51
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Kakkar V, Månsson C, de Mattos EP, Bergink S, van der Zwaag M, van Waarde MAWH, Kloosterhuis NJ, Melki R, van Cruchten RTP, Al-Karadaghi S, Arosio P, Dobson CM, Knowles TPJ, Bates GP, van Deursen JM, Linse S, van de Sluis B, Emanuelsson C, Kampinga HH. The S/T-Rich Motif in the DNAJB6 Chaperone Delays Polyglutamine Aggregation and the Onset of Disease in a Mouse Model. Mol Cell 2016; 62:272-283. [PMID: 27151442 DOI: 10.1016/j.molcel.2016.03.017] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 01/14/2016] [Accepted: 03/10/2016] [Indexed: 01/30/2023]
Abstract
Expanded CAG repeats lead to debilitating neurodegenerative disorders characterized by aggregation of proteins with expanded polyglutamine (polyQ) tracts. The mechanism of aggregation involves primary and secondary nucleation steps. We show how a noncanonical member of the DNAJ-chaperone family, DNAJB6, inhibits the conversion of soluble polyQ peptides into amyloid fibrils, in particular by suppressing primary nucleation. This inhibition is mediated by a serine/threonine-rich region that provides an array of surface-exposed hydroxyl groups that bind to polyQ peptides and may disrupt the formation of the H bonds essential for the stability of amyloid fibrils. Early prevention of polyQ aggregation by DNAJB6 occurs also in cells and leads to delayed neurite retraction even before aggregates are visible. In a mouse model, brain-specific coexpression of DNAJB6 delays polyQ aggregation, relieves symptoms, and prolongs lifespan, pointing to DNAJB6 as a potential target for disease therapy and tool for unraveling early events in the onset of polyQ diseases.
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Affiliation(s)
- Vaishali Kakkar
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Cecilia Månsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Eduardo P de Mattos
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands; Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Steven Bergink
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Marianne van der Zwaag
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Maria A W H van Waarde
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Niels J Kloosterhuis
- Department of Pediatrics, Molecular Genetics Section, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Ronald Melki
- Neuroscience Paris-Saclay Institute of Neuroscience, Centre National de la Recherche Scientifique, 91190 Gif-Sur-Yvette, France
| | - Remco T P van Cruchten
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Salam Al-Karadaghi
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Paolo Arosio
- Department of Chemistry, University of Cambridge, Cambridge CB2 1TN, UK
| | | | | | - Gillian P Bates
- Department of Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK
| | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Bart van de Sluis
- Department of Pediatrics, Molecular Genetics Section, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Harm H Kampinga
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands.
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52
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Punihaole D, Workman RJ, Hong Z, Madura JD, Asher SA. Polyglutamine Fibrils: New Insights into Antiparallel β-Sheet Conformational Preference and Side Chain Structure. J Phys Chem B 2016; 120:3012-26. [PMID: 26947327 DOI: 10.1021/acs.jpcb.5b11380] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the structure of polyglutamine (polyQ) amyloid-like fibril aggregates is crucial to gaining insights into the etiology of at least ten neurodegenerative disorders, including Huntington's disease. Here, we determine the structure of D2Q10K2 (Q10) fibrils using ultraviolet resonance Raman (UVRR) spectroscopy and molecular dynamics (MD). Using UVRR, we determine the fibril peptide backbone Ψ and glutamine (Gln) side chain χ3 dihedral angles. We find that most of the fibril peptide bonds adopt antiparallel β-sheet conformations; however, a small population of peptide bonds exist in parallel β-sheet structures. Using MD, we simulate three different potential fibril structural models that consist of either β-strands or β-hairpins. Comparing the experimentally measured Ψ and χ3 angle distributions to those obtained from the MD simulated models, we conclude that the basic structural motif of Q10 fibrils is an extended β-strand structure. Importantly, we determine from our MD simulations that Q10 fibril antiparallel β-sheets are thermodynamically more stable than parallel β-sheets. This accounts for why polyQ fibrils preferentially adopt antiparallel β-sheet conformations instead of in-register parallel β-sheets like most amyloidogenic peptides. In addition, we directly determine, for the first time, the structures of Gln side chains. Our structural data give new insights into the role that the Gln side chains play in the stabilization of polyQ fibrils. Finally, our work demonstrates the synergistic power and utility of combining UVRR measurements and MD modeling to determine the structure of amyloid-like fibrils.
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Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Riley J Workman
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University , Pittsburgh, Pennsylvania 15282, United States
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Jeffry D Madura
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University , Pittsburgh, Pennsylvania 15282, United States
| | - Sanford A Asher
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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53
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Huntingtin exon 1 fibrils feature an interdigitated β-hairpin-based polyglutamine core. Proc Natl Acad Sci U S A 2016; 113:1546-51. [PMID: 26831073 DOI: 10.1073/pnas.1521933113] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Polyglutamine expansion within the exon1 of huntingtin leads to protein misfolding, aggregation, and cytotoxicity in Huntington's disease. This incurable neurodegenerative disease is the most prevalent member of a family of CAG repeat expansion disorders. Although mature exon1 fibrils are viable candidates for the toxic species, their molecular structure and how they form have remained poorly understood. Using advanced magic angle spinning solid-state NMR, we directly probe the structure of the rigid core that is at the heart of huntingtin exon1 fibrils and other polyglutamine aggregates, via measurements of long-range intramolecular and intermolecular contacts, backbone and side-chain torsion angles, relaxation measurements, and calculations of chemical shifts. These experiments reveal the presence of β-hairpin-containing β-sheets that are connected through interdigitating extended side chains. Despite dramatic differences in aggregation behavior, huntingtin exon1 fibrils and other polyglutamine-based aggregates contain identical β-strand-based cores. Prior structural models, derived from X-ray fiber diffraction and computational analyses, are shown to be inconsistent with the solid-state NMR results. Internally, the polyglutamine amyloid fibrils are coassembled from differently structured monomers, which we describe as a type of "intrinsic" polymorphism. A stochastic polyglutamine-specific aggregation mechanism is introduced to explain this phenomenon. We show that the aggregation of mutant huntingtin exon1 proceeds via an intramolecular collapse of the expanded polyglutamine domain and discuss the implications of this observation for our understanding of its misfolding and aggregation mechanisms.
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54
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Walsh PS, Dean JC, McBurney C, Kang H, Gellman SH, Zwier TS. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences. Phys Chem Chem Phys 2016; 18:11306-22. [PMID: 27054830 DOI: 10.1039/c6cp01062h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase.
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Affiliation(s)
| | - Jacob C. Dean
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Carl McBurney
- Department of Chemistry
- University of Wisconsin-Madison
- Madison
- USA
| | - Hyuk Kang
- Department of Chemistry
- Ajou University
- Republic of Korea
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55
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Rossi M, Fang W, Michaelides A. Stability of Complex Biomolecular Structures: van der Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects. J Phys Chem Lett 2015; 6:4233-8. [PMID: 26722963 DOI: 10.1021/acs.jpclett.5b01899] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Biomolecules are complex systems stabilized by a delicate balance of weak interactions, making it important to assess all energetic contributions in an accurate manner. However, it is a priori unclear which contributions make more of an impact. Here, we examine stacked polyglutamine (polyQ) strands, a peptide repeat often found in amyloid aggregates. We investigate the role of hydrogen bond (HB) cooperativity, van der Waals (vdW) dispersion interactions, and quantum contributions to free energies, including anharmonicities through density functional theory and ab initio path integral simulations. Of these various factors, we find that the largest impact on structural stabilization comes from vdW interactions. HB cooperativity is the second largest contribution as the size of the stacked chain grows. Competing nuclear quantum effects make the net quantum contribution small but very sensitive to anharmonicities, vdW, and the number of HBs. Our results suggest that a reliable treatment of these systems can only be attained by considering all of these components.
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Affiliation(s)
- Mariana Rossi
- Physical and Theoretical Chemistry Lab, University of Oxford , South Parks Road, OX1 3QZ Oxford, United Kingdom
- St. Edmund Hall , Queen's Lane, OX1 4AR Oxford, United Kingdom
| | - Wei Fang
- Thomas Young Centre, London Centre for Nanotechnology, and Department of Chemistry, University College London , 17-19 Gordon Street, WC1H 0AH London, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology, and Department of Chemistry, University College London , 17-19 Gordon Street, WC1H 0AH London, United Kingdom
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56
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Punihaole D, Hong Z, Jakubek RS, Dahlburg EM, Geib S, Asher SA. Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations. J Phys Chem B 2015; 119:13039-51. [PMID: 26392216 PMCID: PMC5065012 DOI: 10.1021/acs.jpcb.5b07651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions.
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Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Elizabeth M. Dahlburg
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Steven Geib
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
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57
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Hernik A, Puławski W, Fedorczyk B, Tymecka D, Misicka A, Filipek S, Dzwolak W. Amyloidogenic Properties of Short α-L-Glutamic Acid Oligomers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10500-10507. [PMID: 26362583 DOI: 10.1021/acs.langmuir.5b02915] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Poly-L-glutamic acid (PLGA) forms amyloid-like β2-fibrils with the main spectral component of vibrational amide I' band unusually shifted below 1600 cm(-1). This distinct infrared feature has been attributed to the presence of bifurcated hydrogen bonds coupling C═O and N-D (N-H) groups of the main chains to glutamate side chains. Here, we investigate how decreasing the chain length of PLGA affects its capacity to form β2-fibrils. A series of acidified aqueous solutions of synthetic (l-Glu)n peptides (n ≈ 200, 10, 6, 5, 4, and 3) were incubated at high temperature. We observed that n = 4 is the critical chain length for which formation of aggregates with the β2-like infrared features is still observed under such conditions. Interestingly, according to atomic force microscopy (AFM), the self-assembly of (L-Glu)n chains varying vastly in length produces fibrils with rather uniform diameters of approximately 4-6 nm. Kinetic experiments on (L-Glu)5 and (L-Glu)200 peptides indicate that the fibrillation is significantly accelerated not only in the presence of homologous seeds but also upon cross-seeding, suggesting thereby a common self-assembly theme for (L-Glu)n chains of various lengths. Our results are discussed in the context of mechanisms of amyloidogenic fibrillation of homopolypeptides.
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Affiliation(s)
- Agnieszka Hernik
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Wojciech Puławski
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Bartłomiej Fedorczyk
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Dagmara Tymecka
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Aleksandra Misicka
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Sławomir Filipek
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Wojciech Dzwolak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
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58
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Fluitt AM, de Pablo JJ. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution. Biophys J 2015; 109:1009-18. [PMID: 26331258 PMCID: PMC4564678 DOI: 10.1016/j.bpj.2015.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/13/2015] [Accepted: 07/15/2015] [Indexed: 11/20/2022] Open
Abstract
Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.
