Coevolving protein residues: Maximum likelihood identification and relationship to structure

The identification of protein sites undergoing correlated evolution (coevol ution) is of great interest due to the possibility that these pairs will te nd to be adjacent in the three-dimensional structure. Identification of suc h pairs should provide useful information for understanding the evolutionar y process, predicting the effects of site-directed substitution, and potent ially for predicting protein structure. Here, we develop and apply a maximu m likelihood method with the aim of improving detection of coevolution. Unl ike previous methods which have had limited success, this method allows for correlations induced by phylogenetic relationships and for variation in ra te of evolution along branches, and does not rely on accurate reconstructio n of ancestral nodes. Tn order to reduce the complexity of coevolutionary r elationships and identify the primary component of pairwise coevolution bet ween two sites, we reduce the data to a two-state system;at each site, rega rdless of the actual number of residues observed at that site. Simulations show that this strategy is good at identifying simple correlations and at r ecognizing cases in which the data are insufficient to distinguish between coevolution and spurious correlations. The new method was tested by using s ize and charge characteristics to group the residues at each site, and then evaluating coevolution in myoglobin sequences. Grouping based on physicoch emical characteristics allows categorization of coevolving sites into posit ive and negative coevolution, depending on the correlation between equilibr ium state frequencies. We detected a striking excess of negative coevolutio n (corresponding to charge) at sites brought into proximity by the periodic ity of the alpha-helix, and there was also a tendency for sites with signif icant likelihood ratios to be close in the three-dimensional structure. Sit es on the surface of the protein appear to coevolve both when they are clos e in the structure, and when they are distant, implying a role for folding and/or avoidance of quaternary structure in the coevolution process. (C) 19 99 Academic Press.