title: Environmental features are important in determining protein secondary structure.
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%.
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA.
authors.forename: J R
authors.initials: JR
authors.lastname: Macdonald
authors.forename: W C
authors.initials: WC
authors.lastname: Johnson
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D008956:Models, Chemical; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D000596:Amino Acids; D010455:Peptides