsky NA, Sawaya MR, Rodriguez JA. Cryo-EM structure of a human LECT2 amyloid fibril reveals a network of polar ladders at its core. Structure 2023; 31:1386-1393.e3. [PMID: 37657439 DOI: 10.1016/j.str.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/29/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023]
Abstract
ALECT2 systemic amyloidosis is associated with deposition of the leukocyte cell-derived chemotaxin-2 (LECT2) protein in the form of fibrils. In ALECT2 amyloidosis, ALECT2 fibrils deposit in the glomerulus, resulting in renal failure. Patients lack effective treatment options outside of renal transplant or dialysis. The structure of globular LECT2 has been determined but structures of ALECT2 amyloid fibrils remain unknown. Using single-particle cryo-EM, we find that recombinant human LECT2 forms robust twisting fibrils with canonical amyloid features. ALECT2 fibrils contain two mating protofilaments spanning residues 55-75 of the LECT2 sequence. The geometry of the ALECT2 fibril displays features in line with other pathogenic amyloids. Its core is tightly packed and stabilized by both hydrophobic contacts and hydrogen-bonded uncharged polar residues. The robustness of ALECT2 fibril cores is illustrated by their resistance to denaturants and proteases. This ALECT2 fibril structure presents a potential new target for treatments against ALECT2 systemic amyloidosis.
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Affiliation(s)
- Logan S Richards
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Maria D Flores
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Samantha Zink
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Natalie A Schibrowsky
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
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13
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Abskharon R, Pan H, Sawaya MR, Seidler PM, Olivares EJ, Chen Y, Murray KA, Zhang J, Lantz C, Bentzel M, Boyer DR, Cascio D, Nguyen BA, Hou K, Cheng X, Pardon E, Williams CK, Nana AL, Vinters HV, Spina S, Grinberg LT, Seeley WW, Steyaert J, Glabe CG, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Structure-based design of nanobodies that inhibit seeding of Alzheimer's patient-extracted tau fibrils. Proc Natl Acad Sci U S A 2023; 120:e2300258120. [PMID: 37801475 PMCID: PMC10576031 DOI: 10.1073/pnas.2300258120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 08/21/2023] [Indexed: 10/08/2023] Open
Abstract
Despite much effort, antibody therapies for Alzheimer's disease (AD) have shown limited efficacy. Challenges to the rational design of effective antibodies include the difficulty of achieving specific affinity to critical targets, poor expression, and antibody aggregation caused by buried charges and unstructured loops. To overcome these challenges, we grafted previously determined sequences of fibril-capping amyloid inhibitors onto a camel heavy chain antibody scaffold. These sequences were designed to cap fibrils of tau, known to form the neurofibrillary tangles of AD, thereby preventing fibril elongation. The nanobodies grafted with capping inhibitors blocked tau aggregation in biosensor cells seeded with postmortem brain extracts from AD and progressive supranuclear palsy (PSP) patients. The tau capping nanobody inhibitors also blocked seeding by recombinant tau oligomers. Another challenge to the design of effective antibodies is their poor blood-brain barrier (BBB) penetration. In this study, we also designed a bispecific nanobody composed of a nanobody that targets a receptor on the BBB and a tau capping nanobody inhibitor, conjoined by a flexible linker. We provide evidence that the bispecific nanobody improved BBB penetration over the tau capping inhibitor alone after intravenous administration in mice. Our results suggest that the design of synthetic antibodies that target sequences that drive protein aggregation may be a promising approach to inhibit the prion-like seeding of tau and other proteins involved in AD and related proteinopathies.
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Affiliation(s)
- Romany Abskharon
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Hope Pan
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Paul M. Seidler
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | | | - Yu Chen
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Molecular Instrumentation Center, UCLA, Los Angeles, CA90095
| | - Kevin A. Murray
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Jeffrey Zhang
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Carter Lantz
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
| | - Megan Bentzel
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - David R. Boyer
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Binh A. Nguyen
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Ke Hou
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Xinyi Cheng
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Els Pardon
- VIB-Vrije Universiteit Brussel Center for Structural Biology, VIB and Vrije Universiteit Brussel, BrusselsB-1050, Belgium
| | - Christopher K. Williams
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
| | - Alissa L. Nana
- Department of Neurology, University of California San Francisco Weill Institute for Neurosciences, University of California, San Francisco, CA94143
| | - Harry V. Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA90095
| | - Salvatore Spina
- Department of Neurology, University of California San Francisco Weill Institute for Neurosciences, University of California, San Francisco, CA94143
| | - Lea T. Grinberg
- Department of Neurology, University of California San Francisco Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Department of Pathology, University of California, San Francisco, CA94143
| | - William W. Seeley
- Department of Neurology, University of California San Francisco Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Department of Pathology, University of California, San Francisco, CA94143
| | - Jan Steyaert
- VIB-Vrije Universiteit Brussel Center for Structural Biology, VIB and Vrije Universiteit Brussel, BrusselsB-1050, Belgium
| | - Charles G. Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA92697
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
| | - David S. Eisenberg
- Department of Chemistry and Biochemistry, UCLA,Los Angeles, CA90095
- Department of Biological Chemistry, UCLA, Los Angeles, CA90095
- HHMI, UCLA, Los Angeles, CA90095
- UCLA-Department of Energy Institute, Molecular Biology Institute, UCLA, Los Angeles, CA90095
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14
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Meador K, Castells-Graells R, Aguirre R, Sawaya MR, Arbing MA, Sherman T, Senarathne C, Yeates TO. A Suite of Designed Protein Cages Using Machine Learning Algorithms and Protein Fragment-Based Protocols. bioRxiv 2023:2023.10.09.561468. [PMID: 37873110 PMCID: PMC10592684 DOI: 10.1101/2023.10.09.561468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, while methods for their creation remain challenging and unpredictable. In the present study, we apply new computational approaches to design a suite of new tetrahedrally symmetric, self-assembling protein cages. For the generation of docked poses, we emphasize a protein fragment-based approach, while for de novo interface design, a comparison of computational protocols highlights the power and increased experimental success achieved using the machine learning program ProteinMPNN. In relating information from docking and design, we observe that agreement between fragment-based sequence preferences and ProteinMPNN sequence inference correlates with experimental success. Additional insights for designing polar interactions are highlighted by experimentally testing larger and more polar interfaces. In all, using X-ray crystallography and cryo-EM, we report five structures for seven protein cages, with atomic resolution in the best case reaching 2.0 Å. We also report structures of two incompletely assembled protein cages, providing unique insights into one type of assembly failure. The new set of designed cages and their structures add substantially to the body of available protein nanoparticles, and to methodologies for their creation.
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Affiliation(s)
- Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | | | - Roman Aguirre
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Michael R. Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
| | - Mark A. Arbing
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
| | - Trent Sherman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Chethaka Senarathne
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
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15
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Castells-Graells R, Meador K, Arbing MA, Sawaya MR, Gee M, Cascio D, Gleave E, Debreczeni JÉ, Breed J, Leopold K, Patel A, Jahagirdar D, Lyons B, Subramaniam S, Phillips C, Yeates TO. Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold. Proc Natl Acad Sci U S A 2023; 120:e2305494120. [PMID: 37669364 PMCID: PMC10500258 DOI: 10.1073/pnas.2305494120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023] Open
Abstract
Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.
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Affiliation(s)
- Roger Castells-Graells
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Mark A. Arbing
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Michael R. Sawaya
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Emma Gleave
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | | | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Karoline Leopold
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | - Ankoor Patel
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | | | - Bronwyn Lyons
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | - Sriram Subramaniam
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Chris Phillips
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Todd O. Yeates
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
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16
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Stewart A, Dershwitz P, Stewart C, Sawaya MR, Yeates TO, Semrau JD, Zischka H, DiSpirito AA, Bobik TA. Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2. Acta Crystallogr F Struct Biol Commun 2023; 79:111-118. [PMID: 37158309 PMCID: PMC10167746 DOI: 10.1107/s2053230x23003035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X-Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.
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Affiliation(s)
- Andrew Stewart
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Philip Dershwitz
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Charles Stewart
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011-3260, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
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17
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Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. Nat Commun 2023; 14:2379. [PMID: 37185252 PMCID: PMC10127185 DOI: 10.1038/s41467-023-37865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP's propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.
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Affiliation(s)
- Einav Tayeb-Fligelman
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Jeannette T Bowler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Christen E Tai
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Michael R Sawaya
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Yi Xiao Jiang
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
| | - Sarah L Griner
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Xinyi Cheng
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Lukasz Salwinski
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Liisa Lutter
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Paul M Seidler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California School of Pharmacy, Los Angeles, CA, 90089-9121, USA
| | - Jiahui Lu
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gregory M Rosenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Ke Hou
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Romany Abskharon
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Hope Pan
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - David R Boyer
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Yan Li
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Daniel H Anderson
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Kevin A Murray
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Genesis Falcon
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Lorena Saelices
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - David S Eisenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
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18
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Richards L, Flores MD, Millán C, Glynn C, Zee CT, Sawaya MR, Gallagher-Jones M, Borges RJ, Usón I, Rodriguez JA. Fragment-Based Ab Initio Phasing of Peptidic Nanocrystals by MicroED. ACS Bio Med Chem Au 2023; 3:201-210. [PMID: 37096030 PMCID: PMC10119933 DOI: 10.1021/acsbiomedchemau.2c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 04/26/2023]
Abstract
Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its de novo determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
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Affiliation(s)
- Logan
S. Richards
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Maria D. Flores
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Claudia Millán
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
| | - Calina Glynn
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Chih-Te Zee
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Michael R. Sawaya
- Department
of Biological Chemistry and Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Howard
Hughes Medical Institute (HHMI), UCLA-DOE Institute for Genomics and
Proteomics, Los Angeles, California 90095, United States
| | - Marcus Gallagher-Jones
- Correlated
Imaging, The Rosalind Franklin Institute, Harwell Science & Innovation
Campus, Rutherford Avenue, Harwell, Didcot OX11 0GD, United Kingdom
| | - Rafael J. Borges
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
- ICREA,
Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
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19
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Richards LS, Flores MD, Zink S, Schibrowsky NA, Sawaya MR, Rodriguez JA. Cryo-EM Structure of a Human LECT2 Amyloid Fibril Reveals a Network of Polar Ladders at its Core. bioRxiv 2023:2023.02.08.527771. [PMID: 36798409 PMCID: PMC9934627 DOI: 10.1101/2023.02.08.527771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
ALECT2 is a type of systemic amyloidosis caused by deposition of the leukocyte cell-derived chemotaxin-2 (LECT2) protein in the form of fibrils. In ALECT2, LECT2 fibril deposits can be found in the glomerulus, resulting in renal failure. Affected patients lack effective treatment options outside of renal transplant or dialysis. While the structure of LECT2 in its globular form has been determined by X-ray crystallography, structures of LECT2 amyloid fibrils remain unknown. Using single particle cryo-EM, we now find that human LECT2 forms robust twisting fibrils with canonical amyloid features. At their core, LECT2 fibrils contain two mating protofilaments, the ordered core of each protofilament spans residues 55-75 of the LECT2 sequence. The overall geometry of the LECT2 fibril displays features in line with other pathogenic amyloids. Its core is tightly packed and stabilized by a network of hydrophobic contacts and hydrogen-bonded uncharged polar residues, while its outer surface displays several charged residues. The robustness of LECT2 fibril cores is illustrated by their limited dissolution in 3M urea and their persistence after treatment with proteinase K. As such, the LECT2 fibril structure presents a potential new target for treatments against ALECT2.
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Affiliation(s)
- Logan S. Richards
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA
| | - Maria D. Flores
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA
| | - Samantha Zink
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA
| | - Natalie A. Schibrowsky
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA
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20
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Seidler PM, Murray KA, Boyer DR, Ge P, Sawaya MR, Hu CJ, Cheng X, Abskharon R, Pan H, DeTure MA, Williams CK, Dickson DW, Vinters HV, Eisenberg DS. Structure-based discovery of small molecules that disaggregate Alzheimer's disease tissue derived tau fibrils in vitro. Nat Commun 2022; 13:5451. [PMID: 36114178 PMCID: PMC9481533 DOI: 10.1038/s41467-022-32951-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/24/2022] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD) is the consequence of neuronal death and brain atrophy associated with the aggregation of protein tau into fibrils. Thus disaggregation of tau fibrils could be a therapeutic approach to AD. The small molecule EGCG, abundant in green tea, has long been known to disaggregate tau and other amyloid fibrils, but EGCG has poor drug-like properties, failing to fully penetrate the brain. Here we have cryogenically trapped an intermediate of brain-extracted tau fibrils on the kinetic pathway to EGCG-induced disaggregation and have determined its cryoEM structure. The structure reveals that EGCG molecules stack in polar clefts between the paired helical protofilaments that pathologically define AD. Treating the EGCG binding position as a pharmacophore, we computationally screened thousands of drug-like compounds for compatibility for the pharmacophore, discovering several that experimentally disaggregate brain-derived tau fibrils in vitro. This work suggests the potential of structure-based, small-molecule drug discovery for amyloid diseases.
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Affiliation(s)
- Paul M Seidler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Kevin A Murray
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David R Boyer
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Peng Ge
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Carolyn J Hu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Xinyi Cheng
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Romany Abskharon
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Hope Pan
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | | | - Christopher K Williams
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Harry V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - David S Eisenberg
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA.
- UCLA-DOE Institute, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Los Angeles, CA, USA.
