Calculate structure
From Proteopedia
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The DSSP determination of helices and β-sheets is in agreement with the generally accepted view of these two structures, but the DSSP determination of turns is not as specific as the generally accepted definition of turns. As described above DSSP identifies turns that have 3, 4, or 5 residues with a backbone hbond being present between the first and the last residues. The presence of the hbond is a requirement to be classified as a turn. [[Psi and Phi Angles|Phi and psi torsional angles]] of the C<sup>α</sup> are not used by the DSSP procedure, but the generally accepted definitions of β and γ turns involve these angles. | The DSSP determination of helices and β-sheets is in agreement with the generally accepted view of these two structures, but the DSSP determination of turns is not as specific as the generally accepted definition of turns. As described above DSSP identifies turns that have 3, 4, or 5 residues with a backbone hbond being present between the first and the last residues. The presence of the hbond is a requirement to be classified as a turn. [[Psi and Phi Angles|Phi and psi torsional angles]] of the C<sup>α</sup> are not used by the DSSP procedure, but the generally accepted definitions of β and γ turns involve these angles. | ||
| - | [[Turns_in_Proteins#Beta Turns|β-turns]] contain four residues and therefore would be included with the 4-turns found by DSSP. The classes of β-turns are defined by the range of psi and phi values for the second and third residues.<ref name=beta>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_p_bturns.html Characteristics of β-turn classes]</ref> There is often a hbond between residues one and four (''i'' + 3) of β-turns, but there is not an absolute requirement for one. In three classes a Pro in the third position has the cis configuration which does not permit the formation of a hbond ([[Turns_in_Proteins# | + | [[Turns_in_Proteins#Beta Turns|β-turns]] contain four residues and therefore would be included with the 4-turns found by DSSP. The classes of β-turns are defined by the range of psi and phi values for the second and third residues.<ref name=beta>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_p_bturns.html Characteristics of β-turn classes]</ref> There is often a hbond between residues one and four (''i'' + 3) of β-turns, but there is not an absolute requirement for one. In three classes a Pro in the third position has the cis configuration which does not permit the formation of a hbond ([[Turns_in_Proteins#Beta Turns|View display of structure.]]). The turns in these three classes are not detected by DSSP since they do not contain a hbond. |
| - | + | [[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> | |
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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 expect 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 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 one needs to determine between which two residues the hbond occurs and thereby which type of n-turn is present. | ||
=== Illustrations === | === Illustrations === | ||
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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. (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) Without displaying the images generated by ''calculate structure'' and ''calculate hbonds structure'' the activities and comparisons described below can not be performed. The α-helices and 3<sub>10</sub>-helices displayed by ''calculate structure'' can easily be associated with the corresponding peptide segments in the summary, but the turns need some additional explanation. | + | 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. (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) Without displaying the images generated by ''calculate structure'' and ''calculate hbonds structure'' the activities and comparisons described below can not be performed. The α-helices and 3<sub>10</sub>-helices displayed by ''calculate structure'' can easily be associated with the corresponding peptide segments in the summary, but the turns need some additional explanation. 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 one 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''. More detail on myohemerytherin's turns and their hbonds are given below with green links and description. Measuring 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 is another way of revealing the nature of the turns, because 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_67/6'>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_63/3'>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_67/6'>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_63/3'>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. | ||
Revision as of 00:30, 15 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.
