Calculate structure

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Basis of Secondary Structure Determination

Calculate structure is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.^[2] 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 Π-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"^[2]. Bends are peptide segments with high curvature, and the determination of curvature involves angles of the C^α. 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 C^α 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.^[3] 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.^[4]

Summary of the use of Calculate structure to identify β and γ-turns

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 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 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 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.

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 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.

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 ()

• 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. 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 . 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 . 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 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 . 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    
T : A:68_A:69     ; run the command calculate hbonds structure in the console to see the hbonds
H : A:70_A:85
T : A:86_A:86    
H : A:93_A:109
T : A:110_A:110    
G : A:111_A:114
T : A:115_A:117    

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 () - 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.
• , 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 , 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 . 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 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

Out of the eleven classic γ-turns identified by Miner-White et. al.^[4] Calculate structure only identifies and displays the hbond of thermolysin. Miner-White et. al. indicate that two hbonds are present in the classic γ-turn in thermolysin (They also state that the turn in thermolysin is the only one of the eleven that has two hbonds.), but Calculate structure only displays one and the T segment of the turn is not listed in the summary displayed in the console. select protein; calculate structure; cartoon; color structure; calculate hbonds structure

• (8TLN, which now supersedes 3TLN which was actually used by Miner-White et. al.); - run 'calculate hbonds structure' to confirm presence of hbond; reported torsional angles are 75,-54.

The hbonds were not identified by Calculate structure in the other ten classic turns and the T segments were not included in the summary displayed in the console. Several illustrations are given.

• ; - run 'calculate hbonds structure' to confirm absence of intra-turn hbond; reported torsional angles are 93, -70.
• (2SGA); - reported torsional angles are 80, -75.
• (6LDH, supersedes 4LDH) - three classic γ-turns high lighted; - none have the appearance of a γ-turn and none have torsional angles that a classic or even an inverse γ-turn would have. Substantial differences between 4LDH and 6LDH could account for the lack of γ-turns in these three sequences.

• 103-106 - T: 102_103 is on the summary, but as indicated by the hbond 101-104 forms a β-turn.
• 208-210 - T: 207_208 is on the summary, but as indicated by the hbond 206-209 forms a β-turn.
• 278-280 - T: 275_276 is the closest segment on the summary.

• (5NLL, supersedes 3FXN) - summary contains G: 122_124 as expected based on the coloration; - torsional angles reported for 3FXN were 35, -94. Classic γ-turn partially nested in a 3₁₀-helix with the helix having priority over the turn.