Cation-pi interactions: Difference between revisions
Eric Martz (talk | contribs) removed two unnecessary mentions of my name |
Eric Martz (talk | contribs) corrected links in first paragraph to firstglance.jmol.org and proteinexplorer.org |
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Cationic sidechain nitrogens (lysine or arginine) within 6.0 Å of the face of an aromatic ring (phenylalanine, tyrosine, or tryptophan) may engage in polar interactions called cation-pi interactions (cation-π interactions) or cation-pi orbital interactions.<br> | Cationic sidechain nitrogens (lysine or arginine) within 6.0 Å of the face of an aromatic ring (phenylalanine, tyrosine, or tryptophan) may engage in polar interactions called cation-pi interactions (cation-π interactions) or cation-pi orbital interactions.<br> | ||
The flat face of an aromatic ring has a partial negative charge due to the pi orbitals. Cationic sidechains (Lys, Arg) or sometimes ligands (including metal ions) often align themselves centered over the faces of aromatic rings. Over one fourth of Trp's in the Protein Data Bank interact with cations, and 99% of significant cation-pi interactions occur within a distance of 6.0 Angstroms <ref name='GD'>PMID: 10449714</ref>. Cation-pi interactions make a significant contribution to the overall stability of most proteins. Gallivan and Dougherty (1999)<ref name='GD' /> conclude that "cation-pi interactions should be considered alongside the more conventional hydrogen bonds, salt bridges, and hydrophobic effects in any analysis of protein structure". They can also contribute significantly to intermolecular contacts and interactions with ligands. | The flat face of an aromatic ring has a partial negative charge due to the pi orbitals. Cationic sidechains (Lys, Arg) or sometimes ligands (including metal ions) often align themselves centered over the faces of aromatic rings. Over one fourth of Trp's in the Protein Data Bank interact with cations, and 99% of significant cation-pi interactions occur within a distance of 6.0 Angstroms <ref name='GD'>PMID: 10449714</ref>. Cation-pi interactions make a significant contribution to the overall stability of most proteins. Gallivan and Dougherty (1999)<ref name='GD' /> conclude that "cation-pi interactions should be considered alongside the more conventional hydrogen bonds, salt bridges, and hydrophobic effects in any analysis of protein structure". They can also contribute significantly to intermolecular contacts and interactions with ligands. | ||
*[http:// | *[http://firstglance.jmol.org First Glance in Jmol] finds and displays potential cation-pi interactions, as described [http://firstglance.jmol.org/notes.htm?#catpi here]. | ||
*[http:// | *[http://proteinexplorer.org Protein Explorer] (requires CHIME plugin) finds and displays potential cation-pi interactions, as described [http://proteinexplorer.org/cationpi.htm here]. | ||
==Background== | ==Background== | ||