Calculate structure
From Proteopedia
(Difference between revisions)
| Line 29: | Line 29: | ||
The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/5'>This turn</scene> serves to illustrate that most often 4-turns (β-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 Proteopedia uses Jmol 11.8, ''calculate hbonds structure'' does not function in the green link, so in order to display the hbonds after clicking a green link the user must run the ''calculate hbonds structure'' command in the console. One can see that the hbond is between residues 67 and 70 making it a 4-turn, and the values for the phi and psi angles of residues 2 and 3 make it a class I β-turn. 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, but the two residues, A:65_A:66, are the last two in the <scene name='Calculate_structure/Turn_63/2'>turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-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 second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/5'>This turn</scene> serves to illustrate that most often 4-turns (β-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 Proteopedia uses Jmol 11.8, ''calculate hbonds structure'' does not function in the green link, so in order to display the hbonds after clicking a green link the user must run the ''calculate hbonds structure'' command in the console. One can see that the hbond is between residues 67 and 70 making it a 4-turn, and the values for the phi and psi angles of residues 2 and 3 make it a class I β-turn. 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, but the two residues, A:65_A:66, are the last two in the <scene name='Calculate_structure/Turn_63/2'>turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-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 two remaining T's have one residue segments, and these could possibly be a 3-turn with that | + | The two remaining T's have one residue segments, and these could possibly be a 3-turn, but displaying <scene name='Calculate_structure/Turns_84_100/1'>backbone</scene> with hbonds reveals that they are 4-turn with some of the other residues also being part of a helix which has priority over a turn. 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 residues 5-8 and 88-91. | + | 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 <scene name='Calculate_structure/Turns_5_88/1'>residues 5-8 and 88-91</scene>. Run ''calculate hbonds structure'' to confirm that there are no hbonds in these turns. |
'''SUMMARY for Myohemerytherin:'''<br> | '''SUMMARY for Myohemerytherin:'''<br> | ||
Revision as of 19:15, 7 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.
| |||||||||||
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
- ↑ Characteristics of γ-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.
