The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential
Date
2001
Authors
Bliznyuk, Andrei
Rendell, Alistair
Allen, Toby
Chung, Shin-Ho
Journal Title
Journal ISSN
Volume Title
Publisher
American Chemical Society
Abstract
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 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.
Description
Keywords
Keywords: Ion permeation; Amino acids; Binding energy; Biochemistry; Electromagnetic wave polarization; Electrostatics; Molecular dynamics; Parameter estimation; Positive ions; Potassium; Proteins; Water; Quantum theory
Citation
Collections
Source
Journal of Physical Chemistry B
Type
Journal article
Book Title
Entity type
Access Statement
License Rights
Restricted until
2037-12-31
Downloads
File
Description