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>. [[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]]. | 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]]. | 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== | ||
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|[[Image:1bl8-ABC-EPM-PyMOL-1.png|330px]] | |[[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}}'''. | | <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%;">→</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]]. | Right<span style="font-size:200%;">→</span>: Map generated by [[iCn3D]], see [[#iCn3D_via_FirstGlance_in_Jmol|method]]. | ||
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[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. | ||
<ol> | |||
<li> Download and install PyMOL. | |||
<li> Enter command "fetch 1pgb". | |||
<ul> | |||
<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!). | ||