title: Composition analysis of alpha-helices in thermophilic organisms.
abstract: We present a statistical comparison of the amino acid composition in a secondary structure element, the alpha-helix, of proteins stable at high temperatures with those which are less so. This study has shown that the temperature-dependent Zimm-Bragg helix propagation value s is not a good predictor for the helix-forming tendency of an amino acid in thermostable proteins. However, we have shown that delta s, the change in s from 20 to 60 degrees C, accurately predicts the direction of the probability shift for 15 amino acids in thermostable protein alpha-helices, although it does not predict the magnitude of that change. The residues tyrosine, glycine and glutamine show a significant increase in residency in alpha-helices for thermostable proteins over their non-thermostable counterparts. Significant decreases in alpha-helix residency occur for the residues valine, glutamic acid, histidine, cysteine and aspartic acid in proteins from thermophilic organisms. Aromatic interactions, hydrogen bonding and a reduction of charge may explain the increase observed for tyrosine and glutamine and the decrease in glutamic acid and aspartic acid, although packing considerations cannot be ruled out. The only physical explanation for the increase in glycine would seem to be its positive delta s value.
authors: Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA.
authors: G L
authors: GL
authors: Warren
authors: G A
authors: GA
authors: Petsko
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D006860:Hydrogen Bonding; D011336:Probability; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013696:Temperature
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins