Protein structures sustain evolutionary drift

A protein sequence folds into a unique three-dimensional protein structure. Different sequences, though, can fold into similar structures. How stable is a protein structure with respect to sequence changes? What percentage of the sequence is 'anchor' residues, that is, residues crucial for protein structure and function? Here, answers to these questions are pursued by analyzing large numbers of structurally homologous protein pairs. Most pairs of similar structures have sequence identity as low as expected from randomly related sequences (8-9%). On average, only 3-4% of all residues are 'anchor' residues. The symmetric shape of the distribution at low sequence identity suggests that for most structures, four billion years of evolution was sufficient to reach an equilibrium. The mean identities for convergent (different ancestor) and divergent (same ancestor) evolution of proteins to similar structures are quite close and hence, in most cases, it is difficult to distinguish between the two effects. In particular, low levels of sequence identity appear not to be indicative of convergent evolution.