Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

ABSTRACT: Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in

SUBMITTER: Wells SA 

PROVIDER: S-EPMC4524684 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature