Protein folds: towards understanding folding from inspection of native structures

Abstract

Following a short summary of some of the principal features of folded proteins, the results of two complementary studies of protein structure are presented, the first concerned with the factors which influence secondary structure propensity and the second an analysis of protein topology. In an attempt to deconvolute the physical contributions to secondary structure propensities, we have calculated intrinsic ɸ,ψ propensities, derived from the coil regions of proteins. Comparison of intrinsic ɸ,ψ propensities with their equivalent secondary structure values show correlations for both helix and strand. This suggests that the local dipeptide, steric and electrostatic interactions have a major influence on secondary structure propensity. We then proceed to inspect the distribution of protein domain folds observed to date. Several folds occur very commonly, so that 46% of the current non-homologous database comprises only nine folds. The implications of these results for protein folding are discussed.