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21
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Bowler JT, Sawaya MR, Boyer DR, Cascio D, Bali M, Eisenberg DS. Micro-electron diffraction structure of the aggregation-driving N-terminus of Drosophila neuronal protein Orb2A reveals amyloid-like β-sheets. J Biol Chem 2022; 298:102396. [PMID: 35988647 PMCID: PMC9556795 DOI: 10.1016/j.jbc.2022.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Amyloid protein aggregation is commonly associated with progressive neurodegenerative diseases, however not all amyloid fibrils are pathogenic. The neuronal cytoplasmic polyadenylation element binding (CPEB) protein is a regulator of synaptic mRNA translation, and has been shown to form functional amyloid aggregates that stabilize long-term memory. In adult Drosophila neurons, the CPEB homolog Orb2 is expressed as two isoforms, of which the Orb2B isoform is far more abundant, but the rarer Orb2A isoform is required to initiate Orb2 aggregation. The N-terminus is a distinctive feature of the Orb2A isoform and is critical for its aggregation. Intriguingly, replacement of phenylalanine in the 5th position of Orb2A with tyrosine (F5Y) in Drosophila impairs stabilization of long-term memory. The structure of endogenous Orb2B fibers was recently determined by cryo-EM, but the structure adopted by fibrillar Orb2A is less certain. Here we use micro-electron diffraction to determine the structure of the first nine N-terminal residues of Orb2A, at a resolution of 1.05 Å. We find that this segment (which we term M9I) forms an amyloid-like array of parallel in-register β-sheets, which interact through side chain interdigitation of aromatic and hydrophobic residues. Our structure provides an explanation for the decreased aggregation observed for the F5Y mutant, and offers a hypothesis for how the addition of a single atom (the tyrosyl oxygen) affects long-term memory. We also propose a structural model of Orb2A that integrates our structure of the M9I segment with the published Orb2B cryo-EM structure.
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Affiliation(s)
- Jeannette T Bowler
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute.
| | - Michael R Sawaya
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - David R Boyer
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - Duilio Cascio
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - Manya Bali
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute
| | - David S Eisenberg
- Molecular Biology Institute, University of California, Los Angeles; Howard Hughes Medical Institute.
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22
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Hazari A, Sawaya MR, Vlahakis N, Johnstone TC, Boyer D, Rodriguez J, Eisenberg D, Raskatov JA. The rippled β-sheet layer configuration-a novel supramolecular architecture based on predictions by Pauling and Corey. Chem Sci 2022; 13:8947-8952. [PMID: 36091211 PMCID: PMC9365095 DOI: 10.1039/d2sc02531k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since observed in countless proteins and peptides and is considered common textbook knowledge. Conversely, the rippled β-sheet only gained a meaningful experimental foundation in the past decade, and the first crystal structural study of rippled β-sheets was published as recently as this year. Noteworthy, the crystallized assembly stopped at the rippled β-dimer stage. It did not form the extended, periodic rippled β-sheet layer topography hypothesized by Pauling and Corey, thus calling the validity of their prediction into question. NMR work conducted since moreover shows that certain model peptides rather form pleated and not rippled β-sheets in solution. To determine whether the periodic rippled β-sheet layer configuration is viable, the field urgently needs crystal structures. Here we report on crystal structures of two racemic and one quasi-racemic aggregating peptide systems, all of which yield periodic rippled antiparallel β-sheet layers that are in excellent agreement with the predictions by Pauling and Corey. Our study establishes the rippled β-sheet layer configuration as a motif with general features and opens the road to structure-based design of unique supramolecular architectures.
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Affiliation(s)
- Amaruka Hazari
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz CA 95064 USA
| | - Michael R Sawaya
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Niko Vlahakis
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Timothy C Johnstone
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz CA 95064 USA
| | - David Boyer
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Jose Rodriguez
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - David Eisenberg
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz CA 95064 USA
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23
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Tetreau G, Sawaya MR, De Zitter E, Andreeva EA, Banneville AS, Schibrowsky NA, Coquelle N, Brewster AS, Grünbein ML, Kovacs GN, Hunter MS, Kloos M, Sierra RG, Schiro G, Qiao P, Stricker M, Bideshi D, Young ID, Zala N, Engilberge S, Gorel A, Signor L, Teulon JM, Hilpert M, Foucar L, Bielecki J, Bean R, de Wijn R, Sato T, Kirkwood H, Letrun R, Batyuk A, Snigireva I, Fenel D, Schubert R, Canfield EJ, Alba MM, Laporte F, Després L, Bacia M, Roux A, Chapelle C, Riobé F, Maury O, Ling WL, Boutet S, Mancuso A, Gutsche I, Girard E, Barends TRM, Pellequer JL, Park HW, Laganowsky AD, Rodriguez J, Burghammer M, Shoeman RL, Doak RB, Weik M, Sauter NK, Federici B, Cascio D, Schlichting I, Colletier JP. De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals. Nat Commun 2022; 13:4376. [PMID: 35902572 PMCID: PMC9334358 DOI: 10.1038/s41467-022-31746-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.
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Affiliation(s)
- Guillaume Tetreau
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
| | - Elke De Zitter
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Elena A Andreeva
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Anne-Sophie Banneville
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Natalie A Schibrowsky
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Nicolas Coquelle
- Large-Scale Structures Group, Institut Laue-Langevin, F-38000, Grenoble, France
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marie Luise Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Marco Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Giorgio Schiro
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Pei Qiao
- Department of Chemistry, Texas A&M University, College Station, TX, 77845, USA
| | - Myriam Stricker
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Dennis Bideshi
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ninon Zala
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Sylvain Engilberge
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Alexander Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Mario Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Irina Snigireva
- European Synchrotron Radiation Facility (ESRF), BP 220, 38043, Grenoble, France
| | - Daphna Fenel
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Ethan J Canfield
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mario M Alba
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | | | | | - Maria Bacia
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | | | - François Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | - Wai Li Ling
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Adrian Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Eric Girard
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Hyun-Woo Park
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Arthur D Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77845, USA
| | - Jose Rodriguez
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Manfred Burghammer
- European Synchrotron Radiation Facility (ESRF), BP 220, 38043, Grenoble, France
| | - Robert L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - R Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Martin Weik
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jacques-Philippe Colletier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France.
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24
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Aoki M, Vinokur J, Motoyama K, Ishikawa R, Collazo M, Cascio D, Sawaya MR, Ito T, Bowie JU, Hemmi H. Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways. J Biol Chem 2022; 298:102111. [PMID: 35690147 PMCID: PMC9254496 DOI: 10.1016/j.jbc.2022.102111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
Mevalonate 3,5-bisphosphate decarboxylase is involved in the recently discovered Thermoplasma-type mevalonate pathway. The enzyme catalyzes the elimination of the 3-phosphate group from mevalonate 3,5-bisphosphate as well as concomitant decarboxylation of the substrate. This entire reaction of the enzyme resembles the latter half-reactions of its homologs, diphosphomevalonate decarboxylase and phosphomevalonate decarboxylase, which also catalyze ATP-dependent phosphorylation of the 3-hydroxyl group of their substrates. However, the crystal structure of mevalonate 3,5-bisphosphate decarboxylase and the structural reasons of the difference between reactions catalyzed by the enzyme and its homologs are unknown. In this study, we determined the X-ray crystal structure of mevalonate 3,5-bisphosphate decarboxylase from Picrophilus torridus, a thermoacidophilic archaeon of the order Thermoplasmatales. Structural and mutational analysis demonstrated the importance of a conserved aspartate residue for enzyme activity. In addition, although crystallization was performed in the absence of substrate or ligands, residual electron density having the shape of a fatty acid was observed at a position overlapping the ATP-binding site of the homologous enzyme, diphosphomevalonate decarboxylase. This finding is in agreement with the expected evolutionary route from phosphomevalonate decarboxylase (ATP-dependent) to mevalonate 3,5-bisphosphate decarboxylase (ATP-independent) through the loss of kinase activity. We found that the binding of geranylgeranyl diphosphate, an intermediate of the archeal isoprenoid biosynthesis pathway, evoked significant activation of mevalonate 3,5-bisphosphate decarboxylase, and several mutations at the putative geranylgeranyl diphosphate-binding site impaired this activation, suggesting the physiological importance of ligand binding as well as a possible novel regulatory system employed by the Thermoplasma-type mevalonate pathway.
