Calculate structure
From Proteopedia
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== Basis of Secondary Structure Determination == | == Basis of Secondary Structure Determination == | ||
| - | <StructureSection load=' | + | <StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene='Globular_Proteins/Anti_helix_erythrin2/1'> |
'''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. | ||
| - | 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 | + | 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. The 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. It is possible for a residue or a segment of residues to be assigned more than one structural type, for that reason the above list 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 that summary for myohemerytherin (2mhr): |
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| + | SUMMARY:<br> | ||
| + | G : A:12_A:14<br> | ||
| + | H : A:19_A:37<br> | ||
| + | H : A:41_A:64<br> | ||
| + | T : A:65_A:66<br> | ||
| + | T : A:68_A:69<br> | ||
| + | H : A:70_A:85<br> | ||
| + | T : A:86_A:86<br> | ||
| + | H : A:93_A:109<br> | ||
| + | T : A:110_A:110<br> | ||
| + | G : A:111_A:114<br> | ||
| + | T : A:115_A:117<br> | ||
| + | |||
| + | Show structure of <scene name='Calculate_structure/Domain_2/1'>domain 2 of chain A glycogen phosphorylase</scene> | ||
SUMMARY:<br> | SUMMARY:<br> | ||
B : A:486_A:486<br> | B : A:486_A:486<br> | ||
Revision as of 17:30, 1 July 2011
An important part of protein structure is the secondary structure which is made up of helices, sheets and turns and Jmol as described in Secondary structure 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 complete job of identifying and displaying the secodnary structures, is available in Jmol ver. 12, but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011.
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 and then click Run.
Basis of Secondary Structure Determination
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References
- ↑ A detailed description is at [1].
- ↑ 2.0 2.1 W. Kabsch & C. Sanders, Biopolymers, 22, 2577-2636, 1983.
