Calculate structure
From Proteopedia
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After Jmol completes the ''calculate structure'' computation the results of the computation is printed in the upper box of the console. One part of that output is a summary of the different types of secondary structure with each type having a one letter identifier. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below is rank ordered in decreasing priority of assignment. With bend having the lowest priority in assignment a structure is identified as a bend only if it is not assigned any other structural type. Below is a copy of the summary for myohemerytherin (2mhr): (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | After Jmol completes the ''calculate structure'' computation the results of the computation is printed in the upper box of the console. One part of that output is a summary of the different types of secondary structure with each type having a one letter identifier. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below is rank ordered in decreasing priority of assignment. With bend having the lowest priority in assignment a structure is identified as a bend only if it is not assigned any other structural type. Below is a copy of the summary for myohemerytherin (2mhr): (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | ||
| - | The user is urged to use the above directions to open version 12 and to perform the ''calculate structure'' command so that the resulting display can be compared with the summary below. Without | + | The user is urged to use the above directions to open Jmol version 12 and to perform the ''calculate structure'' command so that the resulting display can be compared with the summary below. Without displaying the images generated by ''calculate structure'' the activities and comparisons described below can not be done. 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 with a structure that has higher priority, so therefore these overlapping residues are not included in the summary. Another possibility would be that one turn is nested in a second one. Two determinations can be used to clarify the situation. Displaying the hbonds shows the residues between which the hbond occurs and therefore which type of n-turn is present. If it is a β-turn (4-turn) or γ-turn (3-turn), determining the values of the torsional angles determines its class. |
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| - | The turns need some additional explanation. One might expect that the segments that have one residue are 3-turns, | + | |
The second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) 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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) 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 second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) 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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) 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. | ||
Revision as of 21:38, 4 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.
