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Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing (2002)
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| Venue: | CODEN: JMOBAK ISSN |
| Citations: | 24 - 1 self |
BibTeX
@INPROCEEDINGS{Zagrovic02simulationof,
author = {Bojan Zagrovic and Christopher D. Snow and Michael R. Shirts and Vijay S. P},
title = {Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing},
booktitle = {CODEN: JMOBAK ISSN},
year = {2002},
pages = {323--927}
}
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Abstract
By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fastfolding 36-residue a-helical protein from the villin headpiece. The total simulated time exceeds 300 ms, orders of magnitude more than previous simulations of a molecule of this size. Starting from an extended state, we obtained an ensemble of folded structures, which is on average 1.7 A ˚ and 1.9 A ˚ away from the native state in Ca distance-based root-meansquare deviation (dRMS) and Cb dRMS sense, respectively. The folding mechanism of villin is most consistent with the hydrophobic collapse view of folding: the molecule collapses non-specifically very quickly (,20 ns), which greatly reduces the size of the conformational space that needs to be explored in search of the native state. The conformational search in the collapsed state appears to be rate-limited by the formation of the aromatic core: in a significant fraction of our simulations, the C-terminal phenylalanine residue packs improperly with the rest of the hydrophobic core. We suggest that the breaking of this interaction may
Keyphrases
atomistic detail worldwide-distributed computing small alpha-helical protein native state folded structure fastfolding 36-residue a-helical protein previous simulation significant fraction hydrophobic core villin headpiece aromatic core hydrophobic collapse view conformational space extended state conformational search c-terminal phenylalanine residue pack ca distance-based root-meansquare deviation new worldwide-distributed computing technique cb drms sense collapsed state total simulated time
