A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35
Identifieur interne : 000153 ( France/Analysis ); précédent : 000152; suivant : 000154A 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 [Italie] ; Philippe Derreumaux [France] ; Giorgio Colombo [Italie] ; Normand Mousseau [Canada]Source :
- PLoS Computational Biology [ 1553-734X ] ; 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.
Url:
DOI: 10.1371/journal.pcbi.1002051
PubMed: 21625573
PubMed Central: 3098217
Affiliations:
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PMC:3098217Le document en format XML
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GNNQQNY from the Yeast Prion Sup-35</title><author><name sortKey="Nasica Labouze, Jessica" sort="Nasica Labouze, Jessica" uniqKey="Nasica Labouze J" first="Jessica" last="Nasica-Labouze">Jessica Nasica-Labouze</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Département de Physique and GEPROM, Université de Montréal, Montréal, Québec, Canada</addr-line></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Physique and GEPROM, Université de Montréal, Montréal, Québec</wicri:regionArea><wicri:noRegion>Québec</wicri:noRegion></affiliation></author><author><name sortKey="Meli, Massimiliano" sort="Meli, Massimiliano" uniqKey="Meli M" first="Massimiliano" last="Meli">Massimiliano Meli</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Chimica del Riconoscimento Molecolare, CNR, 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last="Colombo">Giorgio Colombo</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano</wicri:regionArea><wicri:noRegion>Milano</wicri:noRegion></affiliation></author><author><name sortKey="Mousseau, Normand" sort="Mousseau, Normand" uniqKey="Mousseau N" first="Normand" last="Mousseau">Normand Mousseau</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Département de Physique and GEPROM, Université de Montréal, Montréal, Québec, Canada</addr-line></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Physique and GEPROM, Université de Montréal, Montréal, Québec</wicri:regionArea><wicri:noRegion>Québec</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS Computational Biology</title><idno type="ISSN">1553-734X</idno><idno type="eISSN">1553-7358</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amyloid (chemistry)</term><term>Molecular Dynamics Simulation</term><term>Oligopeptides (chemistry)</term><term>Peptide Termination Factors (chemistry)</term><term>Prions (chemistry)</term><term>Protein Conformation</term><term>Saccharomyces cerevisiae Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amyloïde ()</term><term>Conformation des protéines</term><term>Facteurs terminaison chaîne peptidique ()</term><term>Oligopeptides ()</term><term>Prions ()</term><term>Protéines de Saccharomyces cerevisiae ()</term><term>Simulation de dynamique moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Amyloid</term><term>Oligopeptides</term><term>Peptide Termination Factors</term><term>Prions</term><term>Saccharomyces cerevisiae Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Molecular Dynamics Simulation</term><term>Protein Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amyloïde</term><term>Conformation des protéines</term><term>Facteurs terminaison chaîne peptidique</term><term>Oligopeptides</term><term>Prions</term><term>Protéines de Saccharomyces cerevisiae</term><term>Simulation de dynamique moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chiti, F" uniqKey="Chiti F">F Chiti</name></author><author><name sortKey="Dobson, Cm" uniqKey="Dobson C">CM Dobson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ross, Ca" uniqKey="Ross C">CA Ross</name></author><author><name sortKey="Poirier, Ma" uniqKey="Poirier M">MA Poirier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Miranker, Ad" uniqKey="Miranker A">AD Miranker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerovnik, E" uniqKey="Zerovnik E">E Zerovnik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dobson, Cm" uniqKey="Dobson C">CM Dobson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sawaya, Mr" 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sortKey="Masino, L" uniqKey="Masino L">L Masino</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li><li>France</li><li>Italie</li></country><region><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><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><name sortKey="Mousseau, Normand" sort="Mousseau, Normand" uniqKey="Mousseau N" first="Normand" last="Mousseau">Normand Mousseau</name></country><country name="Italie"><noRegion><name sortKey="Meli, Massimiliano" sort="Meli, Massimiliano" uniqKey="Meli M" first="Massimiliano" last="Meli">Massimiliano Meli</name></noRegion><name sortKey="Colombo, Giorgio" sort="Colombo, Giorgio" uniqKey="Colombo G" first="Giorgio" last="Colombo">Giorgio Colombo</name></country><country name="France"><region name="Île-de-France"><name sortKey="Derreumaux, Philippe" sort="Derreumaux, Philippe" uniqKey="Derreumaux P" first="Philippe" last="Derreumaux">Philippe Derreumaux</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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