title: Viral channel forming proteins - modeling the target.
abstract: 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.
authors.affiliation: Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan. wfischer@ym.edu.tw
authors.forename: Wolfgang B
authors.initials: WB
authors.lastname: Fischer
authors.forename: Hao-Jen
authors.initials: HJ
authors.lastname: Hsu
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics; D054298:Human Immunodeficiency Virus Proteins / Q000737:chemistry / Q000235:genetics; D007473:Ion Channels / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry / Q000235:genetics; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D007473:Ion Channels; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins