I would like to calculate the number of water molecules replaced before and after complex formation on the binding surface? How we can do this? Any suggestions?
You can calculate solvent accesible surface for complex and free partners. The difference will give you surface of interaction site. From this and water molecule interaction surface you can say aproximately( i saw this surface in a publication somewhere) But it will have error of ~25% :)
But better idea is to add solvent in gromacs and select all water patricles near the surface(PyMol). It should be a little more accurate.
I hope it will help you.
Dear Srinivas,
you might take a look at
http://leonardo.inf.um.es/macromol/programs/hydropro/hydropro.htm
Kind regards
Alfred
If I assume that you have or can model the structures before and after complex formation, you have to consider the following :
Water may serve a dual purpose - simple solvation water, and structural water. The latter is important to keep in mind.
In the complex find out which of the surface atoms / residues that are in van der Waal contact with the protein. Keep track of which residues that are in contact - find their solvent accessible surface from DSSP info (an old but important contribution from Chris Sander and colleagues). Decide which area you will assume appropriate for a single water molecule. You now have a good estimate for the amount of water freplaced by the complex formation.
Thanks a lot to Dr.Alfred Ross , Dr. Steffen Petersen and Dawid Deneka for your valuable suggestions !
If you have the structure of the complex, you can use a tool such as Intervor to compute the interface. It also computes the number of interfacial water molecules, i.e., the water molecules that are squeeze in between the two partners.
If YOU have the structure YOU can try to apply some programs of "Molecular Modeling", otherwise YOU can to try somehow to estimate from, SPR, QCM and AFM.
There is one article attached:
Article AFM study of complement system assembly initiated by antigen...
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