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Computational Analysis

• Computations were done using CHARMM (Brooks et al., 1993)


Contact tables:

Contact table lists the residue pairs in contact at various subunit interfaces of the quarternary arrangement seen for the respective virus structures. A pair of residues from two (different) subunits are considered to be in contact, if the distance between the center of mass of the side chain atoms falls within the distance cut-offs obtained based on the structures available in PDB (Godzik et al., 1992). These contacts were further annotated based on the nature of the contacting residues (e.g., Polar-Polar, Acidic-Basic etc.,). In addition, the table also lists all the interfaces where a particular residue piar is in contact.

For more details on how to read/interpret the contact tables click here.

Inter-subunit Association, Solvation energies & residuewise contributions:

Subunit association energies were calculated based on the atomic buried surface areas multipled by the solvation parameters (Eisenberg et. al., 1989, Horton and Lewis, 1992). Buried surface areas were calculated using the program CHARMM with a probe radius of 1.4A. Extents of associtation energies, Buried surface areas and solvation energies of each interface are listed with links leading to the graphs showing the individual residue contributions to respective properties above are plotted as a function of a.a. residue numbers. Mouse-over/clicking the points of the graphs would highlight the residuewise contributions and contacts that particular residue is involved in respectively.

Structure based 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 in the context of the quaternary structure of the capsid assembly 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, Horton and Lewis, 1992). 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.

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.

Accessible surface profiles:

Accessible residues were identified based on iterative approach eliminating the residues which are exposed but located at the interfaces. The quantity which is plotted is an amplified SASA (min) values by the effective Radius. SASAmin = SASAmax for the exposed residues. Now, the effective radius corresponds to the radius at which a residue located minus(-) inner radius of the virus capsid. This approach (SASA*eff.Radius) dampens the values of the residues, which are exposed at the inside surface of the capsids.


Vijay Reddy


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