Computational protein design quantifies structural constraints on amino acid covariation.

ABSTRACT: Amino acid covariation, where the identities of amino acids at different sequence positions are correlated, is a hallmark of naturally occurring proteins. This covariation can arise from multiple factors, including selective pressures for maintaining protein structure, requirements imposed by a specific function, or from phylogenetic sampling bias. Here we employed flexible backbone computational protein design to quantify the extent to which protein structure has constrained amino acid covariation for 40 diverse protein domains. We find significant similarities between the amino acid covariation in alignments of natural protein sequences and sequences optimized for their structures by computational protein design methods. These results indicate that the structural constraints imposed by p

SUBMITTER: Ollikainen N 

PROVIDER: S-EPMC3828131 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature