Protein-induced DNA bending: the role of phosphate neutralisation

Abstract

An important component of protein–nucleic acid interactions is the formation of salt bridges between cationic amino acid side chains and the anionic phosphate groups of the nucleic acid. We have used molecular mechanics to study the energetic and conformational impact of such interactions. Firstly, crystallographic protein–nucleic acid complexes from the Protein Data Bank were analysed in terms of DNA curvature and the presence of salt bridges. For complexes where the DNA is significantly bent, the contribution of salt bridges to this curvature was modelled by studying the effect of neutralising the appropriate phosphate groups. The number and the distribution of salt bridges vary widely for different DNA binding motifs and appear to have very different effects on DNA. In the case of homeodomain, bZIP and helix–loop–helix proteins, salt bridges induce DNA bending, whereas for prokaryotic helix–turn–helix proteins the number of salt bridges is much smaller and little bending is found. By analysing the components of the DNA deformation energy involved in protein binding we show that salt bridges consistently increase the flexibility of the DNA backbone.