51
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Baek I, Lee M, Na S. Understanding structural characteristics of out-of-register hIAPP amyloid proteins via molecular dynamics. RSC Adv 2016. [DOI: 10.1039/c6ra19100b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We investigated characteristics of out-of-register (OOR) hIAPP amyloids. By varying the length size of OOR hIAPP, we found 8 layers is most stable. In addition, OOR hIAPP has relative structural instability than in-register hAIPP.
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Affiliation(s)
- Inchul Baek
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
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52
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Lee M, Na S. End Capping Alters the Structural Characteristics and Mechanical Properties of Transthyretin (105-115) Amyloid Protofibrils. Chemphyschem 2015; 17:425-32. [DOI: 10.1002/cphc.201500945] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/16/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Myeongsang Lee
- Department of Mechanical Engineering; Korea University; Seoul 02841 Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering; Korea University; Seoul 02841 Republic of Korea
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53
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Fu L, Wang Z, Batista VS, Yan ECY. New Insights from Sum Frequency Generation Vibrational Spectroscopy into the Interactions of Islet Amyloid Polypeptides with Lipid Membranes. J Diabetes Res 2015; 2016:7293063. [PMID: 26697504 PMCID: PMC4677203 DOI: 10.1155/2016/7293063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/24/2015] [Indexed: 11/17/2022] Open
Abstract
Studies of amyloid polypeptides on membrane surfaces have gained increasing attention in recent years. Several studies have revealed that membranes can catalyze protein aggregation and that the early products of amyloid aggregation can disrupt membrane integrity, increasing water permeability and inducing ion cytotoxicity. Nonetheless, probing aggregation of amyloid proteins on membrane surfaces is challenging. Surface-specific methods are required to discriminate contributions of aggregates at the membrane interface from those in the bulk phase and to characterize protein secondary structures in situ and in real time without the use of perturbing spectroscopic labels. Here, we review the most recent applications of sum frequency generation (SFG) vibrational spectroscopy applied in conjunction with computational modeling techniques, a joint experimental and computational methodology that has provided valuable insights into the aggregation of islet amyloid polypeptide (IAPP) on membrane surfaces. These applications show that SFG can provide detailed information about structures, kinetics, and orientation of IAPP during interfacial aggregation, relevant to the molecular mechanisms of type II diabetes. These recent advances demonstrate the promise of SFG as a new approach for studying amyloid diseases at the molecular level and for the rational drug design targeting early aggregation products on membrane surfaces.
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Affiliation(s)
- Li Fu
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Zhuguang Wang
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
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54
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Kim JI, Lee M, Baek I, Yoon G, Na S. The mechanical response of hIAPP nanowires based on different bending direction simulations. Phys Chem Chem Phys 2015; 16:18493-500. [PMID: 25073067 DOI: 10.1039/c4cp02494j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amyloid proteins, implicated in numerous aging-related diseases, possess remarkable mechanical properties. Polymorphism leads to different arrangements of β sheets in amyloid fibrils, which changes the characteristics of the hydrogen bond network that determines their mechanical properties and structural characteristics. We performed bending simulations using molecular dynamics methods under constant-velocity conditions in different bending directions. Two different fibril structures, parallel/homo and parallel/hetero, of hIAPP amyloids were considered. Though the bending configuration influences the toughness of the material, our results indicate that the basic material behavior is affected by the β-sheet arrangement that is determined by the type of polymorphism in amyloid fibrils.
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Affiliation(s)
- J I Kim
- Department of Mechanical Engineering, Korea University, Seoul 136-701, Republic of Korea.
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55
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Relationship between structural composition and material properties of polymorphic hIAPP fibrils. Biophys Chem 2015; 199:1-8. [PMID: 25682214 DOI: 10.1016/j.bpc.2015.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/14/2015] [Accepted: 02/02/2015] [Indexed: 01/21/2023]
Abstract
Amyloid proteins are misfolded, denatured proteins that are responsible for causing several degenerative and neuro-degenerative diseases. Determining the mechanical stability of these amyloids is crucial for understanding the disease mechanisms, which will guide us in treatment. Furthermore, many research groups recognized amyloid proteins as functional biological materials that can be used in nanosensors, bacterial biofilms, coatings, etc. Many in vitro studies have been carried out to determine the characteristics of amyloid proteins via force spectroscopy methods, atomic force microscopy, and optical tweezers. However, computational methods (e.g. molecular dynamics and elastic network model) not only reveal the mechanical properties of the amyloid proteins, but also provide more in-depth information about the amyloids by presenting a visualization of their conformational changes. In this study, we evaluated the various material properties and behaviors of four different polymorphic structures of human islet amyloid polypeptide (hIAPP) by using steered molecular dynamics (SMD) simulations under tensile conditions. From our results, we examined how these mechanical properties may differ with respect to the structural formation of amyloid proteins.
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56
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Yan ECY, Wang Z, Fu L. Proteins at Interfaces Probed by Chiral Vibrational Sum Frequency Generation Spectroscopy. J Phys Chem B 2015; 119:2769-85. [DOI: 10.1021/jp508926e] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, CT 06511, United States
| | - Zhuguang Wang
- Department of Chemistry, Yale University, New Haven, CT 06511, United States
| | - Li Fu
- Department of Chemistry, Yale University, New Haven, CT 06511, United States
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57
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Abstract
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Homomeric self-assembly of peptides
into amyloid fibers is a feature of many diseases. A central role
has been suggested for the lateral fiber surface affecting gains of
toxic function. To investigate this, a protein scaffold that presents
a discrete, parallel β-sheet surface for amyloid subdomains
up to eight residues in length has been designed. Scaffolds that present
the fiber surface of islet amyloid polypeptide (IAPP) were prepared.
