Calculate structure
From Proteopedia
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All types of 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 not an absolute requirement for a hbond, but there is often one between residues one and four (''i'' + 3). 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|View display of structure.]]). The turns in these three classes are not detected by DSSP since they do not contain a hbond. | All types of 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 not an absolute requirement for a hbond, but there is often one between residues one and four (''i'' + 3). 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|View display of structure.]]). The turns in these three classes are not detected by DSSP since they do not contain a hbond. | ||
| - | All γ-turns contain three residues 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> | + | All γ-turns contain three residues 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> In addition to having three residues γ-turns are defined by having a hbond between residues ''i'' and ''i'' + 1. |
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 perform the calculate structure command so that the resulting display can be compared with the summary below. After running the | + | The user is urged to use the above directions to perform the calculate structure command so that the resulting display can be compared with the summary below. After running the commands the segments displayed as α-helices and 3<sub>10</sub>-helices can easily be associated with peptide segments in the summary. The turns need some additional explanation. |
SUMMARY:(Key for the structural components is '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.)<br> | SUMMARY:(Key for the structural components is '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.)<br> | ||
Revision as of 00:57, 2 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.
Basis of Secondary Structure Determination
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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.
