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Helix‐forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing
Author(s) -
Okamoto Yuko
Publication year - 1994
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/prot.340190104
Subject(s) - alpha helix , helix (gastropod) , monte carlo method , steric effects , chemistry , random coil , amino acid , folding (dsp implementation) , crystallography , stereochemistry , mathematics , biochemistry , circular dichroism , biology , statistics , ecology , snail , electrical engineering , engineering
Monte Carlo simulated annealing is applied to the study of the α‐helix‐forming tendencies of seven nonpolar amino acids, Ala, Leu, Met, Phe, Ile, Val, and Gly. Homooligomers of 10 amino acids are used and the helix tendency is calculated by folding α‐helicies from completely random initial conformations. The results of the simulation imply that Met, Ala, and Leu are helix formers and that Val, Ile, and Gly are helix breakers, while Phe comes in between the two groups. The differences between helix formers and breakers turned out to be large in agreement with the recent experiments with short peptides. It is argued from the energy distributions of the obtained conformations that the helix tendency is small for the helix breakers because of steric hindrance of side chains. Homoglycine is shown to favor a random coil conformation. The β‐strand tendencies of the same homooligomers are also considered, and they are shown to agree with the frequencies of amino acids in β‐sheet from the protein data base. © 1994 Wiley‐Liss, Inc.