A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
Identifieur interne : 001E02 ( PubMed/Checkpoint ); précédent : 001E01; suivant : 001E03A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
Auteurs : Jessica Nasica-Labouze [Canada] ; Massimiliano Meli ; Philippe Derreumaux ; Giorgio Colombo ; Normand MousseauSource :
- PLoS computational biology [ 1553-7358 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Amyloid, Oligopeptides, Peptide Termination Factors, Prions, Saccharomyces cerevisiae Proteins.
- Molecular Dynamics Simulation, Protein Conformation.
Abstract
The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided.
DOI: 10.1371/journal.pcbi.1002051
PubMed: 21625573
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moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21625573</PMID><DateCompleted><Year>2011</Year><Month>09</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1553-7358</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>5</Issue><PubDate><Year>2011</Year><Month>May</Month></PubDate></JournalIssue><Title>PLoS computational biology</Title><ISOAbbreviation>PLoS Comput. Biol.</ISOAbbreviation></Journal><ArticleTitle>A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.</ArticleTitle><Pagination><MedlinePgn>e1002051</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pcbi.1002051</ELocationID><Abstract><AbstractText>The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. 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Derreumaux</name><name sortKey="Meli, Massimiliano" sort="Meli, Massimiliano" uniqKey="Meli M" first="Massimiliano" last="Meli">Massimiliano Meli</name><name sortKey="Mousseau, Normand" sort="Mousseau, Normand" uniqKey="Mousseau N" first="Normand" last="Mousseau">Normand Mousseau</name></noCountry><country name="Canada"><noRegion><name sortKey="Nasica Labouze, Jessica" sort="Nasica Labouze, Jessica" uniqKey="Nasica Labouze J" first="Jessica" last="Nasica-Labouze">Jessica Nasica-Labouze</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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