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 torsional angles of the C^α. Bends can overlap with helices and turns.

The results of the calculate structure computation are printed in the upper box of the console. One part of that output is a summary which identifies peptide segments according to their type of secondary structure with each type having a one letter identifier. During the DSSP analysis it is possible for a residue or a segment of residues to be assigned more than one structural type, so the structural types are assigned a priority. (The summary for myohemerytherin (2mhr) is given below with a key for the one letter identifiers which are rank ordered in decreasing priority.) Turns (T) have a lower priority than sheets of helices with bends (S) having the lowest priority. 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 to identify n-turns, 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), but there is not an absolute requirement for a hbond. 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 + 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

Calculate structure was used 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. With isolated turns DSSP reports two, three and four residues for 3-, 4-, and 5-turns, respectively. If the turn is overlapping with a structure of higher priority fewer residues will be included in the segment.
• The presence of a one-residue T segments in the summary indicates that the β-turn overlaps a structure of higher priority (most often a helix). These single blue colored residues can be at the end or interior of the helix, and some in the interior of a helix may not be colored blue (Domain 2 of chain A Glycogen Phosphorylase).
• All two-residue T segments indicate β-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 β-turns have two to three residues colored blue in the structure, rarely four.
• T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4- or 5-turn, isolated or nested 4 or 5-turns.
• After calculate structure and calculate hbonds structure has been run the following methods can be used to identify the different types of turns. Blue coloration and the hbond bond between i and i + 3 can be used to identify overlapping and isolated β-turns. The 4- or 5-turns which are nested in some way are easily identified by residue i being involved in at least two hbonds. β-turns VIa1, VIa2, and VIb can be identified by locating a trace that has the appearance of a β-turns and is not colored blue and checking for a cis-Pro at i + 2. (Hover the cursor over the trace to display the name and number of the residues.) 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.^[3]
• There are two resources at RCSB Protein Data Bank^[5] that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin below.

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 parameters do 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, (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and (β-turn 110-113; 110 is blue, 111-113 are part of a 3₁₀-helix.).
• There are two T segments that contain two residues, (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).
• The last T is a three residue segment, (β-turn 114-117, 4-turn 114-118; 114 is part of a 3₁₀-helix, 115-117 & part of 118 are blue, 118 is partially white.). 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. 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
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   
Key - H: α-helix; B: β-bridge; E: β-strand; G: 3₁₀-helix; I: π-helix; T: 3-, 4-, 5-turn; S: bend.

Identify turns using resourses at RCSB

Follow directions given above. If you select one of the other annotations of secondary structure, you will discover that class VIb β-turns are among the structures being annotated. Use end note to open necessary sites.^[6]

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

• each of the one residue T segments (e.g. T : A:488_A:488) in the summary below along with a few residues on each side of the 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. The only turns that these single residue segments are part of are involved helices.
• 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 with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. 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 the atoms involved in the hbonds.).

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; first three residues are part of a helix with 527 partially colored blue.
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 & a β-turn (805-808) nested in the 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.

Identify turns using resourses at RCSB

When the structure is large and complex as it is in the complete chain A glycogen phosphorylase, you may not be able to see the small high lighted turn after clicking on the annotation bar. The turn or any other secondary structure, when it is selected on the annotation bar, is centered in the Jmol applet so that when the structure is zoomed the turn will become enlarged and visible in the center of the applet. If you want to view the turn in isolation, in the Jmol menu click on 'Select' and choose 'Display Selected Only'. This menu item works as a toogle switch so the complete structure can be turned back on. Run 'calculate hbonds structure' in the lower box of the Jmol console displays all the hbonds involved in the secondary structures. Use end note to open glycogen phosphorylase chain A.^[7]