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Title: Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Authors:
; ; ; ; ;  [1]
  1. Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580 (Japan)
Publication Date:
OSTI Identifier:
22391186
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Conference Proceedings; Journal Volume: 1649; Journal Issue: 1; Conference: IRAGO Conference 2014, Tsukuba-city, Ibaraki (Japan), 6-7 Nov 2014; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; AMINO ACIDS; COMPUTERIZED SIMULATION; DNA; ELECTRONIC STRUCTURE; GENES; LIGANDS; MOLECULAR DYNAMICS METHOD; MOLECULES; MONOMERS; PROTEINS; WATER