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Affiliation(s)
- Aaron M Fluitt
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Juan J de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois; Argonne National Laboratory, Lemont, Illinois.
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59
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Mándity IM, Fülöp F. An overview of peptide and peptoid foldamers in medicinal chemistry. Expert Opin Drug Discov 2015; 10:1163-77. [PMID: 26289578 DOI: 10.1517/17460441.2015.1076790] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Foldamers are artificial self-organizing systems with various critical properties: i) a stable and designable secondary structure; ii) a larger molecular surface as compared with ordinary organic drug molecules; iii) appropriate control of the orientation of the side-chain functional groups; iv) resistance against proteolytic degradation, which leads to potentially increased oral bioavailability and a longer serum half-life relative to ordinary α-peptides; and v) the lower conformational freedom may result in increased receptor binding in comparison with the natural analogs. AREAS COVERED This article covers the general properties and types of foldamers. This includes highlighted examples of medicinal chemical applications, including antibacterial and cargo molecules, anti-Alzheimer compounds and protein-protein interaction modifiers. EXPERT OPINION Various new foldamers have been created with a range of structures and biological applications. Membrane-acting antibacterial foldamers have been introduced. A general property of these structures is their amphiphilic nature. The amphiphilicity can be stationary or induced by the membrane binding. Cell-penetrating foldamers have been described which serve as cargo molecules, and foldamers have been used as autophagy inducers. Anti-Alzheimer compounds too have been created and the greatest breakthrough was attained via the modification of protein-protein interactions. This can serve as the chemical and pharmaceutical basis for the relevance of foldamers in the future.
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Affiliation(s)
| | - Ferenc Fülöp
- a University of Szeged Institute of Pharmaceutical Chemistry , H-6720 Szeged, Eötvös u. 6, Hungary +36 62 545 768 ; +36 62 545 564 ; +36 62 545 705 ; ;
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60
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Arndt JR, Kondalaji SG, Maurer MM, Parker A, Legleiter J, Valentine SJ. Huntingtin N-Terminal Monomeric and Multimeric Structures Destabilized by Covalent Modification of Heteroatomic Residues. Biochemistry 2015; 54:4285-96. [PMID: 26098795 DOI: 10.1021/acs.biochem.5b00478] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early stage oligomer formation of the huntingtin protein may be driven by self-association of the 17-residue amphipathic α-helix at the protein's N-terminus (Nt17). Oligomeric structures have been implicated in neuronal toxicity and may represent important neurotoxic species in Huntington's disease. Therefore, a residue-specific structural characterization of Nt17 is crucial to understanding and potentially inhibiting oligomer formation. Native electrospray ion mobility spectrometry-mass spectrometry (IMS-MS) techniques and molecular dynamics simulations (MDS) have been applied to study coexisting monomer and multimer conformations of Nt17, independent of the remainder of huntingtin exon 1. MDS suggests gas-phase monomer ion structures comprise a helix-turn-coil configuration and a helix-extended-coil region. Elongated dimer species comprise partially helical monomers arranged in an antiparallel geometry. This stacked helical bundle may represent the earliest stages of Nt17-driven oligomer formation. Nt17 monomers and multimers have been further probed using diethylpyrocarbonate (DEPC). An N-terminal site (N-terminus of Threonine-3) and Lysine-6 are modified at higher DEPC concentrations, which led to the formation of an intermediate monomer structure. These modifications resulted in decreased extended monomer ion conformers, as well as a reduction in multimer formation. From the MDS experiments for the dimer ions, Lys6 residues in both monomer constituents interact with Ser16 and Glu12 residues on adjacent peptides; therefore, the decrease in multimer formation could result from disruption of these or similar interactions. This work provides a structurally selective model from which to study Nt17 self-association and provides critical insight toward Nt17 multimerization and, possibly, the early stages of huntingtin exon 1 aggregation.
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Affiliation(s)
- James R Arndt
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Samaneh Ghassabi Kondalaji
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Megan M Maurer
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Arlo Parker
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J Valentine
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
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61
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Hong J, Gierasch LM, Liu Z. Its preferential interactions with biopolymers account for diverse observed effects of trehalose. Biophys J 2015; 109:144-53. [PMID: 26153711 PMCID: PMC4572414 DOI: 10.1016/j.bpj.2015.05.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 10/23/2022] Open
Abstract
Biopolymer homeostasis underlies the health of organisms, and protective osmolytes have emerged as one strategy used by Nature to preserve biopolymer homeostasis. However, a great deal remains unknown about the mechanism of action of osmolytes. Trehalose, as a prominent example, stabilizes proteins against denaturation by extreme temperature and denaturants, preserves membrane integrity upon freezing or in dry conditions, inhibits polyQ-mediated protein aggregation, and suppresses the aggregation of denatured proteins. The underlying thermodynamic mechanisms of such diverse effects of trehalose remain unclear or controversial. In this study, we applied the surface-additive method developed in the Record laboratory to attack this issue. We characterized the key features of trehalose-biopolymer preferential interactions and found that trehalose has strong unfavorable interactions with aliphatic carbon and significant favorable interactions with amide/anionic oxygen. This dissection has allowed us to elucidate the diverse effects of trehalose and to identify the crucial functional group(s) responsible for its effects. With (semi)quantitative thermodynamic analysis, we discovered that 1) the unfavorable interaction of trehalose with hydrophobic surfaces is the dominant factor in its effect on protein stability, 2) the favorable interaction of trehalose with polar amides enables it to inhibit polyQ-mediated protein aggregation and the aggregation of denatured protein in general, and 3) the favorable interaction of trehalose with phosphate oxygens, together with its unfavorable interaction with aliphatic carbons, enables trehalose to preserve membrane integrity in aqueous solution. These results provide a basis for a full understanding of the role of trehalose in biopolymer homeostasis and the reason behind its evolutionary selection as an osmolyte, as well as for a better application of trehalose as a chemical chaperone.
