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Electrostatic potential maps: Difference between revisions

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It is revealing to visualize the distribution of electrostatic charges, [https://en.wikipedia.org/wiki/Electric_potential electrostatic potential], on molecular [https://en.wikipedia.org/wiki/Van_der_Waals_surface 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<ref>This opening paragraph was adapted from text authored by [[User:Karsten Theis]] in [[Jmol/Electrostatic potential]].</ref>. While exploring a structure in [[FirstGlance in Jmol]], electrostatic potential maps can be generated with a few mouse clicks -- see [[#iCn3D via FirstGlance in Jmol|instructions below]].
It is revealing to visualize the distribution of electrostatic charges, [https://en.wikipedia.org/wiki/Electric_potential electrostatic potential], on molecular [https://en.wikipedia.org/wiki/Van_der_Waals_surface 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<ref>This opening paragraph was adapted from text authored by [[User:Karsten Theis]] in [[Jmol/Electrostatic potential]].</ref>. Charged residues modulate enzyme efficiency over considerable distances<ref>PMID: 39928564</ref>. [[Missing residues and incomplete sidechains|Missing atoms or residues]], nearly universal in [[empirical models]], cause [[Missing_residues_and_incomplete_sidechains#Why_Missing_Residues_Matter|errors in the map]]. Therefore it is '''{{font color|red|crucial to use a model without missing atoms}}''', which could be an [[Missing_residues_and_incomplete_sidechains#AlphaFold_models_have_no_missing_atoms|AlphaFold model]].
While exploring a structure in [[FirstGlance in Jmol]], electrostatic potential maps can be generated with a few mouse clicks -- see [[#iCn3D via FirstGlance in Jmol|instructions below]].
==Gallery==
==Gallery==
===Leucine Zipper on DNA===
===Leucine Zipper on DNA===
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|[[Image:5t01-epm-dna.png]]
|[[Image:5t01-epm-dna.png]]
|[[Image:5t01-epm-protein.png]]
|[[Image:5t01-epm-protein.png]]
| <big>'''Leucine zipper'''</big> transcription regulator protein bound to DNA ([[5t01]]). The electrostatic potential maps show '''{{Font color|blue|positively charged protein surface}}''' contacting '''{{Font color|red|negatively charged DNA}}'''.
| style=max-width:400px;|'''Leucine zipper''' transcription regulator protein bound to DNA ([[5t01]]). [[5t01]] has only 5 missing residues, none charged, and 1 incomplete sidechain (Lys311), all at the ends of the protein chains.  The electrostatic potential maps show '''{{Font color|blue|positively charged protein surface}}''' contacting '''{{Font color|red|negatively charged DNA}}'''.


Maps generated via [http://firstglance.jmol.org/fg.htm?mol=5t01 FirstGlance in Jmol] using [[iCn3D]].
<span style="font-size:200%;">&larr;</span> Left maps generated via [http://firstglance.jmol.org/fg.htm?mol=5t01 FirstGlance in Jmol] using [[iCn3D]], see [[#iCn3D via FirstGlance in Jmol|below]].
 
Right <span style="font-size:200%;">&rarr;</span> maps generated with [[ChimeraX]], see [[#ChimeraX|below]].
|[[Image:5t01-epm-dna-chimerax-180px.png]]
|[[Image:5t01-epm-protein-chimerax-180px.png]]
|}
|}


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{| class="wikitable"
{| class="wikitable"
|-
|-
|[[Image:1bl8-ABC-chimerax-epm-330px.gif]]
|[[Image:1bl8ABC-cap2-trimmed.gif]]
|[[Image:1bl8ABC-cap2-trimmed.gif]]
| <big>'''Potassium channel'''</big> ([[1bl8]]). The electrostatic potential map shows '''{{Font color|red|negatively charged protein surface}}''' lining the channel containing '''{{Font color|#00b000|K<sup>+</sup> ions}}'''.
| <big>'''Potassium channel'''</big> ([[1bl8]]). The electrostatic potential map shows '''{{Font color|red|negatively charged protein surface}}''' lining the channel containing '''{{Font color|#00b000|K<sup>+</sup> 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.
<span style="font-size:200%;">&larr;</span>Left: Map generated by [[ChimeraX]]<ref>Colors of the electrostatic potential map generated by ChimeraX were intensified by reducing the range from default -10 to 10 with the command "coulombic sel range -4,4".</ref>, see [[#ChimeraX|method]].
 
Right<span style="font-size:200%;">&rarr;</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]].
 
Map generated from a PDB file from which one of the 4 chains was removed with a [[plain text editor]] to reveal the inside surface of the channel.
 
'''Caution''': Map generated with [[1bl8]] which has, in each of the 3 chains, 3 Arginines and 1 Glutamic acid with [[Missing residues and incomplete sidechains#Incomplete Sidechains|incomplete sidechains]].
|}
 
{| class="wikitable"
|-
|[[Image:1bl8-ABC-EPM-PyMOL-1.png|330px]]
|[[Image:1bl8-ABC-EPM-PyMOL-2.png|330px]]
| <big>'''Potassium channel'''</big> ([[1bl8]]). The electrostatic potential map shows '''{{Font color|red|negatively charged protein surface}}''' lining the channel containing '''{{Font color|#00b000|K<sup>+</sup> ions}}'''.
 
Map generated by [[PyMOL]], see [[#PyMOL|method]].
 
Right<span style="font-size:200%;">&rarr;</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]].
 
Map generated from a PDB file from which one of the 4 chains was removed with a [[plain text editor]] to reveal the inside surface of the channel.
 
