Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 by computer modeling based on neural network methods.
A neural network computer program, trained to predict secondary structure of proteins by exposing it to matching sets of primary and secondary structures from a database, was used to analyze the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 from their amino acid sequences. The results are compared to those obtained by the Chou-Fasman analysis. Two alpha-helical sequences corresponding to the putative fusigenic domain and to the transmembrane domain of gp41 could be predicted, as well as a possible binding site between p17 and gp41. On the basis of the secondary structure predictions, a three-dimensional model of p17 was constructed. This model was found to represent a stable conformation by an analysis using an energy-minimization program. The model predicts that p17 is attached to the membrane only by the acylated N-terminus, in analogy with the N-terminus of the gag protein of other retroviruses and also with the src oncogene protein p60src. The intracellular C-terminal part of gp41 may act as a receptor by electrostatic interaction with p17.
Laboratory for Protein Chemistry, University of Copenhagen, Denmark.
H
H
Andreassen
H
H
Bohr
J
J
Bohr
S
S
Brunak
T
T
Bugge
R M
RM
Cotterill
C
C
Jacobsen
P
P
Kusk
B
B
Lautrup
S B
SB
Petersen
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D015686:Gene Products, env / Q000032:analysis; D015683:Gene Products, gag; D015488:HIV Antigens; D015699:HIV Envelope Protein gp120; D019302:HIV Envelope Protein gp160; D015700:HIV Envelope Protein gp41; D015497:HIV-1 / Q000032:analysis*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011498:Protein Precursors / Q000032:analysis; D012984:Software; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus
D015686:Gene Products, env; D015683:Gene Products, gag; D015488:HIV Antigens; D015699:HIV Envelope Protein gp120; D019302:HIV Envelope Protein gp160; D015700:HIV Envelope Protein gp41; D011498:Protein Precursors; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1