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Affiliation(s)
- Jiang Hong
- School of Life Science, Shanghai University, Shanghai, China.
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts
| | - Zhicheng Liu
- School of Life Science, Shanghai University, Shanghai, China
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62
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Mompeán M, Hervás R, Xu Y, Tran TH, Guarnaccia C, Buratti E, Baralle F, Tong L, Carrión-Vázquez M, McDermott AE, Laurents DV. Structural Evidence of Amyloid Fibril Formation in the Putative Aggregation Domain of TDP-43. J Phys Chem Lett 2015; 6:2608-15. [PMID: 26266742 PMCID: PMC5568655 DOI: 10.1021/acs.jpclett.5b00918] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
TDP-43 can form pathological proteinaceous aggregates linked to ALS and FTLD. Within the putative aggregation domain, engineered repeats of residues 341-366 can recruit endogenous TDP-43 into aggregates inside cells; however, the nature of these aggregates is a debatable issue. Recently, we showed that a coil to β-hairpin transition in a short peptide corresponding to TDP-43 residues 341-357 enables oligomerization. Here we provide definitive structural evidence for amyloid formation upon extensive characterization of TDP-43(341-357) via chromophore and antibody binding, electron microscopy (EM), solid-state NMR, and X-ray diffraction. On the basis of these findings, structural models for TDP-43(341-357) oligomers were constructed, refined, verified, and analyzed using docking, molecular dynamics, and semiempirical quantum mechanics methods. Interestingly, TDP-43(341-357) β-hairpins assemble into a novel parallel β-turn configuration showing cross-β spine, cooperative H-bonding, and tight side-chain packing. These results expand the amyloid foldome and could guide the development of future therapeutics to prevent this structural conversion.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física Rocasolano, CSIC Serrano 119, 28006 Madrid, Spain
- Corresponding Authors: (M.M.) Tel: +34 91-745-9543. Fax: +34 91-564-2431. . (D.V.L.)
| | - Rubén Hervás
- Instituto Cajal, CSIC Avda, Doctor Arce 37, E-28002 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Crta. de Cantoblanco no. 8, E-28049 Cantoblanco, Madrid, Spain
| | - Yunyao Xu
- Department of Chemistry, Columbia University, 344 Havemeyer Hall, New York, New York 10027, United States
| | - Timothy H. Tran
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Francisco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Mariano Carrión-Vázquez
- Instituto Cajal, CSIC Avda, Doctor Arce 37, E-28002 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Crta. de Cantoblanco no. 8, E-28049 Cantoblanco, Madrid, Spain
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, 344 Havemeyer Hall, New York, New York 10027, United States
| | - Douglas V. Laurents
- Instituto de Química Física Rocasolano, CSIC Serrano 119, 28006 Madrid, Spain
- Corresponding Authors: (M.M.) Tel: +34 91-745-9543. Fax: +34 91-564-2431. . (D.V.L.)
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63
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Bochicchio B, Pepe A, Crudele M, Belloy N, Baud S, Dauchez M. Tuning self-assembly in elastin-derived peptides. SOFT MATTER 2015; 11:3385-3395. [PMID: 25811498 DOI: 10.1039/c5sm00072f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Elastin-derived peptides are gaining increasing interest as potential biomaterials. Previous studies have demonstrated that short elastin-derived peptides are able to self-assemble into fibrils as the entire elastin protein. The motif responsible for that is the XGGZG motif at least three-fold repeated. In this work we have synthesized and studied, at molecular and supramolecular levels, four pentadecapeptides obtained by switching the X and Z residue with leucine and/or valine. We found that the four peptides formed different supramolecular structures corresponding to specific molecular conformations. Our results show that not only the residue type but also the exact position occupied by the residue in the motif is crucial in driving the self-aggregation. The aim of this work is to provide the basis for designing elastin-derived peptides with tunable supramolecular architecture.
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Affiliation(s)
- Brigida Bochicchio
- Department of Science, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy.
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64
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Man VH, Roland C, Sagui C. Structural determinants of polyglutamine protofibrils and crystallites. ACS Chem Neurosci 2015; 6:632-45. [PMID: 25604626 DOI: 10.1021/cn500358g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Nine inherited neurodegenerative diseases are associated with the expansion of the CAG codon. Once the translated polyglutamine expansion becomes longer than ~36 residues, it triggers the formation of intraneural protein aggregates that often display the signature of cross-β amyloid fibrils. Here, we use fully atomistic molecular dynamics simulations to probe the structural stability and conformational dynamics of both previously proposed and new polyglutamine aggregate models. We test the relative stability of parallel and antiparallel β sheets, and characterize possible steric interfaces between neighboring sheets and the effects of different alignments of the side-chain carboxamide dipoles. Results indicate that (i) different initial oligomer structures converge to crystals consistent with available diffraction data, after undergoing cooperative side-chain rotational transitions and quarter-stagger displacements on a microsecond time scale, (ii) structures previously deemed stable on a hundred nanosecond time scale are unstable over the microsecond time scale, and (iii) conversely, structures previously deemed unstable did not account for the correct side-chain packing and once the correct symmetry is considered the structures become stable for over a microsecond, due to tightly interdigitated side chains, which lock into highly regular polar zippers with inter-side-chain and backbone-side-chain hydrogen bonds. With these insights, we built Q40 monomeric models with different combinations of arc and hairpin turns and tested them for stability. The stable monomers were further probed as a function of repeat length. Our results are consistent with the aggregation threshold. These results explain and reconcile previously reported experimental and model discrepancies about polyglutamine aggregate structures.
