Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein
Joint Authors
Witter, Raiker
Möllhoff, Margit
Koch, Frank-Thomas
Sternberg, Ulrich
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-14, 14 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-09-30
Country of Publication
Egypt
No. of Pages
14
Main Subjects
Abstract EN
Polarization of atoms plays a substantial role in molecular interactions.
Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins.
Changes in charge distributions can be included into molecular mechanics calculations by various methods.
Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT).
Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations.
Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated.
A refined parameterization yielded excellent correlation of R = 0.9967 .
The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus.
Our calculations show that moderate changes of side chain torsion angle χ 1 and small variations of χ 2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.
American Psychological Association (APA)
Witter, Raiker& Möllhoff, Margit& Koch, Frank-Thomas& Sternberg, Ulrich. 2015. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein. Journal of Chemistry،Vol. 2015, no. 2015, pp.1-14.
https://search.emarefa.net/detail/BIM-1067681
Modern Language Association (MLA)
Witter, Raiker…[et al.]. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein. Journal of Chemistry No. 2015 (2015), pp.1-14.
https://search.emarefa.net/detail/BIM-1067681
American Medical Association (AMA)
Witter, Raiker& Möllhoff, Margit& Koch, Frank-Thomas& Sternberg, Ulrich. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein. Journal of Chemistry. 2015. Vol. 2015, no. 2015, pp.1-14.
https://search.emarefa.net/detail/BIM-1067681
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1067681