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Affiliation(s)
- Mizuki Aoki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - Jeffrey Vinokur
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Kento Motoyama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - Rino Ishikawa
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - Michael Collazo
- Departments of Biological Chemistry, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Duilio Cascio
- Departments of Biological Chemistry, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Michael R Sawaya
- UCLA-DOE Institute of Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Tomokazu Ito
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan.
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25
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Gray ALH, Sawaya MR, Acharyya D, Lou J, Edington EM, Best MD, Prosser RA, Eisenberg DS, Do TD. Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices. Protein Sci 2022; 31:716-727. [PMID: 34954854 PMCID: PMC8862425 DOI: 10.1002/pro.4268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Atomic structures of amyloid oligomers that capture the neurodegenerative disease pathology are essential to understand disease-state causes and finding cures. Here we investigate the G6W mutation of the cytotoxic, hexameric amyloid model KV11. The mutation results into an asymmetric dodecamer composed of a pair of 30° twisted antiparallel β-sheets. The complete break between adjacent β-strands is unprecedented among amyloid fibril crystal structures and supports that our structure is an oligomer. The poor shape complementarity between mated sheets reveals an interior channel for binding lipids, suggesting that the toxicity may be due to a perturbation of lipid transport rather than a direct disruption of membrane integrity. Viability assays on mouse suprachiasmatic nucleus, anterior hypothalamus, and cerebral cortex demonstrated selective regional vulnerability consistent with Alzheimer's disease. Neuropeptides released from the brain slices may provide clues to how G6W initiates cellular injury.
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Affiliation(s)
- Amber L. H. Gray
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Michael R. Sawaya
- HHMIUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Energy Institute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Debalina Acharyya
- Department of Biochemistry & Cellular and Molecular BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Jinchao Lou
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | | | - Michael D. Best
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Rebecca A. Prosser
- Department of Biochemistry & Cellular and Molecular BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - David S. Eisenberg
- HHMIUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Energy Institute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Thanh D. Do
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
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26
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Murray KA, Evans D, Hughes MP, Sawaya MR, Hu CJ, Houk KN, Eisenberg D. Extended β-Strands Contribute to Reversible Amyloid Formation. ACS Nano 2022; 16:2154-2163. [PMID: 35132852 DOI: 10.1021/acsnano.1c08043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The assembly of proteins into fibrillar amyloid structures was once considered to be pathologic and essentially irreversible. Recent studies reveal amyloid-like structures that form reversibly, derived from protein low-complexity domains which function in cellular metabolism. Here, by comparing atomic-level structures of reversible and irreversible amyloid fibrils, we find that the β-sheets of reversible fibrils are enriched in flattened (as opposed to pleated) β-sheets formed by stacking of extended β-strands. Quantum mechanical calculations show that glycine residues favor extended β-strands which may be stabilized by intraresidue interactions between the amide proton and the carbonyl oxygen, known as C5 hydrogen-bonds. Larger residue side chains favor shorter strands and pleated sheets. These findings highlight a structural element that may regulate reversible amyloid assembly.
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27
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Xiao Jiang Y, Cao Q, Sawaya MR, Abskharon R, Ge P, DeTure M, Dickson DW, Eisenberg DS. Amyloid fibrils from frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) are composed of TMEM106B, rather than TDP-43. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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28
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Murray KA, Hughes MP, Hu CJ, Sawaya MR, Salwinski L, Pan H, French SW, Seidler PM, Eisenberg DS. Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies. Nat Struct Mol Biol 2022; 29:529-536. [PMID: 35637421 PMCID: PMC9205782 DOI: 10.1038/s41594-022-00774-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/08/2022] [Indexed: 01/19/2023]
Abstract
Proteins including FUS, hnRNPA2, and TDP-43 reversibly aggregate into amyloid-like fibrils through interactions of their low-complexity domains (LCDs). Mutations in LCDs can promote irreversible amyloid aggregation and disease. We introduce a computational approach to identify mutations in LCDs of disease-associated proteins predicted to increase propensity for amyloid aggregation. We identify several disease-related mutations in the intermediate filament protein keratin-8 (KRT8). Atomic structures of wild-type and mutant KRT8 segments confirm the transition to a pleated strand capable of amyloid formation. Biochemical analysis reveals KRT8 forms amyloid aggregates, and the identified mutations promote aggregation. Aggregated KRT8 is found in Mallory-Denk bodies, observed in hepatocytes of livers with alcoholic steatohepatitis (ASH). We demonstrate that ethanol promotes KRT8 aggregation, and KRT8 amyloids co-crystallize with alcohol. Lastly, KRT8 aggregation can be seeded by liver extract from people with ASH, consistent with the amyloid nature of KRT8 aggregates and the classification of ASH as an amyloid-related condition.
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Affiliation(s)
- Kevin A. Murray
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
| | - Michael P. Hughes
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
| | - Carolyn J. Hu
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
| | - Michael R. Sawaya
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
| | - Lukasz Salwinski
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
| | - Hope Pan
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
| | - Samuel W. French
- grid.19006.3e0000 0000 9632 6718Department of Pathology & Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Paul M. Seidler
- grid.42505.360000 0001 2156 6853Department of Pharmacology and Pharmaceutical Science, University of Southern California, Los Angeles, CA USA
| | - David S. Eisenberg
- grid.19006.3e0000 0000 9632 6718Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA USA
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29
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Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis. Cell 2021; 184:4857-4873. [PMID: 34534463 PMCID: PMC8772536 DOI: 10.1016/j.cell.2021.08.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 02/05/2023]
Abstract
The hidden world of amyloid biology has suddenly snapped into atomic-level focus, revealing over 80 amyloid protein fibrils, both pathogenic and functional. Unlike globular proteins, amyloid proteins flatten and stack into unbranched fibrils. Stranger still, a single protein sequence can adopt wildly different two-dimensional conformations, yielding distinct fibril polymorphs. Thus, an amyloid protein may define distinct diseases depending on its conformation. At the heart of this conformational variability lies structural frustrations. In functional amyloids, evolution tunes frustration levels to achieve either stability or sensitivity according to the fibril's biological function, accounting for the vast versatility of the amyloid fibril scaffold.
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Affiliation(s)
- Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jose A Rodriguez
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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30
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Cao Q, Boyer DR, Sawaya MR, Abskharon R, Saelices L, Nguyen BA, Lu J, Murray KA, Kandeel F, Eisenberg DS. Cryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril cores. Nat Struct Mol Biol 2021; 28:724-730. [PMID: 34518699 PMCID: PMC10396428 DOI: 10.1038/s41594-021-00646-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Amyloidosis of human islet amyloid polypeptide (hIAPP) is a pathological hallmark of type II diabetes (T2D), an epidemic afflicting nearly 10% of the world's population. To visualize disease-relevant hIAPP fibrils, we extracted amyloid fibrils from islet cells of a T2D donor and amplified their quantity by seeding synthetic hIAPP. Cryo-EM studies revealed four fibril polymorphic atomic structures. Their resemblance to four unseeded hIAPP fibrils varies from nearly identical (TW3) to non-existent (TW2). The diverse repertoire of hIAPP polymorphs appears to arise from three distinct protofilament cores entwined in different combinations. The structural distinctiveness of TW1, TW2 and TW4 suggests they may be faithful replications of the pathogenic seeds. If so, the structures determined here provide the most direct view yet of hIAPP amyloid fibrils formed during T2D.
