Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function

Here, we provide an analysis of molecular evolution of five of the most pop ulated protein folds: immunoglobulin fold, oligonucleotide-binding fold, Ro ssman fold, alpha/beta plait, and TIM barrels. In order to distinguish betw een "historic", functional and structural reasons for amino acid conservati ons, we consider proteins that acquire the same fold and have no evident se quence homology. For each fold we identify positions that are conserved wit hin each individual family and coincide when nonhomologous proteins are str ucturally superimposed. As a baseline for statistical assessment we use the conservatism expected based on the solvent accessibility. The analysis is based on a new concept of "conservatism-of-conservatism". This approach all ows us to identify the structural features that are stabilized in all prote ins having a given fold, despite the fact that actual interactions that pro vide such stabilization may vary from protein to protein. Comparison with e xperimental data on thermodynamics, folding kinetics and function of the pr oteins reveals that such universally conserved clusters correspond to eithe r: (i) super-sites (common location of active site in proteins having commo n tertiary structures but not function) or (ii) folding nuclei whose stabil ity is an important determinant of folding rate, or both (in the case of Ro ssman fold). The analysis also helps to clarify the relation between foldin g and function that is apparent for some folds. (C) 1999 Academic Press.