Combining experiments and simulations to examine the temperature-dependent behaviour of a disordered protein

Abstract

AbstractIntrinsically disordered proteins are a class of proteins that lack stable folded conformations and instead adopt a range of conformations that determine their biochemical functions. The temperature-dependent behaviour of such disordered proteins is complex and can vary depending on the specific protein and environment. Here, we have used molecular dynamics simulations and previously published experimental data to investigate the temperature-dependent behaviour of Histatin 5, a 24-residue-long polypeptide. We examined the hypothesis that Histatin 5 undergoes a loss of polyproline II structure with increasing temperature, leading to more compact conformations. We found that the conformational ensembles generated by the simulations generally agree with small-angle X-ray scattering data for Histatin 5, but show some discrepancies with the hydrodynamic radius as probed by pulsed-field gradient nuclear magnetic resonance spectroscopy, and with the secondary structure information derived from circular dichroism. We attempted to reconcile these differences by reweighting the conformational ensembles against the scattering and NMR data. By doing so, we were in part able to capture the temperature-dependent behaviour of Histatin 5 and to link the observed decrease in hydrodynamic radius with increasing temperature to a loss of polyproline II structure. We were, however, unable to achieve agreement with both the scattering and NMR data within experimental errors. We discuss different possibilities for this outcome including inaccuracies in the force field, differences in conditions of the NMR and scattering experiments, and issues related to the calculation of the hydrodynamic radius from conformational ensembles. Our study highlights the importance of integrating multiple types of experimental data when modelling conformational ensembles of disordered proteins and how environmental factors such as the temperature influence them.