Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement

摘要: Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) shift calculation and driven structure refinement. A new parameterization for BPT amide nitrogen has been derived from MP2 ab initio calculations successfully evaluated using crystalline tripeptides. computed of small globular ubiquitin, demonstrating that can match results obtained at DFT level very low computational cost. In addition tensors, allows gradients consequently geometry optimizations. applied refinement conformational analysis a set Trypanosoma brucei (the causative agent African sleeping sickness) tryparedoxin peroxidase Px III structures. found interaction with its reaction partner Tpx seems be governed by selection rather than induced fit.