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Affiliation(s)
- Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
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65
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Goyal B, Patel K, Srivastava KR, Durani S. De novo design of stereochemically-bent sixteen-residue β-hairpin as a hydrolase mimic. RSC Adv 2015. [DOI: 10.1039/c5ra19015k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Stepwise design of sixteen-residue β-hairpin as a hydrolase mimic involving fold design by stereochemical mutation followed by inverse-design of sequence.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | - Kirti Patel
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
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66
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Arndt JR, Brown RJ, Burke KA, Legleiter J, Valentine SJ. Lysine residues in the N-terminal huntingtin amphipathic α-helix play a key role in peptide aggregation. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:117-126. [PMID: 25601683 DOI: 10.1002/jms.3504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
Huntington's disease is a genetic neurodegenerative disorder caused by an expansion in a polyglutamine domain near the N-terminus of the huntingtin (htt) protein that results in the formation of protein aggregates. Here, htt aggregate structure has been examined using hydrogen-deuterium exchange techniques coupled with tandem mass spectrometry. The focus of the study is on the 17-residue N-terminal flanking region of the peptide that has been shown to alter htt aggregation kinetics and morphology. A top-down sequencing strategy employing electron transfer dissociation is utilized to determine the location of accessible and protected hydrogens. In these experiments, peptides aggregate in a deuterium-rich solvent at neutral pH and are subsequently subjected to deuterium-hydrogen back-exchange followed by rapid quenching, disaggregation, and tandem mass spectrometry analysis. Electrospray ionization of the peptide solution produces the [M + 5H](5+) to [M + 10H](10+) charge states and reveals the presence of multiple peptide sequences differing by single glutamine residues. The [M + 7H](7+) to [M + 9](9+) charge states corresponding to the full peptide are used in the electron transfer dissociation analyses. Evidence for protected residues is observed in the 17-residue N-terminal tract and specifically points to lysine residues as potentially playing a significant role in htt aggregation.
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Affiliation(s)
- James R Arndt
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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67
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Mishra R, Thakur AK. Amyloid nanospheres from polyglutamine rich peptides: assemblage through an intermolecular salt bridge interaction. Org Biomol Chem 2015; 13:4155-9. [DOI: 10.1039/c4ob02589j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amyloid fiber formation by two polyglutamine peptides through a nucleation polymerization pathway. An intermolecular salt bridge between the positively charged lysine and the negatively charged glutamate induces the formation of nanospherical amyloids through a non-nucleated pathway.
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Affiliation(s)
- Rahul Mishra
- Department of Biological Sciences and Bioengineering
- Indian Institute of Technology
- Kanpur
- India
| | - Ashwani K. Thakur
- Department of Biological Sciences and Bioengineering
- Indian Institute of Technology
- Kanpur
- India
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68
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An improved capping unit for stabilizing the ends of associated β-strands. FEBS Lett 2014; 588:4749-53. [PMID: 25451230 DOI: 10.1016/j.febslet.2014.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/14/2014] [Accepted: 11/06/2014] [Indexed: 12/25/2022]
Abstract
Understanding protein beta structures has been hindered by the challenge of designing small, well-folded β-sheet systems. A β-capping motif was previously designed to help solve this problem, but not without limitations, as the termini of this β-cap were not fully available for chain extension. Combining Coulombic side chain attractions with a Trp/Trp edge-to-face interaction we produced a new capping motif that provided greater β-sheet stability. This stability was maintained even in systems lacking a turn locus with a high propensity for chain direction reversal. The Coulombic cap was shown to improve β-sheet stability in a number of difficult systems, hence providing an additional tool for protein structure and folding studies.
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69
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Assembly of Aβ proceeds via monomeric nuclei. J Mol Biol 2014; 427:287-90. [PMID: 25451026 DOI: 10.1016/j.jmb.2014.10.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/21/2014] [Accepted: 10/26/2014] [Indexed: 11/21/2022]
Abstract
Aggregation of amyloid-β (Aβ) peptides is fundamental to Alzheimer's disease. It has now been shown that nucleated proliferation of Aβ fibrils utilizes a secondary mechanism with existing fibrils catalyzing the formation of new ones. Here it is shown that the data for Aβ40 and Aβ42 require that the nuclei be monomeric; that is, an initial, unfavorable conformational change is rate limiting for the processes that appear to be nucleation. Following the conformational change, the assembly process is "downhill" despite clear lag times and significant concentration dependence. The similarity to polyglutamine nucleation suggests that monomeric nuclei may be widespread in amyloid formation.
