Calculate structure
From Proteopedia
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'''γ-turns''' | '''γ-turns''' | ||
| - | * In the SUMMARY for Domain 2 of Chain A Glycogen Phosphorylase there are six T labeled segments which contain one residue and are 3-turns because they all have a hbond between ''i'' and ''i + 2''. The phi values for residue ''i + 1'' are negative, but the psi values are also negative. These six 3-turns could be inverse γ-turns, if the range for psi values given by Miner-White, et. al. is extended to negative values.<ref name=Miner /> | + | * In the SUMMARY for Domain 2 of Chain A Glycogen Phosphorylase there are six T labeled segments which contain one residue and are 3-turns because they all have a hbond between ''i'' and ''i + 2''. The phi values for residue ''i + 1'' are negative, but the psi values are also negative. These six 3-turns could be inverse γ-turns, if the range for psi values given by Miner-White, et. al. is extended to negative values.<ref name=Miner /> Miner-White, et. al. seem to allow for this by stating in the legend of Table 1, "To qualify for a classic γ-turn, the value of the mainchain dihedral angle φ of residue ''i'' + 1 has to be greater than 0°; for an inverse γ-turn it has to be less than 0°." The values that they report for psi are the means of the values that they found in the 54 proteins that they investigated. |
| + | * ''Calculate structure'' did not find classic γ-turns in many of the proteins in which Miner-White, et. al. had found the classic turns. This occurred because the DSSP identified those residues as the end of a helix. | ||
In the SUMMARY for Myohemerytherin given below observe that all the segments that are labeled T (Turn) are composed of one, two, or three residues. One might suspect that the segments that have one residue, two residues, and three residues are the interior residues of 3-turns, 4-turn and 5-turns, respectively, and that the 3-turns are γ-turns and the 4-turns are β-turns. This is often the case, but in many cases it is not this simple. As illustrated below only one out of the five turns identified by DSSP in myohemerytherin have a two residue segment in the summary, but all five are β-turns. One reason for this is that the turns may partially overlap structures that have higher priority (In myohemerytherin they are helices.), so that a one residue segment in the summary represents a 4-turn. DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. Another possibility could be that one turn is nested in a second one. This occurs with the three residue segment in the myohemerytherin summary. In order to identify which type of turn is actually present from these different possibilities, one needs to determine between which two residues the hbond occurs and thereby determine which type of n-turn is present. | In the SUMMARY for Myohemerytherin given below observe that all the segments that are labeled T (Turn) are composed of one, two, or three residues. One might suspect that the segments that have one residue, two residues, and three residues are the interior residues of 3-turns, 4-turn and 5-turns, respectively, and that the 3-turns are γ-turns and the 4-turns are β-turns. This is often the case, but in many cases it is not this simple. As illustrated below only one out of the five turns identified by DSSP in myohemerytherin have a two residue segment in the summary, but all five are β-turns. One reason for this is that the turns may partially overlap structures that have higher priority (In myohemerytherin they are helices.), so that a one residue segment in the summary represents a 4-turn. DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. Another possibility could be that one turn is nested in a second one. This occurs with the three residue segment in the myohemerytherin summary. In order to identify which type of turn is actually present from these different possibilities, one needs to determine between which two residues the hbond occurs and thereby determine which type of n-turn is present. | ||
Revision as of 00:50, 17 July 2011
An important part of protein structure is the secondary structure which is made up of helices, sheets and turns, and with limitations as described in How Jmol Determines Secondary Structure Jmol is capable of determining and displaying these three types of structures. The calculate structure[1] command which re-calculates the secondary structure does a more fundamental identification of these secondary structures but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011 but is available in Jmol ver. 12. Calculate hbonds structure is also available in ver. 12, and it identifies and displays the hbonds involved in these three types of secondary structures[1].
Any one page of Proteopedia can be run in the signed ver. 12 by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and reloading the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank, whereas in the unsigned version it is grey. Click on the Jmol frank, in the main menu which opens click on Console, in the bottom box enter the commands:select protein; calculate structure; cartoon; color structure; calculate hbonds structure and then click Run.
The objectives of this article is:
- To describe briefly what structures are identified by calculate structure and how it is done.
- To compare its results with other ways of identifying and classifying these structures.
- To illustrate with two examples.
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References
- ↑ 1.0 1.1 A detailed description is at [1].
- ↑ 2.0 2.1 W. Kabsch & C. Sanders, Biopolymers, 22, 2577-2636, 1983.
- ↑ Characteristics of β-turn classes
- ↑ 4.0 4.1 Miner-White, EJ, et. al. One type of gamma turn, rather than the other, gives rise to chain reversal in proteins. J. Mol. Bio. 204, 1983, pp. 777-782.
