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Molecular dynamics simulations of helix folding: The effects of amino acid substitution
Author(s) -
Sung ShenShu,
Wu XiongWu
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(199711)42:6<633::aid-bip2>3.0.co;2-v
Subject(s) - chemistry , molecular dynamics , alanine , amino acid , helix (gastropod) , folding (dsp implementation) , peptide , valine , protein folding , stereochemistry , leucine , crystallography , computational chemistry , biochemistry , ecology , snail , electrical engineering , biology , engineering
Molecular dynamics simulations were applied to helix folding of alanine‐based synthetic peptides. A single alanine residue in the middle of the peptide was substituted with various nonpolar amino acids (leucine, isoleucine, valine, glycine or proline) to study the effect of the substitution. Unlike many other molecular dynamics simulations, nonhelical initial conformations were used in our simulations to study the folding process. An average solvent effect was included in the energy function to simplify the solvent calculation and to overcome the multiple minima problem. During the simulations, the peptides folded into helices in nanoseconds. Compact structures containing two helical segments were also observed. The calculated helical ratios of the peptides showed the same rank order as observed experimentally for the alanine‐based peptides. Within a peptide, the helical ratio of each residue was calculated and a minimum was found near the center of the sequence for all peptides. The substitutions had different asymmetric effects on the helical ratios of the residues preceding and following the substitution site, indicating different helix capping preferences of the substituting amino acids. © 1997 John Wiley & Sons, Inc. Biopoly 42: 633–644, 1997