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70
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Hoop CL, Lin HK, Kar K, Hou Z, Poirier MA, Wetzel R, van der Wel PCA. Polyglutamine amyloid core boundaries and flanking domain dynamics in huntingtin fragment fibrils determined by solid-state nuclear magnetic resonance. Biochemistry 2014; 53:6653-66. [PMID: 25280367 PMCID: PMC4211650 DOI: 10.1021/bi501010q] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
In Huntington’s disease, expansion
of a polyglutamine (polyQ)
domain in the huntingtin (htt) protein leads to misfolding and aggregation.
There is much interest in the molecular features that distinguish
monomeric, oligomeric, and fibrillar species that populate the aggregation
pathway and likely differ in cytotoxicity. The mechanism and rate
of aggregation are greatly affected by the domains flanking the polyQ
segment within exon 1 of htt. A “protective” C-terminal
proline-rich flanking domain inhibits aggregation by inducing polyproline
II structure (PPII) within an extended portion of polyQ. The N-terminal
flanking segment (httNT) adopts an α-helical structure
as it drives aggregation, helps stabilize oligomers and fibrils, and
is seemingly integral to their supramolecular assembly. Via solid-state
nuclear magnetic resonance (ssNMR), we probe how, in the mature fibrils,
the htt flanking domains impact the polyQ domain and in particular
the localization of the β-structured amyloid core. Using residue-specific
and uniformly labeled samples, we find that the amyloid core occupies
most of the polyQ domain but ends just prior to the prolines. We probe
the structural and dynamical features of the remarkably abrupt β-sheet
to PPII transition and discuss the potential connections to certain
htt-binding proteins. We also examine the httNT α-helix
outside the polyQ amyloid core. Despite its presumed structural and
demonstrated stabilizing roles in the fibrils, quantitative ssNMR
measurements of residue-specific dynamics show that it undergoes distinct
solvent-coupled motion. This dynamical feature seems reminiscent of
molten-globule-like α-helix-rich features attributed to the
nonfibrillar oligomeric species of various amyloidogenic proteins.
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Affiliation(s)
- Cody L Hoop
- Department of Structural Biology, University of Pittsburgh School of Medicine , Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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71
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Röthlein C, Miettinen MS, Borwankar T, Bürger J, Mielke T, Kumke MU, Ignatova Z. Architecture of polyglutamine-containing fibrils from time-resolved fluorescence decay. J Biol Chem 2014; 289:26817-26828. [PMID: 25092288 DOI: 10.1074/jbc.m114.581991] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The disease risk and age of onset of Huntington disease (HD) and nine other repeat disorders strongly depend on the expansion of CAG repeats encoding consecutive polyglutamines (polyQ) in the corresponding disease protein. PolyQ length-dependent misfolding and aggregation are the hallmarks of CAG pathologies. Despite intense effort, the overall structure of these aggregates remains poorly understood. Here, we used sensitive time-dependent fluorescent decay measurements to assess the architecture of mature fibrils of huntingtin (Htt) exon 1 implicated in HD pathology. Varying the position of the fluorescent labels in the Htt monomer with expanded 51Q (Htt51Q) and using structural models of putative fibril structures, we generated distance distributions between donors and acceptors covering all possible distances between the monomers or monomer dimensions within the polyQ amyloid fibril. Using Monte Carlo simulations, we systematically scanned all possible monomer conformations that fit the experimentally measured decay times. Monomers with four-stranded 51Q stretches organized into five-layered β-sheets with alternating N termini of the monomers perpendicular to the fibril axis gave the best fit to our data. Alternatively, the core structure of the polyQ fibrils might also be a zipper layer with antiparallel four-stranded stretches as this structure showed the next best fit. All other remaining arrangements are clearly excluded by the data. Furthermore, the assessed dimensions of the polyQ stretch of each monomer provide structural evidence for the observed polyQ length threshold in HD pathology. Our approach can be used to validate the effect of pharmacological substances that inhibit or alter amyloid growth and structure.
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Affiliation(s)
- Christoph Röthlein
- Institute of Biochemistry and Biologie and University of Potsdam, 14467 Potsdam.
| | - Markus S Miettinen
- Department of Theory of Biological Soft Matter Systems, Institute of Theoretical Physics, Free University Berlin, 14195 Berlin
| | - Tejas Borwankar
- Institute of Biochemistry and Biologie and University of Potsdam, 14467 Potsdam
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, and
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael U Kumke
- Institute of Chemistry, University of Potsdam, 14467 Potsdam
| | - Zoya Ignatova
- Institute of Biochemistry and Biologie and University of Potsdam, 14467 Potsdam.
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72
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Sahoo B, Singer D, Kodali R, Zuchner T, Wetzel R. Aggregation behavior of chemically synthesized, full-length huntingtin exon1. Biochemistry 2014; 53:3897-907. [PMID: 24921664 PMCID: PMC4075985 DOI: 10.1021/bi500300c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Repeat
length disease thresholds vary among the 10 expanded polyglutamine
(polyQ) repeat diseases, from about 20 to about 50 glutamine residues.
