In my study there was two enzymes structurally very diverse but they have same enzymatic activity. I want to know how we can predict that both have same surface charges or potential or sequence independent similar arrangement of electron density.
If the atomic coordinates of the protein tertiary structures are available, the surface potential is easy to be displayed by softwares, such as PyMol. Otherwise, you may estimate the tertiary structures by the homology modeling.
But, first of all, why do you investigated the surface charges to investigate the emzyme activity? Have the catalytic sites of the molecules been identified?
Surface potentials can be calculated by programs such as DelPhi (see link below), which can then be viewed by numerous visualizers: GRASP, PyMol, Chimera. Many of the molecular visualizers also have a built in interface for DelPhi.
Good luck!
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi
Ultimately, there are a number of tools for a similar problem (I once used yasara, see yasara.org). However, you should perform a MD-simulation first in order and calculate a few snapshots to display the surface potential to make sure you are not up to compare artefactual differences / similarities (whatever you discuss as a general feature should be present in a vast majority of your snapshots).
Continuum Electrostatics can easily be calculated by solving the Poisson-Boltzmann equation, using software such as APBS, CHARMM PBEQ or DelPhi and visualized with PyMOL, UCSF Chimera or VMD (all three have built-in APBS GUI interfaces, and Chimera and VMD also have a GUI for DelPhi). APBS, combined with PDB2PQR for atomic radii and charge assignment can be very straightforward. You can find more about it (including a number of tutorials) in the Poisson-Boltzmann website:
http://www.poissonboltzmann.org/
For an example of how surface electrostatics can be used to compare properties of a binding site in a group of proteins, you can check this paper, which uses some of the software mentioned:
http://www.sciencedirect.com/science/article/pii/S1047847713000750
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