Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

We present a novel method to identify sites under selection in protein-coding genes. Our method combines the traditional Goldman-Yang model of coding-sequence evolution with the information obtained from the 3D structure of the evolving protein, specifically the relative solvent accessibility (RSA) of individual residues. We develop a random-effects likelihood sites model in which rate classes are RSA dependent. The RSA dependence is modeled with linear functions. We demonstrate that our RSA-dependent model provides a significantly better fit to molecular sequence data than does a traditional, RSA-independent model. We further show that our model provides a natural, RSA-dependent neutral baseline for the evolutionary rate ratio omega = dN/dS Sites that deviate from this neutral baseline likely experience selection pressure for function. We apply our method to the influenza proteins hemagglutinin and neuraminidase. For hemagglutinin, our method recovers positively selected sites near the sialic acid-binding site and negatively selected sites that may be important for trimerization. For neuraminidase, our method recovers the oseltamivir resistance site and otherwise suggests that few sites deviate from the neutral baseline. Our method is broadly applicable to any protein sequences for which structural data are available or can be obtained via homology modeling or threading.