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 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. 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 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.^[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. 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 determined and compared to the values expected for classes VIa1, VIa2, and VIb.

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.^[4]

Summary of observations obtained from using Calculate structure

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.
• 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.
• 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.

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 ()

• There are two T segments that contain one residue ( and ), and both mark β-turns. Descriptions of both are included in the summary below.
• There are two T segments that contain two residues ( and ), and both mark β-turns. Descriptions of both are included in the summary below.
• The 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 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:
G : A:12_A:14
H : A:19_A:37
H : A:41_A:64     (run the command calculate hbonds structure in the console to see the hbonds)
T : A:65_A:66 β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.
T : A:68_A:69 β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue. ;
H : A:70_A:85
T : A:86_A:86 β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.
H : A:93_A:109
T : A:110_A:110 β-turn 110-113; 110 is blue, 111-113 are part of a helix.
G : A:111_A:114
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.
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

• all of the one residue T segments (e.g. T : A:488_A:488) in the summary below along with some residues on each side of each single residue. Improve the view by displaying these . (Remember to display the hbonds by running calculate hbonds structure from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T: segments. None of the residues labeled with T: on the summary are part of an isolated turn. Those involved in turns are part of a helix.
• Reveal the nature of the . Displaying these makes it easier to observe the hbonds. 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 4-turn and two 5-turns. 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.).
• Are there any β-turns that do not have hbonds but do have a Pro at position 3?

SUMMARY of T's for Domain 2 of Chain A Glycogen Phosphorylase:(All other segments deleted.)
T : A:488_A:488    488 (colored blue) is between a sheet & 3₁₀-helix.
T : A:495_A:495    495 is at the end of α-helix.
T : A:525_A:526   β-turn 524-527; but first three residues are part of a helix.
T : A:594_A:595   β-turn 593-596; 594 & 595 are colored blue, 593 is end of a sheet.
T : A:611_A:612   β-turn 610-613; 611 & 612 are colored blue, other two are white.
T : A:635_A:638   β-turn 633-636; 635 &636 colored blue; β-turn 636-639, 637 & 638 blue.
T : A:669_A:670   β-turn 668-671; 669 & 670 blue, other two are white.
T : A:676_A:677   β-turn 675-678; last three residues part of helix, 675 is white.
T : A:683_A:685   β-turn 682-685; 682 & 683 are the end of a helix, other two are blue.
T : A:694_A:695   β-turn 693-696; last two residues are part of a helix, 694 is blue, 693 is white.
T : A:728_A:728    728 is the first residue of an α-helix
T : A:747_A:750   β-turn 748-751; 748-750 are blue, 751 is white.
T : A:752_A:753   β-turn 751-754; 752 & 753 are blue, 754 is white.
T : A:773_A:773    773 is the first residue in an α-helix
T : A:777_A:777    777 is part of same α-helix as 773
T : A:807_A:807    807 is part of an α-helix
T : A:822_A:825   5-turns at 820-825 & 821-826; 822-824 are part of helix, 825 is blue, 826 is white.

486-490,493-497,726-730,771-775,776-779,804-809; 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.