New paper on force-field choice when studying Von Willebrand Factor dynamics

By using temperature replica-exchange molecular dynamics simulations, we find that some force fields indeed rise to the challenge and capture the structural and dynamical features of the NMR ensemble and, therefore, are the appropriate choice for simulations of proteins with partially structured domains.

Kuzmanic, A., Pritchard, R. B., Hansen, D. F. & Gervasio, F. L. Importance of the Force-Field Choice in Capturing Functionally Relevant Dynamics in Von Willebrand Factor. J. Phys. Chem. Lett. acs.jpclett.9b00517 (2019). doi:10.1021/acs.jpclett.9b00517.

Abstract:

Whether recent updates and new releases of atomistic force fields can model the structural and dynamical properties of proteins containing both folded and partially disordered domains is still unclear. To address this fundamental question, we tested eight recently released force fields against our set of nuclear magnetic resonance (NMR) observables for a complex and medically relevant system, the major factor VIII binding region on von Willebrand factor. This biomedically important region comprises both a folded and a partially structured domain. By using an enhanced sampling technique (temperature replica-exchange molecular dynamics simulations), we find that some force fields indeed rise to the challenge and capture the structural and dynamical features of the NMR ensemble and, therefore, are the appropriate choice for simulations of proteins with partially structured domains. What is more, we show that only such force fields can qualitatively capture the effects of a pathogenic mutation on the structural ensemble.