Analysis Of Side-chain Dynamics Of PhoB Dna Binding/transactivation Domain Using Molecular Dynamics Simulations

Abstract

PhoB is a transcription activator protein involved in the regulation of 39 genes constituting the pho regulon of bacteria. The DNA-binding/transactivation domain is a C-terminal functional domain of the PhoB for binding of the pho box, which is situated upstream of the pho regulon. The NMR structure of the DNA binding form of the PhoB DNA-binding/transactivation domain was solved by our group (PDB: 2z33) (1). In addition, backbone and side-chain dynamics of PhoB-DNA binding/transactivation domain were analyzed using the NMR relaxation spectroscopy (2).In the present study, molecular dynamics (MD) simulations of the free-form and DNA- binding form of PhoB-DNA binding/transactivation domain were carried out, and resulting backbone and side-chain dynamics were compared with those of NMR relaxation experiments. The model-free order parameters for the backbone N-H bond (S2NH) and the methyl-averaging axis (S2axis) obtained from the MD simulations were in agreement with experimental values. It was found that S2NH and S2axis correlate well with the root-mean-square fluctuation (RMSF) of the backbone nitrogen atoms and the methyl carbon atoms obtained from the MD simulations, respectively, in contrast to weak correlations between the order parameters and crystal temperature factors. The S2aixs - RMSF plot showed the clear dependence of S2aixs on amino-acid species and the positions of the methyl groups in the side-chains, suggesting that dynamics of the methyl group in side chains are strongly affected by geometry of side chains in amino-acid species.(1) T. Yamane et al., Proteins 2008:71, 1970-1983.(2) H. Okamura et al., J. Mol. Biol. 2007:367, 1093-1117.