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The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential

Bliznyuk, Andrei; Rendell, Alistair; Allen, Toby; Chung, Shin-Ho

Description

The molecular electrostatic potential inside the potassium channel protein from Streptomyces lividans has been investigated using linear scaling semiempirical quantum chemical method, for a variety of geometries, with and without solvating water molecules. The results are compared with those given by a number of popular molecular mechanics force-fields. The difference between the quantum and molecular mechanics electrostatic potentials due to the protein exceeds 30 kcal/mol within the narrow...[Show more]

dc.contributor.authorBliznyuk, Andrei
dc.contributor.authorRendell, Alistair
dc.contributor.authorAllen, Toby
dc.contributor.authorChung, Shin-Ho
dc.date.accessioned2015-12-10T23:19:45Z
dc.identifier.issn1520-6106
dc.identifier.urihttp://hdl.handle.net/1885/66036
dc.description.abstractThe molecular electrostatic potential inside the potassium channel protein from Streptomyces lividans has been investigated using linear scaling semiempirical quantum chemical method, for a variety of geometries, with and without solvating water molecules. The results are compared with those given by a number of popular molecular mechanics force-fields. The difference between the quantum and molecular mechanics electrostatic potentials due to the protein exceeds 30 kcal/mol within the narrow selectivity filter of the channel and is attributed to the neglect of electronic effects, e.g., polarization, in the molecular mechanics force-fields. In particular, mutual electronic interactions between four threonine residues in the selectivity filter are found to have a large effect on the electrostatic potential. Calculations in the presence of water molecules suggest that molecular mechanics methods also overestimate the stabilization of the cation inside the ion channel. The molecular electrostatic potentials computed by molecular mechanics force-fields expressed relative to bulk water, however, reveal a much smaller error.
dc.publisherAmerican Chemical Society
dc.sourceJournal of Physical Chemistry B
dc.subjectKeywords: Ion permeation; Amino acids; Binding energy; Biochemistry; Electromagnetic wave polarization; Electrostatics; Molecular dynamics; Parameter estimation; Positive ions; Potassium; Proteins; Water; Quantum theory
dc.titleThe Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential
dc.typeJournal article
local.description.notesImported from ARIES
local.description.refereedYes
local.identifier.citationvolume105
dc.date.issued2001
local.identifier.absfor030701 - Quantum Chemistry
local.identifier.ariespublicationMigratedxPub1205
local.type.statusPublished Version
local.contributor.affiliationBliznyuk, Andrei, Administrative Division, ANU
local.contributor.affiliationRendell, Alistair, College of Engineering and Computer Science, ANU
local.contributor.affiliationAllen, Toby, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationChung, Shin-Ho, College of Physical and Mathematical Sciences, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.startpage12674
local.bibliographicCitation.lastpage12679
local.identifier.doi10.1021/jp013069h
dc.date.updated2015-12-10T10:17:23Z
local.identifier.scopusID2-s2.0-0035924827
CollectionsANU Research Publications

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