Molecular dynamics simulation of protein folding by essential dynamics sampling: Folding landscape of horse heart cytochrome c

被引:56
作者
Daidone, I
Amadei, A
Roccatano, D
Di Nola, A [1 ]
机构
[1] Univ Roma La Sapienza, Dept Chem, I-00185 Rome, Italy
[2] Univ Roma Tor Vergata, Dipartimento Sci & Tecnol Chim, Rome, Italy
[3] Univ Aquila, Dipartimento Chim Ingn Chim & Mat, I-67100 Laquila, Italy
关键词
D O I
10.1016/S0006-3495(03)74709-2
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
A new method for simulating the folding process of a protein is reported. The method is based on the essential dynamics sampling technique. In essential dynamics sampling, a usual molecular dynamics simulation is performed, but only those steps, not increasing the distance from a target structure, are accepted. The distance is calculated in a configurational subspace defined by a set of generalized coordinates obtained by an essential dynamics analysis of an equilibrated trajectory. The method was applied to the folding process of horse heart cytochrome c, a protein with; 30008 of freedom. Starting from structures, with a root-mean-square deviation of similar to20 Angstrom from the crystal structure, the correct folding was obtained, by utilizing only 106 generalized degrees of freedom, chosen among those accounting for the backbone carbon atoms motions, hence not containing any information on the side chains. The folding pathways found are in agreement with experimental data on the same molecule.
引用
收藏
页码:2865 / 2871
页数:7
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