The designs show sequence-specific surface effects apparent in that
they gain the capacity to attenuate rates of IAPP self-assembly in
solution and affect IAPP-induced toxicity in insulin-secreting cells.
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Affiliation(s)
- Marisa A Rubio
- Department of Molecular Biophysics and Biochemistry, Yale University , 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
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58
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Andreasen M, Skeby KK, Zhang S, Nielsen EH, Klausen LH, Frahm H, Christiansen G, Skrydstrup T, Dong M, Schiøtt B, Otzen D. The Importance of Being Capped: Terminal Capping of an Amyloidogenic Peptide Affects Fibrillation Propensity and Fibril Morphology. Biochemistry 2014; 53:6968-80. [DOI: 10.1021/bi500674u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Andreasen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
| | - Katrine Kirkeby Skeby
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus, Denmark
| | - Shuai Zhang
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Erik Holm Nielsen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus, Denmark
| | - Lasse Hyldgaard Klausen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Heidi Frahm
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
| | - Gunna Christiansen
- Department
of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, DK-8000 Aarhus, Denmark
| | - Troels Skrydstrup
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus, Denmark
| | - Mingdong Dong
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus, Denmark
| | - Daniel Otzen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO) at the Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
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59
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Sinopoli A, Magrì A, Milardi D, Pappalardo M, Pucci P, Flagiello A, Titman JJ, Nicoletti VG, Caruso G, Pappalardo G, Grasso G. The role of copper(II) in the aggregation of human amylin. Metallomics 2014; 6:1841-52. [PMID: 25080969 DOI: 10.1039/c4mt00130c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Amylin is a 37-residue peptide hormone produced by the islet β-cells of pancreas and the formation of amylin aggregates is strongly associated with β-cell degeneration in type 2 diabetes, as demonstrated by more than 95% of patients exhibiting amylin amyloid upon autopsy. It is widely recognized that metal ions such as copper(II) have been implicated in the aggregation process of amyloidogenic peptides such as Aβ and α-synuclein and there is evidence that amylin self-assembly is also largely affected by copper(II). For this reason, in this work, the role of copper(II) in the aggregation of amylin has been investigated by several different experimental approaches. Mass spectrometric investigations show that copper(II) induces significant changes in the amylin structure, which decrease the protein fibrillogenesis as observed by ThT measurements. Accordingly, solid-state NMR experiments together with computational analysis carried out on a model amylin fragment confirmed the non-fibrillogenic nature of the copper(II) induced aggregated structure. Finally, the presence of copper(II) is also shown to have a major influence on amylin proneness to be degraded by proteases and cytotoxicity studies on different cell cultures are reported.
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Affiliation(s)
- Alessandro Sinopoli
- Dottorato Internazionale in Biomedicina Traslazionale, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
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60
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Poojari C, Xiao D, Batista VS, Strodel B. Membrane permeation induced by aggregates of human islet amyloid polypeptides. Biophys J 2014; 105:2323-32. [PMID: 24268144 DOI: 10.1016/j.bpj.2013.09.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 09/12/2013] [Accepted: 09/30/2013] [Indexed: 01/23/2023] Open
Abstract
Several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases as well as nonneuropathic diseases such as type II diabetes and atrial amyloidosis are associated with aggregation of amyloid polypeptides into fibrillar structures, or plaques. In this study, we use molecular dynamics simulations to test the stability and orientation of membrane-embedded aggregates of the human islet amyloid polypeptide (hIAPP) implicated in type II diabetes. We find that in both monolayers and bilayers of dipalmitoylphosphatidylglycerol (DPPG) hIAPP trimers and tetramers remain inside the membranes and preserve their β-sheet secondary structure. Lipid bilayer-inserted hIAPP trimers and tetramers orient inside DPPG at 60° relative to the membrane/water interface and lead to water permeation and Na(+) intrusion, consistent with ion-toxicity in islet β-cells. In particular, hIAPP trimers form a water-filled β-sandwich that induce water permeability comparable with channel-forming proteins, such as aquaporins and gramicidin-A. The predicted disruptive orientation is consistent with the amphiphilic properties of the hIAPP aggregates and could be probed by chiral sum frequency generation (SFG) spectroscopy, as predicted by the simulated SFG spectra.
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Affiliation(s)
- Chetan Poojari
- Forschungszentrum Jülich GmbH, Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
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61
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Yang YI, Gao YQ. Computer Simulation Studies of Aβ37–42 Aggregation Thermodynamics and Kinetics in Water and Salt Solution. J Phys Chem B 2014; 119:662-70. [DOI: 10.1021/jp502169b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Y. Isaac Yang
- Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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62
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63
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Yoon G, Lee M, Kim JI, Na S, Eom K. Role of sequence and structural polymorphism on the mechanical properties of amyloid fibrils. PLoS One 2014; 9:e88502. [PMID: 24551113 PMCID: PMC3925137 DOI: 10.1371/journal.pone.0088502] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/13/2014] [Indexed: 11/25/2022] Open
Abstract
Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP) fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD) simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of β strands (peptide chain). Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of β strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture.
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Affiliation(s)
- Gwonchan Yoon
- Department of Mechanical Engineering, Korea University, Seoul, Republic of Korea
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Myeongsang Lee
- Department of Mechanical Engineering, Korea University, Seoul, Republic of Korea
| | - Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, Republic of Korea
- * E-mail: (KE); (SN)
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University, Suwon, Republic of Korea
- * E-mail: (KE); (SN)
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64
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Guo J, Zhang Y, Ning L, Jiao P, Liu H, Yao X. Stabilities and structures of islet amyloid polypeptide (IAPP22–28) oligomers: From dimer to 16-mer. Biochim Biophys Acta Gen Subj 2014; 1840:357-66. [DOI: 10.1016/j.bbagen.2013.09.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/11/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022]
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65
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He L, Wang X, Zhao C, Zhu D, Du W. Inhibition of human amylin fibril formation by insulin-mimetic vanadium complexes. Metallomics 2014; 6:1087-96. [DOI: 10.1039/c4mt00021h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inhibition of human amylin fibril formation by insulin-mimetic vanadium complexes.
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Affiliation(s)
- Lei He
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Xuesong Wang
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Cong Zhao
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Dengsen Zhu
- Department of Chemistry
- Renmin University of China
- Beijing, China
| | - Weihong Du
- Department of Chemistry
- Renmin University of China
- Beijing, China
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66
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Matthes D, Daebel V, Meyenberg K, Riedel D, Heim G, Diederichsen U, Lange A, de Groot BL. Spontaneous Aggregation of the Insulin-Derived Steric Zipper Peptide VEALYL Results in Different Aggregation Forms with Common Features. J Mol Biol 2014; 426:362-76. [DOI: 10.1016/j.jmb.2013.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 10/09/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
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67
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Bernhardt NA, Berhanu WM, Hansmann UHE. Mutations and seeding of amylin fibril-like oligomers. J Phys Chem B 2013; 117:16076-85. [PMID: 24294935 DOI: 10.1021/jp409777p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Seeding a protein solution with preformed fibrils can dramatically enhance the growth rate of amyloids. As the seeds do not need to be of the same protein, seeding may account for the observed correlations between amyloid diseases. In an effort to understand better the molecular mechanisms behind cross seeding we have studied in silico the effect of mutations on the seeding of amylin fibrils. Our investigations of the structural stability of decamers of wild type amylin peptides, of Y37L mutants, and of heteroassemblies of wild-type and mutant amylin molecules show that the experimentally observed efficient cross seeding can be explained based on similarity in fibril structure of components. We find that amyloids with similar side chains packing at the β-sheet interface are structurally compatible, acting as a good template for the congruent incorporation of homologues peptides. In the Y37L mutants, lack of tyrosine-specific interactions causes significant higher flexibility of the C terminal than observed in the wild-type fibril. This effects elongation of the mutant fibril leading to the longer lag times during aggregation that are observed in experiments. Our study gives guidelines for the design of ligands that could stabilize amylin fibrils.
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Affiliation(s)
- Nathan A Bernhardt
- Department of Biology, Southwestern Oklahoma State University , Weatherford, Oklahoma 73096, United States
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68
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Palmieri LC, Melo-Ferreira B, Braga CA, Fontes GN, Mattos LJ, Lima LMT. Stepwise oligomerization of murine amylin and assembly of amyloid fibrils. Biophys Chem 2013; 180-181:135-44. [DOI: 10.1016/j.bpc.2013.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 01/15/2023]
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69
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Ndlovu H, Ashcroft AE, Radford SE, Harris SA. Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2013; 4:429-440. [PMID: 23946911 PMCID: PMC3740767 DOI: 10.3762/bjnano.4.50] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 06/24/2013] [Indexed: 06/02/2023]
Abstract
We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.
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Affiliation(s)
- Hlengisizwe Ndlovu
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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70
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Forman CJ, Fejer SN, Chakrabarti D, Barker PD, Wales DJ. Local frustration determines molecular and macroscopic helix structures. J Phys Chem B 2013; 117:7918-28. [PMID: 23724893 DOI: 10.1021/jp4040503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Decorative domains force amyloid fibers to adopt spiral ribbon morphologies, as opposed to the more common twisted ribbon. We model the effect of decorating domains as a perturbation to the relative orientation of β strands in a bilayered extended β-sheet. The model consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting ellipsoids. The relative orientation of the ellipsoids dictates the morphology of the resulting assembly. Amyloid structures derived from experiment are consistent with our model, and we use magnets to demonstrate that the frustration principle is scale and system independent. In contrast to other models of amyloid, our model isolates the effect of frustration from the fundamental interactions between building blocks to reveal the frustration rather than dependence of morphology on the physical interactions. Consequently, amyloid is viewed as a discrete molecular version of the more general macroscopic frustrated bilayer that is exemplified by Bauhinia seedpods. The model supports the idea that the interactions arising from an arbitrary peptide sequence can support an amyloid structure if a bilayer can form first, which suggests that supplementary protein sequences, such as chaperones or decorative domains, could play a significant role in stabilizing such bilayers and therefore in selecting morphology during nucleation. Our model provides a foundation for exploring the effects of frustration on higher-order superstructural polymorphic assemblies that may exhibit complex functional behavior. Two outstanding examples are the systematic kinking of decorated fibers and the nested frustration of the Bauhinia seedpod.
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Affiliation(s)
- Christopher J Forman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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71
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Lovas S, Zhang Y, Yu J, Lyubchenko YL. Molecular mechanism of misfolding and aggregation of Aβ(13-23). J Phys Chem B 2013; 117:6175-86. [PMID: 23642026 DOI: 10.1021/jp402938p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The misfolding and self-assembly of the amyloid-beta (Aβ) peptide into aggregates is a molecular signature of the development of Alzheimer's disease, but molecular mechanisms of the peptide aggregation remain unknown. Here, we combined Atomic Force Microscopy (AFM) and Molecular Dynamics (MD) simulations to characterize the misfolding process of an Aβ peptide. Dynamic force spectroscopy AFM analysis showed that the peptide forms stable dimers with a lifetime of ∼1 s. During MD simulations, isolated monomers gradually adopt essentially similar nonstructured conformations independent from the initial structure. However, when two monomers approach their structure changes dramatically, and the conformational space for the two monomers become restricted. The arrangement of monomers in antiparallel orientation leads to the cooperative formation of β-sheet conformation. Interactions, including hydrogen bonds, salt bridges, and weakly polar interactions of side chains stabilize the structure of the dimer. Under the applied force, the dimer, as during the AFM experiments, dissociates in a cooperative manner. Thus, misfolding of the Aβ peptide proceeds via the loss of conformational flexibility and formation of stable dimers suggesting their key role in the subsequent Aβ aggregation process.
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Affiliation(s)
- Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States.
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72
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Comellas G, Rienstra CM. Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys 2013; 42:515-36. [DOI: 10.1146/annurev-biophys-083012-130356] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology,
- Department of Chemistry, and
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
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73
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Mukherjee S, Dey SG. Heme Bound Amylin: Spectroscopic Characterization, Reactivity, and Relevance to Type 2 Diabetes. Inorg Chem 2013; 52:5226-35. [DOI: 10.1021/ic4001413] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Soumya Mukherjee
- Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
| | - Somdatta Ghosh Dey
- Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
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74
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Profit AA, Felsen V, Chinwong J, Mojica ERE, Desamero RZB. Evidence of π-stacking interactions in the self-assembly of hIAPP(22-29). Proteins 2013; 81:690-703. [PMID: 23229921 PMCID: PMC3594381 DOI: 10.1002/prot.24229] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/29/2012] [Accepted: 11/28/2012] [Indexed: 12/16/2022]
Abstract
The role aromatic amino acids play in the formation of amyloid is a subject of controversy. In an effort to clarify the contribution of aromaticity to the self-assembly of human islet amyloid polypeptide (hIAPP)22-29 , peptide analogs containing electron donating groups (EDGs) or electron withdrawing groups (EWGs) as substituents on the aromatic ring of Phe-23 at the para position have been synthesized and characterized using turbidity measurements in conjunction with Raman and fluorescence spectroscopy. Results indicate the incorporation of EDGs on the aromatic ring of Phe-23 virtually abolish the ability of hIAPP22-29 to form amyloid. Peptides containing EWGs were still capable of forming aggregates. These aggregates were found to be rich in β-sheet secondary structure. Transmission electron microscopy images of the aggregates confirm the presence of amyloid fibrils. The observed difference in amyloidogenic propensity between peptides containing EDGs and those with EWGs appears not to be based on differences in peptide hydrophobicity. Fluorescence and Raman spectroscopic investigations reveal that the environment surrounding the aromatic ring becomes more hydrophobic and ordered upon aggregation. Furthermore, Raman measurements of peptide analogs containing EWGs, conclusively demonstrate a distinct downshift in the CC ring mode (ca. 1600 cm(-1) ) upon aggregation that has previously been shown to be indicative of π-stacking. While previous work has demonstrated that π-stacking is not an absolute requirement for fibrillization, our findings indicate that Phe-23 also contributes to fibril formation through π-stacking interactions and that it is not only the hydrophobic nature of this residue that is relevant in the self-assembly of hIAPP22-29 . © Proteins 2013. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Adam A. Profit
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Valentina Felsen
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Justina Chinwong
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Elmer-Rico E. Mojica
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Ruel Z. B. Desamero
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
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75
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Coexistence of ribbon and helical fibrils originating from hIAPP(20-29) revealed by quantitative nanomechanical atomic force microscopy. Proc Natl Acad Sci U S A 2013; 110:2798-803. [PMID: 23388629 DOI: 10.1073/pnas.1209955110] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uncontrolled misfolding of proteins leading to the formation of amyloid deposits is associated with more than 40 types of diseases, such as neurodegenerative diseases and type-2 diabetes. These irreversible amyloid fibrils typically assemble in distinct stages. Transitions among the various intermediate stages are the subject of many studies but are not yet fully elucidated. Here, we combine high-resolution atomic force microscopy and quantitative nanomechanical mapping to determine the self-assembled structures of the decapeptide hIAPP(20-29), which is considered to be the fibrillating core fragment of the human islet amyloid polypeptide (hIAPP) involved in type-2 diabetes. We successfully follow the evolution of hIAPP(20-29) nanostructures over time, calculate the average thickening speed of small ribbon-like structures, and provide evidence of the coexistence of ribbon and helical fibrils, highlighting a key step within the self-assembly model. In addition, the mutations of individual side chains of wide-type hIAPP(20-29) shift this balance and destabilize the helical fibrils sufficiently relative to the twisted ribbons to lead to their complete elimination. We combine atomic force microscopy structures, mechanical properties, and solid-state NMR structural information to build a molecular model containing β sheets in cross-β motifs as the basis of self-assembled amyloids.
