ArticleThe journal of physical chemistry. B2010
Soft wall ion channel in continuum representation with application to modeling ion currents in α-hemolysin.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 33 citations in OpenAlex.
- Article
- Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model.Entropy (Basel, Switzerland) · 2020Review
- Membrane Position Dependency of the pKThe Journal of membrane biology · 2018Article
- Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process.The journal of physical chemistry. B · 2015Article
- Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials.Journal of computational chemistry · 2014Article
- Multiscale Multiphysics and Multidomain Models I: Basic Theory.Journal of theoretical & computational chemistry · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores.Journal of chemical theory and computation · 2012Article
- Variational multiscale models for charge transport.SIAM review. Society for Industrial and Applied Mathematics · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A soft repulsion (SR) model of short-range interactions between mobile ions and protein atoms is introduced in the framework of continuum representation of the protein and solvent. The Poisson-Nernst-Plank (PNP) theory of ion transport through biological channels is modified to incorporate this soft wall protein model. Two sets of SR parameters are introduced. The first is parametrized for all essential amino acid residues using all atom molecular dynamic simulations; the second is a truncated Lennard-Jones potential. We have further designed an energy-based algorithm for the determination of the ion accessible volume, which is appropriate for a particular system discretization. The effects of these models of short-range interactions were tested by computing current-voltage characteristics of the α-hemolysin channel. The introduced SR potentials significantly improve prediction of channel selectivity. In addition, we studied the effect of the choice of some space-dependent diffusion coefficient distributions on the predicted current-voltage properties. We conclude that the diffusion coefficient distributions largely affect total currents and have little effect on rectifications, selectivity, or reversal potential. The PNP-SR algorithm is implemented in a new efficient parallel Poisson, Poisson-Boltzmann, and PNP equation solver, also incorporated in a graphical molecular modeling package HARLEM.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.