Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

ABSTRACT: ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the n

SUBMITTER: Invernizzi G 

PROVIDER: S-EPMC4154638 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature