Publication Date:
1998-10-23
Description:
An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude longer than the longest simulation of a protein in water reported to date. Starting with an unfolded state of villin headpiece subdomain, hydrophobic collapse and helix formation occur in an initial phase, followed by conformational readjustments. A marginally stable state, which has a lifetime of about 150 nanoseconds, a favorable solvation free energy, and shows significant resemblance to the native structure, is observed; two pathways to this state have been found.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duan, Y -- Kollman, P A -- GM-29072/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Oct 23;282(5389):740-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9784131" target="_blank"〉PubMed〈/a〉
Keywords:
Carrier Proteins/*chemistry
;
*Computer Simulation
;
Mathematical Computing
;
Microfilament Proteins/*chemistry
;
*Models, Molecular
;
Neurofilament Proteins/*chemistry
;
Nuclear Magnetic Resonance, Biomolecular
;
Peptide Fragments/*chemistry
;
Protein Conformation
;
*Protein Folding
;
Protein Structure, Secondary
;
Protein Structure, Tertiary
;
Thermodynamics
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
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