Calculate structure

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An important part of protein structure is the secondary structure which is made up of helices, sheets and turns, and with limitations as described in How Jmol Determines Secondary Structure Jmol is capable of determining and displaying these three types of structures. The calculate structure^[1] command which re-calculates the secondary structure does a more fundamental identification of these secondary structures but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011 but 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 one 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 which opens click on Console, in the bottom box 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 briefly what structures are identified by calculate structure and how it is done.
To compare its results with other ways of identifying and classifying these structures.
To illustrate with two examples.

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.

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 each class has a different 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 classes are not detected by DSSP since they do not contain a hbond.

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 perform the calculate structure command so that the resulting display can be compared with the summary below. After running the command the residues involved in the α-helices and the 3₁₀-helices can easily be identified. The turns need some additional explanation.

SUMMARY:(Key for the structural components is H: α-helix; B: β-bridge; E: β-strand; G: 3₁₀-helix; I: π-helix; T: 3-, 4-, 5-turn; S: bend.)

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
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

Show structure of

SUMMARY:
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

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

Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, Jaime Prilusky, Wayne Decatur

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Calculate structure

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Basis of Secondary Structure Determination

References

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