Determining Valine Side-Chain Rotamer Conformations in Proteins from Methyl 13C Chemical Shifts: Application to the 360 kDa Half-Proteasome

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Abstract
A method is presented for determining Val side-chain χ1 rotamer distributions in proteins based exclusively on measured 13Cγ1 and 13Cγ2 chemical shifts. The approach selects an ensemble of 20 χ1 values, calculates average methyl 13Cγ1,γ2 chemical shifts via theoretical quantum chemical calculations and maximizes the agreement with the experimentally measured shifts using a genetic algorithm. The methodology is validated with an application involving six proteins for which 13Cγ chemical shifts and three-bond methyl-backbone scalar couplings are available. The utility of the methodology is demonstrated with an application to the 360 kDa ‘half-proteasome’ where the χ1 rotameric distributions of Val residues are calculated on the basis of chemical shifts. For the most part the χ1 profiles so obtained compare very well with those generated from the high-resolution (2.3 Å) X-ray structure of the proteasome. Both NMR and X-ray distributions are cross-validated by comparing calculated 1H–13C methyl residual dipolar couplings with measured values, and the level of agreement is at least as good for the NMR derived χ1 values. Notably, as the resolution of the X-ray data improves (rotamer distributions from 3.4 and 2.3 Å X-ray structures are compared with the NMR data), the agreement with the NMR gets significantly better. This emphasizes the importance of NMR approaches for the study of high molecular weight complexes that can be recalcitrant to high resolution X-ray analysis.

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