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Affiliation(s)
- Qin Cao
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - David R Boyer
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Lorena Saelices
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA.,Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Binh A Nguyen
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA.,Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jiahui Lu
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Kevin A Murray
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Fouad Kandeel
- Department of Translational Research & Cellular Therapeutics, City of Hope, Duarte, CA, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA.
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31
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Ochoa JM, Mijares O, Acosta AA, Escoto X, Leon-Rivera N, Marshall JD, Sawaya MR, Yeates TO. Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments. Acta Crystallogr F Struct Biol Commun 2021; 77:275-285. [PMID: 34473104 PMCID: PMC8411931 DOI: 10.1107/s2053230x21007470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/21/2021] [Indexed: 11/08/2023] Open
Abstract
Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.
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Affiliation(s)
- Jessica M. Ochoa
- UCLA Molecular Biology Institute, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Oscar Mijares
- Whittier College, 13406 East Philadelphia Street, Whittier, CA 90602, USA
| | - Andrea A. Acosta
- Whittier College, 13406 East Philadelphia Street, Whittier, CA 90602, USA
| | - Xavier Escoto
- Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Nancy Leon-Rivera
- Whittier College, 13406 East Philadelphia Street, Whittier, CA 90602, USA
| | - Joanna D. Marshall
- Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- UCLA–DOE Institute of Genomics and Proteomics, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- UCLA Molecular Biology Institute, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- UCLA–DOE Institute of Genomics and Proteomics, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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32
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Abstract
Protein molecules bring a rich functionality to the field of designed nanoscale architectures. High-symmetry protein cages are rapidly finding diverse applications in biomedicine, nanotechnology, and imaging, but methods for their reliable and predictable construction remain challenging. In this study we introduce an approach for designing protein assemblies that combines ideas and favorable elements adapted from recent work. Cubically symmetric cages can be created by combining two simpler symmetries, following recently established principles. Here, two different oligomeric protein components are brought together in a geometrically specific arrangement by their separate genetic fusion to individual components of a heterodimeric coiled-coil polypeptide motif of known structure. Fusions between components are made by continuous α-helices to limit flexibility. After a computational design, we tested 10 different protein cage constructions experimentally, two of which formed larger assemblies. One produced the intended octahedral cage, ∼26 nm in diameter, while the other appeared to produce the intended tetrahedral cage as a minor component, crystallizing instead in an alternate form representing a collapsed structure of lower stoichiometry and symmetry. Geometric distinctions between the two characterized designs help explain the different degrees of success, leading to clearer principles and improved prospects for the routine creation of nanoscale protein architectures using diverse methods.
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Affiliation(s)
- Joshua Laniado
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Kevin A Cannon
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Michael R Sawaya
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095, United States
| | - Dan E McNamara
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
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33
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Tayeb-Fligelman E, Cheng X, Tai C, Bowler JT, Griner S, Sawaya MR, Seidler PM, Jiang YX, Lu J, Rosenberg GM, Salwinski L, Abskharon R, Zee CT, Hou K, Li Y, Boyer DR, Murray KA, Falcon G, Anderson DH, Cascio D, Saelices L, Damoiseaux R, Guo F, Eisenberg DS. Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2. bioRxiv 2021. [PMID: 33688654 DOI: 10.1101/2021.03.05.434000] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 Nucleoprotein (NCAP) functions in RNA packaging during viral replication and assembly. Computational analysis of its amino acid sequence reveals a central low-complexity domain (LCD) having sequence features akin to LCDs in other proteins known to function in liquid-liquid phase separation. Here we show that in the presence of viral RNA, NCAP, and also its LCD segment alone, form amyloid-like fibrils when undergoing liquid-liquid phase separation. Within the LCD we identified three 6-residue segments that drive amyloid fibril formation. We determined atomic structures for fibrils formed by each of the three identified segments. These structures informed our design of peptide inhibitors of NCAP fibril formation and liquid-liquid phase separation, suggesting a therapeutic route for Covid-19. One Sentence Summary Atomic structures of amyloid-driving peptide segments from SARS-CoV-2 Nucleoprotein inform the development of Covid-19 therapeutics.
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34
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Mulligan VK, Kang CS, Sawaya MR, Rettie S, Li X, Antselovich I, Craven TW, Watkins AM, Labonte JW, DiMaio F, Yeates TO, Baker D. Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Sci 2021; 29:2433-2445. [PMID: 33058266 PMCID: PMC7679966 DOI: 10.1002/pro.3974] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022]
Abstract
Cyclic symmetry is frequent in protein and peptide homo‐oligomers, but extremely rare within a single chain, as it is not compatible with free N‐ and C‐termini. Here we describe the computational design of mixed‐chirality peptide macrocycles with rigid structures that feature internal cyclic symmetries or improper rotational symmetries inaccessible to natural proteins. Crystal structures of three C2‐ and C3‐symmetric macrocycles, and of six diverse S2‐symmetric macrocycles, match the computationally‐designed models with backbone heavy‐atom RMSD values of 1 Å or better. Crystal structures of an S4‐symmetric macrocycle (consisting of a sequence and structure segment mirrored at each of three successive repeats) designed to bind zinc reveal a large‐scale zinc‐driven conformational change from an S4‐symmetric apo‐state to a nearly inverted S4‐symmetric holo‐state almost identical to the design model. These symmetric structures provide promising starting points for applications ranging from design of cyclic peptide based metal organic frameworks to creation of high affinity binders of symmetric protein homo‐oligomers. More generally, this work demonstrates the power of computational design for exploring symmetries and structures not found in nature, and for creating synthetic switchable systems. PDB Code(s): 6UFU, 6UG2, 6UG3, 6UG6, 6UGB, 6UGC, 6UCX, 6UD9, 6UDR, 6UDW, 6UDZ, 6UF4, 6UF7, 6UF8, 6UFA and 6UF9;
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Affiliation(s)
- Vikram Khipple Mulligan
- Systems Biology, Center for Computational Biology, Flatiron Institute, New York, New York, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Christine S Kang
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA.,Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, University of California-Los Angeles (UCLA), Los Angeles, California, USA.,UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, Los Angeles, California, USA
| | - Stephen Rettie
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Inna Antselovich
- Department of Chemistry and Biochemistry, University of California-Los Angeles (UCLA), Los Angeles, California, USA.,UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, Los Angeles, California, USA
| | - Timothy W Craven
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Jason W Labonte
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania, USA.,Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Frank DiMaio
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California-Los Angeles (UCLA), Los Angeles, California, USA.,UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, Los Angeles, California, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
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35
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Abstract
Structural elucidation of small macromolecules such as peptides has recently been facilitated by a growing number of technological advances to existing crystallographic methods. The emergence of electron micro-diffraction (MicroED) of protein nanocrystals under cryogenic conditions has enabled the interrogation of crystalline peptide assemblies only hundreds of nanometers thick. Collection of atomic or near-atomic resolution data by these methods has permitted the ab initio determination of structures of various amyloid-forming peptides, including segments derived from prions and ice-nucleating proteins. This chapter focuses on the process of ab initio structural determination from nano-scale peptide assemblies and other similar molecules.
