A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

ABSTRACT: Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two

SUBMITTER: Lai J 

PROVIDER: S-EPMC3423504 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature