-
Associtation energies + Buried surface areas:
Total surface area buried at the interfaces of the interacting
subunits are calculated by estimating loss of accessible surface areas. The
Accessible surface areas are computed using the method of
Lee, B. and Richards, F.M. (1971), J.Mol. Biol., 55 , 379-400.
with a probe radius of 1.4Ang.
The association energies are estimated my multiplying the atomic solvation
parameters with the buried surface areas of the individual atoms as described
in
Eisenberg, D. & McLachlan A.D. (1986), Nature, 319, 199-203.
Horton, N. and Lewis, M. (1992), Protein Science, 1 , 169-181.
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Residuewise contributions at various interfaces:
Contributions of individual residues to the inter-subunit interaction energy
is estimated as the sum of electrostatic and van der Waals energies between
the residue and the interacting subunits. The electrostatic and van der Waals
energies are estimated based on the continuum electrostatic potentials and
Lennard Jones 6-12 potential respectively.
The non-bonded parameters and
the partial charges were taken from the CHARMM22 force field. The electrostatic
potentials are obtained by calculating finite difference solutions to the
POISSON-BOLTZMANN equation using the Program DELPHI (Sharp, K.A & Honig, B. (1990), Biophys. Biophys. Chem., 19, 301-332).
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Combinatorial Assembly pathways:
Given a set of association energies for the unique subunit-subunit interfaces
present in the viral capsid, a preferred pathway of assembling the multiple
copies of the subunits into a particle is obtained using combinatorial method.
The method is decribed in the following references:
Reddy, V.S., Giesing, H.A., Morton, R.T., Kumar, A., Post, C.B., Brooks, C.L. & Johnson J.E. (1998),
Biophys. J.,74, 546-558.
Horton, N. and Lewis, M. (1992), Protein Science, 1 , 169-181.
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A table of quasi-equivalent contacts:
Various non-covalent interactions (at the residue level) occur at the unique
inter-subunit interfaces are identified based on the simple distance and atomtype
criteria and arranged in the form of a table.
This table is useful in quickly identifying the presence/absence of quasi-equivalent
interactions across the various quasi-symmetry related interfaces.
(Reddy, V.S. and Johnson, J.E. (unplublished results))
The input coordinates should be orthogonalized in Angstrom units and
should be given in one of the standard orientations of icosahedron (Z35X or Z35Y).
These coordinates should be in the Protein Data Bank (PDB) format. The
individual chains must be identified by a separate chain indentifier (e.g.,
A/B/C etc., at the column 22 of ecah 'ATOM ' line) .
As in the PDB format, each
line, listing coordinates of an atom should start with an 'ATOM' or 'HETATM' tag.
e.g.,
ATOM 1 N ARG A 58 -8.811 41.857 105.551 1.00100.00
These are the rotation matrices required to generate the neighbouring subunits of the assembly in order to create the subunit interface of interest.
The matrices should be given in the following order:
- A matrix to generate 5-fold related asymmetric unit
- A matrix to generate 3-fold related asymmetric unit
- A matrix to generate 2-fold related asymmetric unit
These 4x3 matrices can be given in FREE FORMAT
but in 4 lines.
e.g., for standard Z35X convention (eg., BBV, FHV)
0.3090 0.8090 -0.5000
-0.8090 0.5000 0.3090
0.5000 0.3090 0.8090
0.0000 0.0000 0.0000
-0.3090 0.8090 -0.5000
-0.8091 -0.5000 -0.3090
-0.5000 0.3090 0.8090
0.0000 0.0000 0.0000
-1.0000 0.0000 0.0000
0.0000 -1.0000 0.0000
0.0000 0.0000 1.0000
0.0000 0.0000 0.0000
e.g., for standard Z35Y convention (eg., CCMV, HRV16)
0.5000 0.8090 0.3090
-0.8090 0.3090 0.5000
0.3090 -0.5000 0.8090
0.0000 0.0000 0.0000
-0.5000 0.8091 -0.3090
-0.8090 -0.3090 0.5000
0.3090 0.5000 0.8090
0.0000 0.0000 0.0000
-1.0000 0.0000 0.0000
0.0000 -1.0000 0.0000
0.0000 0.0000 1.0000
0.0000 0.0000 0.0000
Please do make sure that the given matrices correspond to the input coordinates.
Vijay Reddy
Last modified: Tue Sep 15 10:17:31 PDT 1998