Capturing the Polarization Response of Solvated Proteins under Constant Electric Fields in Molecular Dynamics Simulations

We capture and compare the polarization response of a solvated globular protein ubiquitin to static electric (E-fields) using atomistic molecular dynamics simulations. We collectively follow E-field induced changes, electrical and structural, occurring across multiple trajectories using the magnitude of the protein dipole vector (P-p). E-fields antiparallel to P-p induce faster structural changes and more facile protein unfolding relative to parallel fields of the same strength. While weak E-fields (0.1-0.5 V/nm) do not unfold ubiquitin and produce a reversible polarization, strong E-fields (1-2 V/nm) unfold the protein through a pathway wherein the helix:beta-strand interactions rupture before those for the beta 1-beta 5 clamp. Independent of E-field direction, high E-field induced structural changes are also reversible if the field is switched off before P-p exceeds 2 times its equilibrium value. We critically examine the dependence of water properties, protein rotational diffusion and E-field induced protein unfolding pathways on the thermostat/barostat parameters used in our simulations.

Automated summary

We investigated the polarization response of ubiquitin to static electric fields using molecular dynamics simulations. We found that antiparallel fields induce faster structural changes and protein unfolding compared to parallel fields of the same strength. Strong electric fields unfold the protein through specific pathways, while weak fields produce reversible polarization. The dependence of water properties, protein diffusion, and unfolding pathways on simulation parameters were critically examined.