Computational modelling of local fluctuations causing transient solvent exposure of protein amides

Abstract

Hydrogen exchange (HX) between protein amides and solvent water molecules can function as a probe for protein dynamics and provide a bridge between the experimental and computational worlds. However, it is important that the underlying assumptions are tested on well-known systems. Here we perform an analysis of a long MD simulation of BPTI, which has previously been used by Persson and Halle to propose a functional definition of the exchange-competent configurations. We find support for the hypothesis that the exchange-competent configurations typically do not constitute a metastable state per se, but rather occur as the outermost tail of the water distribution around a metastable broken state directly identifiable as having a broken intermolecular hydrogen bond and increased solvent-exposure. Furthermore, we estimate the lifetime of these broken states and the probability that exchange-competent configurations occur in them. We have also tested various sampling protocols and their ability to enhance the exploration of the broken states. Computational protocol used in this study can be applied to a broad range of sys-tems to gain valuable insight into the nature of the broken state, although further development is needed to devise a generally applicable quantitative method.