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Affiliation(s)
- Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Ambarneil Saha
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry, Chemistry & Biochemistry, and Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
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36
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Ochoa JM, Nguyen VN, Nie M, Sawaya MR, Bobik TA, Yeates TO. Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization. Protein Sci 2020; 29:2201-2212. [PMID: 32885887 DOI: 10.1002/pro.3941] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
Bacterial microcompartments are protein-based organelles that carry out specialized metabolic functions in diverse bacteria. Their outer shells are built from several thousand protein subunits. Some of the architectural principles of bacterial microcompartments have been articulated, with lateral packing of flat hexameric BMC proteins providing the basic foundation for assembly. Nonetheless, a complete understanding has been elusive, partly owing to polymorphic mechanisms of assembly exhibited by most microcompartment types. An earlier study of one homologous BMC shell protein subfamily, EutS/PduU, revealed a profoundly bent, rather than flat, hexameric structure. The possibility of a specialized architectural role was hypothesized, but artifactual effects of crystallization could not be ruled out. Here we report a series of crystal structures of an orthologous protein, CutR, from a glycyl-radical type choline-utilizing microcompartment from the bacterium Streptococcus intermedius. Depending on crystal form, expression construct, and minor mutations, a range of novel quaternary architectures was observed, including two spiral hexagonal assemblies. A new graphical approach helps illuminate the variations in BMC hexameric structure, with results substantiating the idea that the EutS/PduU/CutR subfamily of BMC proteins may endow microcompartment shells with flexible modes of assembly.
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Affiliation(s)
- Jessica M Ochoa
- UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Vy N Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Mengxiao Nie
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Michael R Sawaya
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Thomas A Bobik
- Department of Biochemistry, Biophysics and Molecular Biology; Iowa State University, Ames, Iowa, USA
| | - Todd O Yeates
- UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA
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37
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Lu J, Cao Q, Hughes MP, Sawaya MR, Boyer DR, Cascio D, Eisenberg DS. CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid. Nat Commun 2020; 11:4090. [PMID: 32796831 PMCID: PMC7427792 DOI: 10.1038/s41467-020-17905-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/14/2020] [Indexed: 01/02/2023] Open
Abstract
hnRNPA2 is a human ribonucleoprotein (RNP) involved in RNA metabolism. It forms fibrils both under cellular stress and in mutated form in neurodegenerative conditions. Previous work established that the C-terminal low-complexity domain (LCD) of hnRNPA2 fibrillizes under stress, and missense mutations in this domain are found in the disease multisystem proteinopathy (MSP). However, little is known at the atomic level about the hnRNPA2 LCD structure that is involved in those processes and how disease mutations cause structural change. Here we present the cryo-electron microscopy (cryoEM) structure of the hnRNPA2 LCD fibril core and demonstrate its capability to form a reversible hydrogel in vitro containing amyloid-like fibrils. Whereas these fibrils, like pathogenic amyloid, are formed from protein chains stacked into β-sheets by backbone hydrogen bonds, they display distinct structural differences: the chains are kinked, enabling non-covalent cross-linking of fibrils and disfavoring formation of pathogenic steric zippers. Both reversibility and energetic calculations suggest these fibrils are less stable than pathogenic amyloid. Moreover, the crystal structure of the disease-mutation-containing segment (D290V) of hnRNPA2 suggests that the replacement fundamentally alters the fibril structure to a more stable energetic state. These findings illuminate how molecular interactions promote protein fibril networks and how mutation can transform fibril structure from functional to a pathogenic form. hnRNPA2 is involved in RNA metabolism and can form both functional amyloid-like fibrils in membraneless organelles, and pathogenic fibrils in neurodegenerative conditions. Here, the authors present the cryo-EM fibril structure of the wild-type hnRNPA2 low-complexity domain (LCD) and the crystal structure of a LCD segment with the disease causing D290V variant and discuss how mutations can transform fibril structure from a functional to a pathogenic form.
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Affiliation(s)
- Jiahui Lu
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Qin Cao
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA.,Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David R Boyer
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Duilio Cascio
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, CA, USA.
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38
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Richards LS, Millán C, Miao J, Martynowycz MW, Sawaya MR, Gonen T, Borges RJ, Usón I, Rodriguez JA. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol 2020; 76:703-712. [PMID: 32744252 PMCID: PMC7397493 DOI: 10.1107/s2059798320008049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.
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Affiliation(s)
- Logan S. Richards
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Jennifer Miao
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Rafael J. Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
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39
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Cao Q, Boyer DR, Sawaya MR, Ge P, Eisenberg DS. Cryo-EM structure and inhibitor design of human IAPP (amylin) fibrils. Nat Struct Mol Biol 2020; 27:653-659. [PMID: 32541896 PMCID: PMC8579859 DOI: 10.1038/s41594-020-0435-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) functions as a glucose-regulating hormone but deposits as amyloid fibrils in more than 90% of patients with type II diabetes (T2D). Here we report the cryo-EM structure of recombinant full-length hIAPP fibrils. The fibril is composed of two symmetrically related protofilaments with ordered residues 14-37. Our hIAPP fibril structure (i) supports the previous hypothesis that residues 20-29 constitute the core of the hIAPP amyloid; (ii) suggests a molecular mechanism for the action of the hIAPP hereditary mutation S20G; (iii) explains why the six residue substitutions in rodent IAPP prevent aggregation; and (iv) suggests regions responsible for the observed hIAPP cross-seeding with β-amyloid. Furthermore, we performed structure-based inhibitor design to generate potential hIAPP aggregation inhibitors. Four of the designed peptides delay hIAPP aggregation in vitro, providing a starting point for the development of T2D therapeutics and proof of concept that the capping strategy can be used on full-length cryo-EM fibril structures.
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Affiliation(s)
- Qin Cao
- Department of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - David R Boyer
- Department of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peng Ge
- California NanoSystem Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - David S Eisenberg
- Department of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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40
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Abskharon R, Seidler PM, Sawaya MR, Cascio D, Yang TP, Philipp S, Williams CK, Newell KL, Ghetti B, DeTure MA, Dickson DW, Vinters HV, Felgner PL, Nakajima R, Glabe CG, Eisenberg DS. Crystal structure of a conformational antibody that binds tau oligomers and inhibits pathological seeding by extracts from donors with Alzheimer's disease. J Biol Chem 2020; 295:10662-10676. [PMID: 32493775 DOI: 10.1074/jbc.ra120.013638] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Indexed: 11/06/2022] Open
Abstract
Soluble oligomers of aggregated tau accompany the accumulation of insoluble amyloid fibrils, a histological hallmark of Alzheimer disease (AD) and two dozen related neurodegenerative diseases. Both oligomers and fibrils seed the spread of Tau pathology, and by virtue of their low molecular weight and relative solubility, oligomers may be particularly pernicious seeds. Here, we report the formation of in vitro tau oligomers formed by an ionic liquid (IL15). Using IL15-induced recombinant tau oligomers and a dot blot assay, we discovered a mAb (M204) that binds oligomeric tau, but not tau monomers or fibrils. M204 and an engineered single-chain variable fragment (scFv) inhibited seeding by IL15-induced tau oligomers and pathological extracts from donors with AD and chronic traumatic encephalopathy. This finding suggests that M204-scFv targets pathological structures that are formed by tau in neurodegenerative diseases. We found that M204-scFv itself partitions into oligomeric forms that inhibit seeding differently, and crystal structures of the M204-scFv monomer, dimer, and trimer revealed conformational differences that explain differences among these forms in binding and inhibition. The efficiency of M204-scFv antibodies to inhibit the seeding by brain tissue extracts from different donors with tauopathies varied among individuals, indicating the possible existence of distinct amyloid polymorphs. We propose that by binding to oligomers, which are hypothesized to be the earliest seeding-competent species, M204-scFv may have potential as an early-stage diagnostic for AD and tauopathies, and also could guide the development of promising therapeutic antibodies.
