Ramachandran outlier
From Proteopedia
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==Ramachandran outlier== | ==Ramachandran outlier== | ||
<StructureSection load='' size='340' side='right' caption='' scene='76/762493/1ea5_color_sec_struct/3'> | <StructureSection load='' size='340' side='right' caption='' scene='76/762493/1ea5_color_sec_struct/3'> | ||
| - | The [[Ramachandran Plot]] was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. <ref>pmid 13990617</ref> | + | The [[Ramachandran Plot]] was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. <ref>pmid 13990617</ref>. See [[Dihedral/Index]] for explanations. |
| - | Ramachandran outliers are those amino acids with non favorable dihedral angles, and Ramachandran plot is a powerful tool for making those evident. Most of the | + | Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing. |
| - | However, sometimes | + | However, sometimes Ramachandran outliers might play a special role in function. See for example the case of Ser-200 in the structure <scene name='76/762493/1ea5_color_sec_struct/3'>1ea5</scene>. Let's draw its <jmol><jmolLink><script>calculate structure;select protein;cartoon only;color structure;plot ramachandran</script><text>Ramachandran Plot</text></jmolLink></jmol>. |
Notice that the residues in <jmol><jmolLink><script>display sheet</script><text>beta sheets</text></jmolLink></jmol> are colored in yellow, the residues in <jmol><jmolLink><script>display helix</script><text>alpha helix</text></jmolLink></jmol> colored in magenta, <jmol><jmolLink><script>display turn</script><text>beta turn</text></jmolLink></jmol> in blue and <jmol><jmolLink><script>display all; hide sheet,helix,turn;</script><text>others</text></jmolLink></jmol> in white. At any time you may <jmol><jmolLink><script>display all</script><text>display all</text></jmolLink></jmol> residues. | Notice that the residues in <jmol><jmolLink><script>display sheet</script><text>beta sheets</text></jmolLink></jmol> are colored in yellow, the residues in <jmol><jmolLink><script>display helix</script><text>alpha helix</text></jmolLink></jmol> colored in magenta, <jmol><jmolLink><script>display turn</script><text>beta turn</text></jmolLink></jmol> in blue and <jmol><jmolLink><script>display all; hide sheet,helix,turn;</script><text>others</text></jmolLink></jmol> in white. At any time you may <jmol><jmolLink><script>display all</script><text>display all</text></jmolLink></jmol> residues. | ||
| - | Only Gly are allowed in the lower right | + | Only Gly are allowed in the lower right quarter. If we <jmol><jmolLink><script>display all; hide Gly</script><text>hide Gly</text></jmolLink></jmol> from the plot, will find the <jmol><jmolLink><script>select [SER]200:A;color selectionHalos green;selectionHalos on;label "\u03C6 =\u20%5.1[phi]\uB0|\u03C8 =\u20%5.1[psi]\uB0";set labelOffset 10 0;</script><text>Ser 200</text></jmolLink></jmol>, with phi/psi angles considered non-favourable for Serine. |
| - | However, in this case a misplaced residue (Ser 200) seems to play an important role in the function of this structure, | + | However, in this case, a Ramachandran-misplaced residue (Ser 200) seems to play an important role in the function of this structure, a member of the alpha/beta hydrolase fold <ref>pmid 1409539</ref>. |
Revision as of 15:19, 15 July 2018
Ramachandran outlier
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References
- ↑ RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963 Jul;7:95-9. PMID:13990617
- ↑ Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, et al.. The alpha/beta hydrolase fold. Protein Eng. 1992 Apr;5(3):197-211. PMID:1409539
