A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.

ABSTRACT:

Background

Since thermodynamic stability is a global property of proteins that has to be conserved during evolution, the selective pressure at a given site of a protein sequence depends on the amino acids present at other sites. However, models of molecular evolution that aim at reconstructing the evolutionary history of macromolecules become computationally intractable if such correlations between sites are explicitly taken into account.

Results

We introduce an evolutionary model with sites evolving independently under a global constraint on the conservation of structural stability. This model consists of a selection process, which depends on two hydrophobicity parameters that can be computed from protein sequences without any fit, and a mutation process for which we consid

SUBMITTER: Bastolla U 

PROVIDER: S-EPMC1570368 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature