DNA curvature and phosphate neutralization: An important aspect of specific protein binding

A theoretical study is presented of the influence of salt bridges between p rotein cationic side chains and DNA phosphates on DNA conformation and flex ibility. Two DNA sequences are studied containing respectively the HNF3 and CAP binding sites. The effect of salt bridges is modelled by the neutralis ation of net phosphate charges for the groups involved in such interactions in the complex. Energy optimised conformations are obtained by molecular m echanics calculations using the JUMNA program. Base sequence dependence is studied by moving the phosphate neutralisation pattern along the sequence, while normal mode analysis is used to evaluate DNA flexibility The results show that phosphate neutralisation has a strong influence on DNA conformati on. For the HNF3 binding Sequence, the free oligomer is bent in direction v ery different from that observed in the protein complex. Phosphate neutrali sation changes this direction by 45 degrees to within only 4 degrees of the direction in the complex, without changing the bending angle. For the CAP binding sequence, the free oligomer is already intrinsically curved in the direction favoured by the protein, but phosphate neutralisation increases t he bending angle. For both oligomers studied these effects are strongly seq uence dependent. It is also shown that oligomer flexibility cannot be expla ined by a simple superposition of the properties of successive dinucleotide steps. Important long range coupling effects are observed. However, for bo th sequence studied, phosphate neutralisation however leads to a reduction in oligomer flexibility.