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A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

Published: 11 November 2006 Publication History

Abstract

We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system---a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for Coulomb force calculations; this is the highest-ever performance reported for classical molecular dynamics simulations. Amyloid fibril formation is known to be related to the occurrence of severe diseases such as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob diseases. The Sup35 protein is a "yeast prion protein," which forms mini-crystals due to aggregation; it forms an effective platform for studying the formation process of amyloid fibrils. In these simulations, we first elucidate that the amyloid-forming peptides GNNQQNY aggregate at a higher frequency than non-amyloid-forming peptides SQNGNQQRG; further, the GNNQQNY peptides tend to form parallel two-stranded ß-sheets that would grow into a cross-ß amyloid nucleus. The results are consistent with those obtained experimentally. Furthermore, we could observe an early elongation of the amyloid nucleus. This result is expected to contribute toward a deeper understanding of the amyloid growth mechanism.

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cover image ACM Conferences
SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing
November 2006
746 pages
ISBN:0769527000
DOI:10.1145/1188455
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 11 November 2006

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