NMR Study of Rapidly Exchanging Backbone Amide Protons in Staphylococcal Nuclease and the Correlation with Structural and Dynamic Properties

Abstract

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 so...