Secondary structure
From Proteopedia
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==How Jmol Determines Secondary Structure== | ==How Jmol Determines Secondary Structure== | ||
===From PDB files=== | ===From PDB files=== | ||
| - | [[PDB files]] usually contain HELIX and SHEET records, in their headers. These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix. | + | [[PDB files]] usually contain HELIX and SHEET records, in their headers. (Many PDB files used to contain TURN records, but in revision 3.2 of the [[PDB files|PDB data format]], TURN records were abolished.) These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix. |
Jmol's standard color scheme for secondary structure (see [[Help:Color_Keys]]): | Jmol's standard color scheme for secondary structure (see [[Help:Color_Keys]]): | ||
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===Jmol's objective calculation=== | ===Jmol's objective calculation=== | ||
| - | When the PDB file lacks HELIX and SHEET records | + | When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. '[[Calculate structure]]' is the Jmol command which does this re-determination. The complete script required to display the ''Secondary Structure'' color scheme and hydrogen bonds (hbonds) contained in the secondary structures is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'. At the present time 'calculate hbonds structure' messes up the post-processing by Proteopedia, and any scene whose script contains this command is not displayed. The above scenes which colors the helices, sheets and turns without displaying the hbonds were constructed using only 'select protein; calculate structure; cartoon; color structure'. If 'calculate hbonds strucutre' is run through the Jmol console as described below, the hbonds in these three types of structures will be displayed. |
<blockquote> | <blockquote> | ||
| - | + | Hbonds in secondary structures can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the command: <span style='background-color:yellow;'>calculate hbonds structure</span> | |
| - | <span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> | + | and then clicking ''Run''.</blockquote> |
| - | + | <blockquote> | |
| + | If a Proteopedia page does not contain the more detailed ''Secondary Structure'' information, it can be displayed by running the script: | ||
| + | <span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> in the Jmol console as described above. | ||
</blockquote> | </blockquote> | ||
| + | See [[Calculate structure]] for more details. | ||
===Examples=== | ===Examples=== | ||
If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the <font color=#FF0080>'''alpha helices'''</font> being displayed the <font color=#A00080>'''3<sub>10</sub> helices'''</font> and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed above, all four chains will be initially displayed, but clicking the ''domain 2 of glycogen phosphorylase'' green link (above) will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]]. | If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the <font color=#FF0080>'''alpha helices'''</font> being displayed the <font color=#A00080>'''3<sub>10</sub> helices'''</font> and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed above, all four chains will be initially displayed, but clicking the ''domain 2 of glycogen phosphorylase'' green link (above) will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]]. | ||
Revision as of 23:54, 20 June 2012
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Secondary structure of a protein refers to the three-dimensional structure of local segments of a protein. Each type of secondary structure has segments that have a repeating conformational pattern which is produced by a repeating pattern of values for the phi and psi torsional angles. For this reason, on a Ramachandran plot, the values for phi and psi are located at a particular area of the plot for each secondary structure.
There are three common secondary structures - helices, β-pleated sheets and turns, and there are several variations of each one of them.
- Helices. Alpha helix, pi helix and 310 helix are the three types of helices with the alpha helix being the most important. The characteristics of these three helices are given at Helices in Proteins. Jmol colors them alpha helix, 310 helix and pi helix as shown in Helices in Proteins.
- Strands. The strands making up the sheets can be parallel or antiparallel and the pleats in the sheet can be twisted as well as being parallel. These structural differences and other characteristics of β-sheets can be seen at Sheets in Proteins.
- Turns. β-turn and γ-turn are the two types of turns. β-turns are composed of four amino acids and can have several difference conformations. γ-turns are made up of only three amino acids and are therefore a much tighter turn. More detail and illustrations of these turns are at Turns in Proteins.
The structure of a human transferrin n-lobe mutant (PDB code 1dtg) is shown in cartoon and colored structure to highlight its secondary structure, with alpha-helices in magenta and beta-sheets in yellow. Another example is (PDB code 1abb).
Contents |
How Jmol Determines Secondary Structure
From PDB files
PDB files usually contain HELIX and SHEET records, in their headers. (Many PDB files used to contain TURN records, but in revision 3.2 of the PDB data format, TURN records were abolished.) These represent the authors' determinations, and when present, Jmol obeys them (see secondary structure colors). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix.
Jmol's standard color scheme for secondary structure (see Help:Color_Keys):
Alpha Helices, Beta Strands , Turns.
Jmol's objective calculation
When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol command language, you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. 'Calculate structure' is the Jmol command which does this re-determination. The complete script required to display the Secondary Structure color scheme and hydrogen bonds (hbonds) contained in the secondary structures is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'. At the present time 'calculate hbonds structure' messes up the post-processing by Proteopedia, and any scene whose script contains this command is not displayed. The above scenes which colors the helices, sheets and turns without displaying the hbonds were constructed using only 'select protein; calculate structure; cartoon; color structure'. If 'calculate hbonds strucutre' is run through the Jmol console as described below, the hbonds in these three types of structures will be displayed.
Hbonds in secondary structures can be displayed by clicking on the Jmol frank which opens the main menu, clicking on Console, in the bottom console box entering the command: calculate hbonds structure and then clicking Run.
If a Proteopedia page does not contain the more detailed Secondary Structure information, it can be displayed by running the script: select protein; calculate structure; cartoon; color structure; calculate hbonds structure in the Jmol console as described above.
See Calculate structure for more details.
Examples
If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the alpha helices being displayed the 310 helices and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed above, all four chains will be initially displayed, but clicking the domain 2 of glycogen phosphorylase green link (above) will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at Calculate structure.
See Also
External Resources
- The PSIPRED Protein Structure Prediction Server has a highly accurate method for protein secondary structure prediction for proteins where there is no empirically-determined 3D structure.
Proteopedia Page Contributors and Editors (what is this?)
Wayne Decatur, Karl Oberholser, Eric Martz, Joel L. Sussman, Karsten Theis, Eran Hodis
