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Octyl glucoside (OG) is a detergent widely employed in structural and functional studies of membrane proteins. To better understand the nature of protein-OG interactions, molecular dynamics simulations (duration 10 ns) have been used to explore an alpha-helical membrane protein, GlpF, in OG micelles and in DMPC bilayers. Greater conformational drift of the extramembraneous protein loops, from the initial X-ray structure, is seen for the GlpF-OG simulations than for the GlpF-DMPC simulation. The mobility of the transmembrane alpha-helices is approximately 1.3x higher in the GlpF-OG than the GlpF-DMPC simulations. The detergent is seen to form an irregular torus around the protein. The presence of the protein leads to a small perturbation in the behavior of the alkyl chains in the OG micelle, namely an approximately 15% increase in the trans-gauche(-)-gauche(+) transition time. Aromatic side chains (Trp, Tyr) and basic side chains (Arg, Lys) play an important role in both protein-detergent (OG) and protein-lipid (DMPC) interactions.

Original publication

DOI

10.1021/jp046727h

Type

Journal article

Journal

J Phys Chem B

Publication Date

13/01/2005

Volume

109

Pages

575 - 582

Keywords

Aquaporins, Computer Simulation, Escherichia coli Proteins, Glucosides, Lipid Bilayers, Membrane Proteins, Micelles, Models, Molecular, Protein Conformation, Protein Structure, Secondary, Structure-Activity Relationship, Time Factors