Secondary structure: Difference between revisions
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[[PDB files]] usually contain HELIX, SHEET, and sometimes contain TURN 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, SHEET, and sometimes contain TURN 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. | ||
When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria | 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. ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. You must permit the signed version of Jmol to open in order to use ver. 12. The signed ver. has a red frank whereas the unsigned is grey. Open the Jmole console (Right click the Jmol frank and select Console.), enter into the lower box the commands: select protein; calculate structure; cartoon; color structure and then click run. | ||
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. ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. You must permit the signed version of Jmol to open in order to use ver. 12. The signed ver. has a red frank whereas the unsigned is grey. Open the Jmole console (Right click the Jmol frank and select Console.), enter into the lower box the commands: select protein; calculate structure; cartoon; color structure and then click run. | |||
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, all four chains will be initially displayed but clicking the 'domain 2 of glycogen phosphorylase' green link 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, all four chains will be initially displayed but clicking the 'domain 2 of glycogen phosphorylase' green link 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]]. | ||
== External Links == | == External Links == | ||
For more information | For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | ||
Revision as of 21:25, 27 June 2011
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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).
How Jmol Determines Secondary StructureHow Jmol Determines Secondary Structure
PDB files usually contain HELIX, SHEET, and sometimes contain TURN records, in their headers. 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.
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. This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the Jmol/Application (version 12). You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. You must permit the signed version of Jmol to open in order to use ver. 12. The signed ver. has a red frank whereas the unsigned is grey. Open the Jmole console (Right click the Jmol frank and select Console.), enter into the lower box the commands: select protein; calculate structure; cartoon; color structure and then click run.
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, all four chains will be initially displayed but clicking the 'domain 2 of glycogen phosphorylase' green link 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.
External LinksExternal Links
For more information, see Wikipedia's page on secondary structure.