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Affiliation(s)
- Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute UCLA, Los Angeles, California, USA.,Howard Hughes Medical Institute UCLA, Los Angeles, California, USA
| | - Paul M Seidler
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute UCLA, Los Angeles, California, USA.,Howard Hughes Medical Institute UCLA, Los Angeles, California, USA
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute UCLA, Los Angeles, California, USA.,Howard Hughes Medical Institute UCLA, Los Angeles, California, USA
| | - Duilio Cascio
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute UCLA, Los Angeles, California, USA.,Howard Hughes Medical Institute UCLA, Los Angeles, California, USA
| | - Tianxiao P Yang
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute UCLA, Los Angeles, California, USA.,Howard Hughes Medical Institute UCLA, Los Angeles, California, USA
| | - Stephan Philipp
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Christopher Kazu Williams
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael A DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Harry V Vinters
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Philip L Felgner
- Vaccine Research and Development Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Rie Nakajima
- Vaccine Research and Development Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Charles G Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute UCLA, Los Angeles, California, USA .,Howard Hughes Medical Institute UCLA, Los Angeles, California, USA
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41
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Glynn C, Sawaya MR, Ge P, Gallagher-Jones M, Short CW, Bowman R, Apostol M, Zhou ZH, Eisenberg DS, Rodriguez JA. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Nat Struct Mol Biol 2020; 27:417-423. [PMID: 32284600 PMCID: PMC7338044 DOI: 10.1038/s41594-020-0403-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/28/2020] [Indexed: 01/22/2023]
Abstract
Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease.
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Affiliation(s)
- Calina Glynn
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael R Sawaya
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Peng Ge
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Connor W Short
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ronquiajah Bowman
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marcin Apostol
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
- ADRx, Thousand Oaks, CA, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - David S Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA.
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42
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Boyer DR, Li B, Sun C, Fan W, Zhou K, Hughes MP, Sawaya MR, Jiang L, Eisenberg DS. The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure. Proc Natl Acad Sci U S A 2020; 117:3592-3602. [PMID: 32015135 PMCID: PMC7035510 DOI: 10.1073/pnas.1917914117] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Aggregation of α-synuclein is a defining molecular feature of Parkinson's disease, Lewy body dementia, and multiple systems atrophy. Hereditary mutations in α-synuclein are linked to both Parkinson's disease and Lewy body dementia; in particular, patients bearing the E46K disease mutation manifest a clinical picture of parkinsonism and Lewy body dementia, and E46K creates more pathogenic fibrils in vitro. Understanding the effect of these hereditary mutations on α-synuclein fibril structure is fundamental to α-synuclein biology. We therefore determined the cryo-electron microscopy (cryo-EM) structure of α-synuclein fibrils containing the hereditary E46K mutation. The 2.5-Å structure reveals a symmetric double protofilament in which the molecules adopt a vastly rearranged, lower energy fold compared to wild-type fibrils. We propose that the E46K misfolding pathway avoids electrostatic repulsion between K46 and K80, a residue pair which form the E46-K80 salt bridge in the wild-type fibril structure. We hypothesize that, under our conditions, the wild-type fold does not reach this deeper energy well of the E46K fold because the E46-K80 salt bridge diverts α-synuclein into a kinetic trap-a shallower, more accessible energy minimum. The E46K mutation apparently unlocks a more stable and pathogenic fibril structure.
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Affiliation(s)
- David R Boyer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Energy Institute, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - Binsen Li
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Chuanqi Sun
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Weijia Fan
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Kang Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Michael P Hughes
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Energy Institute, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Energy Institute, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - Lin Jiang
- Molecular Biology Institute, University of California, Los Angeles, CA 90095;
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - David S Eisenberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Energy Institute, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
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43
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Basavalingappa V, Bera S, Xue B, Azuri I, Tang Y, Tao K, Shimon LJW, Sawaya MR, Kolusheva S, Eisenberg DS, Kronik L, Cao Y, Wei G, Gazit E. Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid. Nat Commun 2019; 10:5256. [PMID: 31748568 PMCID: PMC6868146 DOI: 10.1038/s41467-019-13250-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/23/2019] [Indexed: 01/25/2023] Open
Abstract
The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m-1 and Young's modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free "basket" formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.
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Affiliation(s)
- Vasantha Basavalingappa
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Ido Azuri
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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44
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Seidler PM, Boyer DR, Murray KA, Yang TP, Bentzel M, Sawaya MR, Rosenberg G, Cascio D, Williams CK, Newell KL, Ghetti B, DeTure MA, Dickson DW, Vinters HV, Eisenberg DS. Structure-based inhibitors halt prion-like seeding by Alzheimer's disease-and tauopathy-derived brain tissue samples. J Biol Chem 2019; 294:16451-16464. [PMID: 31537646 PMCID: PMC6827308 DOI: 10.1074/jbc.ra119.009688] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/13/2019] [Indexed: 01/04/2023] Open
Abstract
In Alzheimer's disease (AD) and tauopathies, tau aggregation accompanies progressive neurodegeneration. Aggregated tau appears to spread between adjacent neurons and adjacent brain regions by prion-like seeding. Hence, inhibitors of this seeding offer a possible route to managing tauopathies. Here, we report the 1.0 Å resolution micro-electron diffraction structure of an aggregation-prone segment of tau with the sequence SVQIVY, present in the cores of patient-derived fibrils from AD and tauopathies. This structure illuminates how distinct interfaces of the parent segment, containing the sequence VQIVYK, foster the formation of distinct structures. Peptide-based fibril-capping inhibitors designed to target the two VQIVYK interfaces blocked proteopathic seeding by patient-derived fibrils. These VQIVYK inhibitors add to a panel of tau-capping inhibitors that targets specific polymorphs of recombinant and patient-derived tau fibrils. Inhibition of seeding initiated by brain tissue extracts differed among donors with different tauopathies, suggesting that particular fibril polymorphs of tau are associated with certain tauopathies. Donors with progressive supranuclear palsy exhibited more variation in inhibitor sensitivity, suggesting that fibrils from these donors were more polymorphic and potentially vary within individual donor brains. Our results suggest that a subset of inhibitors from our panel could be specific for particular disease-associated polymorphs, whereas inhibitors that blocked seeding by extracts from all of the tauopathies tested could be used to broadly inhibit seeding by multiple disease-specific tau polymorphs. Moreover, we show that tau-capping inhibitors can be transiently expressed in HEK293 tau biosensor cells, indicating that nucleic acid-based vectors can be used for inhibitor delivery.