The unique amino acid sequences flanking the polyQ segment are thought
to contribute to these repeat length thresholds. The specific portions
of the flanking sequences that modulate polyQ properties are not always
clear, however. This ambiguity may be important in Huntington’s
disease (HD), for example, where in vitro studies
of aggregation mechanisms have led to distinctly different mechanistic
models. Most in vitro studies of the aggregation
of the huntingtin (HTT) exon1 fragment implicated in the HD mechanism
have been conducted on inexact molecules that are imprecise either
on the N-terminus (recombinantly produced peptides) or on the C-terminus
(chemically synthesized peptides). In this paper, we investigate the
aggregation properties of chemically synthesized HTT exon1 peptides
that are full-length and complete, containing both normal and expanded
polyQ repeat lengths, and compare the results directly to previously
investigated molecules containing truncated C-termini. The results
on the full-length peptides are consistent with a two-step aggregation
mechanism originally developed based on studies of the C-terminally
truncated analogues. Thus, we observe relatively rapid formation of
spherical oligomers containing from 100 to 600 HTT exon1 molecules
and intermediate formation of short protofibril-like structures containing
from 500 to 2600 molecules. In contrast to this relatively rapid assembly,
mature HTT exon1 amyloid requires about one month to dissociate in vitro, which is similar to the time required for neuronal
HTT exon1 aggregates to disappear in vivo after HTT
production is discontinued.
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Affiliation(s)
- Bankanidhi Sahoo
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
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73
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Moran SD, Zanni MT. How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy. J Phys Chem Lett 2014; 5:1984-1993. [PMID: 24932380 PMCID: PMC4051309 DOI: 10.1021/jz500794d] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 05/16/2014] [Indexed: 05/17/2023]
Abstract
There is an enormous amount of interest in the structures and formation mechanisms of amyloid fibers. In this Perspective, we review the most common structural motifs of amyloid fibers and discuss how infrared spectroscopy and isotope labeling can be used to identify their structures and aggregation kinetics. We present three specific strategies, site-specific labeling to obtain residue-by-residue structural information, isotope dilution of uniformly labeled proteins for identifying structural folds and protein mixtures, and expressed protein ligation for studying the domain structures of large proteins. For each of these methods, vibrational couplings are the source of the identifying features in the infrared spectrum. Examples are provided using the proteins hIAPP, Aβ, polyglutamine, and γD-crystallin. We focus on FTIR spectroscopy but also describe new observables made possible by 2D IR spectroscopy.
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74
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Miettinen MS, Monticelli L, Nedumpully-Govindan P, Knecht V, Ignatova Z. Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains-but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers. Biophys J 2014; 106:1721-8. [PMID: 24739171 PMCID: PMC4008795 DOI: 10.1016/j.bpj.2014.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/03/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022] Open
Abstract
A common thread connecting nine fatal neurodegenerative protein aggregation diseases is an abnormally expanded polyglutamine tract found in the respective proteins. Although the structure of this tract in the large mature aggregates is increasingly well described, its structure in the small early aggregates remains largely unknown. As experimental evidence suggests that the most toxic species along the aggregation pathway are the small early ones, developing strategies to alleviate disease pathology calls for understanding the structure of polyglutamine peptides in the early stages of aggregation. Here, we present a criterion, grounded in available experimental data, that allows for using kinetic stability of dimers to assess whether a given polyglutamine conformer can be on the aggregation path. We then demonstrate that this criterion can be assessed using present-day molecular dynamics simulations. We find that although the α-helical conformer of polyglutamine is very stable, dimers of α-helices lack the kinetic stability necessary to support further oligomerization. Dimers of steric zipper, β-nanotube, and β-pseudohelix conformers are also too short-lived to initiate aggregation. The β-hairpin-containing conformers, instead, invariably form very stable dimers when their side chains are interdigitated. Combining these findings with the implications of recent solid-state NMR data on mature fibrils, we propose a possible pathway for the initial stages of polyglutamine aggregation, in which β-hairpin-containing conformers act as templates for fibril formation.
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Affiliation(s)
- Markus S Miettinen
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | - Luca Monticelli
- Institut National de la santé et de la recherche medicale, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | | | - Volker Knecht
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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75
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Landrum E, Wetzel R. Biophysical underpinnings of the repeat length dependence of polyglutamine amyloid formation. J Biol Chem 2014; 289:10254-10260. [PMID: 24596088 DOI: 10.1074/jbc.c114.552943] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
There are now 10 expanded CAG repeat diseases in which both disease risk and age of onset are strongly dependent on the repeat length of the polyglutamine (polyQ) sequence in the disease protein. Large, polyQ-rich inclusions in patient brains and in cell and animal models are consistent with the involvement of polyQ aggregation in the disease mechanism. This possibility is reinforced by studies showing strong repeat length dependence to the aggregation process, qualitatively mirroring the repeat length dependence of disease risk. Our understanding of the underlying biophysical principles that mediate the repeat length dependence of aggregation, however, is far from complete. A previous study of simple polyQ peptides showed that N*, the size of the critical nucleus that controls onset of aggregation, decreases from unfavorable tetramer to favorable monomer over the range Q23 to Q26. These data, however, do not explain why, for all peptides exhibiting N* ∼ 1, spontaneous aggregation rates continue to increase with increasing repeat length. Here we describe a novel kinetics analyses that maps out the nonlinear dependence with repeat length of a nucleation efficiency term that is likely related to aspects of nucleus structure. This trend accounts for why nucleus size increases to tetrameric at repeat lengths of Q23 or below. Intriguingly, both aggregation and age of onset trend with repeat length in similar ways, exhibiting large changes per added Gln at low repeat lengths and small changes per added Gln at relatively long repeat lengths. Fibril stability also increases with repeat length in a nonlinear fashion.
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Affiliation(s)
- Elizabeth Landrum
- Department of Structural Biology and the Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Ronald Wetzel
- Department of Structural Biology and the Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260.
