  Several recent works have shown that protein structure can predict
site-specific evolutionary sequence variation. In particular, sites that are
buried and/or have many contacts with other sites in a structure have been
shown to evolve more slowly, on average, than surface sites with few contacts.
Here, we present a comprehensive study of the extent to which numerous
structural properties can predict sequence variation. The quantities we
considered include buriedness (as measured by relative solvent accessibility),
packing density (as measured by contact number), structural flexibility (as
measured by B factors, root-mean-square fluctuations, and variation in dihedral
angles), and variability in designed structures. We obtained structural
flexibility measures both from molecular dynamics simulations performed on 9
non-homologous viral protein structures and from variation in homologous
variants of those proteins, where available. We obtained measures of
variability in designed structures from flexible-backbone design in the Rosetta
software. We found that most of the structural properties correlate with site
variation in the majority of structures, though the correlations are generally
weak (correlation coefficients of 0.1 to 0.4). Moreover, we found that
buriedness and packing density were better predictors of evolutionary variation
than was structural flexibility. Finally, variability in designed structures
was a weaker predictor of evolutionary variability than was buriedness or
packing density, but it was comparable in its predictive power to the best
structural flexibility measures. We conclude that simple measures of buriedness
and packing density are better predictors of evolutionary variation than are
more complicated predictors obtained from dynamic simulations, ensembles of
homologous structures, or computational protein design.
