Molecular dynamics simulations on the first two helices of Vpu from HIV-1

Biophys J. 2003 May;84(5):3276-84. doi: 10.1016/S0006-3495(03)70052-6.


Vpu is an 81 amino acid protein of HIV-1 with two phosphorylation sites. It consists of a short N-terminal end traversing the bilayer and a longer cytoplasmic part. The dual functional role of Vpu is attributed to these topological distinct regions of the protein. The first 52 amino acids of Vpu (HV1H2) have been simulated, which are thought to be embedded in a fully hydrated lipid bilayer and to consist of a transmembrane helix (helix-1) connected via a flexible linker region, including a Glu-Tyr-Arg (EYR) motif, with a second helix (helix-2) residing with its helix long axis on the bilayer surface. Repeated molecular dynamics simulations show that Glu-28 is involved in salt bridge formation with Lys-31 and Arg-34 establishing a kink between the two helices. Helix-2 remains in a helical conformation indicating its stability and function as a "peptide float," separating helix-1 from the rest of the protein. This leads to the conclusion that Vpu consists of three functional modules: helix-1, helix-2, and the remaining residues toward the C-terminal end.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry
  • Computer Simulation
  • HIV-1 / chemistry*
  • Human Immunodeficiency Virus Proteins
  • Lipid Bilayers / chemistry*
  • Membrane Proteins / chemistry*
  • Models, Molecular*
  • Molecular Sequence Data
  • Motion*
  • Phosphatidylcholines / chemistry*
  • Protein Conformation
  • Protein Structure, Secondary
  • Viral Regulatory and Accessory Proteins / chemistry*


  • Amino Acids
  • Human Immunodeficiency Virus Proteins
  • Lipid Bilayers
  • Membrane Proteins
  • Phosphatidylcholines
  • Viral Regulatory and Accessory Proteins
  • vpu protein, Human immunodeficiency virus 1
  • 1-palmitoyl-2-oleoylphosphatidylcholine