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We present the ProCS method for the rapid and accurate prediction of proteinbackbone amide proton chemical shifts - sensitive probes of the geometry of keyhydrogen bonds that determine protein structure. ProCS is parameterized againstquantum mechanical (QM) calculations and reproduces high level QM resultsobtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS isinterfaced with the PHAISTOS protein simulation program and is used to inferstatistical protein ensembles that reflect experimentally measured amide protonchemical shift values. Such chemical shift-based structural refinements,starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMNTudor Domain, result in average chemical shifts, hydrogen bond geometries, andtrans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellentagreement with experiment. We show that the structural sensitivity of theQM-based amide proton chemical shift predictions is needed to refine proteinstructures to this agreement. The ProCS method thus offers a powerful new toolfor refining the structures of hydrogen bonding networks to high accuracy withmany potential applications such as protein flexibility in ligand binding.

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics