Molecular Recognition through Concerted Ubiquitin Backbone and Side Chain Motion Determined from NMR and MD Simulations

Abstract

Motion is involved in a large number of protein functions. For ubiquitin, residual dipolar coupling (RDC) derived ensembles have suggested it recognizes binding partners via conformational selection through motions occurring on the supra tau-c (>4 ns) timescale [1]. Subsequent relaxation dispersion (RD) studies identified microsecond fluctuations for six backbone atoms [2,3]. However, it has not been clear if these motions are independent or collective, and what role side chains play. To address those questions, we have conducted an in-depth RD analysis of the backbone and side chain methyl groups. This survey showed a large number of atoms (>30) with microsecond fluctuations. These atoms are distributed throughout the structure and nearly all show the same exchange rate, which suggests that ubiquitin undergoes collective motion involving both the backbone and side chains. The presence of microsecond side chain motion agrees with previous RDC measurements of methyl groups within ubiquitin [4]. Furthermore, comparison of different methyl nuclei indicates that the nature of the side chain fluctuations is almost entirely due to changes in rotamer populations. This is borne out in molecular dynamics simulations of ubiquitin trapped in different conformational states by binding partners [5]. Residues showing RD were significantly more likely to show changes in rotamer populations in the simulations. Put together, this leads to a model where collective microsecond backbone motion is coupled to redistribution of side chain rotamer populations. The correlation with binding partner simulations implicates this motion in conformational selection.1. Lange et al. Science. 320:1471-1475 (2008)2. Ban et al. Angew Chem Int Ed. 50:11437-1144 (2011)3. Ban et al. J Magn Reson. 221:1-4 (2012)4. Fares et al. J Biomol NMR. 45:23-44 (2009)5. Peters et al. PLoS Comput Biol. Accepted (2012)