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Biophys. J. BioFAST: First Published November 4, 2005. doi:10.1529/biophysj.105.071407
© 2005 by the Biophysical Society.

A more recent version of this article appeared on February 1, 2006.
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BIOPHYSICAL THEORY AND MODELING

ANIONIC PHOSPHOLIPID INTERACTIONS WITH THE POTASSIUM CHANNEL KCSA: SIMULATION STUDIES

Sundeep S Deol 1, Carmen Domene 1, Peter J Bond 1 and Mark S.P. Sansom 1*

1 Univ of Oxford

* To whom correspondence should be addressed. E-mail: mark{at}biop.ox.ac.uk.

Submitted on July 25, 2005
Revised on August 23, 2005
Accepted on 18 October 2005


  Abstract
Molecular dynamics (MD) simulations have been used to unmask details of specific interactions of anionic phospholipids with inter-subunit binding sites on the surface of the bacterial potassium channel KcsA. Crystallographic data on a diacyl glycerol fragment at this site were used to model phosphatidyl ethanolamine (PE), or phosphatidyl glycerol (PG), or phosphatidic acid (PA) at the inter-subunit binding sites. Each of these models of a KcsA-lipid complex was embedded in phosphatidyl choline bilayer and explored in a 20 ns MD simulation. H-bond analysis revealed that in terms of lipid/protein interactions PA > PG >> PE and revealed how anionic lipids (PG and PA) bind to a site provided by two key arginine residues (R64 and R89) at the interface between adjacent subunits. A 27 ns simulation was performed in which KcsA (without any lipids initially modelled at the R64/R89 sites) was embedded in a PE/PG bilayer. There was a progressive specific increase over the course of the simulation in the number of H-bonds of PG with KcsA. Furthermore, two specific PG binding events at R64/R89 sites were observed. The phosphate oxygen atoms of bound PG formed H-bonds to the guanidinium group of R89, whilst the terminal glycerol H-bonded to R64. Overall, this study suggests that simulations can help identify and characterise sites for specific lipid interactions on a membrane protein surface.

Key Words: ion channel, lipid bilayer, molecular dynamics, non-annular lipid, potassium channel




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Copyright © 2005 by the Biophysical Society.