Computer simulation molecular dynamics (MD) calculations are proposed to complement experiments designed to elucidate structural characteristics of virus protein U (Vpu), an 81-residue protein which is encoded exclusively by human immunodeficiency virus type 1, HIV-1. Vpu has two distinct biological activities that are controlled by separate structural domains: Induction of the degradation of the CD4 receptor in the endoplasmic reticulum (ER) and augmentation of virus particle release from the plasma membrane. The former function involves the cytoplasmic (CYTO) sequences of Vpu and the latter the transmembrane (TM) domain. The goal of this project is to utilize new constant pressure and temperature MD methodologies to detail how, and where, HIV-1-specific Vpu interacts with cellular components. We have already published MD simulation results for the biologically relevant bilayer phase of the phospholipid dipalmitoylphosphatidylcholine (DPPC), which a well-recognized model membrane system. We have also recently carried out a simulation study of a membrane-spanning synthetic ion channel formed by a four- helix bundle of 21-residue peptides. We propose to build on these MD simulation results and explore the interactions of the hydrophobic Vpu TM domain peptide (Vpu 1-27) with a model membrane. Next, in light of their potential to act as biological channel for monvalent cations, we propose to determine the behavior of oligomers of the wild-type peptide Vpu 1-27 in a lipid bilayer. The MD technique will also be used to investigate the solution structure of the Vpu CYTO domain (peptide Vpu 32-81) to compare with contemporary experiments. To do so, we will carry out extensive MD simulation is aqueous and mixed hydrophilic and hydrophobic solvents. Finally, if the afore mentioned studies are successful, we will then attempt to characterize the behavior of HIV-1-specific Vpu in other membrane- mimetic environments including, bilayers, micelles and Langmuir monolayers. These computer simulation studies are designed to complement NMR and diffraction experiments, which will be carried out at UPENN and elsewhere, on HIV-1-specific Vpu.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM056538-03
Application #
6204290
Study Section
Project Start
1999-08-01
Project End
2000-11-30
Budget Start
1997-10-01
Budget End
1998-09-30
Support Year
3
Fiscal Year
1999
Total Cost
Indirect Cost
Name
University of Pennsylvania
Department
Type
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Sinha, Neeraj; Grant, Christopher V; Wu, Chin H et al. (2005) SPINAL modulated decoupling in high field double- and triple-resonance solid-state NMR experiments on stationary samples. J Magn Reson 177:197-202
Kochendoerfer, Gerd G; Jones, David H; Lee, Sangwon et al. (2004) Functional characterization and NMR spectroscopy on full-length Vpu from HIV-1 prepared by total chemical synthesis. J Am Chem Soc 126:2439-46
Becker, Christian F W; Oblatt-Montal, Myrta; Kochendoerfer, Gerd G et al. (2004) Chemical synthesis and single channel properties of tetrameric and pentameric TASPs (template-assembled synthetic proteins) derived from the transmembrane domain of HIV virus protein u (Vpu). J Biol Chem 279:17483-9
Zheng, Songyan; Strzalka, Joseph; Jones, David H et al. (2003) Comparative structural studies of Vpu peptides in phospholipid monolayers by x-ray scattering. Biophys J 84:2393-415
Opella, Stanley J (2003) Membrane protein NMR studies. Methods Mol Biol 227:307-20
Montal, M (2003) Structure-function correlates of Vpu, a membrane protein of HIV-1. FEBS Lett 552:47-53
Nevzorov, Alexander A; Opella, Stanley J (2003) Structural fitting of PISEMA spectra of aligned proteins. J Magn Reson 160:33-9
Mesleh, M F; Valentine, K G; Opella, S J et al. (2003) Myristoylation as a general method for immobilization and alignment of soluble proteins for solid-state NMR structural studies. J Biomol NMR 25:55-61
Sun, Feng (2003) Molecular dynamics simulation of human immunodeficiency virus protein U (Vpu) in lipid/water Langmuir monolayer. J Mol Model 9:114-23
Mesleh, Michael F; Opella, Stanley J (2003) Dipolar Waves as NMR maps of helices in proteins. J Magn Reson 163:288-99

Showing the most recent 10 out of 33 publications