Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.

ABSTRACT: PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane-associated protein complexes by binding to the carboxyl termini of their partners. PDZ domains are thought also to play a signal transduction role by propagating the information that binding has occurred to remote sites. In this study, a molecular dynamics (MD) simulation-based approach, referred to as an interaction correlation analysis, is applied to the PDZ2 domain to identify the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlations between all residue pairs obtained from the MD simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical cl

SUBMITTER: Kong Y 

PROVIDER: S-EPMC2605193 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature