Abstract
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.
Highlights
Chemical shifts hold valuable structural information that is being used increasingly in the determination of protein structure and dynamics[1]
We show for a number of small proteins that structural refinement against experimental dH values using ProCS leads to hydrogen bond geometries that are in closer agreement with high-resolution X-ray structures and experimental trans-hydrogen bond spin-spin coupling constants (h3JNC0 ) compared to using an energy function based on the empirical chemical shift predictor CamShift [7] or solely using a force field (OPLS-AA/L [16] with the GB/SA continuum solvent model [17])
ProCS is a quantum mechanical (QM)-based backbone amide proton chemical shift predictor that can deliver QM quality chemical shift predictions for a protein structure in a millisecond. dH-values predicted using X-ray structures are in worse agreement with experiment, compared to those of the popular empirical chemical shift-predictors CamShift, SHIFTS, SHIFTX, and SPARTA+
Summary
Chemical shifts hold valuable structural information that is being used increasingly in the determination of protein structure and dynamics[1]. While these methods generally offer quite accurate predictions, the predicted chemical shifts of backbone amide protons (dH) tend to be significantly less accurate than, for example, the proton on the a-carbon [8,9] This is unfortunate since 15N-HSQC forms a large fraction of all protein NMR studies and dH holds valuable information about the hydrogen bond geometry of the ubiquitous amide-amide hydrogen bonds that are key to protein secondary structure. The method by Parker et al addresses this problem by parameterization against dH-values obtained by quantum mechanical (QM) calculations, and is similar in spirit to the QM-based a-carbon chemical shift predictor CheShift developed by Vila et al [13,14] Both studies noted that the QMbased chemical shift predictors tend to be more sensitive to small structural changes compared to popular empirical chemical shift predictors and promises to be valuable tools in protein structure validation and refinement. We show for a number of small proteins that structural refinement against experimental dH values using ProCS leads to hydrogen bond geometries that are in closer agreement with high-resolution X-ray structures and experimental trans-hydrogen bond spin-spin coupling constants (h3JNC0 ) compared to using an energy function based on the empirical chemical shift predictor CamShift [7] or solely using a force field (OPLS-AA/L [16] with the GB/SA continuum solvent model [17])
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