Calculate structure

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 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"^[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.

Comparison to Other Models

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 turns involve these angles.

All types of β-turns contain four residues and therefore would be included with the 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] There is not an absolute requirement for a hbond, but there is often one between residues one and four (i + 3). In three classes 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.

All γ-turns contain three residues and would be included with the 3-turns found by DSSP. The classic γ-turns have phi and psi values at residue i + 1 of +75.0 ± 40 and -64 ± 40, respectively, and the inverse γ-turns have phi and psi values at residue i + 1 of -79 ± 40 and +69 ± 40, respectively.^[4][5] In addition to having three residues γ-turns are defined by having a hbond between residues i and i + 1.

Illustrations

After Jmol completes the calculate structure computation the results of the computation is 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. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below 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. Below is a copy of the summary for myohemerytherin (2mhr): ()

The user is urged to use the above directions to open version 12 and to perform the calculate structure command so that the resulting display can be compared with the summary below. Without doing this the images described below can not be observed. After running the commands the segments displayed as α-helices and 3₁₀-helices can easily be associated with peptide segments in the summary.

The turns need some additional explanation. One might expect that the segments that have one residue are 3-turns, the segments with two residues are 4-turn and the segments with three residues are 5-turns. This is often the case, but in many cases it is more complex. The turn may overlap with a structure that has higher priority, so therefore these overlapping residues are not included in the summary. Another possibility would be that one turn is nested in a second one. Two determinations can be used to clarify the situation. Displaying the hbonds shows the residues between which the hbond occurs and therefore which type of n-turn is present. If it is a β-turn (4-turn) or γ-turn (3-turn), determining the values of the torsional angles determines its class.

The second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) serves to illustrate that most often 4-turns (β-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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions to display these angles) make it a class I β-turn. 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, but the two residues, A:65_A:66, are the last two in the turn (Display with green link below). Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-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 with calculate hbonds structure showing 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 have one residue segments, and these could possibly be a 3-turn with that one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn. This seems to be the case for the turns that are identified as A:86_A:86 and A:110_A:110. As described above the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn.

There are two β-turns that are not detected by DSSP, and they are both class IVB which do not have a hbond. They are located at residues 5-8 and 88-91.

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.

Show structure of

SUMMARY for Domain 2 of Chain A Glycogen Phosphorylase:
B : A:486_A:486
T : A:488_A:488
I : A:489_A:494
T : A:495_A:495
H : A:497_A:507
G : A:510_A:513
G : A:515_A:524
T : A:525_A:526
H : A:528_A:551
E : A:562_A:567
G : A:572_A:574
H : A:576_A:592
T : A:594_A:595
E : A:601_A:606
T : A:611_A:612
H : A:614_A:632
T : A:635_A:638
E : A:640_A:644
H : A:650_A:659
E : A:662_A:665
T : A:669_A:670
T : A:676_A:677
H : A:678_A:682
T : A:683_A:685
E : A:687_A:691
T : A:694_A:695
H : A:696_A:703
G : A:705_A:707
E : A:709_A:711
H : A:715_A:724
T : A:728_A:728
H : A:729_A:734
H : A:736_A:746
T : A:747_A:750
T : A:752_A:753
G : A:755_A:758
H : A:759_A:768
T : A:773_A:773
G : A:774_A:776
T : A:777_A:777
H : A:778_A:791
H : A:794_A:806
T : A:807_A:807
G : A:808_A:811
B : A:812_A:812
H : A:813_A:821
T : A:822_A:825