1
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Kreutzer AG, Parrocha CMT, Haerianardakani S, Guaglianone G, Nguyen JT, Diab MN, Yong W, Perez-Rosendahl M, Head E, Nowick JS. Antibodies Raised Against an Aβ Oligomer Mimic Recognize Pathological Features in Alzheimer's Disease and Associated Amyloid-Disease Brain Tissue. ACS CENTRAL SCIENCE 2024; 10:104-121. [PMID: 38292607 PMCID: PMC10823522 DOI: 10.1021/acscentsci.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024]
Abstract
Antibodies that target the β-amyloid peptide (Aβ) and its associated assemblies are important tools in Alzheimer's disease research and have emerged as promising Alzheimer's disease therapies. This paper reports the creation and characterization of a triangular Aβ trimer mimic composed of Aβ17-36 β-hairpins and the generation and study of polyclonal antibodies raised against the Aβ trimer mimic. The Aβ trimer mimic is covalently stabilized by three disulfide bonds at the corners of the triangular trimer to create a homogeneous oligomer. Structural, biophysical, and cell-based studies demonstrate that the Aβ trimer mimic shares characteristics with oligomers of full-length Aβ. X-ray crystallography elucidates the structure of the trimer and reveals that four copies of the trimer assemble to form a dodecamer. SDS-PAGE, size exclusion chromatography, and dynamic light scattering reveal that the trimer also forms higher-order assemblies in solution. Cell-based toxicity assays show that the trimer elicits LDH release, decreases ATP levels, and activates caspase-3/7 mediated apoptosis. Immunostaining studies on brain slices from people who lived with Alzheimer's disease and people who lived with Down syndrome reveal that the polyclonal antibodies raised against the Aβ trimer mimic recognize pathological features including different types of Aβ plaques and cerebral amyloid angiopathy.
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Affiliation(s)
- Adam G Kreutzer
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Chelsea Marie T Parrocha
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, United States
| | - Sepehr Haerianardakani
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Gretchen Guaglianone
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Jennifer T Nguyen
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, United States
| | - Michelle N Diab
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - William Yong
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California 92697, United States
| | - Mari Perez-Rosendahl
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California 92697, United States
| | - Elizabeth Head
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California 92697, United States
| | - James S Nowick
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, United States
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2
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Kreutzer AG, Guaglianone G, Yoo S, Parrocha CMT, Ruttenberg SM, Malonis RJ, Tong K, Lin YF, Nguyen JT, Howitz WJ, Diab MN, Hamza IL, Lai JR, Wysocki VH, Nowick JS. Probing differences among Aβ oligomers with two triangular trimers derived from Aβ. Proc Natl Acad Sci U S A 2023; 120:e2219216120. [PMID: 37216514 PMCID: PMC10235986 DOI: 10.1073/pnas.2219216120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The assembly of the β-amyloid peptide (Aβ) to form oligomers and fibrils is closely associated with the pathogenesis and progression of Alzheimer's disease. Aβ is a shape-shifting peptide capable of adopting many conformations and folds within the multitude of oligomers and fibrils the peptide forms. These properties have precluded detailed structural elucidation and biological characterization of homogeneous, well-defined Aβ oligomers. In this paper, we compare the structural, biophysical, and biological characteristics of two different covalently stabilized isomorphic trimers derived from the central and C-terminal regions Aβ. X-ray crystallography reveals the structures of the trimers and shows that each trimer forms a ball-shaped dodecamer. Solution-phase and cell-based studies demonstrate that the two trimers exhibit markedly different assembly and biological properties. One trimer forms small soluble oligomers that enter cells through endocytosis and activate capase-3/7-mediated apoptosis, while the other trimer forms large insoluble aggregates that accumulate on the outer plasma membrane and elicit cellular toxicity through an apoptosis-independent mechanism. The two trimers also exhibit different effects on the aggregation, toxicity, and cellular interaction of full-length Aβ, with one trimer showing a greater propensity to interact with Aβ than the other. The studies described in this paper indicate that the two trimers share structural, biophysical, and biological characteristics with oligomers of full-length Aβ. The varying structural, assembly, and biological characteristics of the two trimers provide a working model for how different Aβ trimers can assemble and lead to different biological effects, which may help shed light on the differences among Aβ oligomers.
