Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials
 
research article

Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials

Bucher, D.  
•
Guidoni, L.  
•
Maurer, P.
Show more
2009
Journal of Chemical Theory and Computation

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside the selectivity filter of the KcsA potassium channel. A comparison is made with the result of classical electrostatic calculations with nonpolarizable MM force fields (AMBER, CHARMM, and GRO-MOS). An effective procedure is proposed to improve force field charges by performing a fit on the electrostatic potential computed along QM/MM simulations, using a dynamical electrostatic potential derived charge set. The optimized charge set is able to reproduce the QM/MM electrostatic potentials along the channel axis within 1-2 kcal/mol, which represents an improvement relative to the corresponding electrostatic potentials obtained with popular MM force fields. By providing quantum mechanical benchmark charges and energies for the KcsA selectivity filter, we hope to facilitate developments toward the modeling of ion channels by providing an objective test as to whether a given implementation of a new, polarizable, model represents a real improvement over existing fixed point charge models.

  • Details
  • Metrics
Type
research article
DOI
10.1021/ct9001619
Web of Science ID

WOS:000268720100021

Author(s)
Bucher, D.  
Guidoni, L.  
Maurer, P.
Rothlisberger, U.  
Date Issued

2009

Published in
Journal of Chemical Theory and Computation
Volume

5

Start page

2173

End page

2179

Subjects

Molecular-Dynamics Simulations

•

Potassium-Ion Channel

•

K+/Na+ Selectivity

•

Permeation

•

Coordination

•

Conduction

•

Energetics

•

State

•

Block

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBC  
Available on Infoscience
December 1, 2009
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/44562
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés