Introducing electrostatic stimulation to normal mode analysis.

Abstract

Normal Mode Analysis (NMA) has proven to be a powerful tool to understand the macromolecular movement of protein complexes. While less precise than an all-atom molecular dynamics simulation, it allows to predict movements on timescales that are not yet accessible to MD simulations on a routine basis. In this work, we build on the previous successful implementation EnCoM to include electrostatic interactions in the NMA analysis. The motivation behind this step is to study the conformational rearrangements of voltage-gated ion channels that are sensitive to the electric field over the membrane. We show here preliminary results on the extension of the inter-residue interactions to include electrostatics and first results on the effect of an electric field on the normal modes of a voltage-gated potassium (Kv) channel.