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Affiliation(s)
- Adam G. Kreutzer
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | | | - Stan Yoo
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | | | | | - Ryan J. Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Karen Tong
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Yu-Fu Lin
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH43210
| | - Jennifer T. Nguyen
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA92697
| | - William J. Howitz
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Michelle N. Diab
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Imane L. Hamza
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH43210
| | - James S. Nowick
- Department of Chemistry, University of California Irvine, Irvine, CA92697
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA92697
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3
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Randall JR, DuPai CD, Cole TJ, Davidson G, Groover KE, Slater SL, Mavridou DA, Wilke CO, Davies BW. Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. SCIENCE ADVANCES 2023; 9:eade0008. [PMID: 36630516 PMCID: PMC9833666 DOI: 10.1126/sciadv.ade0008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Peptide macrocycles are a rapidly emerging class of therapeutic, yet the design of their structure and activity remains challenging. This is especially true for those with β-hairpin structure due to weak folding properties and a propensity for aggregation. Here, we use proteomic analysis and common antimicrobial features to design a large peptide library with macrocyclic β-hairpin structure. Using an activity-driven high-throughput screen, we identify dozens of peptides killing bacteria through selective membrane disruption and analyze their biochemical features via machine learning. Active peptides contain a unique constrained structure and are highly enriched for cationic charge with arginine in their turn region. Our results provide a synthetic strategy for structured macrocyclic peptide design and discovery while also elucidating characteristics important for β-hairpin antimicrobial peptide activity.
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Affiliation(s)
- Justin R. Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Cory D. DuPai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - T. Jeffrey Cole
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Gillian Davidson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Kyra E. Groover
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Sabrina L. Slater
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Claus O. Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Bryan W. Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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4
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D'mello VC, Goldsztejn G, Rao Mundlapati V, Brenner V, Gloaguen E, Charnay‐Pouget F, Aitken DJ, Mons M. Characterization of Asx Turn Types and Their Connate Relationship with β‐Turns. Chemistry 2022; 28:e202104328. [DOI: 10.1002/chem.202104328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Viola C. D'mello
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Graphene Research Labs KIADB IT Park Near Airport Bengaluru 562149 India
| | - Gildas Goldsztejn
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Université Paris-Saclay, CNRS Institut des Sciences Moléculaires d'Orsay (ISMO) 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Institut de Recherche en Astrophysique et Planétologie (IRAP) Université de Toulouse (UPS), CNRS, CNES 9 Avenue du Colonel Roche 31028 Toulouse France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Florence Charnay‐Pouget
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
- Present address: Université Clermont Auvergne, CNRS SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | - David J. Aitken
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
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5
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Richaud AD, Zhao G, Hobloss S, Roche SP. Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops. J Org Chem 2021; 86:13535-13547. [PMID: 34499510 PMCID: PMC8576641 DOI: 10.1021/acs.joc.1c01442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Samir Hobloss
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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6
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Graham KA, Byrne A, Mason M, Andersen NH. Optimizing the fold stability of the circularly permuted Trp-cage motif. Biopolymers 2019; 110:e23327. [PMID: 31479150 DOI: 10.1002/bip.23327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/11/2019] [Accepted: 08/13/2019] [Indexed: 11/09/2022]
Abstract
Through optimization of the linker region and key stabilizing mutations, it has been possible to improve the stability of the circularly permuted (cp) Trp-cage miniprotein. However, even the most stable Trp-cage circular permutants are still less stable than the analogous standard topology (std) Trp-cages. Extending mutational studies of Trp-cage fold stability to cp-species, including analogs lacking chain terminal charges, has uncovered and quantitated some additional stabilizing and destabilizing interactions. Upon protonation, the circular permutants are destabilized to a much greater extent than the standard topology series. End effects, particularly Coulombic interactions, appear to be more important for the cp-series while the Y10/P4 interaction in the cp-series is not as significant a stabilizing feature as the corresponding Y3/P19 in the standard topology series.
