NMR study of rapidly exchanging backbone amide protons in staphylococcal nuclease and the correlation with structural arid dynamic properties

Exchange rates of rapidly exchanging (>1.0 s^-1) backbone amide protons with solvent water in staphylococcal nuclease (SN) were measured at pH 6.03- 7.03 with a 2D heteronuclear water exchange filter sequence (WEX II-FHSQC). Comparison of the exchange data with crystal structure data reveals the following: (1) Non-hydrogen-bonding and exposed residues have protection factors (predicted exchange rate in random coil/measured exchange rate) of less than 15 for non-hydrophobic residues and 10 or higher for hydrophobic residues. Among non-hydrophobic residues, Gly tends to have a higher protection factor (10-15), whereas other residues are below 10. (2) Protection factors for buried and non-hydrogen-bonded protons vary over a wide range (6-10⁴). Low protection factors (<25) may indicate fluctuations in structure resulting in substantial solvent exposure. (3) Some hydrogen- bonded and buried protons show rapid exchange, and the protection factors are 25-400. This indicates kinetically labile hydrogen bonds and solvent exposure by structural fluctuations. On the other hand, many protons in this category exchange slower than the detection limit (<1.0 s^-1) and are mainly observed in α helices and β sheets, or hydrophobic residues. Although a good correlation between NMR exchange measurements and X-ray structural properties was observed, discrepancies were also found for several residues, namely ⁸⁰Gln, ⁸²Thr, and ¹³⁸Asn. The measured pH dependence revealed unusual behavior for ⁷⁷Asn, possibly due to a tightly bound water molecule. Our data indicate that it is possible to use the exchange rates of rapidly exchanging protons as a probe for studying hydrogen bonding, solvent accessibility, or regional kinetic lability of protein structures in solution at physiological pH.