Calculate structure
From Proteopedia
(Difference between revisions)
| Line 5: | Line 5: | ||
The objectives of this article are: | The objectives of this article are: | ||
* Describe briefly how ''calculate structure'' identifies secondary structures, with a focus on turns, and relate its turn identification to β and γ-turns. | * Describe briefly how ''calculate structure'' identifies secondary structures, with a focus on turns, and relate its turn identification to β and γ-turns. | ||
| - | * Summarize the | + | * Summarize the observations obtained from using ''calculate structure '' to identify turns in two proteins. |
* Show details of the above identifications. | * Show details of the above identifications. | ||
| Line 21: | Line 21: | ||
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 4, 5, or 6 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 4, 5, or 6 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 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#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. If a trace is not colored blue but has the 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. |
[[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 2 and therefore are not included among 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> | [[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 2 and therefore are not included among 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 turns | + | ===Summary of observations obtained from using ''Calculate structure''=== |
| - | Two proteins is a small sample, but it does give some indication of the nature of the T: segments (turns) reported in the summary and of the trace segments | + | These observations are from the use of ''Calculate structure'' to identify the turns in myohemerthyrin and Domain 2 of chain A Glycogen Phosphorylase. Two proteins is a small sample, but it does give some indication of the nature of the T: segments (turns) reported in the summary and of the pattern of blue colored trace segments in the displayed structure. There are additional samples, which you can analyze, following these two proteins. |
| + | |||
* Most T: segments in the summary contain one or two residues but a few contain three or four residues. | * Most T: segments in the summary contain one or two residues but a few contain three or four residues. | ||
| - | * The presence of a one-residue T: segments in the summary is not necessarily an indicator of a n-turn. Some of these single residues are found in the interior of a helix and are not colored blue ( | + | * The presence of a one-residue T: segments in the summary is not necessarily an indicator of a n-turn. Some of these single residues are found in the interior of a helix and are not colored blue (found in Domain 2 of chain A Glycogen Phosphorylase). Even if the single residue is colored blue in the structure, the turn in which it is located is not an isolated turn but part of a helix. These single blue colored residues can be at the end or interior of the helix. |
* All two-residue T: segments indicate 3-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated 3-turns (β-turns) have two to three residues colored blue in the structure, rarely four. This coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify β-turns. | * All two-residue T: segments indicate 3-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated 3-turns (β-turns) have two to three residues colored blue in the structure, rarely four. This coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify β-turns. | ||
* T: segments that have more than two residues indicate two contiguous or nested β-turn, β-turn nested in a 4 or 5-turn, isolated or nested 4 or 5-turns. These nested turns are easily identified by residue ''i'' being involved in two hbonds. | * T: segments that have more than two residues indicate two contiguous or nested β-turn, β-turn nested in a 4 or 5-turn, isolated or nested 4 or 5-turns. These nested turns are easily identified by residue ''i'' being involved in two hbonds. | ||
| - | * DSSP does not identify these classes of β-turns VIa1, VIa2, and VIb because of the lack of a hbond. If a segment is not colored blue but has the 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. | ||
| - | |||
=== Illustrations === | === Illustrations === | ||
| Line 41: | Line 40: | ||
* There are two T segments that contain two residues (<scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> and <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene>), and both mark β-turns. Descriptions of both are included in the summary below. | * There are two T segments that contain two residues (<scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> and <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene>), and both mark β-turns. Descriptions of both are included in the summary below. | ||
* The <scene name='Calculate_structure/Turn_114/2'>last T</scene> is a three residue segment, and ''Calculate hbonds structure'' shows hbonds between 114 and 117 (β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. | * The <scene name='Calculate_structure/Turn_114/2'>last T</scene> is a three residue segment, and ''Calculate hbonds structure'' shows hbonds between 114 and 117 (β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. | ||
| - | * Can you locate the two turns that are not | + | * Can you locate the two turns that are not colored with blue traces and do not contain 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. |
'''SUMMARY for Myohemerytherin:'''<br> | '''SUMMARY for Myohemerytherin:'''<br> | ||
| Line 55: | Line 54: | ||
G : A:111_A:114<br> | G : A:111_A:114<br> | ||
T : A:115_A:117 β-turn 114-117, 4-turn 114-118 - 114 is part of a helix, 115-117 & part of 118 are blue, 118 is partially white. <scene name='Calculate_structure/Turn_114/2'>Display turn</scene><br> | T : A:115_A:117 β-turn 114-117, 4-turn 114-118 - 114 is part of a helix, 115-117 & part of 118 are blue, 118 is partially white. <scene name='Calculate_structure/Turn_114/2'>Display turn</scene><br> | ||
| - | <scene name='Calculate_structure/Turns_5_88/1'>Display the two class VIb turns</scene><br> | ||
Key - '''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> | Key - '''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> | ||
| + | (<scene name='Calculate_structure/Turns_5_88/1'>Display the two class VIb turns</scene>)<br> | ||
'''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br> | '''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br> | ||
Revision as of 20:36, 5 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 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 briefly how calculate structure identifies secondary structures, with a focus on turns, and relate its turn identification to β and γ-turns.
- Summarize the observations obtained from using calculate structure to identify turns in two proteins.
- Show details of the above identifications.
| |||||||||||
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.
