Hydrogen bond geometry and 2H/1H fractionation in proteins

Measurement of H-2/H-1 equilibrium exchange (Phi) is commonly applied as an indirect probe of hydrogen bonds in small molecules. To expand the limited set of protein Phi measurements and to gain insight into the putative correlation between low Phi, and hydrogen bond strength, we report measurements for two proteins, src SH3 and ubiquitin. A hydrogen bond network in Gallus gallus src SH3 domain, involving residues 30, 47, and 50, contributes similar to 2.0 kcal/mol to native state stability and provides an excellent system in which to test the purported connection between hydrogen bonding networks and protium enrichment. All observed sites in src SH3 had fractionation factors greater than unity. In particular, the backbone protons associated with the hydrogen bond network at residues Glu30, Ser47;, and Thr50 all exhibit moderate deuterium enrichment. Measured fractionation values in ubiquitin range from Phi = 1.52 for the amide of residue Ser20 to a remarkably low Phi = 0.29 for the amide of Thr9. The majority (75%) of backbone amides fall between 0.9 < Phi < 1.3, with an average Phi = 1.07, closely matching the average Phi = 1.11 previously determined by another triple resonance method, and consistent with the fractionation observed in other weak hydrogen bonding amide systems. A survey of protein sites exhibiting low fractionation show a conservation of hydrogen bonding geometry. Our data, in combination with other studies, suggest that H-1/H-2 fractionation at protein backbone amides is a product of the complex three dimensional and static protein hydrogen bonding environment that restricts or enhances specific vibrational modes and is largely independent of hydrogen bonding strength.