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76
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Jha A, Narayan S, Udgaonkar JB, Krishnamoorthy G. Solvent-induced tuning of internal structure in a protein amyloid protofibril. Biophys J 2013; 103:797-806. [PMID: 22947941 DOI: 10.1016/j.bpj.2012.07.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 07/06/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022] Open
Abstract
An important goal in studies of protein aggregation is to obtain an understanding of the structural diversity that is characteristic of amyloid fibril and protofibril structures at the molecular level. In this study, what to our knowledge are novel assays based on time-resolved fluorescence anisotropy decay and dynamic quenching measurements of a fluorophore placed at different specific locations in the primary structure of a small protein, barstar, have been used to determine the extent to which the protein sequence participates in the structural core of protofibrils. The fluorescence measurements reveal the structural basis of how modulating solvent polarity results in the tuning of the protofibril conformation from a pair of parallel β-sheets in heat-induced protofibrils to a single parallel β-sheet in trifluorethanol-induced protofibrils. In trifluorethanol-induced protofibrils, the single β-sheet is shown to be built up from in-register β-strands formed by nearly the entire protein sequence, while in heat-induced protofibrils, the pair of β-sheets motif is built up from β-strands formed by only the last two-third of the protein sequence.
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Affiliation(s)
- Anjali Jha
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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77
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Young L, Ndlovu H, Knapman TW, Harris SA, Radford SE, Ashcroft AE. Monitoring oligomer formation from self-aggregating amylin peptides using ESI-IMS-MS. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-012-0115-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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78
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Sabaté R, Ventura S. Cross-β-sheet supersecondary structure in amyloid folds: techniques for detection and characterization. Methods Mol Biol 2013; 932:237-257. [PMID: 22987357 DOI: 10.1007/978-1-62703-065-6_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The formation of protein aggregates is linked to the onset of several human disorders of increasing prevalence, ranging from dementia to diabetes. In most of these diseases, the toxic effect is exerted by the self-assembly of initially soluble proteins into insoluble amyloid-like fibrils. Independently of the protein origin, all these macromolecular assemblies share a common supersecondary structure: the cross-β-sheet conformation, in which a core of β-strands is aligned perpendicularly to the fibril axis forming extended regular β-sheets. Due to this ubiquity, the presence of cross-β-sheet conformational signatures is usually exploited to detect, characterize, and screen for amyloid fibrils in protein samples. Here we describe in detail some of the most commonly used methods to analyze such supersecondary structure.
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Affiliation(s)
- Raimon Sabaté
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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79
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Rabiee A, Ebrahim-Habibi A, Ghasemi A, Nemat-Gorgani M. How curcumin affords effective protection against amyloid fibrillation in insulin. Food Funct 2013; 4:1474-80. [DOI: 10.1039/c3fo00019b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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80
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He L, Wang X, Zhao C, Wang H, Du W. Ruthenium complexes as novel inhibitors of human islet amyloid polypeptide fibril formation. Metallomics 2013; 5:1599-603. [DOI: 10.1039/c3mt00146f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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81
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Surmacz-Chwedoruk W, Nieznańska H, Wójcik S, Dzwolak W. Cross-seeding of fibrils from two types of insulin induces new amyloid strains. Biochemistry 2012; 51:9460-9. [PMID: 23127165 DOI: 10.1021/bi301144d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The irreversibility and autocatalytic character of amyloidogenesis and the polymorphism of amyloid fibrils underlie the phenomenon of self-propagating strains, wherein the mother seed, rather than the seeding environment, determines the properties of daughter fibrils. Here we study the formation of amyloid fibrils from bovine insulin and the recombinant Lys(B31)-Arg(B32) human insulin analog. The two polypeptides are similar enough to cross-seed but, upon spontaneous aggregation, form amyloid fibrils with distinct spectral features in the infrared amide I' band region. When bovine insulin is cross-seeded with the analog amyloid (and vice versa), the shape, absorption maximum, and even fine fingerprint features of the amide I' band are passed from the mother to daughter fibrils with a high degree of fidelity. Although the differences in primary structure between bovine insulin and the Lys(B31)-Arg(B32) analog of human insulin lie outside of the polypeptide's critical amyloidogenic regions, they affect the secondary structure of fibrils, possibly the formation of intermolecular salt bridges, and the susceptibility to dissection and denaturation with dimethyl sulfoxide (DMSO). All these phenotypic features of mother fibrils are imprinted in daughter amyloid upon cross-seeding. Analysis of noncooperative DMSO-induced denaturation of daughter fibrils suggests that the self-propagating polymorphism underlying the emergence of new amyloid strains is encoded on the level of secondary structure. Our findings have been discussed in the context of polymorphism of fibrils, amyloid strains, and possible implications for mechanisms of amyloidogenesis.
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82
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Pan YX, Liu CJ, Zhang S, Yu Y, Dong M. 2D-Oriented Self-Assembly of Peptides Induced by Hydrated Electrons. Chemistry 2012; 18:14614-7. [DOI: 10.1002/chem.201200745] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 08/09/2012] [Indexed: 11/11/2022]
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83
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Yau J, Sharpe S. Structures of amyloid fibrils formed by the prion protein derived peptides PrP(244-249) and PrP(245-250). J Struct Biol 2012; 180:290-302. [PMID: 22929126 DOI: 10.1016/j.jsb.2012.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 08/08/2012] [Accepted: 08/13/2012] [Indexed: 10/28/2022]
Abstract
While the formation of amyloid fibrils from diverse peptide and protein sequences is well established, the molecular determinants of structure and assembly are not well understood. In particular, the relationship between amino acid sequence and the type of internal steric zipper packing adopted in amyloid fibrils has not been established. Here we report the structures of two cytotoxic amyloid peptides derived from the mammalian prion protein, PrP(244-249) and PrP(245-250), determined using solid state NMR. While the amino acid composition of these two hexapeptides is very similar (ISFLIF and SFLIFL), the intermolecular interactions that give rise to the intersheet packing within the fibrils differ significantly. PrP(245-250) adopts a class 1 steric zipper, with parallel sheets stacked in an antiparallel face to face arrangement, stabilized by N- to C-terminal salt bridges. PrP(244-249), by contrast, forms two different intersheet interfaces within amyloid fibrils, with parallel opposing sheets in either a face to face (class 3) or face to back (class 2) arrangement. The fibrils formed by this peptide are primarily stabilized by close packing of the hydrophobic side chains, with contributions from side-chain to backbone hydrogen bonding (class 2 only). Thus, the structures presented here provide new insight into the relationship between amino acid sequence and the types of interactions stabilizing amyloid fibrils.
