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

The calculation of free-energy landscapes in proteins is a challenge for modern numerical simulations. As to the case of potassium ion 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.

Computational Analysis of Current and Noise Properties of a Single Open Ion Channel.

This paper presents a computational analysis of the noise associated with the ion current in single open ion channels. The study is performed by means of a coupled molecular dynamics/Monte Carlo approach able to simulate the conduction process on the basis of all microscopic information today available from protein structural data and atomistic simulations. The case of potassium ions permeating the KcsA channel is considered in the numerical calculations.