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Computational Analysis

Types of Analyses*:

Contact Tables
Inter-subunit association energies & residuewise contributions
Accessible Surface Profiles
Outside SASA
Net Surface Charge
Dimensions

*Computations were done using the program CHARMM

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.


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.


Outside SASA:

The outside SASA is sum of the solvent accessible surface area (SASA) of all the surface exposed residues in the icosahedral asymmetric unit. This SASA is conventional estimate, calculated based on Lee and Richards method, but not the effective SASA calculated as in the ASA profiles.


Net Surface Charge:

The net surface charge is calculated by adding the charges of surface-exposed residues(both positive and negative) to obtain a net charge. For example, 20 positively charged residues and 20 negatively charged residues would yield a net charge of 0.


Radius, Diameter, and Volume:

The inner and outer radii are the minimum and maximum distance calculated from the origin (0,0,0) going over all the atoms. Diameter is twice the radius and spherical volumes are based on the standard formula, 4/3(Pi*Radius^3).

The average radii is not simply the average of the minimum and maximum radii. If a virus is spiky, the average radius will be underestimated. This is an effort to match the sizes estimated form the EM micrographs using a scalebar or even Small Angle X-ray Scattering (SAXS) studies. To account for this, we divide/define 1Å thin or thick shells starting from the minimum radius, x, then x+1, x+2, x+3... until the maximum radius is reached. Then the number of atoms (# of counts) that are present in each shell is calculated and the shell that has the maximum number of atoms is identified. Next, the shell with the highest radius that has more than 10% of the maximum number of counts is identified by cycling through all the shells. The outer radius of this shell is then defined as the average radius.

For example for Black Beetle Virus (2BBV) the calculated inner, average, outer radii are 102, 166, 172, respectively. Using the above method, the average radius is notably much closer to maximum radius. The average radius (166Å) is closer to ~156Å radius determined using solution scattering studies (Hosur et al., 1984, Virology, 133:119-127) than the 137Å that comes from taking the average of 102 and 172Å.

Contact Vijay Reddy for more information


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