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76
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Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy. Proc Natl Acad Sci U S A 2014; 111:5796-801. [PMID: 24550484 DOI: 10.1073/pnas.1401587111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyglutamine (polyQ) sequences are found in a variety of proteins, and mutational expansion of the polyQ tract is associated with many neurodegenerative diseases. We study the amyloid fibril structure and aggregation kinetics of K2Q24K2W, a model polyQ sequence. Two structures have been proposed for amyloid fibrils formed by polyQ peptides. By forming fibrils composed of both (12)C and (13)C monomers, made possible by protein expression in Escherichia coli, we can restrict vibrational delocalization to measure 2D IR spectra of individual monomers within the fibrils. The spectra are consistent with a β-turn structure in which each monomer forms an antiparallel hairpin and donates two strands to a single β-sheet. Calculated spectra from atomistic molecular-dynamics simulations of the two proposed structures confirm the assignment. No spectroscopically distinct intermediates are observed in rapid-scan 2D IR kinetics measurements, suggesting that aggregation is highly cooperative. Although 2D IR spectroscopy has advantages over linear techniques, the isotope-mixing strategy will also be useful with standard Fourier transform IR spectroscopy.
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77
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Roland BP, Kodali R, Mishra R, Wetzel R. A serendipitous survey of prediction algorithms for amyloidogenicity. Biopolymers 2013; 100:780-9. [PMID: 23893755 PMCID: PMC3918212 DOI: 10.1002/bip.22305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 05/28/2013] [Indexed: 01/16/2023]
Abstract
The 17- amino acid N-terminal segment of the Huntingtin protein, htt(NT), grows into stable α-helix rich oligomeric aggregates when incubated under physiological conditions. We examined 15 scrambled sequence versions of an htt(NT) peptide for their stabilities against aggregation in aqueous solution at low micromolar concentration and physiological conditions. Surprisingly, given their derivation from a sequence that readily assembles into highly stable α-helical aggregates that fail to convert into β-structure, we found that three of these scrambled peptides rapidly grow into amyloid-like fibrils, while two others also develop amyloid somewhat more slowly. The other 10 scrambled peptides do not detectibly form any aggregates after 100 h incubation under these conditions. We then analyzed these sequences using four previously described algorithms for predicting the tendencies of peptides to grow into amyloid or other β-aggregates. We found that these algorithms-Zyggregator, Tango, Waltz, and Zipper-varied greatly in the number of sequences predicted to be amyloidogenic and in their abilities to correctly identify the amyloid forming members of this scrambled peptide collection. The results are discussed in the context of a review of the sequence and structural factors currently thought to be important in determining amyloid formation kinetics and thermodynamics.
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Affiliation(s)
- Bartholomew P Roland
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Biomedical Sciences Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15260
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78
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Todd TW, Lim J. Aggregation formation in the polyglutamine diseases: protection at a cost? Mol Cells 2013; 36:185-94. [PMID: 23794019 PMCID: PMC3800151 DOI: 10.1007/s10059-013-0167-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/02/2013] [Indexed: 12/30/2022] Open
Abstract
Mutant protein aggregation is a hallmark of many neurodegenerative diseases, including the polyglutamine disorders. Although the correlation between aggregation formation and disease pathology originally suggested that the visible inclusions seen in patient tissue might directly contribute to pathology, additional studies failed to confirm this hypothesis. Current opinion in the field of polyglutamine disease research now favors a model in which large inclusions are cytoprotective and smaller oligomers or misfolded monomers underlie pathogenesis. Nonetheless, therapies aimed at reducing or preventing aggregation show promise. This review outlines the debate about the role of aggregation in the polyglutamine diseases as it has unfolded in the literature and concludes with a brief discussion on the manipulation of aggregation formation and clearance mechanisms as a means of therapeutic intervention.
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Affiliation(s)
- Tiffany W. Todd
- Department of Genetics, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Janghoo Lim
- Department of Genetics, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA
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79
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Burke KA, Yates EA, Legleiter J. Biophysical insights into how surfaces, including lipid membranes, modulate protein aggregation related to neurodegeneration. Front Neurol 2013; 4:17. [PMID: 23459674 PMCID: PMC3585431 DOI: 10.3389/fneur.2013.00017] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/09/2013] [Indexed: 11/13/2022] Open
Abstract
There are a vast number of neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD), associated with the rearrangement of specific proteins to non-native conformations that promotes aggregation and deposition within tissues and/or cellular compartments. These diseases are commonly classified as protein-misfolding or amyloid diseases. The interaction of these proteins with liquid/surface interfaces is a fundamental phenomenon with potential implications for protein-misfolding diseases. Kinetic and thermodynamic studies indicate that significant conformational changes can be induced in proteins encountering surfaces, which can play a critical role in nucleating aggregate formation or stabilizing specific aggregation states. Surfaces of particular interest in neurodegenerative diseases are cellular and subcellular membranes that are predominately comprised of lipid components. The two-dimensional liquid environments provided by lipid bilayers can profoundly alter protein structure and dynamics by both specific and non-specific interactions. Importantly for misfolding diseases, these bilayer properties can not only modulate protein conformation, but also exert influence on aggregation state. A detailed understanding of the influence of (sub)cellular surfaces in driving protein aggregation and/or stabilizing specific aggregate forms could provide new insights into toxic mechanisms associated with these diseases. Here, we review the influence of surfaces in driving and stabilizing protein aggregation with a specific emphasis on lipid membranes.
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Affiliation(s)
- Kathleen A Burke
- C. Eugene Bennett Department of Chemistry, West Virginia University Morgantown, WV, USA
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