Calculate structure
From Proteopedia
(Difference between revisions)
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The user is urged to use the above directions to open Jmol version 12 and to run the ''calculate structure'' and the accompanying commands so that the resulting display can be compared with the summary below. Without displaying the images generated by ''calculate structure'' and ''calculate hbonds structure'' the activities and comparisons described below can not be performed. After displaying the secondary structure formed by ''calculate structure'' the displayed α-helices and 3<sub>10</sub>-helices can easily be associated with peptide segments in the summary. The turns need some additional explanation. One might expect that the segments in the summary that have one residue, two residues, and three residues are the interior residues of 3-turns, 4-turn and 5-turns, respectively. This is often the case, but in many cases it is not this simple. The turn may overlap or partially overlap with a structure that has higher priority, so that a one residue segment in the summary could represent a 4-turn. Another possibility could be that one turn is nested in a second one. In order to clarify the specific nature of the turn on needs to determine between which two residues the hbond occurs and thereby which type of n-turn is present. Looking closely at a blue colored trace find the dashed line representing a hbond, and hovering over the trace where the dashed line meets the trace reveals the number of the residue that is hydrogen bonded. Go to the other end of the dashed line and determine the residue number at that end. The two numbers should be ''i'' and ''i + n''. Green links are used below to display the hbonds of the turns in myohemerytherin in more detail. Another clarifying determination is to measure the values of the torsional angles (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) of the interior residues of the turn. These values can be used to classify the turn as a β-turn or γ-turn. The description below identifies the β-turn class of each of the turns. | The user is urged to use the above directions to open Jmol version 12 and to run the ''calculate structure'' and the accompanying commands so that the resulting display can be compared with the summary below. Without displaying the images generated by ''calculate structure'' and ''calculate hbonds structure'' the activities and comparisons described below can not be performed. After displaying the secondary structure formed by ''calculate structure'' the displayed α-helices and 3<sub>10</sub>-helices can easily be associated with peptide segments in the summary. The turns need some additional explanation. One might expect that the segments in the summary that have one residue, two residues, and three residues are the interior residues of 3-turns, 4-turn and 5-turns, respectively. This is often the case, but in many cases it is not this simple. The turn may overlap or partially overlap with a structure that has higher priority, so that a one residue segment in the summary could represent a 4-turn. Another possibility could be that one turn is nested in a second one. In order to clarify the specific nature of the turn on needs to determine between which two residues the hbond occurs and thereby which type of n-turn is present. Looking closely at a blue colored trace find the dashed line representing a hbond, and hovering over the trace where the dashed line meets the trace reveals the number of the residue that is hydrogen bonded. Go to the other end of the dashed line and determine the residue number at that end. The two numbers should be ''i'' and ''i + n''. Green links are used below to display the hbonds of the turns in myohemerytherin in more detail. Another clarifying determination is to measure the values of the torsional angles (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) of the interior residues of the turn. These values can be used to classify the turn as a β-turn or γ-turn. The description below identifies the β-turn class of each of the turns. | ||
| - | The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/ | + | The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/2'>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. If one desires to show all the hbonds in in the protein and not just the ones in the turn, ''select protein'' must be run along with ''calculate hbonds structure''. This bond qualifies it as a 4-turn, and 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 turn (Display with green link below). 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 with ''calculate hbonds structure'' showing 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 one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn. This seems to be the case for the turns that are identified as A:86_A:86 and A:110_A:110. As described above the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn. | The two remaining T's have one residue segments, and these could possibly be a 3-turn with that one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn. This seems to be the case for the turns that are identified as A:86_A:86 and A:110_A:110. As described above the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn. | ||
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H : A:41_A:64<br> | H : A:41_A:64<br> | ||
T : A:65_A:66 <scene name='Calculate_structure/Turn_63/1'>Display turn</scene><br> | T : A:65_A:66 <scene name='Calculate_structure/Turn_63/1'>Display turn</scene><br> | ||
| - | T : A:68_A:69 <scene name='Calculate_structure/Turn_67/ | + | T : A:68_A:69 <scene name='Calculate_structure/Turn_67/2'>Display turn</scene>; run the command ''calculate hbonds structure'' in the console to see the hbonds<br> |
H : A:70_A:85<br> | H : A:70_A:85<br> | ||
T : A:86_A:86 <scene name='Calculate_structure/Turn_84/1'>Display turn</scene><br> | T : A:86_A:86 <scene name='Calculate_structure/Turn_84/1'>Display turn</scene><br> | ||
Revision as of 20:28, 6 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
- ↑ 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.