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Affiliation(s)
- Katherine A Graham
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Aimee Byrne
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Micheal Mason
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
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7
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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8
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Sivanesam K, Kier BL, Whedon SD, Chatterjee C, Andersen NH. Biological consequences of improving the structural stability of hairpins that have antimicrobial activity. J Pept Sci 2018; 23:899-906. [PMID: 29193517 DOI: 10.1002/psc.3054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 11/11/2022]
Abstract
Designing new antimicrobial peptides (AMPs) focuses heavily on the activity of the peptide and less on the elements that stabilize the secondary structure of these peptides. Studies have shown that improving the structure of naturally occurring AMPs can affect activity and so here we explore the relationship between structure and activity of two non-naturally occurring AMPs. We have used a backbone-cyclized peptide as a template and designed an uncyclized analogue of this peptide that has antimicrobial activity. We focused on beta-hairpin-like structuring features. Improvements to the structure of this peptide reduced the activity of the peptide against gram-negative, Escherichia coli but improved the activity against gram-positive, Corynebacterium glutamicum. Distinctions in structuring effects on gram-negative versus gram-positive activity were also seen in a second peptide system. Structural improvements resulted in a peptide that was more active than the native against gram-positive bacterium but less active against gram-negative bacterium. Our results show that there is not always a correlation between improved hairpin-structuring and activity. Other factors such as the type of bacteria being targeted as well as net positive charge can play a role in the potency of AMPs. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Kalkena Sivanesam
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Samuel D Whedon
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
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9
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Schulte M, Panwalkar V, Freischem S, Willbold D, Dingley AJ. Proline Restricts Loop I Conformation of the High Affinity WW Domain from Human Nedd4-1 to a Ligand Binding-Competent Type I β-Turn. J Phys Chem B 2018; 122:4219-4230. [PMID: 29595969 DOI: 10.1021/acs.jpcb.7b11637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence alignment of the four WW domains from human Nedd4-1 (neuronal precursor cell expressed developmentally down-regulated gene 4-1) reveals that the highest sequence diversity exists in loop I. Three residues in this type I β-turn interact with the PPxY motif of the human epithelial Na+ channel (hENaC) subunits, indicating that peptide affinity is defined by the loop I sequence. The third WW domain (WW3*) has the highest ligand affinity and unlike the other three hNedd4-1 WW domains or other WW domains studied contains the highly statistically preferred proline at the ( i + 1) position found in β-turns. In this report, molecular dynamics simulations and experimental data were combined to characterize loop I stability and dynamics. Exchange of the proline to the equivalent residue in WW4 (Thr) results in the presence of a predominantly open seven residue Ω loop rather than the type I β-turn conformation for the wild-type apo-WW3*. In the presence of the ligand, the structure of the mutated loop I is locked into a type I β-turn. Thus, proline in loop I ensures a stable peptide binding-competent β-turn conformation, indicating that amino acid sequence modulates local flexibility to tune binding preferences and stability of dynamic interaction motifs.
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Affiliation(s)
- Marianne Schulte
- ICS-6 (Strukturbiochemie) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40225 Düsseldorf , Germany
| | - Vineet Panwalkar
- ICS-6 (Strukturbiochemie) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40225 Düsseldorf , Germany
| | - Stefan Freischem
- ICS-6 (Strukturbiochemie) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40225 Düsseldorf , Germany
| | - Dieter Willbold
- ICS-6 (Strukturbiochemie) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40225 Düsseldorf , Germany
| | - Andrew J Dingley
- ICS-6 (Strukturbiochemie) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40225 Düsseldorf , Germany
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10
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Zamora-Carreras H, Maestro B, Strandberg E, Ulrich AS, Sanz JM, Jiménez MÁ. Roles of Amphipathicity and Hydrophobicity in the Micelle-Driven Structural Switch of a 14-mer Peptide Core from a Choline-Binding Repeat. Chemistry 2018; 24:5825-5839. [PMID: 29369425 DOI: 10.1002/chem.201704802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 01/16/2023]
Abstract
Choline-binding repeats (CBRs) are ubiquitous sequences with a β-hairpin core that are found in the surface proteins of several microorganisms such as S. pneumoniae (pneumococcus). Previous studies on a 14-mer CBR sequence derived from the pneumoccal LytA autolysin (LytA239-252 peptide) have demonstrated a switch behaviour for this peptide, so that it acquires a stable, native-like β-hairpin conformation in aqueous solution but is reversibly transformed into an amphipathic α-helix in the presence of detergent micelles. With the aim of understanding the factors responsible for this unusual β-hairpin to α-helix transition, and to specifically assess the role of peptide hydrophobicity and helical amphipathicity in the process, we designed a series of LytA239-252 variants affecting these two parameters and studied their interaction with dodecylphosphocholine (DPC) micelles by solution NMR, circular dichroism and fluorescence spectroscopies. Our results indicate that stabilising cross-strand interactions become essential for β-hairpin stability in the absence of optimal turn sequences. Moreover, both amphipathicity and hydrophobicity display comparable importance for helix stabilisation of CBR-derived peptides in micelles, indicating that these sequences represent a novel class of micelle/membrane-interacting peptides.
