Journal article
Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization
Journal of chemical theory and computation, v 14(5), pp 2743-2750
08 May 2018
PMID: 29570282
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K
ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.
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Details
- Title
- Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization
- Creators
- S Alexis Paz - INFIQC, CONICET , X5000HUA , Córdoba , ArgentinaLuca Maragliano - Center for Synaptic Neuroscience and Technology , Fondazione Istituto Italiano di Tecnologia , 16132 Genoa , ItalyCameron F Abrams - Department of Chemical and Biological Engineering , Drexel University , Philadelphia , Pennsylvania 19104 , United States
- Publication Details
- Journal of chemical theory and computation, v 14(5), pp 2743-2750
- Publisher
- American Chemical Society; Washington, DC
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000431926500042
- Scopus ID
- 2-s2.0-85046792185
- Other Identifier
- 991014969875304721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Chemistry, Physical
- Physics, Atomic, Molecular & Chemical