Biased Molecular Simulations for Free-Energy Mapping: A Comparison on the KcsA Channel as a Test Case

Abstract

The calculation of free-energy landscapes in proteins is a challenge for modern numerical simulations. As to the case of potassium io channels is concerned, it is particularly interesting because of the nanometric dimensions of the selectivity filter, where the complex electrostatics is highly relevant. The present study aims at comparing three different techniques used to bias molecular dynamics simulations, namely Umbrella Sampling, Steered Molecular Dynamics, and Metadynamics, never applied all together in the past to the same channel protein. Our test case is represented by potassium ions permeating the selectivity filter in the KcsA channe