Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin

Background: The recent merger of computation and protein design has resulte d in a burst of success in the generation of novel proteins with native-lik e properties. A critical component of this coupling between theory acid exp eriment is a detailed analysis of the structures and stabilities of designe d proteins to assess and improve the accuracy of design algorithms. Results: Here we report the solution structure of a hydrophobic core varian t of ubiquitin, referred to as 1D7, which was designed with the core-repack ing algorithm ROC. As a measure of conformational specificity, we also pres ent amide exchange protection factors and backbone and sidechain dynamics. The results indicate that 1D7 is similar to wild-type (WT) ubiquitin in bac kbone structure and degree of conformational specificity. We also observe a good correlation between experimentally determined sidechain structures an d those predicted by ROC. However, evaluation of the core sidechain conform ations indicates that, in general, 1D7 has more sidechains in less statisti cally favorable conformations than WT. Conclusions: Our results provide an explanation for the lower stability of 1D7 compared to WT, and suggest modifications to design algorithms that may improve the accuracy with which structure and stability are predicted. The results also demonstrate that core packing can affect conformational flexi bility in subtle ways that are likely to be important for the design of fun ction and protein-ligand interactions.