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Affiliation(s)
- Paul Matthew Seidler
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - David R Boyer
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Kevin A Murray
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Tianxiao P Yang
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Megan Bentzel
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Gregory Rosenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Duilio Cascio
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Christopher Kazu Williams
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - Kathy L Newell
- Indiana University School of Medicine, Indianapolis, Indiana 46202
| | | | - Michael A DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224
| | - Harry V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
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45
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Makam P, Yamijala SSRKC, Tao K, Shimon LJW, Eisenberg DS, Sawaya MR, Wong BM, Gazit E. Non-proteinaceous hydrolase comprised of a phenylalanine metallo-supramolecular amyloid-like structure. Nat Catal 2019; 2:977-985. [PMID: 31742246 PMCID: PMC6861134 DOI: 10.1038/s41929-019-0348-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Enzymatic activity is crucial for various technological applications, yet the complex structures and limited stability of enzymes often hinder their use. Hence, de novo design of robust biocatalysts that are much simpler than their natural counterparts and possess enhanced catalytic activity has long been a goal in biotechnology. Here, we present evidence for the ability of a single amino acid to self-assemble into a potent and stable catalytic structural entity. Spontaneously, phenylalanine (F) molecules coordinate with zinc ions to form a robust, layered, supramolecular amyloid-like ordered architecture (F-Zn(ii)) and exhibit remarkable carbonic anhydrase-like catalytic activity. Notably, amongst the reported artificial biomolecular hydrolases, F-Zn(ii) displays the lowest molecular mass and highest catalytic efficiency, in addition to reusability, thermal stability, substrate specificity, stereoselectivity and rapid catalytic CO2 hydration ability. Thus, this report provides a rational path towards future de novo design of minimalistic biocatalysts for biotechnological and industrial applications.
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Affiliation(s)
- Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Linda J. W. Shimon
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - David S. Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael R. Sawaya
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bryan M. Wong
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Department of Physics and Astronomy, and Materials Science and Engineering Program, University of California, Riverside, CA, USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
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46
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Griner SL, Seidler P, Bowler J, Murray KA, Yang TP, Sahay S, Sawaya MR, Cascio D, Rodriguez JA, Philipp S, Sosna J, Glabe CG, Gonen T, Eisenberg DS. Structure-based inhibitors of amyloid beta core suggest a common interface with tau. eLife 2019; 8:46924. [PMID: 31612856 PMCID: PMC6850776 DOI: 10.7554/elife.46924] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 10/04/2019] [Indexed: 01/04/2023] Open
Abstract
Alzheimer’s disease (AD) pathology is characterized by plaques of amyloid beta (Aβ) and neurofibrillary tangles of tau. Aβ aggregation is thought to occur at early stages of the disease, and ultimately gives way to the formation of tau tangles which track with cognitive decline in humans. Here, we report the crystal structure of an Aβ core segment determined by MicroED and in it, note characteristics of both fibrillar and oligomeric structure. Using this structure, we designed peptide-based inhibitors that reduce Aβ aggregation and toxicity of already-aggregated species. Unexpectedly, we also found that these inhibitors reduce the efficiency of Aβ-mediated tau aggregation, and moreover reduce aggregation and self-seeding of tau fibrils. The ability of these inhibitors to interfere with both Aβ and tau seeds suggests these fibrils share a common epitope, and supports the hypothesis that cross-seeding is one mechanism by which amyloid is linked to tau aggregation and could promote cognitive decline.
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Affiliation(s)
- Sarah L Griner
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Paul Seidler
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Jeannette Bowler
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Kevin A Murray
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Tianxiao Peter Yang
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Shruti Sahay
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Michael R Sawaya
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Duilio Cascio
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Jose A Rodriguez
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
| | - Stephan Philipp
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
| | - Justyna Sosna
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
| | - Charles G Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States.,Biochemistry Department, Faculty of Science and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tamir Gonen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - David S Eisenberg
- UCLA-DOE Institute, Department of Biological Chemistry, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
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47
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Warmack RA, Boyer DR, Zee CT, Richards LS, Sawaya MR, Cascio D, Gonen T, Eisenberg DS, Clarke SG. Structure of amyloid-β (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface. Nat Commun 2019; 10:3357. [PMID: 31350392 PMCID: PMC6659688 DOI: 10.1038/s41467-019-11183-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
Amyloid-β (Aβ) harbors numerous posttranslational modifications (PTMs) that may affect Alzheimer's disease (AD) pathogenesis. Here we present the 1.1 Å resolution MicroED structure of an Aβ 20-34 fibril with and without the disease-associated PTM, L-isoaspartate, at position 23 (L-isoAsp23). Both wild-type and L-isoAsp23 protofilaments adopt β-helix-like folds with tightly packed cores, resembling the cores of full-length fibrillar Aβ structures, and both self-associate through two distinct interfaces. One of these is a unique Aβ interface strengthened by the isoaspartyl modification. Powder diffraction patterns suggest a similar structure may be adopted by protofilaments of an analogous segment containing the heritable Iowa mutation, Asp23Asn. Consistent with its early onset phenotype in patients, Asp23Asn accelerates aggregation of Aβ 20-34, as does the L-isoAsp23 modification. These structures suggest that the enhanced amyloidogenicity of the modified Aβ segments may also reduce the concentration required to achieve nucleation and therefore help spur the pathogenesis of AD.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - David R Boyer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Logan S Richards
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Tamir Gonen
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1737, USA.,Department of Physiology, University of California, Los Angeles, Los Angeles, CA, 90095-1751, USA
| | - David S Eisenberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1737, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095-1570, USA.
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Warmack RA, Boyer DR, Zee CT, Richards LS, Sawaya MR, Cascio D, Gonen T, Eisenberg DS, Clarke SG. Visualization of the core of a modified Amyloid-β polymorph with MicroED. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s010876731909617x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abskharon R, Seidler P, Sawaya MR, Cascio D, Philipp S, Glabe CG, Eisenberg DS. P4‐697: ATOMIC STRUCTURES OF A SINGLE CHAIN ANTIBODY THAT BINDS AND INHIBITS SEEDING BY TAU OLIGOMERS. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.09.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | - Paul Seidler
- University of California Los Angeles Los Angeles CA USA
| | | | - Duilio Cascio
- University of California Los Angeles Los Angeles CA USA
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Siegel SD, Amer BR, Wu C, Sawaya MR, Gosschalk JE, Clubb RT, Ton-That H. Erratum for Siegel et al., "Structure and Mechanism of LcpA, a Phosphotransferase That Mediates Glycosylation of a Gram-Positive Bacterial Cell Wall-Anchored Protein". mBio 2019; 10:e00617-19. [PMID: 30992357 PMCID: PMC6469975 DOI: 10.1128/mbio.00617-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sara D Siegel
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Brendan R Amer
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Chenggang Wu
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
| | - Michael R Sawaya
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Jason E Gosschalk
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Hung Ton-That
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas, USA
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California, USA
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