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Affiliation(s)
- Héctor Zamora-Carreras
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Beatriz Maestro
- Instituto de Biología MolecularyCelular, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021, Karlsruhe, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Jesús M Sanz
- Instituto de Biología MolecularyCelular, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain.,Biological Research Centre (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Ángeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
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11
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Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Habka S, Sohn WY, Vaquero-Vara V, Géléoc M, Tardivel B, Brenner V, Gloaguen E, Mons M. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins. Phys Chem Chem Phys 2018; 20:3411-3423. [DOI: 10.1039/c7cp07605c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.
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Affiliation(s)
- S. Habka
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - W. Y. Sohn
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | | | - M. Géléoc
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - B. Tardivel
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - V. Brenner
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - E. Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - M. Mons
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
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13
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Anderson JM, Andersen NH. A pH Switch for β-Sheet Protein Folding. Angew Chem Int Ed Engl 2017; 56:7074-7077. [PMID: 28523654 PMCID: PMC5607017 DOI: 10.1002/anie.201700860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/26/2017] [Indexed: 01/24/2023]
Abstract
Protein design advancements have led to biotechnological strategies based on more stable and more specific structures. Herein we present a 6-residue sequence (HPATGK) that acts as a stable structure-nucleating turn at physiological and higher pH but is notably unfavorable for chain direction reversal at low pH. When placed into the turn of a β-sheet, this leads to a pH switch of folding. Using a standard 3-stranded β-sheet model, the WW domain, it was found that the pH switch sequence insertion caused minimal change at pH 8 but a ca. 50 °C drop in the melting temperature (Tm ) was observed at pH 2.5: ΔΔGF ≥11.3 kJ mol-1 . Using the strategies demonstrated in this article, the redesign of β-sheets to contain a global, or local, pH-dependent conformational switch should be possible.
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14
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A pH Switch for β-Sheet Protein Folding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Kreutzer AG, Yoo S, Spencer RK, Nowick JS. Stabilization, Assembly, and Toxicity of Trimers Derived from Aβ. J Am Chem Soc 2017; 139:966-975. [PMID: 28001392 PMCID: PMC5256483 DOI: 10.1021/jacs.6b11748] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Oligomers
of the β-amyloid peptide Aβ have emerged
as important contributors to neurodegeneration in Alzheimer’s
disease. Mounting evidence suggests that Aβ trimers and higher-order
oligomers derived from trimers have special significance in the early
stages of Alzheimer’s disease. Elucidating the structures of
these trimers and higher-order oligomers is paramount for understanding
their role in neurodegeneration. This paper describes the design,
synthesis, X-ray crystallographic structures, and biophysical and
biological properties of two stabilized trimers derived from the central
and C-terminal regions of Aβ. These triangular
trimers are stabilized through three disulfide cross-links between
the monomer subunits. The X-ray crystallographic structures reveal
that the stabilized trimers assemble hierarchically to form hexamers,
dodecamers, and annular porelike structures. Solution-phase biophysical
studies reveal that the stabilized trimers assemble in solution to
form oligomers that recapitulate some of the higher-order assemblies
observed crystallographically. The stabilized trimers share many of
the biological characteristics of oligomers of full-length Aβ,
including toxicity toward a neuronally derived human cell line, activation
of caspase-3 mediated apoptosis, and reactivity with the oligomer-specific
antibody A11. These studies support the biological significance of
the triangular trimer assembly of Aβ β-hairpins and may
offer a deeper understanding of the molecular basis of Alzheimer’s
disease.
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Affiliation(s)
- Adam G Kreutzer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Stan Yoo
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Ryan K Spencer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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