The Site-Specific Amino Acid Preferences of Homologous Proteins Depend on Sequence Divergence.

ABSTRACT: The propensity of protein sites to be occupied by any of the 20 amino acids is known as site-specific amino acid preferences (SSAP). Under the assumption that SSAP are conserved among homologs, they can be used to parameterize evolutionary models for the reconstruction of accurate phylogenetic trees. However, simulations and experimental studies have not been able to fully assess the relative conservation of SSAP as a function of sequence divergence between protein homologs. Here, we implement a computational procedure to predict the SSAP of proteins based on the effect of changes in thermodynamic stability upon mutation. An advantage of this computational approach is that it allows us to interrogate a large and unbiased sample of homologous proteins, over the entire spectrum of sequence d

SUBMITTER: Ferrada E 

PROVIDER: S-EPMC6326188 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature