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Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association (143 visite)

Vitagliano L, Esposito L, Pedone C, De Simone A

Biochem Biophys Res Commun (ISSN: 1090-2104, 0006-291x, 1090-2104electronic), 2008 Dec 26; 377(4): 1036-1041.

Tipo di articolo: Journal Article, Research Support, Non-U. S. Gov'T,

Impact factor: 2.648

Impact factor a 5 anni: 2.823

Parole chiave: Amyloid, Neurodegenerative Diseases, Protein Aggregation, Yeast Prion, Glycylasparaginylasparaginylglutaminylglutaminylasparaginyltyrosine, Peptide, Unclassified Drug, Article, Beta Sheet, Molecular Dynamics, Peptide Analysis, Priority Journal, Protein Interaction, Protein Stability, Amino Acid Sequence, Humans, Protein Structure, Secondary,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-56349091416&partnerID=40&md5=a280de3e705594e8f8eff363be369913

Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel beta-sheets. The data show that GNNQQNY preference for parallel or antiparallel beta-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.
*** IBB - CNR ***

Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy.

Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
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5 Records (4 escludendo Abstract e Conferenze).
Impact factor totale: 12.716 (12.716 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 12.225 (12.225 escludendo Abstract e Conferenze).

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