β-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease

Abstract

Refolding of staphylococcal nuclease has been studied recently by hydrogen–deuterium exchange and NMR spectroscopy. These studies infer that β-hairpin formed by strand 2 and strand 3 connected by reverse turn forms early during the refolding of nuclease. Typically, hydrogen–deuterium exchange NMR techniques are usually carried out on a time scale of milliseconds whereas β-hairpins are known to fold on a much shorter time scale. It follows that in the experiments, the hydrogen–deuterium exchange protection patterns could be arising from a significant population of fully formed hairpins. In order to demonstrate it is the fully formed hairpins which gives rise to the hydrogen–deuterium exchange protection patterns, we have considered molecular dynamics simulation of the peptide 21DTVKLM YKGQPMTFR 35 from staphylococcal nuclease corresponding to the β-hairpin region, using GROMOS96 force field under NVT conditions. Starting from unfolded conformational states, the peptide folds into hairpin conformations with native-like and non-native hydrogen bonding patterns. Subsequent to folding, equilibrium conditions prevail. The computed protection factors and atom depth values, at equilibrium, of the various amide protons agree qualitatively with experimental observations. A collection of molecules following the trajectories observed in the simulations can account for experimental observations. These simulations provide a molecular picture of the formed hairpins and their conformational features during the refolding experiments on nuclease, monitored by hydrogen–deuterium exchange.