Calculate structure
From Proteopedia
(Difference between revisions)
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* To illustrate with two examples. | * To illustrate with two examples. | ||
== Basis of Secondary Structure Determination == | == Basis of Secondary Structure Determination == | ||
| - | <StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene=' | + | <StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene='Calculate_structure/Erythrin/1/1'> |
''Calculate structure'' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name="DSSP">W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms used in DSSP are based mainly on hydrogen-bonding patterns along with geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression ''i'' + ''n'' (''i'' is a residue that forms a hydrogen bond with a residue n residues removed from residue ''i''.) where n = 3, 4 or 5. These values define three types of turns. A peptide segment that has repeating turns of the same type are called 3<sub>10</sub>-helix, α-helix, or п-helix, respectively. If the turn is isolate, it is simply called an n-turn. The other recognized pattern is a hydrogen bond which is between residues which are not close together in sequence. This type of hydrogen bond is called a bridge. Kabsch & Sanders define a ladder as a "set of one or more consecutive bridges of identical type" and a sheet as a "set of one or more ladders connected by shared residues"<ref name="DSSP" />. Bends are peptide segments with high curvature, and the determination of curvature involves angles of the C<sup>α</sup>. Bends can overlap with helices and turns. | ''Calculate structure'' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name="DSSP">W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms used in DSSP are based mainly on hydrogen-bonding patterns along with geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression ''i'' + ''n'' (''i'' is a residue that forms a hydrogen bond with a residue n residues removed from residue ''i''.) where n = 3, 4 or 5. These values define three types of turns. A peptide segment that has repeating turns of the same type are called 3<sub>10</sub>-helix, α-helix, or п-helix, respectively. If the turn is isolate, it is simply called an n-turn. The other recognized pattern is a hydrogen bond which is between residues which are not close together in sequence. This type of hydrogen bond is called a bridge. Kabsch & Sanders define a ladder as a "set of one or more consecutive bridges of identical type" and a sheet as a "set of one or more ladders connected by shared residues"<ref name="DSSP" />. Bends are peptide segments with high curvature, and the determination of curvature involves angles of the C<sup>α</sup>. Bends can overlap with helices and turns. | ||
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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 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 because as you can see in the summary the segments labeled with a T do not contain the same number of residues. The ones that contain one residue 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 marked as being at A:86_A:86 and A:110_A:110. As described below 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 | + | 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 because as you can see in the summary the segments labeled with a T do not contain the same number of residues. The ones that contain one residue 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 marked as being at A:86_A:86 and A:110_A:110. As described below 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. |
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> | ||
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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> | ||
H : A:93_A:109<br> | H : A:93_A:109<br> | ||
| - | T : A:110_A:110<br> | + | T : A:110_A:110 <scene name='Calculate_structure/Turn_110/1'>Display turn</scene><br> |
G : A:111_A:114<br> | G : A:111_A:114<br> | ||
T : A:115_A:117<br> | T : A:115_A:117<br> | ||
Revision as of 22:35, 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.
