Vibrational spectrum and randomness of water at the interface of a protein–DNA complex

Abstract

Molecular dynamics simulations have been carried out to explore the effect of complex formation between the N-terminal domain of the λ-repressor protein (in dimeric form) and the corresponding DNA operator on low-frequency intermolecular vibrational modes of water confined at the interface. The calculations demonstrated enhanced back-scattering of interfacial water due to increased caging effects, the effect being greater for water molecules that are associated with direct binding process. Highest degree of caging effect has been identified with the water molecules that are engaged in forming hydrogenbonded bridges either near directly bound residues or in establishing contacts between the unbound DNA and protein residues. This leads to blue shifts of thewater and the effect is maximum for the bridged Vibrational Spectrum and Randomness of Water at the Interface of a Protein-DNA C water. The analyses further demonstrated that the local randomness of the interfacial water molecules strongly depends on the conformational rigidity of the DNA and the protein components.