Calculate structure
From Proteopedia
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'''Myohemerytherin''' (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | '''Myohemerytherin''' (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | ||
* Locate any β-turns that are not being displayed by blue trace because there is not a hbond between the first and the last residues of the turn. Remember that you can confirm the presence of this type of β-turn by showing the presence of a Pro at position three. (Hover the cursor over the trace to display the name and number of the residues.) There are two class VIb β-turns in myohemerytherin. | * Locate any β-turns that are not being displayed by blue trace because there is not a hbond between the first and the last residues of the turn. Remember that you can confirm the presence of this type of β-turn by showing the presence of a Pro at position three. (Hover the cursor over the trace to display the name and number of the residues.) There are two class VIb β-turns in myohemerytherin. | ||
| - | * The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/6'>This turn</scene> serves to illustrate that most often 4-turns are identified in the summary by their two central residues. Most of the β-turns in myohemerythrin are exceptions to this generalization, but in glycogen phosphorylase (below) it does hold in the majority of cases. (Since ''calculate hbonds structure'' does not function in the green links of Proteopedia using Jmol 11.8, the ''calculate hbonds structure'' command must be run in the console to display the hbonds after clicking a green link.) One can see that the hbond is between residues 67 and 70 making it a 4-turn (β-turn), and | + | * The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/6'>This turn</scene> serves to illustrate that most often 4-turns are identified in the summary by their two central residues. Most of the β-turns in myohemerythrin are exceptions to this generalization, but in glycogen phosphorylase (below) it does hold in the majority of cases. (Since ''calculate hbonds structure'' does not function in the green links of Proteopedia using Jmol 11.8, the ''calculate hbonds structure'' command must be run in the console to display the hbonds after clicking a green link.) One can see that the hbond is between residues 67 and 70 making it a 4-turn (β-turn), and if the values for the phi and psi angles of residues 2 and 3 were displayed one could confirm it as a β-turn (class I). Notice, however, that part of residues 67 and 68 are colored white rather than blue. |
| - | * The first T is identified by a two residue segment, A:65_A:66, but | + | * The first T is identified by a two residue segment, A:65_A:66, but these two residues are the last two in the <scene name='Calculate_structure/Turn_63/3'>turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-turn (β-turn) and the torsional angles classify it as type I β-turn. As shown by their coloration the first two residues also qualify as α-helix and are displayed as such since a helix has priority over a turn. |
* The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>5-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (4-turn and type II β-turn) and between 114 and 118 (5-turn). A β-turn is nested in a 5-turn. Residue 114 is part of the 3<sub>10</sub>-helix so it is not colored blue. | * The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>5-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (4-turn and type II β-turn) and between 114 and 118 (5-turn). A β-turn is nested in a 5-turn. Residue 114 is part of the 3<sub>10</sub>-helix so it is not colored blue. | ||
| - | * The two remaining T's have one residue segments, and these could possibly be a 3-turn, but | + | * The two remaining T's each have one residue segments, and these could possibly be a 3-turn, but looking closely at the <scene name='Calculate_structure/Turns_84_100_one/1'>location of the hbonds</scene> reveals that they are 4-turn with some of the other residues also being part of a helix which has priority over a turn. Showing more detail of <scene name='Calculate_structure/Turns_84_100/1'>hydrogen bonding with backbone</scene>. Both of these turns are class I β-turn. |
| - | There are two β-turns that are not detected by DSSP, and they are both class IVB which do not have a hbond. They are located at . Run ''calculate hbonds structure'' to confirm that there are no hbonds in these turns. | ||
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'''SUMMARY for Myohemerytherin:'''<br> | '''SUMMARY for Myohemerytherin:'''<br> | ||
G : A:12_A:14<br> | G : A:12_A:14<br> | ||
Revision as of 19:38, 18 July 2011
An important part of protein structure is the secondary structure which is made up of helices, sheets and turns, and Jmol is capable of determining and displaying these three types of structures with limitations as described in How Jmol Determines Secondary Structure . The calculate structure[1] is a command which does a more fundamental identification of these secondary structures by re-calculating the secondary structure, but it is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. It 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 click on Console, in the bottom box of the console 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 what structures are identified by calculate structure and briefly how it is done.
- To identify problems associated with using the results of calculate structure to identify β and γ-turns.
- To illustrate with 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.
- ↑ 3.0 3.1 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.
