Analysis of protein-protein interface by MolSurfer
Instructions:
After opening this page, 2 windows should
have appeared: the Molsurfer window showing a 2-dimensional map
of the interface; and the WebMol window showing a 3-dimensional
view of a protein-protein complex and its interface.
Use menu File--Open to switch between the
interfaces;
Use menu View to switch between the properties
to be displayed on the 2D map;
Use Mouse to move/drag/click across the map
to navigate in the 3D structure;
To adjust the range for displaying properties
on 2D map, click left/right mouse button on the color bar;
Use features of WebMol while viewing 3D -
stereo, colouring, selecting etc;
Use menu File--Quit when done.
All images of 2D maps can be found here. Note that the parameter ranges there have fixed initial values; these can only be altered on the interactive maps.
Details of interface mapping for the
tutorial demo:
Each PDB file was split into 2 parts giving
coordinates of the first and the second proteins forming the interface;
A quasi rectangular mesh with ca 1 Å
spacing was generated on the analytically defined interface between these
2 proteins;
Points for which the sum of the distances
to the closest atoms of proteins 1 and 2 exceeds 6 Å were deleted;
Heteroatoms that lie within 3 Å of any
interface point were added;
The properties of each protein were projected
onto every point of the interface; these are the properties assigned to
the closest atom to the point;
Electrostatic potential of each (isolated)
protein was computed with the UHBD program by solving the finite difference
linearized Poisson-Boltzmann equation and the potential values were interpolated
at each interface point.
Additionally, the changes in binding free
energy upon alanine mutation were assigned to each side-chain atom of the
corresponding residue. This data can be obtained from the
Alanine Scanning Energetics database for example.
Residue hydrophobicities were assigned according
to the residue name and following the parameters in Eisenberg D., Weiss
R.M., Terwilliger T.C. and Wilcox W. (1982) Farad. Symp. Chem. Soc.,
17,
109-120, namely:
ALA 0.25
GLN -0.69 LEU 0.53
SER -0.26 ARG -1.80 GLU
-0.62 LYS -1.10
THR -0.18 ASN -0.64 GLY
0.16 MET 0.26
TRP 0.37 ASP -0.72 HIS
-0.40 PHE 0.61
TYP 0.02 CYS 0.04
ILE 0.73 PRO -0.07
VAL 0.54 none of the above
0.00
Atomic hydrophobicities were assigned according
to the atom name and follow Eisenberg D., Wesson M., Yamashita M.
(1989) Chem. Scrip., 29A, 217-221, namely: