Assessing the chemical accuracy of protein structures via peptide acidity

Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~ 60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~ 0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses.

Highlights► The acidity of protein amides is exquisitely sensitive to the surrounding charge and dielectric volume distribution. ► Poisson-Boltzmann (PB) predictions appear sensitive to the resolution of independent crystal structure determinations. ► X-ray structures of four proteins yield amide exchange predictions superior to homology model and NMR structures. ► The previously reported RECOORD re-refinement of chymotrypsin inhibitor 2 markedly improves the peptide acidity predictions.