Generality of the structurally constrained protein evolution model: assessment on representatives of the four main...

The Structurally Constrained Protein Evolution (SCPE) model simulates protein evolution by introducing random mutations into the evolving sequences and selecting them against too much structural perturbation. Given a single protein structure, the SCPE model can be used to obtain a whole set of site-dependent amino acid substitution matrices. The set of SCPE substitution matrices for a given protein family can be seen as an independent-sites model of evolution for that family. Thus, these matrices can be compared with other substitution-matrix-based models of evolution. So far, SCPE has been tested only on left-handed parallel beta helix (LbetaH) proteins. Here, we address the question of generality by assessing the SCPE model on representatives of the four main classes of folds: alpha, beta, alpha+beta, and alpha/beta. We compare with other models using the likelihood ratio test with parametric bootstrapping. We show that SCPE performs better than the popular JTT model for all cases considered. Furthermore, by considering the relative contributions of mutation and selection, we found that the key to the success of the SCPE model is the selection step.