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Affiliation(s)
- Jason Yau
- Molecular Structure and Function Programme, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada
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84
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Milton NGN, Harris JR. Fibril formation and toxicity of the non-amyloidogenic rat amylin peptide. Micron 2012; 44:246-53. [PMID: 22854213 DOI: 10.1016/j.micron.2012.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 01/09/2023]
Abstract
Full-length native rat amylin 1-37 has previously been widely shown to be unable to form fibrils and to lack the toxicity of the human amylin form leading to its use as a non-amyloidogenic control peptide. A recent study has suggested that rat amylin 1-37 forms amyloidogenic β-sheet structures in the presence of the human amylin form and suggested that this property could promote toxicity. Using TEM analysis we show here fibril formation by synthetic rat amylin 1-37 and 8-37 peptides when the lyophilized HPLC purified peptides are initially dissolved in 20 mM Tris-HCl. Dissolution of synthetic rat amylin 1-37 and 8-37 peptides in H(2)O or phosphate buffered saline failed to produce fibrils. Addition of 20 mM Tris-HCl to synthetic rat amylin 1-37 and 8-37 peptides initially dissolved in H(2)O also failed to induce fibril formation. The rat amylin fibrils have a uniform structure and bind Congo red suggesting that they are amyloid fibrils. The rat amylin fibrils also bind catalase, which could be inhibited by Amyloid-β 31-35 and a catalase amyloid-β binding domain-like peptide (R9). The rat amylin 1-37 and 8-37 fibrils are toxic in both human pancreatic islet and neuronal cell culture systems. The toxicity of rat amylin fibrils can be inhibited by an amylin receptor antagonist (AC187) and a caspase inhibitor (zVAD-fmk) in a similar manner to previous observations for human amylin toxicity. Chemically induced rat amylin fibril formation of uniform structured fibrils provides a potentially novel anti-amyloid drug discovery tool.
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Affiliation(s)
- Nathaniel G N Milton
- Department of Human & Health Sciences, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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85
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Liu G, Robbins KJ, Sparks S, Selmani V, Bilides KM, Gomes EE, Lazo ND. Helix-Dipole Effects in Peptide Self-Assembly to Amyloid. Biochemistry 2012; 51:4167-74. [DOI: 10.1021/bi3001616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gai Liu
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Kevin J. Robbins
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Samuel Sparks
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Veli Selmani
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Kalin M. Bilides
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Erin E. Gomes
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
| | - Noel D. Lazo
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts
01610, United States
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86
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Lopez del Amo JM, Schmidt M, Fink U, Dasari M, Fändrich M, Reif B. An asymmetric dimer as the basic subunit in Alzheimer's disease amyloid β fibrils. Angew Chem Int Ed Engl 2012; 51:6136-9. [PMID: 22565601 DOI: 10.1002/anie.201200965] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Juan Miguel Lopez del Amo
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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87
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Lopez del Amo JM, Schmidt M, Fink U, Dasari M, Fändrich M, Reif B. An Asymmetric Dimer as the Basic Subunit in Alzheimer’s Disease Amyloid β Fibrils. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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88
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Seo M, Rauscher S, Pomès R, Tieleman DP. Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides. J Chem Theory Comput 2012; 8:1774-1785. [PMID: 22582033 PMCID: PMC3348680 DOI: 10.1021/ct200876v] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Indexed: 01/05/2023]
Abstract
We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)(4) are used to examine peptide aggregation in different environments, in water, and at the water-octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.
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Affiliation(s)
- Mikyung Seo
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University
of Calgary, Calgary, Alberta, Canada
| | - Sarah Rauscher
- Molecular Structure and Function,
Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Régis Pomès
- Molecular Structure and Function,
Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - D. Peter Tieleman
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University
of Calgary, Calgary, Alberta, Canada
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89
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Chatani E, Yagi H, Naiki H, Goto Y. Polymorphism of β2-microglobulin amyloid fibrils manifested by ultrasonication-enhanced fibril formation in trifluoroethanol. J Biol Chem 2012; 287:22827-37. [PMID: 22566695 DOI: 10.1074/jbc.m111.333310] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The polymorphic property of amyloid structures has been focused on as a molecular basis of the presence and propagation of different phenotypes of amyloid diseases, although little is known about the molecular mechanism for expressing diverse structures from only one protein sequence. Here, we have found that, in combination with an enhancing effect of ultrasonication on nucleation, β(2)-microglobulin, a protein responsible for dialysis-related amyloidosis, generates distinct fibril conformations in a concentration-dependent manner in the presence of 2,2,2-trifluoroethanol (TFE). Although the newly formed fibrils all exhibited a similar needle-like morphology with an extensive cross-β core, as suggested by Fourier transform infrared absorption spectra, they differed in thioflavin T intensity, extension kinetics, and tryptophan fluorescence spectra even in the same solvents, representing polymorphic structures. The hydrophobic residues seemed to be more exposed in the fibrils originating at higher concentrations of TFE, as indicated by the increased binding of 1-anilinonaphthalene-8-sulfonic acid, suggesting that the modulation of hydrophobic interactions is critical to the production of polymorphic amyloid structures. Interestingly, the fibrils formed at higher TFE concentrations showed significantly higher stability against guanidium hydrochloride, the perturbation of ionic strength, and, furthermore, pressurization. The cross-β structure inside the fibrils seems to have been more idealized, resulting in increased stability when nucleation occurred in the presence of the alcohol, indicating that a weaker contribution of hydrophobic interactions is intrinsically more amenable to the formation of a non-defective amyloid structure.
