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

Abstract

Abstract. 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.

Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding

“…This observation corroborates earlier experimental studies that showed significant changes in the locations and interactions of residues in the phosphate-binding cassette (residues GLY-71 to ALA-84) of CAP upon binding of cAMP . In particular, ARG-82 broke its salt bridge with GLU-129 and entered into the cAMP-binding pocket to establish a new salt bridge with the phosphate unit of cAMP. ,, In addition, two other salt bridges involving GLU-77, GLU-78, and ARG-122 were broken, and a new salt bridge was formed between ARG-122 and GLU-129 after cAMP binds to CAP …”

“…84 In particular, ARG-82 broke its salt bridge with GLU-129 and entered into the cAMP-binding pocket to establish a new salt bridge with the phosphate unit of cAMP. 58,85,86 In addition, two other salt bridges involving GLU-77, GLU-78, and ARG-122 were broken, and a new salt bridge was formed between ARG-122 and GLU-129 after cAMP binds to CAP. 37 The F-helices have zero interaction with the cAMP molecules in the cAMP-CAP complex due to the lack of direct contact between them.…”

“…A large number of experimental − and computational ,− studies examining the allosteric coupling between cAMP binding sites and the DNA binding domains have shown that upon binding to cAMP-loaded CAP the DNA duplex is bent to optimize the electrostatic complementarity between the DNA and CAP . Although earlier studies have shown that the apo- and singly loaded CAP have been known to recognize and bind to DNA, their binding affinity for DNA is significantly lower than that of doubly loaded CAP .…”