Calculate structure
From Proteopedia
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=== Basis of Secondary Structure Determination === | === Basis of Secondary Structure Determination === | ||
| - | ''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 its completion the results of ''calculate structure'' computation are 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, and for this reason the key of structural types 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. The summary for myohemerytherin (2mhr) is given below. | + | ''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 its completion the results of ''calculate structure'' computation are 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, and for this reason the key of structural types 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. The summary for myohemerytherin (2mhr) is given below. | ||
=== Relationship to β and γ Turns === | === Relationship to β and γ Turns === | ||
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[[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> | [[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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| + | ===Points to consider when identifying β and γ-turns with ''Calculate Structure''=== | ||
| + | '''β-turns''' | ||
| + | * DSSP does not report classes VIa1, VIa2, and VIb because of the lack of a hbond. If a segment is not colored blue but appears that it may be a β-turns, check for a cis-Pro at ''i + 2''. Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[determined|Phi and Psi Angles]]. | ||
| + | * Segments with one residue | ||
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 suspect 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 turns may partially overlap structures that have higher priority (In myohemerytherin they are turns.), so that a one residue segment in the summary represents a 4-turn. DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. Another possibility could be that one turn is nested in a second one. This occurs with the three residue segment in the myohemerytherin summary. In order to identify which type of turn is actually present from these different possibilities, one needs to determine between which two residues the hbond occurs and thereby determine which type of n-turn is present. | 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 suspect 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 turns may partially overlap structures that have higher priority (In myohemerytherin they are turns.), so that a one residue segment in the summary represents a 4-turn. DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. Another possibility could be that one turn is nested in a second one. This occurs with the three residue segment in the myohemerytherin summary. In order to identify which type of turn is actually present from these different possibilities, one needs to determine between which two residues the hbond occurs and thereby determine which type of n-turn is present. | ||
Revision as of 16:40, 16 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.
