Electrostatic potential maps

From Proteopedia

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^[1]. While exploring a structure in FirstGlance in Jmol, electrostatic potential maps can be generated with a few mouse clicks -- see instructions below.

Gallery

Leucine Zipper on DNA

Leucine zipper transcription regulator protein bound to DNA (5t01). The electrostatic potential maps show positively charged protein surface contacting negatively charged DNA. Maps generated via FirstGlance in Jmol using iCn3D.

Potassium Channel

Potassium channel (1bl8). The electrostatic potential map shows negatively charged protein surface lining the channel containing K+ ions. Map generated by iCn3D after uploading a PDB file from which one of the 4 chains was removed to reveal the inside surface of the channel.

Ribosome

Large ribosomal subunit (4ioa). The electrostatic potential maps of the many proteins show positively charged protein surfaces where protein contacts, or is buried within RNA (gray), while protein surfaces exposed to solvent have approximately net neutral mixtures of charges. Map generated by iCn3D.

Map Comparisons

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 with "Potential contour" set to 4. Method.	Van der Waals model colored by charge with FirstGlance in Jmol. Sidechain nitrogens on Arg/Lys; oxygens on Asp/Glu. Method.

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

iCn3D via FirstGlance in Jmol

1. Start FirstGlance in Jmol.
2. Enter the desired PDB Id, such as 5SZE.
3. Click the Views tab, then click Show More Views.
4. Click Electrostatic Potential Map.
5. Click Protein or DNA/RNA^[2]. iCn3D will open in a new browser tab showing the electrostatic potential map.
6. Optionally, in iCn3D, Menu: Style, Background, White.
7. To spin, iCn3D Menu: View, Rotate, Auto Rotation.

In iCn3D

1. Start the iCn3D web application.
2. Enter the desired PDB Id, such as 1pgb, and click one of the Load buttons^[2].
3. Menu: Select, Defined Sets. In the list that appears, click on proteins (or optionally on nucleotices).
4. Menu: Analysis, DelPhi Potential, DelPhi Potential. Click the Surface with Potential tab.
5. Optional (to expand white regions), change Potential contour from 2 to a higher value.
6. Click the button Surface with Potential.
7. Menu (optional): Style, Background, White.
8. To spin, Menu: View, Rotate, Auto Rotation.

To remove the yellow selection halo, enter the command (in the slot at the bottom) "select sets nothing".

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!).

Coloring Charged Atoms

1. Start FirstGlance in Jmol.
2. Enter the desired PDB Id, such as 1ijw.
3. Click the Views tab, then click Charge...

See Also

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

References

1. ↑ This opening paragraph was adapted from text authored by User:Karsten Theis in Jmol/Electrostatic potential.
2. ↑ ^{2.0 2.1} To visualize the differences between the biological unit and asymmetric unit, view the PDB Id in http://firstglance.jmol.org, then click on Biological Unit 1.