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
seqments were predicted in regions displaying profound sequence
variation, one in a region suggested to be critical for CD4
biding. 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 sub-unit vaccine candidates.
Original language | English |
---|---|
Journal | Proteins: Structure, Function, and Bioinformatics |
Volume | 25 |
Issue number | 1 |
Pages (from-to) | 1-11 |
ISSN | 0887-3585 |
DOIs | |
Publication status | Published - 1996 |