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Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Nussinov, Ruth Ma, Buyong
Description	Country affiliation: United States Author Affiliation: Ma B ( Laboratory of Experimental and Computational Biology, National Cancer Institute at Frederick, Maryland 21702, USA.)
Abstract	The aggregation observed in protein conformational diseases is the outcome of significant new beta-sheet structure not present in the native state. Peptide model systems have been useful in studies of fibril aggregate formation. Experimentally, it was found that a short peptide AGAAAAGA is one of the most highly amyloidogenic peptides. This peptide corresponds to the Syrian hamster prion protein (ShPrP) residues 113-120. The peptide was observed to be conserved in all species for which the PrP sequence has been determined. We have simulated the stabilities of oligomeric AGAAAAGA and AAAAAAAA (A8) by molecular dynamic simulations. Oligomers of both AGAAAAGA and AAAAAAAA were found to be stable when the size is 6 to 8 (hexamer to octamer). Subsequent simulation of an additional alpha-helical AAAAAAAA placed on the A8-octamer surface has revealed molecular events related to conformational change and oligomer growth. Our study addresses both the minimal oligomeric size of an aggregate seed and the mechanism of seed growth. Our simulations of the prion-derived 8-residue amyloidogenic peptide and its variant have indicated that an octamer is stable enough to be a seed and that the driving force for stabilization is the hydrophobic effect.
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science
Issue Number	10
Volume Number	11
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2002-10-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Amyloid Metabolism Computer Simulation Models, Molecular Peptides Protein Conformation Protein Structure, Secondary Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, P.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation

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