title: Prediction of the secondary structure of HIV-1 gp120.
abstract: The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, beta-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV subunit vaccine candidates.
authors.affiliation: Laboratory for Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Denmark.
authors.forename: J E
authors.initials: JE
authors.lastname: Hansen
authors.forename: O
authors.initials: O
authors.lastname: Lund
authors.forename: J O
authors.initials: JO
authors.lastname: Nielsen
authors.forename: S
authors.initials: S
authors.lastname: Brunak
authors.forename: J E
authors.initials: JE
authors.lastname: Hansen
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D015704:CD4 Antigens / Q000378:metabolism; D017124:Conserved Sequence; D016208:Databases, Factual; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1 / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D017510:Protein Folding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D015704:CD4 Antigens; D015699:HIV Envelope Protein gp120