Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers

Single-stranded DNA binding (SSB) proteins bind with single-stranded DNA (ss-DNA) segments that are generated as intermediates during DNA metabolic processes. The primary function of an SSB protein is to protect the ss-DNA from being degraded so that other enzymes can effectively act on it. We have performed atomistic molecular dynamics simulations of the two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers in aqueous solutions. Attempts have been made to study the effects of complexation on the internal motions of the protein domains and the correlated dynamics of the amino acid residue side chains. In agreement with experiments, KH3 domain has been found to be relatively more flexible in the complexed state. The calculations reveal increased long-range anticorrelated motions among several amino acid residues in the complexed forms. Compared to the KH4 domain, noticeable increase in N–H dipole ordering on complexation has been observed for the KH3 domain. Importantly, it is demonstrated that the effects of the DNA strands on the side chain orientations of the arginine and lysine residues and their ordering and dynamics play critical roles in forming the complexes and their structural stability.