Paper Citing NAMD - Abstract
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 135101, OCT 7 2011
Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner. (C) 2011 American Institute of Physics. [doi:10.1063/1.3634004]
