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Direct computation of long time processes in peptides and proteins: Reaction path study of the coil‐to‐helix transition in polyalanine
Author(s) -
Huo Shuanghong,
Straub John E.
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19990801)36:2<249::aid-prot10>3.0.co;2-1
Subject(s) - computation , helix (gastropod) , path (computing) , electromagnetic coil , chemistry , transition (genetics) , chemical physics , statistical physics , computational chemistry , crystallography , materials science , physics , computer science , biochemistry , algorithm , biology , snail , gene , programming language , quantum mechanics , ecology
The MaxFlux reaction path algorithm was used to isolate optimal transition pathways for the coil‐to‐helix transition in polyalanine. Eighteen transition pathways, each connecting one random coil configuration with an ideal α‐helical configuration, were computed and analyzed. The transition pathway energetics and mechanism were analyzed in terms of the progression of the peptide nonbonded contact formation, helicity, end‐to‐end distance and energetics. It was found that (1) localized turns characterized by i, i + 3 hydrogen bonds form in the early stages of the coil‐to‐helix transition, (2) the peptide first collapses and then becomes somewhat more extended in the final stage of helix formation, and (3) 3 10 ‐helix formation does not appear to be a necessary step in the transition from coil to helix. These conclusions are in agreement with the results of more computationally intensive direct molecular dynamics simulations. Proteins 1999;36:249–261. © 1999 Wiley‐Liss, Inc.