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. Our test case is represented by potassium ions permeating the selectivity filter of the KcsA channel.
E. Piccinini, M. Ceccarelli, F. Affinito, R. Brunetti, C. Jacoboni (2008). Biased Molecular Simulations for Free-Energy Mapping: A Comparison on the KcsA Channel as a Test Case. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 173-183 [10.1021/ct7001896].
Biased Molecular Simulations for Free-Energy Mapping: A Comparison on the KcsA Channel as a Test Case
PICCININI, ENRICO;
2008
Abstract
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. Our test case is represented by potassium ions permeating the selectivity filter of the KcsA channel.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
