Calculate structure
From Proteopedia
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* To illustrate with two examples. | * To illustrate with two examples. | ||
| - | <StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene='Calculate_structure/Erythrin/1'> | + | <StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene='Calculate_structure/Erythrin/1'>__NOTOC__ |
=== Basis of Secondary Structure Determination === | === Basis of Secondary Structure Determination === | ||
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[[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 1 and would be included with the 3-turns found by DSSP. The classic γ-turns have phi and psi values at residue ''i'' + 1 of +75.0 ± 40 and -64 ± 40, respectively, and the inverse γ-turns have phi and psi values at residue ''i'' + 1 of -79 ± 40 and +69 ± 40, respectively.<ref>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.</ref> | [[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 1 and would be included with the 3-turns found by DSSP. The classic γ-turns have phi and psi values at residue ''i'' + 1 of +75.0 ± 40 and -64 ± 40, respectively, and the inverse γ-turns have phi and psi values at residue ''i'' + 1 of -79 ± 40 and +69 ± 40, respectively.<ref>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.</ref> | ||
| - | ===Points to consider when identifying β and γ-turns | + | ===Points to consider when identifying β and γ-turns=== |
| + | See below for more detail and illustrations of these points. | ||
'''β-turns''' | '''β-turns''' | ||
* DSSP does not report classes VIa1, VIa2, and VIb because of the lack of a hbond. If a segment is not colored blue but appears that it may be a β-turns, check for a cis-Pro at ''i + 2''. Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[determined|Phi and Psi Angles]]. | * DSSP does not report classes VIa1, VIa2, and VIb because of the lack of a hbond. If a segment is not colored blue but appears that it may be a β-turns, check for a cis-Pro at ''i + 2''. Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[determined|Phi and Psi Angles]]. | ||
| - | * Segments with one residue | + | * Segments labeled with T and contain one residue may not be a 3-turn, but a β-turn (4-turn) that partially overlaps a structure that has a higher priority, and only the non-overlapping residue is reported as a 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. If the hbonds displays between ''i + 3'', the turn is a β-turn. |
| + | * A β-turn can be nested in a 5-turn, and in the Summary this turn will show as a three residue segment. A β-turn nested in a 5-turn contains two hbonds. One located between ''i'' and ''i + 3'', and the other one is between ''i'' and ''i + 4''. | ||
| - | 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 | + | '''γ-turns''' |
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| + | 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 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'', but they do not qualify to be called neither classic nor inverse γ-turns because with all of them the phi and the psi values are both negative. by definition one or the other needs to be positive. When calculate structure is run on proteins that have been identified as having a γ-turn, the γ-turn is not always identified as a 3-turn. | 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'', but they do not qualify to be called neither classic nor inverse γ-turns because with all of them the phi and the psi values are both negative. by definition one or the other needs to be positive. When calculate structure is run on proteins that have been identified as having a γ-turn, the γ-turn is not always identified as a 3-turn. | ||
Revision as of 20:21, 16 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
- ↑ 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.
