title: Domain assembly, surface accessibility and sequence conservation in full length HIV-1 Nef.
abstract: The accessory Nef protein from human and simian immunodeficiency viruses is critical for efficient viral replication and pathogenesis. Here we present an assembly of the full length structure of HIV-1 Nef, allele NL4-3, based on the previously solved anchor and core domain structures. The center part of the 33 residue encompassing flexible loop at the C-terminus of Nef, involved in Nef internalization and CD4 endocytosis, has been modelled. The degree of sequence conservation in HIV-1 Nef proteins was determined using a total of 186 different strains from five different subtypes. The sequence conservation has been correlated with the accessible surface area and with secondary structure features for individual residues. The high amount of flexible regions in Nef accounts for the large surface and the multiple interaction sites the protein exhibits.
authors.affiliation: Howard Hughes Medical Institute, University of California, San Francisco, CA 94143-0703, USA. mgeyer@cc.ucsf.edu
authors.forename: M
authors.initials: M
authors.lastname: Geyer
authors.forename: B M
authors.initials: BM
authors.lastname: Peterlin
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D015704:CD4 Antigens / Q000737:chemistry; D017124:Conserved Sequence; D004705:Endocytosis; D015693:Gene Products, nef / Q000737:chemistry*; D015497:HIV-1 / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013045:Species Specificity; D054311:nef Gene Products, Human Immunodeficiency Virus
chemical_list: D015704:CD4 Antigens; D015693:Gene Products, nef; D054311:nef Gene Products, Human Immunodeficiency Virus