Calculate structure
From Proteopedia
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The objectives of this article are: | The objectives of this article are: | ||
* Describe what structures are identified by ''calculate structure'' and briefly how it is done. | * Describe what structures are identified by ''calculate structure'' and briefly how it is done. | ||
| - | * Summarize the results of using ''calculate structure '' to identify β | + | * Summarize the results of using ''calculate structure '' to identify β in several proteins. |
* Show details of the above identifications. | * Show details of the above identifications. | ||
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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 are | + | [[Turns_in_Proteins#Beta Turns|β-turns]] contain four residues and therefore are 3-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> β-turns often have a hbond between residues one and four (''i'' + 3) of β-turns, but there is not an absolute requirement for one. In three classes (VIa1, VIa2, VIb) 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'' + | + | [[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 2 and therefore are not included the turns found by DSSP. The classic γ-turns have phi and psi values at residue ''i'' + 1 of +75.0 and -64, respectively, and the inverse γ-turns have phi and psi values at residue ''i'' + 1 of -79 and +69, respectively.<ref name="Miner">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> |
| - | ===Summary of the use of ''Calculate structure'' to identify β | + | ===Summary of the use of ''Calculate structure'' to identify β-turns=== |
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| - | * DSSP does not report classes VIa1, VIa2, and VIb because of the lack of a hbond. If a segment is not colored blue but has appearance of 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 [[Psi and Phi Angles|determined]]. | + | * DSSP does not report classes VIa1, VIa2, and VIb because of the lack of a hbond. If a segment is not colored blue but has appearance of 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 [[Psi and Phi Angles|determined]] and compared to the values expected for classes VIa1, VIa2, and VIb. |
* Segments labeled with T and contain one residue may not be a 3-turn, but a β-turn (4-turn) that partially overlaps a structure that has a higher priority, and only the non-overlapping residue is reported as a 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. If a T segment in the Summary is only one residue long, it can be identified as a β-turn by the presence of a hbond between ''i'' and ''i + 3''. | * Segments labeled with T and contain one residue may not be a 3-turn, but a β-turn (4-turn) that partially overlaps a structure that has a higher priority, and only the non-overlapping residue is reported as a 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. If a T segment in the Summary is only one residue long, it can be identified as a β-turn by the presence of a hbond between ''i'' and ''i + 3''. | ||
* A β-turn can be nested in a 5-turn, and in the Summary this turn will show as a three residue segment. A β-turn nested in a 5-turn contains two hbonds. One located between ''i'' and ''i + 3'', and the other one is between ''i'' and ''i + 4''. | * A β-turn can be nested in a 5-turn, and in the Summary this turn will show as a three residue segment. A β-turn nested in a 5-turn contains two hbonds. One located between ''i'' and ''i + 3'', and the other one is between ''i'' and ''i + 4''. | ||
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* In the SUMMARY for Domain 2 of Chain A Glycogen Phosphorylase there are six T labeled segments which contain one residue. Each of the three residue segments if viewed in isolation appear as if they are involved in 3-turns, but none of them have a hbond between ''i'' and ''i + 2''. These residues are colored to indicate they are involved in helices, a sheet and non-repetitive, ordered segment, but only one is colored blue. | * In the SUMMARY for Domain 2 of Chain A Glycogen Phosphorylase there are six T labeled segments which contain one residue. Each of the three residue segments if viewed in isolation appear as if they are involved in 3-turns, but none of them have a hbond between ''i'' and ''i + 2''. These residues are colored to indicate they are involved in helices, a sheet and non-repetitive, ordered segment, but only one is colored blue. | ||
* ''Calculate structure'' found a classic γ-turns in only one of the proteins in which Miner-White, et. al. had found eleven classic turns. Reasons for this are ''Calculate structure'' did not identify the hbond, there is a partial overlap with a helix which has priority over the turn. | * ''Calculate structure'' found a classic γ-turns in only one of the proteins in which Miner-White, et. al. had found eleven classic turns. Reasons for this are ''Calculate structure'' did not identify the hbond, there is a partial overlap with a helix which has priority over the turn. | ||
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'''Myohemerytherin''' (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | '''Myohemerytherin''' (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | ||
* Locate any β-turns that are not being displayed by blue trace because there is not a hbond between the first and the last residues of the turn. Remember that you can confirm the presence of this type of β-turn by showing the presence of a Pro at position three. (Hover the cursor over the trace to display the name and number of the residues.) There are two class VIb β-turns in myohemerytherin. | * Locate any β-turns that are not being displayed by blue trace because there is not a hbond between the first and the last residues of the turn. Remember that you can confirm the presence of this type of β-turn by showing the presence of a Pro at position three. (Hover the cursor over the trace to display the name and number of the residues.) There are two class VIb β-turns in myohemerytherin. | ||
| - | * 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 | + | * 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 3-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 ''calculate hbonds structure'' does not function in the green links of Proteopedia using Jmol 11.8, the ''calculate hbonds structure'' command must be run in the console to display the hbonds after clicking a green link.) One can see that the hbond is between residues 67 and 70 making it a 3-turn (β-turn), and if the values for the phi and psi angles of residues 2 and 3 were displayed one could confirm it as a class I. Notice that part of residues 67 and 68 are colored white rather than blue. |
| - | * The first T is identified by a two residue segment, A:65_A:66, but these two residues 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 | + | * The first T is identified by a two residue segment, A:65_A:66, but these two residues 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 3-turn (β-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'> | + | * The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>4-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (3-turn and type II β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. Residue 114 is part of the 3<sub>10</sub>-helix so it is not colored blue. |
| - | * The two remaining T's each have one residue segments, and these could possibly be a 3-turn, but looking closely at the <scene name='Calculate_structure/Turns_84_100_one/1'>location of the hbonds</scene> reveals that they are | + | * The two remaining T's each have one residue segments, and these could possibly be a 3-turn, but looking closely at the <scene name='Calculate_structure/Turns_84_100_one/1'>location of the hbonds</scene> reveals that they are 3-turn with some of the other residues also being part of a helix which has priority over a turn. Showing more detail of <scene name='Calculate_structure/Turns_84_100/1'>hydrogen bonding with backbone</scene>. Both of these turns are class I β-turn. |
<blockquote>'''SUMMARY for Myohemerytherin:'''<br> | <blockquote>'''SUMMARY for Myohemerytherin:'''<br> | ||
Revision as of 02:45, 1 August 2011
An important part of protein structure is the secondary structure which is made up of helices, sheets and turns, and Jmol is capable of determining and displaying these three types of structures with limitations as described in How Jmol Determines Secondary Structure . The calculate structure[1] is a command which does a more fundamental identification of these secondary structures by re-calculating the secondary structure, but it is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. It 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 click on Console, in the bottom box of the console enter the commands:select protein; calculate structure; cartoon; color structure; calculate hbonds structure and then click Run.
The objectives of this article are:
- Describe what structures are identified by calculate structure and briefly how it is done.
- Summarize the results of using calculate structure to identify β in several proteins.
- Show details of the above identifications.
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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
- ↑ 4.0 4.1 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.
