Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins

Abstract

A computational methodology for backbone amide proton chemical shift (delta(H)) predictions based on ab initio quantum mechanical treatment of part of the protein is presented. The method is used to predict and interpret 13 delta(H) values in protein G and ubiquitin. The predicted amide-amide delta(H) values are within 0.6 ppm of experiment, with a root-mean-square deviation (RMSD) of 0.3 ppm. We show that while the hydrogen bond geometry is the most important delta(H)-determinant, longer-range cooperative effects of extended hydrogen networks make significant contributions to delta(H). We present a simple model that accurately relates the protein structure to delta(H).