Electrostatic potential maps

From Proteopedia

proteopedia linkproteopedia link

It is revealing to visualize the distribution of electrostatic charges, electrostatic potential, on molecular van der Waals surfaces. Most protein-protein and protein-ligand interactions are largely electrostatic in nature, via hydrogen bonds and ionic interactions. Their strengths are modulated by the nature of the solvent: pure water or high ionic strength aqueous solution.

Contents 1 Gallery 2 Methods 2.1 PyMOL 3 See Also 4 References

Gallery

Protein 1pgb is in the same orientation in all images. Positive + / Negative -
Electrostatic potential map rendered by PyMOL using default molecular surface probe radius 1.4 Å. Method.	Electrostatic potential map rendered by iCn3D.	Van der Waals model colored by charge with FirstGlance in Jmol. Sidechain nitrogens on Arg/Lys; oxygens on Asp/Glu.

Electrostatic potential map of 1tsj made with the Embedded Python Molecular Viewer from the Center for Computational Structural Biology of the Scripps Research Institute. Click on the image to enlarge.

Methods

===iCn3D

PyMOL

PyMOL has a license fee, but is free for students and educators.

1. Download and install PyMOL.
2. Enter command "fetch 1pgb".
3. Menu: All, Action, remove waters.
4. Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local).
5. Enter command "bg_color white".

Optional: The probe radius used to generate the molecular surface can be changed, and the previously generated surface will immediately change. The command is "set solvent_radius, 1.2" (don't overlook the comma!).

See Also

• Electrostatic interactions in Proteopedia.
• Jmol/Electrostatic potential methods.
• Isopotential Map in Wikipedia
• Delphi Web Server

References