X-ray vs. NMR structures as templates for computational protein design

Certain protein-design calculations involve using an experimentally determined high-resolution structure as a template to identify new sequences that can adopt the same fold. This approach has led to the successful design of many novel, well-folded, native-like proteins. Although any atomic-resolution structure can serve as a template in such calculations, most successful designs have used high-resolution crystal structures. Because there are many proteins for which crystal structures are not available, it is of interest whether nuclear magnetic resonance (NMR) templates are also appropriate. We have analyzed differences between using X-ray and NMR templates in side-chain repacking and design calculations. We assembled a database of 29 proteins for which both a high-resolution X-ray structure and an ensemble of NMR structures are available. Using these pairs, we compared the rotamericity, chi(1)-angle recovery, and native-sequence recovery of X-ray and NMR templates. We carried out design using RosettaDesign on both types of templates, and compared the energies and packing qualities of the resulting structures. Overall, the X-ray structures were better templates for use with Rosetta. However, for approximately 20% of proteins, a member of the reported NMR ensemble gave rise to designs with similar properties. Re-evaluating RosettaDesign structures with other energy functions indicated much smaller differences between the two types of templates. Ultimately, experiments are required to confirm the utility of particular X-ray and NMR templates. But our data suggest that the lack of a high-resolution X-ray structure should not preclude attempts at computational design if an NMR ensemble is available.