Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association(638 views) 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.
Keywords: 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,
Affiliations: *** 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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Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association
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.
Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association
Petraglia F, Singh AA, Carafa V, Nebbioso A, Conte M, Scisciola L, Valente S, Baldi A, Mandoli A, Petrizzi VB, Ingenito C, De Falco S, Cicatiello V, Apicella I, Janssen-megens EM, Kim B, Yi G, Logie C, Heath S, Ruvo M, Wierenga ATJ, Flicek P, Yaspo ML, Della Valle V, Bernard O, Tomassi S, Novellino E, Feoli A, Sbardella G, Gut I, Vellenga E, Stunnenberg HG, Mai A, Martens JHA, Altucci L * Combined HAT/EZH2 modulation leads to cancer-selective cell death(288 views) Oncotarget (ISSN: 1949-2553electronic, 1949-2553linking), 2018 May 22; 9(39): 25630-25646. Impact Factor:5.008 ViewExport to BibTeXExport to EndNote