Electrostatic potential calculation Link
The surface electrostatic potential of the proteins in their quaternary form was calculated
using the program DELPHI [45]. Salt concentration was set equal to 0, since identical environmental conditions
can better delineate differences between the electrostatic potential of the halophilic
and non-halophilic homolog. Internal and solvent dielectric constants were set to
4.0 [46] and 80.0 respectively. The other parameters used were set to the default values:
grid scale = 1.2, box fill = 60%, probe radius = 1.4 Å, and van der Waals surface.
To compare the potential of halophilic and non-halophilic proteins of different lengths,
the average atomic potential (AAP) was calculated dividing the total electrostatic
potential by the total number of atoms.
4.2. Calculations of electrostatic potentials and free energies Link
Continuum electrostatic calculations were performed using the finite difference Poisson–Boltzmann (FDPB) method, implemented in the Delphi program.
Atomic radii and charges were taken from the param22 parameter set of the CHARMM program. An accurate algorithm for molecular surface generation was employed.
The interior of a protein and water were modeled as dielectric media
with dielectric constants of 2 and 80, respectively. The choice of the
dielectric constant of 2 is dictated by the fact that we have assumed no
conformational changes upon binding so that we need to account for
electronic but not nuclear relaxation. The ionic strength of the
solution was set to 0.1 M and the ion exclusion radius to 2.0 Å.
Boundary conditions were approximated by the Debye–Huckel potential of
the charge distribution being treated. Calculations were run until the
total energy converged to within 10−4kBT, where kB is the Boltzmann constant and T is the absolute temperature.
The
calculations of the electrostatic contributions of individual groups to
binding were performed on a lattice with 2.5 grids per ångstrom. These
calculations are relatively insensitive to the variations in grid
resolution. In a test performed on the barnase–barstar complex, a
variation of the grid resolution by 0.2 grid/Å (to 2.3 and 2.7 grids/Å)
resulted in δ(ΔΔGelecν)<0.5 kcal/mol for all residues (the root-mean-square variance of residue contributions, 〈δ(ΔΔGelecν)〉=0.2 kcal/mol).
