Jmol/Electrostatic potential
Why look at the electrostatic potential?Why look at the electrostatic potential?
Many protein: ligand interactions are largely electrostatic in nature (e.g. via hydrogen bonds and ionic interactions), and their strength is modulated by the nature of the solvent (e.g. pure water or high ionic strength aqueous solution). Many of the intramolecular interactions within a protein are electrostatic in nature as well, and are different in strength depending whether they occur on the surface or in the hydrophobic core of a protein.
Calculating electrostatic potential and visualizing it in JmolCalculating electrostatic potential and visualizing it in Jmol
Jmol has two ways of importing electrostatic information, either as atomic partial charges or as values on a three-dimensional grid (the latter allows looking at long-range effects as well).
Atomic partial chargesAtomic partial charges
Mapping atomic partial charges on a surface is done with the "MEP" keyword in the "isosurface" command:
load C6H6.smol;isosurface solvent map mep
MEP stands for molecular electrostatic potential. In the example, the partial charges were loaded with the coordinates from a .smol file from a electrostatic potential calculation in Spartan.
Electrostatic potential mapElectrostatic potential map
Mapping values from a 3D grid onto the protein surface is also done with the "isosurface" command, loading the data directly when the command is issued:
load 1F36_pbeq.pdb; isosurface ID test solvent 1.4 color range -5.0 5.0 map "1F36_pbeq.dx"
The "color range" keyword results in all values above 5 having the same color (blue in this case), all value below -5 having the same color (red in this case), and values in between shown in colors in between. In the example, the .dx file containing the potential map is from a calculation done in CHARMM.
Sources for obtaining electrostatic potential dataSources for obtaining electrostatic potential data
http://www.charmm-gui.org/?doc=input/pbeqsolver
https://www.chemtube3d.com/category/structure-and-bonding/dipoles-and-electrostatic-surfaces/
https://pinostriccoli.altervista.org/le-superfici-molecolari-elettrostatiche-mep/
molcalc.org, e.g. http://molcalc.org/calculation/cc11a07f2bb4579391c1e0603665f673#/solvation
Some theory on the Poisson Boltzmann equation: DOI:10.1002/jmr.577
Example 1: waterElectrostatic potential of based on partial charges calculated in molcalc.org. Use this checkbox to toggle the potential on and off:
After loading the .smol file, the following command was used to show the potential: isosurface molecular map mep color translucent
Example 2: the DNA-binding protein FISDNA-binding (and DNA-bending) of is believed to be mostly electrostatic, explaining the low sequence-specificity and the high sensitive of interactions to ionic strength of the solvent. Use this checkbox to toggle the potential on and off:
|
| ||||||||||