Case Study: Immunogen Design for HIV-1.
The V3-CTB construct (ribbon and transparent surface) was modeled using ICM-Pro
Introduction
Possibly the most efficient means of preventing the spread of AIDS is to develop an HIV-1 vaccine. One approach to developing an AIDS vaccine is to target the immune response on the regions of gp120 that are known to bind neutralizing antibodies such as the V3 region.
Using MolSoft's
ICM-Pro and
ICM-Homology software Totrov et al designed two V3-scaffold immunogen constructs based on Cholera toxin subunit B (CTB). The template was chosen by searching the Protein Data Bank for surface exposed beta turns that could be superimposed on the V3 loop. The designed constructs were then expressed and characterized.
Although V3 is highly variable at the sequence level it still maintains conserved structure in order to interact with chemokine receptors on the surface of the cell. This information was exploited to design a full length and a shorter more-focused V3 loop.
Methods
The full length graft was designed by:
- The crystal structure of HIV-1 gp120 was analyzed to identify grafting sites.
- A pair of gp120 residues immediately before and after a key disulfide bridge (C296-C331) were used to scan the CTB structure (PDB code 3CHB) for a pair of matching residues.
- 3D conformations of the grafts were then clustered by RMSD using ICM-Pro.
- The grafts were then inserted into the CTB structure and the energy of the structure was assessed removing grafts which made significant clashes with the rest of the CTB structure.
The shorter more focused V3 graft was designed by sampling the energy of a beta-hairpin turn using the Biased Probability Monte Carlo method in ICM-Pro (Abagyan and Totrov 1994). The beta-hairpin turn was predicted based on evidence from V3 structures.
Results
The full length gaft was shown to boost the immune response in testing in rabbits. The modeling methods developed in this work can be used for the development of other epitope specific immunogens for HIV-1.
References
Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S.
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold.
Virology. 2010 Sep 30;405(2):513-23. [NCBI_Abstract]
Abagyan, R.A. and Totrov, M.M.
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations For Peptides and Proteins
J. Mol. Biol. 1994 235, 983-1002 [NCBI_Abstract]
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The V3-CTB construct (ribbon and transparent surface) was modeled using ICM-Pro