'''Caution''': Map generated with [[1bl8]] which has, in each of the 3 chains, 3 Arginines and 1 Glutamic acid with [[Missing residues and incomplete sidechains#Incomplete Sidechains|incomplete sidechains]].
|}
|}


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Map generated by [[iCn3D]].
Map generated by [[iCn3D]].
'''Caution''': Map generated with [[4ioa]], which has 162 amino acids modeled as alpha carbons only, and has 369 missing amino acids that include nearly 100 missing charged residues.
|}
|}


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{| class="wikitable"
{| class="wikitable"
|-
|-
! scope="colgroup" colspan="3" | Protein [[1pgb]] is in the same orientation in all images. '''{{Font color|blue|Positive +}}''' / '''{{Font color|red|Negative -}}'''
! scope="colgroup" colspan="3" | Protein [[1pgb]] (no missing atoms) is in the same orientation in all images. '''{{Font color|blue|Positive +}}''' / '''{{Font color|red|Negative -}}'''
|-
|-
|style="width: 250;" width="250"| [[Image:1pgb-EPM-PyMOL.png|250 px]]
|style="width: 250;" width="250"| [[Image:1pgb-EPM-PyMOL.png|250 px]]
|style="width: 250;" width="250"| [[Image:1pgb-epm-chimerax.png|250px]]
|style="width: 250;" width="250"| [[Image:1pgb-EPM-iCn3D.png|230 px]]
|style="width: 250;" width="250"| [[Image:1pgb-EPM-iCn3D.png|230 px]]
|style="width: 250;" width="250"| [[Image:1pgb-charge-fgij.png|250 px]]
|style="width: 250;" width="250"| [[Image:1pgb-charge-fgij.png|250 px]]
|-
|-
| Electrostatic potential map rendered by [[PyMOL]] using default molecular surface probe radius 1.4 &Aring;. [[#PyMOL|Method]].
| Electrostatic potential map rendered by [[PyMOL]] using default molecular surface probe radius 1.4 &Aring;. [[#PyMOL|Method]].
| Electrostatic potential map rendered by [[ChimeraX]]. [[#ChimeraX|Method]].
| Electrostatic potential map rendered by [[iCn3D]] with "Potential contour" set to 4. [[#iCn3D|Method]].
| Electrostatic potential map rendered by [[iCn3D]] with "Potential contour" set to 4. [[#iCn3D|Method]].
| Van der Waals model colored by charge with [[FirstGlance in Jmol]]. Sidechain '''{{Font color|blue|nitrogens}}''' on Arg/Lys; '''{{Font color|red|oxygens}}''' on Asp/Glu. [[#Coloring Charged Atoms|Method]].
| Van der Waals model colored by charge with [[FirstGlance in Jmol]]. Sidechain '''{{Font color|blue|nitrogens}}''' on Arg/Lys; '''{{Font color|red|oxygens}}''' on Asp/Glu. [[#Coloring Charged Atoms|Method]].
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# Optionally, in iCn3D, Menu: Style, Background, White.
# Optionally, in iCn3D, Menu: Style, Background, White.
# To spin, iCn3D Menu: View, Rotate, Auto Rotation.
# To spin, iCn3D Menu: View, Rotate, Auto Rotation.
# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]].


====In iCn3D====
====In iCn3D====
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# Menu (optional): Style, Background, White.
# Menu (optional): Style, Background, White.
# To spin, Menu: View, Rotate, Auto Rotation.
# 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".
# See [[#Converting MOV or MP4 to GIF|Capturing MOV or MP4 and converting to GIF]].
===ChimeraX===
[[ChimeraX]] is free for non-commercial use.


To remove the yellow selection halo, enter the command (in the slot at the bottom) "select sets nothing".
# Download and install ChimeraX.
# Drag and drop a PDB file into ChimeraX, or use the File dropdown menu, Fetch by ID, PDB.
# Check the select checkbox (pointing finger icon) in the Models box (lower right) to select all, or use the Select dropdown menu to select a chain, or to select both chains C and D, enter the command "select /C,D".
# In the ''Molecule Display'' tab, click on ''electrostatic''.
# After the surface appears, try the Lighting & Effects options in the ''Graphics'' tab.
# De-select with the checkbox in the Models box.
# To save an MP4 movie to the Desktop, click the ''Spin movie'' icon in the Home tab: [[Image:Chimerax-movie-icon.png|30px]]
# See [[#Converting MOV or MP4 to GIF|Converting MP4 to GIF]].


===PyMOL===
===PyMOL===
[https://pymol.org PyMOL] has a license fee, but is free for students and educators.
[https://pymol.org PyMOL] has a license fee, but is free for students and educators.


# Download and install PyMOL.
<ol>
# Enter command "fetch 1pgb".
<li> Download and install PyMOL.
# Menu: All, Action, remove waters.
<li> Enter command "fetch 1pgb".
# Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local).
<ul>
# Enter command "bg_color white".
<li> The above command loads the asymmetric unit. Commands to load biological assembly 1:
<li> fetch 7mgp, type=pdb1
<li> split_state 7mgp
</ul>
<li> Menu: All, Action, remove waters.
<li> Menu: 1pgb, Action, generate, vacuum electrostatics, protein contact potential (local). For a biological assembly, it appears that you will have to repeat this command for every part.
<li> Enter command "bg_color white".
</ol>


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!).
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!).
===Converting MOV or MP4 to GIF===
Please see at FirstGlance in Jmol: [http://firstglance.jmol.org/videocapture.htm Video Capture & Conversion].


===Coloring Charged Atoms===
===Coloring Charged Atoms===

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