A method for validating the accuracy of NMR protein structures

Nicholas J Fowler,Mike P Williamson,Adnan Sljoka,Adnan Sljoka

doi:10.1038/s41467-020-20177-1

Abstract

We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.

Highlights

We present a method that measures the accuracy of nuclear magnetic resonance (NMR) protein structures
Because it is expected that crystal structures and solution structures have the same physical forces underlying them, the geometrical tests for crystal and NMR structures are identical, and include clashscore, an analysis of Ramachandran outliers, and an analysis of sidechain outliers
We demonstrate the power of the method by using it to make comparisons between crystal structures and NMR structures

Summary

Introduction

We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). The quantity of information comprising the experimental restraints is far less for NMR, and the information is much more local This makes NMR structures inherently less precise, and probably less accurate too, and means that cross-validation by missing out 10% of the data, as used for Rfree, is not generally possible for NMR structures[12]. NMR structures tend to be validated using an unsatisfactory set of restraint comparisons, typically comprising number of restraints per residue, restraint violations, and structure precision (RMS distance between members of the ensemble)[5,13] None of these is a direct comparison to the input data, and the third of these is explicitly a measure of precision, not of accuracy, and it is already well established that there is little relationship between precision and accuracy[14,15,16,17]. We demonstrate the power of the method by using it to make comparisons between crystal structures and NMR structures

Methods

Results

Conclusion