FirstGlance/Evaluating Protein Crosslinks: Difference between revisions
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Below are step-by-step instructions for evaluating putative [[protein crosslinks]] reported by FirstGlance in Jmol. Genuine crosslink bonds are illustrated, along with [[clashes]] that are irregularities in the model, not crosslink bonds. | Below are step-by-step instructions for evaluating putative [[protein crosslinks]] reported by FirstGlance in Jmol. Genuine crosslink bonds are illustrated, along with [[clashes]] that are irregularities in the model, not crosslink bonds. | ||
==Instructions for an Isopeptide Bond== | ==Instructions for an Isopeptide Bond== | ||
1. | 1. Go to [http://firstglance.jmol.org FirstGlance in Jmol] (right click link, open in new tab), and enter [[PDB code]] <b>2xi9</b>. | ||
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<table class="wikitable"><tr><td>[[Image:Fgij-xl1.png]]</td></tr></table> | <table class="wikitable"><tr><td>[[Image:Fgij-xl1.png]]</td></tr></table> | ||
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==Clashes== | ==Clashes== | ||
FirstGlance suggests the presence of a "putative crosslink" based solely on the distances between relevant atoms (click the link '''Detailed Methods''' in FirstGlance). Sometimes, instead of a real covalent bond crosslink, the proximity of the relevant atoms is due to errors in the atomic model that produce [[clashes]]. | FirstGlance suggests the presence of a "putative crosslink" based solely on the distances between relevant atoms (click the link '''Detailed Methods''' in FirstGlance). Sometimes, instead of a real covalent bond crosslink, the proximity of the relevant atoms is due to [[alternate locations]] or small errors in the atomic model that produce [[clashes]]. | ||
For each putative crosslink suggested by FirstGlance, it is the responsibility of the user to evaluate whether it is a real covalent crosslink, or a clash. FirstGlance makes this responsibility clear (see the bottom paragraph in the snapshot under step #4 above). | For each putative crosslink suggested by FirstGlance, it is the responsibility of the user to evaluate whether it is a real covalent crosslink, or a clash. FirstGlance makes this responsibility clear (see the bottom paragraph in the snapshot under step #4 above). | ||
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===Bonds=== | ===Bonds=== | ||
It is important not to take the bonds displayed by FirstGlance/Jmol literally. [[Atomic coordinate files]] from the [[wwPDB]] do not specify most covalent bonds. Rather, Jmol draws covalent "bond" sticks between atoms wherever two atoms are sufficiently close. In the case of carbon, nitrogen and oxygen, this is wherever a pair of those atoms is separated by ≤1.81 Å<ref name="bondlengths">Actual covalent bond lengths are approximately C-C: 1.4 Å; C-N: 1.4 Å; C-O: 1.4 Å; C=O: 1.2 Å C-S: 1.7 Å ([https://en.wikipedia.org/wiki/Covalent_radius Covalent radii in Wikipedia]).</ref>. In perfectly accurate models, this works correctly, but the errors in [[empirical models]] sometimes lead to bonds being drawn incorrectly. Thus, Jmol may show bond sticks where the reality is a clash, not a bond; and Jmol may fail to show bond sticks between atoms that are believed to be covalently bonded, but are too far apart in the model. | It is important not to take the bonds displayed by FirstGlance/Jmol literally. [[Atomic coordinate files]] from the [[wwPDB]] do not specify most covalent bonds. Rather, Jmol draws covalent "bond" sticks between atoms wherever two atoms are sufficiently close. In the case of carbon, nitrogen and oxygen, this is wherever a pair of those atoms is separated by ≤1.81 Å (for actual bond lengths, see footnote<ref name="bondlengths">Actual covalent bond lengths are approximately C-C: 1.4 Å; C-N: 1.4 Å; C-O: 1.4 Å; C=O: 1.2 Å; C-S: 1.7 Å ([https://en.wikipedia.org/wiki/Covalent_radius Covalent radii in Wikipedia]).</ref>). In perfectly accurate models, this works correctly, but the errors in [[empirical models]] sometimes lead to bonds being drawn incorrectly. Thus, Jmol may show bond sticks where the reality is a clash, not a bond; and Jmol may fail to show bond sticks between atoms that are believed to be covalently bonded, but are too far apart in the model. | ||
==Case Illustrations== | ==Case Illustrations== | ||