Viral channel forming proteins - modeling the target

Biochim Biophys Acta. 2011 Feb;1808(2):561-71. doi: 10.1016/j.bbamem.2010.05.014. Epub 2010 May 28.


The cellular and subcellular membranes encounter an important playground for the activity of membrane proteins encoded by viruses. Viral membrane proteins, similar to their host companions, can be integral or attached to the membrane. They are involved in directing the cellular and viral reproduction, the fusion and budding processes. This review focuses especially on those integral viral membrane proteins which form channels or pores, the classification to be so, modeling by in silico methods and potential drug candidates. The sequence of an isolate of Vpu from HIV-1 is aligned with host ion channels and a toxin. The focus is on the alignment of the transmembrane domains. The results of the alignment are mapped onto the 3D structures of the respective channels and toxin. The results of the mapping support the idea of a 'channel-pore dualism' for Vpu.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Amino Acid Sequence
  • Computer Simulation
  • HIV-1 / chemistry
  • HIV-1 / genetics
  • Human Immunodeficiency Virus Proteins / chemistry
  • Human Immunodeficiency Virus Proteins / genetics
  • Ion Channels / chemistry*
  • Ion Channels / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Viral Proteins / chemistry*
  • Viral Proteins / genetics
  • Viral Regulatory and Accessory Proteins / chemistry
  • Viral Regulatory and Accessory Proteins / genetics


  • Human Immunodeficiency Virus Proteins
  • Ion Channels
  • Viral Proteins
  • Viral Regulatory and Accessory Proteins
  • vpu protein, Human immunodeficiency virus 1