• Computations were done using the program CHARMM

Contact tables:

Contacting residues at the various subunit interfaces, in the quarternary arrangement seen in the respective virus structures, were identified and tabulated based on simple distance criteria. Two residues are considered to be in contact, if the distance between the CB-atom of side chain atoms falls within the distance limits obtained based on the structures available in PDB (courtesy: Skolnick and coworkers). These contacts were further classified based on the nature of the contacting residues (e.g., Polar-Polar, Acidic-Basic etc.,)

Inter-subunit association energies & residuewise contributions:

Subunit association energies were calculated based on the atomic buried surface areas times the solvation parameters (Eisenberg and McLachlan, (1986) Nature, 319, 199-203). At each interface, contribution of individual residues were estimated and plotted as a function of residue numbers. In addition, the residue wise contributions (for each side of the interface) were sorted in the decreasing order and the top 10 residues and their contributions are listed.

Identification of assembly intermediates and pathways:

The inter-subunit association energies were used as the basis set to identify potential assembly intermediates, by sampling (nearly) all possible configurations for a given number of associating subunits. These configurations were sorted according to their energies and the top configuration(s) are identified as the likely intermediates (Reddy et.al.,(1998) Biophys. J., 74, 546-558). These likely configurations were identified at every step of the way going from 2 to full complement of coat protein subunits that are required to form the complete virus capsid. The trajectory of the intermediates perhaps represents the likely pathway for the virus assembly.

Simulations:

Molecular dynamics simulations and normal mode analysis are being done on a few virus structures. The results would be documented, as and when they get published.

Crystal contacts between the particles in the unit cell:

Contacts between the virus particles as they pack in the unit cell of the crystal were calculated by generating the neighboring particles related by the crystal symmetry (Natarajan and Johnson (1998), J.Struc.Biol.,121,295-305). These inter-particle contact regions have been suggested to be putative antigenic determinants and receptor binding sites.