Side-Chain χ1 Conformations in Urea-Denatured Ubiquitin and Protein G from 3J Coupling Constants and Residual Dipolar Couplings

Abstract

Current NMR information on side-chain conformations of unfolded protein states is sparse due to the poor dispersion particularly of side-chain proton resonances. We present here optimized schemes for the detection of (3)J(HalphaHbeta), (3)J(NHbeta), and (3)J(C'Hbeta) scalar and (1)D(CbetaHbeta) residual dipolar couplings (RDCs) in unfolded proteins. For urea-denatured ubiquitin and protein G, up to six (3)J-couplings to (1)H(beta) are detected, which define the chi(1) angle at very high precision. Interpretation of the (3)J couplings by a model of mixed staggered chi(1) rotamers yields excellent agreement and also provides stereoassignments for (1)H(beta) methylene protons. For all observed amino acids with the exception of leucine, the chemical shift of (1)H(beta3) protons was found downfield from (1)H(beta2). For most residues, the precision of individual chi(1) rotamer populations is better than 2%. The experimental chi(1) rotamer populations are in the vicinity of averages obtained from coil regions in folded protein structures. However, individual variations from these averages of up to 40% are highly significant and indicate sequence- and residue-specific interactions. Particularly strong deviations from the coil average are found for serine and threonine residues, an effect that may be explained by a weakening of side-chain to backbone hydrogen bonds in the urea-denatured state. The measured (1)D(CbetaHbeta) RDCs correlate well with predicted RDCs that were calculated from a sterically aligned coil model ensemble and the (3)J-derived chi(1) rotamer populations. This agreement supports the coil model as a good first approximation of the unfolded state. Deviations between measured and predicted values at certain sequence locations indicate that the description of the local backbone conformations can be improved by incorporation of the RDC information. The ease of detection of a large number of highly precise side-chain RDCs opens the possibility for a more rigorous characterization of both side-chain and backbone conformations in unfolded proteins.