Amino acid coevolution induces an evolutionary Stokes shift.

ABSTRACT: The process of amino acid replacement in proteins is context-dependent, with substitution rates influenced by local structure, functional role, and amino acids at other locations. Predicting how these differences affect replacement processes is difficult. To make such inference easier, it is often assumed that the acceptabilities of different amino acids at a position are constant. However, evolutionary interactions among residue positions will tend to invalidate this assumption. Here, we use simulations of purple acid phosphatase evolution to show that amino acid propensities at a position undergo predictable change after an amino acid replacement at that position. After a replacement, the new amino acid and similar amino acids tend to become gradually more acceptable over time at that po

SUBMITTER: Pollock DD 

PROVIDER: S-EPMC3361410 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature