Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing.
Monte Carlo simulated annealing is applied to the study of the alpha-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 alpha-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 beta-strand tendencies of the same homooligomers are also considered, and they are shown to agree with the frequencies of amino acids in beta-sheet from the protein data base.
Okamoto
Y
Y
Department of Physics, Nara Women's University, Japan.
D000409:Alanine / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D005998:Glycine / Q000737:chemistry; D006860:Hydrogen Bonding; D007532:Isoleucine / Q000737:chemistry; D007930:Leucine / Q000737:chemistry; D008715:Methionine / Q000737:chemistry; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry; D010649:Phenylalanine / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D014633:Valine / Q000737:chemistry
D000596:Amino Acids; D009842:Oligopeptides; D007532:Isoleucine; D010649:Phenylalanine; D008715:Methionine; D007930:Leucine; D014633:Valine; D000409:Alanine; D005998:Glycine