Calcium binding to the purple membrane: A molecular dynamics study

Wassenaar, Tsjerk A., Daura, Xavier, Padros, Esteve and Mark, Alan E. (2009) Calcium binding to the purple membrane: A molecular dynamics study. Proteins Structure Function Bioinformatics, 74 3: 669-681. doi:10.1002/prot.22182


Author Wassenaar, Tsjerk A.
Daura, Xavier
Padros, Esteve
Mark, Alan E.
Title Calcium binding to the purple membrane: A molecular dynamics study
Journal name Proteins Structure Function Bioinformatics   Check publisher's open access policy
ISSN 0887-3585
Publication date 2009-02-01
Year available 2008
Sub-type Article (original research)
DOI 10.1002/prot.22182
Volume 74
Issue 3
Start page 669
End page 681
Total pages 13
Place of publication United States
Publisher John Wiley & Sons, Inc
Collection year 2009
Language eng
Subject C1
060112 Structural Biology (incl. Macromolecular Modelling)
970106 Expanding Knowledge in the Biological Sciences
Formatted abstract
The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca2+ near the Schiff base and another one near the Glu194-Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations. Proteins 2009. © 2008 Wiley-Liss, Inc.
Keyword bacteriorhodopsin
cation binding
bond valence sum
simulation
model
Q-Index Code C1
Q-Index Status Confirmed Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2009 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
 
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Created: Wed, 25 Mar 2009, 01:17:27 EST by Jennifer Falknau on behalf of School of Chemistry & Molecular Biosciences