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Biophys J, September 2002, p. 1259-1267, Vol. 83, No. 3

Molecular Dynamics Investigation of Membrane-Bound Bundles of the Channel-Forming Transmembrane Domain of Viral Protein U from the Human Immunodeficiency Virus HIV-1

Carlos F. Lopez,dagger Mauricio Montal,* J. Kent Blasie,dagger Michael L. Klein,dagger and Preston B. Mooredagger

 *Division of Biology, University of California, La Jolla, California 92093-0346; and  dagger Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 USA

Molecular dynamics (MD) simulations have been carried out on bundles of the channel-forming transmembrane (TM) domain of the viral protein U (VPU1-27 and VPU6-27) from the human immunodeficiency virus (HIV-1). Simulations of hexameric and pentameric bundles of VPU6-27 in an octane/water membrane mimetic system suggested that the pentamer is the preferred oligomer. Accordingly, an unconstrained pentameric helix bundle of VPU1-27 was then placed in a hydrated palmitoyl-oleyl-3-n-glycero-phosphatidylethanolamine (POPE) lipid bilayer and its structural properties calculated from a 3-ns MD run. Some water molecules, initially inside the channel lumen, were expelled halfway through the simulation and the bundle adopted a conical structure reminiscent of previous MD results obtained for VPU6-27 in an octane/water system. The pore constriction generated may correspond to a closed state of the channel and underlies the relocation of the W residue toward the pore lumen. The relative positions of the helices with respect to the bilayer and their interactions with the lipids are discussed. The observed structure is stabilized via specific interactions between the VPU helices and the carbonyl oxygen atoms of the lipid molecules, particularly at the Q and S residues.

Biophys J, September 2002, p. 1259-1267, Vol. 83, No. 3
© 2002 by the Biophysical Society   0006-3495/02/09/1259/09  $2.00


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