Calculate structure

An important part of protein structure is the secondary structure which is made up of Phi and psi torsional angles, β-turns and View display of structure., and Jmol is capable of determining and displaying these three types of structures with limitations as described in γ-turns. The calculate structure 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.

Any one page of Proteopedia can be run in the signed ver. 12 by appending "?JMOLJAR=https://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 is:

• To describe what structures are identified by calculate structure and briefly how it is done.
• To identify problems associated with using the results of calculate structure to identify β and γ-turns.
• To illustrate with examples.

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Basis of Secondary Structure Determination Calculate structure is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal. The secondary structure recognition algorithms used in DSSP are based mainly on hydrogen-bonding patterns along with some 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 310-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". Bends are peptide segments with high curvature, and the determination of curvature involves angles of the Cα. 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. (The summary for myohemerytherin (2mhr) is given below with a key for the 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 for the identifiers 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 helices and sheets which are identified on the summary can easily be associated with the corresponding structures in the applet, but the turns need some additional explanation. Relationship to β and γ Turns 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. Phi and psi torsional angles of the Cα are not used by the DSSP procedure, but the generally accepted definitions of β and γ turns involve these angles. β-turns contain four residues and therefore are 4-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. 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 (View display of structure.). The turns in these three classes are not detected by DSSP since they do not contain a hbond. γ-turns contain three residues having a hbond between residues i and i + 1 and are included with the 3-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. Problems encountered when identifying β and γ-turns See below for more details and illustrations of these problems. 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. 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 turn segment in the Summary is only one residue long and that segment is displayed as a blue trace short than four residues, it is still a β-turn if there is a hbond between 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. γ-turns 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 did not find classic γ-turns in many of the proteins in which Miner-White, et. al. had found the classic turns. This occurred because the DSSP identified those residues as the end of a helix. Illustrations The user is urged to use the above directions to open Jmol version 12 and to run the calculate structure and the accompanying commands so that the resulting display can be compared with the summary below. Without displaying the images generated by calculate structure and calculate hbonds structure the activities and comparisons described below can not be performed. Unless a green link is designed to change the color and structural representation these two display characteristics will not change after they have been set by calculate structure, but all hbonds are deleted by clicking a green link so calculate hbonds structure has to be run from the console after every green link click in order to display hbonds. Myohemerytherin (Restore initial 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. The second T in the myohemerytherin summary is identified as segment A:68_A:69. This turn serves to illustrate that most often 4-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 4-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 β-turn (class I). Notice, however, 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 turn. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-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 5-turn. Calculate hbonds structure shows hbonds between 114 and 117 (4-turn and type II β-turn) and between 114 and 118 (5-turn). A β-turn is nested in a 5-turn. Residue 114 is part of the 310-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 location of the hbonds reveals that they are 4-turn with some of the other residues also being part of a helix which has priority over a turn. Showing more detail of hydrogen bonding with backbone. Both of these turns are class I β-turn. SUMMARY for Myohemerytherin: G : A:12_A:14 H : A:19_A:37 H : A:41_A:64 T : A:65_A:66     Display turn T : A:68_A:69     Display turn; run the command calculate hbonds structure in the console to see the hbonds H : A:70_A:85 T : A:86_A:86     Display turn H : A:93_A:109 T : A:110_A:110     Display turn G : A:111_A:114 T : A:115_A:117     Display turn Display the two class VIb turns Key - H: α-helix; B: β-bridge; E: β-strand; G: 310-helix; I: π-helix; T: 3-, 4-, 5-turn; S: bend. Domain 2 of chain A Glycogen Phosphorylase (Load Structure) - 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. After clicking on the above green link, open the console and run the script: select protein; calculate structure; cartoon; color structure; calculate hbonds structure Using the method used for myohemerytherin above, look for β-turns that have a Pro at position 3 but do not have hbonds. High lite, as three or four residue segments, the one residue segments in the summary below. (Remember to display the hbonds by running calculate hbonds structure from the console.) Only one segment has a residue colored blue, indicating a turn, and the other residues are colored as being part of a helix, sheet or non-secondary structure (white). Improve the view by displaying these segments in isolation, and reveal that they look very much like γ-turns. None of these segments have the hbond required for 3-turn, but three of the segments have hbonds involved in 4-turns (773-776, 774-777, 805-808) and 5-turns (772-776, 774-778), and none of the residues involved are colored blue. One has to wonder why the segments without hbonds are listed in the summary as T segments. As can be seen in the summary below the values of the torsional angles of the central residue of the three residue segments are similar to those for inverse γ-turns, but the psi values are all negative. Reveal the nature of the remaining T segments. Inspecting them for hbonds (after running calculate hbonds structure from the console) reveals that all but one of these T segments are part of β-turns, and that segment (822-825) is part of a 5-turn and two 6-turns (A type of turn not described by Miner-White, et. al.). Displaying these turns in isolation makes it easier to observe the hbonds. Using the residue numbers in the summary one can determine which residues make up the turns. At two places the β-turns overlap. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying hbonds.). SUMMARY of T's for Domain 2 of Chain A Glycogen Phosphorylase:(All other segments deleted.) T : A:488_A:488    torsional angles: -60, -15; T : A:495_A:495    torsional angles: -81, -18; T : A:525_A:526   β-turn 524-527 T : A:594_A:595   β-turn 593-596 T : A:611_A:612   β-turn 610-613 T : A:635_A:638   β-turn 633-636,636-639 T : A:669_A:670   β-turn 668-671 T : A:676_A:677   β-turn 675-678 T : A:683_A:685   β-turn 682-685 T : A:694_A:695   β-turn 693-696 T : A:728_A:728    torsional angles: -34, -22; T : A:747_A:750   β-turn 748-751 T : A:752_A:753   β-turn 751-754 T : A:773_A:773    torsional angles: -77; -79; T : A:777_A:777    torsional angles: -74, -65; T : A:807_A:807    torsional angles: -93, -8; T : A:822_A:825   5-turn & two 6-turn 820-826 487-489,494-496,727-729,772-774,776-778,805-808; 524-527,593-596,610-613,633-636,636-639,668-671,675-678,682-685,693-696,748-751,751-754,820-826 Detection of Known γ-turns Calculate structure only identifies one out of the eleven classic γ-turns identified by Miner-White et. al.. The hbond of the classic γ-turn in thermolysin is displayed and Thermolysin (8TLN, which now supersedes 3TLN which was actually used by Miner-White et. al.); Isolated view. The hbonds were not identified by Calculate structure in the other ten classic turns and the turn segments were not included in the summary displayed in the console. Several illustrations are given. α-lytic protease - Isolated turn Proteinase A (2SGA); Isolated turn However, with some of these turns a residue making up the turn is included along with contiguous residues in a T segment of the summary.

Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, Wayne Decatur, Jaime Prilusky