Molecular modelling study of HIV p17gag (MA) protein shell utilising data from electron microscopy and X-ray crystallography

• Published in: Journal of molecular biology 2000-05, Vol.298 (5), p.841-857
• Main Authors: Forster, M.J., Mulloy, B., Nermut, M.V.
• Format: Article
• Language: English
• Subjects: AIDS/HIV; Computer Simulation; Crystallography, X-Ray; electron microscopy; gag Gene Products, Human Immunodeficiency Virus; gag protein; Gene Products, gag - chemistry; Gene Products, gag - genetics; Gene Products, gag - metabolism; Gene Products, gag - ultrastructure; HIV; HIV - chemistry; HIV - genetics; HIV - growth & development; HIV - physiology; HIV Antigens - chemistry; HIV Antigens - genetics; HIV Antigens - metabolism; HIV Antigens - ultrastructure; Human immunodeficiency virus; Hydrogen Bonding; matrix protein; Microscopy, Electron; Models, Molecular; molecular modelling; p17 protein; Protein Binding; Protein Structure, Quaternary; Solvents; Static Electricity; Thermodynamics; Viral Proteins; Virus Assembly
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.2000.3715

The matrix protein p17gag (MA) is a product of proteolytic cleavage of the gag gene encoded polyprotein (pr55gag) and is formed when HIV particles undergo the process of maturation. The MA protein is associated with the inner surface of the viral membrane and determines the overall shape of the virion. Previous studies have shown the existence of trimers of MA in solution and in the crystalline state. Here, we used molecular modelling methods to identify feasible interactions between pairs of MA trimers and have related this to structural data from electron microscopy. A systematic search docking procedure was able to identify many energetically favourable conformations for a pair of trimers, including some which have been previously reported. These conformations were used to generate several networks of MA trimers, which were then evaluated against structural observations of the MA network. The model suggested here provides a good match with experimental data such as the spacing between gag protein rings, the number and disposition of glycoprotein (gp41-gp120) knobs and the number of copies of MA in a virus particle. It also rationalises the observed distribution of sizes of virus particles and is consistent with the presence of icosahedral organisation in mature HIV. Energy minimisation performed with explicit water and counter ions, was used to identify residues participating in inter-trimer interactions. The nature of these interactions is discussed in relation to the conservation of these residues in reported variants of the HIV and SIV MA protein sequences.