Alpha/gamma transitions in the B-DNA backbone.

摘要: In the crystal structures of protein complexes with B DNA, a and ? DNA backbone torsion angles often exhibit non canonical values. It is not known if these alternative conformations are easily accessible in solution can contribute to specific recognition by proteins. We have analysed coupled transition within central GpC step dodecamer computer simulations. Five stable or metastable a/? sub states found. The most favourable pathway from structure any unusual form involves counter rotation ?, via trans conformation. However, corresponding free energy indicates that spontaneous flipping torsions improbable DNA. This supported an analysis available high resolution crystallographic showing only encountered complexed An structural consequences transitions shows geometry influences essentially roll twist values reduces equilibrium dispersion parameters. Our results support hypothesis backbones arise during protein?DNA complexation, assisting fine adjustments between two partners playing role overall complexation energy.