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Affiliation(s)
- Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Hyogo 657-8501, Japan.
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90
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Portillo AM, Krasnoslobodtsev AV, Lyubchenko YL. Effect of electrostatics on aggregation of prion protein Sup35 peptide. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:164205. [PMID: 22466073 PMCID: PMC3482402 DOI: 10.1088/0953-8984/24/16/164205] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Self-assembly of misfolded proteins into ordered fibrillar structures is a fundamental property of a wide range of proteins and peptides. This property is also linked with the development of various neurodegenerative diseases such as Alzheimer's and Parkinson's. Environmental conditions modulate the misfolding and aggregation processes. We used a peptide, CGNNQQNY, from yeast prion protein Sup35, as a model system to address effects of environmental conditions on aggregate formation. The GNNQQNY peptide self-assembles in fibrils with structural features that are similar to amyloidogenic proteins. Atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence assay were employed to follow the aggregation process at various pHs and ionic strengths. We also used single molecule AFM force spectroscopy to probe interactions between the peptides under various conditions. The ThT fluorescence data showed that the peptide aggregates fast at pH values approaching the peptide isoelectric point (pI = 5.3) and the kinetics is 10 times slower at acidic pH (pH 2.0), suggesting that electrostatic interactions contribute to the peptide self-assembly into aggregates. This hypothesis was tested by experiments performed at low (11 mM) and high (150 mM) ionic strengths. Indeed, the aggregation lag time measured at pH 2 at low ionic strength (11 mM) is 195 h, whereas the lag time decreases ~5 times when the ionic strength is increased to 150 mM. At conditions close to the pI value, pH 5.6, the aggregation lag time is 12 ± 6 h under low ionic strength, and there is minimal change to the lag time at 150 mM NaCl. The ionic strength also influences the morphology of aggregates visualized with AFM. In pH 2.0 and at high ionic strength, the aggregates are twofold taller than those formed at low ionic strength. In parallel, AFM force spectroscopy studies revealed minimal contribution of electrostatics to dissociation of transient peptide dimers.
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Affiliation(s)
- Alexander M. Portillo
- Department of Pharmaceutical Science, College of Pharmacy, COP 1012, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Alexey V. Krasnoslobodtsev
- Department of Pharmaceutical Science, College of Pharmacy, COP 1012, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Science, College of Pharmacy, COP 1012, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
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91
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Shaw CP, Middleton DA, Volk M, Lévy R. Amyloid-derived peptide forms self-assembled monolayers on gold nanoparticle with a curvature-dependent β-sheet structure. ACS NANO 2012; 6:1416-26. [PMID: 22242947 DOI: 10.1021/nn204214x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Using a combination of Fourier transform infrared (FTIR) spectroscopy and solid-state nuclear magnetic resonance (SSNMR) techniques, the secondary structure of peptides anchored on gold nanoparticles of different sizes is investigated. The structure of the well-studied CALNN-capped nanoparticles is compared to the structure of nanoparticles capped with a new cysteine-terminated peptide, CFGAILSS. The design of that peptide is derived from the minimal amyloidogenic sequence FGAIL of the human islet polypeptide amylin. We demonstrate that CFGAILSS forms extended fibrils in solution. When constrained at a nanoparticle surface, CFGAILSS adopts a secondary structure markedly different from CALNN. Taking into account the surface selection rules, the FTIR spectra of CFGAILSS-capped gold nanoparticles indicate the formation of β-sheets which are more prominent for 25 nm diameter nanoparticles than for 5 nm nanoparticles. No intermolecular (13)C-(13)C dipolar coupling is detected with rotational resonance SSNMR for CALNN-capped nanoparticles, while CALNN is in a random coil configuration. Coupling is detected for CFGAILSS-capped gold nanoparticles, however, consistent with an intermolecular (13)C-(13)C distance of 5.0 ± 0.3 Å, in agreement with intermolecular hydrogen bonding in a parallel β-sheet structure.
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Affiliation(s)
- Christopher P Shaw
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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92
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Effect of sequence variation on the mechanical response of amyloid fibrils probed by steered molecular dynamics simulation. Biophys J 2012; 102:587-96. [PMID: 22325282 DOI: 10.1016/j.bpj.2011.12.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 12/01/2011] [Accepted: 12/09/2011] [Indexed: 11/20/2022] Open
Abstract
The mechanical failure of mature amyloid fibers produces fragments that act as seeds for the growth of new fibrils. Fragmentation may also be correlated with cytotoxicity. We have used steered atomistic molecular dynamics simulations to study the mechanical failure of fibrils formed by the amyloidogenic fragment of human amylin hIAPP20-29 subjected to force applied in a variety of directions. By introducing systematic variations to this peptide sequence in silico, we have also investigated the role of the amino-acid sequence in determining the mechanical stability of amyloid fibrils. Our calculations show that the force required to induce mechanical failure depends on the direction of the applied stress and upon the degree of structural order present in the β-sheet assemblies, which in turn depends on the peptide sequence. The results have implications for the importance of sequence-dependent mechanical properties on seeding the growth of new fibrils and the role of breakage events in cytotoxicity.
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93
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Andreasen M, Nielsen SB, Mittag T, Bjerring M, Nielsen JT, Zhang S, Nielsen EH, Jeppesen M, Christiansen G, Besenbacher F, Dong M, Nielsen NC, Skrydstrup T, Otzen DE. Modulation of fibrillation of hIAPP core fragments by chemical modification of the peptide backbone. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:274-85. [DOI: 10.1016/j.bbapap.2011.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/14/2011] [Accepted: 10/24/2011] [Indexed: 11/30/2022]
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94
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Doran TM, Kamens AJ, Byrnes NK, Nilsson BL. Role of amino acid hydrophobicity, aromaticity, and molecular volume on IAPP(20-29) amyloid self-assembly. Proteins 2012; 80:1053-65. [DOI: 10.1002/prot.24007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 11/12/2011] [Accepted: 11/18/2011] [Indexed: 01/22/2023]
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95
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Reif B. Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR. Methods Mol Biol 2012; 831:279-301. [PMID: 22167680 DOI: 10.1007/978-1-61779-480-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.
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Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
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96
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Madine J, Davies HA, Shaw C, Hamley IW, Middleton DA. Fibrils and nanotubes assembled from a modified amyloid-β peptide fragment differ in the packing of the same β-sheet building blocks. Chem Commun (Camb) 2012; 48:2976-8. [DOI: 10.1039/c2cc17118j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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97
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Abstract
Amyloid fibrils are polymeric assemblies of normally soluble proteins or peptides. To investigate their structure, it is generally not possible to use conventional methods of crystallography and solution nuclear magnetic resonance. To examine the repeating crystalline structure along the fibre axis, X-ray fibre diffraction has been a useful tool. Here we discuss the methods by which amyloid-like fibrils may be prepared to form a sample suitable for structural analysis and describe how data may be collected and then analysed to arrive at a potential model structure.
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98
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Amphiphilic adsorption of human islet amyloid polypeptide aggregates to lipid/aqueous interfaces. J Mol Biol 2011; 421:537-47. [PMID: 22210153 DOI: 10.1016/j.jmb.2011.12.035] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 12/15/2011] [Accepted: 12/17/2011] [Indexed: 11/23/2022]
Abstract
Many amyloid proteins misfold into β-sheet aggregates upon interacting with biomembranes at the onset of diseases, such as Parkinson's disease and type II diabetes. The molecular mechanisms triggering aggregation depend on the orientation of β-sheets at the cell membranes. However, understanding how β-sheets adsorb onto lipid/aqueous interfaces is challenging. Here, we combine chiral sum frequency generation (SFG) spectroscopy and ab initio quantum chemistry calculations based on a divide-and-conquer strategy to characterize the orientation of human islet amyloid polypeptides (hIAPPs) at lipid/aqueous interfaces. We show that the aggregates bind with β-strands oriented at 48° relative to the interface. This orientation reflects the amphiphilic properties of hIAPP β-sheet aggregates and suggests the potential disruptive effect on membrane integrity.
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99
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Davies HA, Madine J, Middleton DA. Solid-state NMR reveals differences in the packing arrangements of peptide aggregates derived from the aortic amyloid polypeptide medin. J Pept Sci 2011; 18:65-72. [PMID: 22102261 DOI: 10.1002/psc.1418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/15/2011] [Accepted: 08/25/2011] [Indexed: 11/11/2022]
Abstract
Several polypeptides aggregate into insoluble amyloid fibrils associated with pathologies such as Alzheimer's disease, Parkinson's disease and type 2 diabetes. Understanding the structural and sequential motifs that drive fibrillisation may assist in the discovery and refinement of effective therapies. Here we investigate the effects of three predicted amyloidogenic regions on the structure of aggregates formed by medin, a poorly characterised polypeptide associated with aortic medial amyloidosis. Solid-state NMR is used to compare the dynamics and sheet packing arrangement of the C-terminal region encompassing residues F(43) GSV within full-length medin (Med(1-50) ) and two shorter peptide fragments, Med(30-50) and Med(42-49) , lacking specific sequences predicted to be amyloidogenic.(.) Results show that all three peptides have different aggregate morphologies, and Med(30-50) and Med(1-50) have different sheet packing arrangements and dynamics to Med(42-49) . These results imply that at least two of the three predicted amyloidogenic regions are required for the formation and elongation of medin fibres observed in the disease state.
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Affiliation(s)
- Hannah A Davies
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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100
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Yang Z, Shi B, Lu H, Xiu P, Zhou R. Dewetting Transitions in the Self-Assembly of Two Amyloidogenic β-Sheets and the Importance of Matching Surfaces. J Phys Chem B 2011; 115:11137-44. [DOI: 10.1021/jp2046454] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zaixing Yang
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Biyun Shi
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Hangjun Lu
- Department of Physics, Zhejiang Normal University, 321004, Jinhua, China
| | - Peng Xiu
- Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
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