Environmental features are important in determining protein secondary structure

Protein Sci. 2001 Jun;10(6):1172-7. doi: 10.1110/ps.420101.

Abstract

We have investigated amino acid features that determine secondary structure: (1) the solvent accessibility of each side chain, and (2) the interaction of each side chain with others one to four residues apart. Solvent accessibility is a simple model that distinguishes residue environment. The pairwise interactions represent a simple model of local side chain to side chain interactions. To test the importance of these features we developed an algorithm to separate alpha-helices, beta-strands, and "other" structure. Single residue and pairwise probabilities were determined for 25,141 samples from proteins with <30% homology. Combining the features of solvent accessibility with pairwise probabilities allows us to distinguish the three structures after cross validation at the 82.0% level. We gain 1.4% to 2.0% accuracy by optimizing the propensities, demonstrating that probabilities do not necessarily reflect propensities. Optimization of residue exposures, weights of all probabilities, and propensities increased accuracy to 84.0%.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Amino Acids / chemistry
  • Models, Chemical
  • Models, Statistical
  • Peptides / chemistry
  • Protein Folding*
  • Protein Structure, Secondary*

Substances

  • Amino Acids
  • Peptides