Secondary structure: Difference between revisions
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<applet load='1dtg' size='400' frame='true' align='right' caption='' scene='Secondary_structure/1dtg_ss/ | <applet load='1dtg' size='400' frame='true' align='right' caption='' scene='Secondary_structure/1dtg_ss/6'/>__NOTOC__ | ||
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 [[Psi and Phi Angles|phi and psi torsional angles]]. For this reason, on a [[Ramachandran Plots|Ramachandran plot]], the values for phi and psi are located at a particular area of the plot for each secondary structure. | 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 [[Psi and Phi Angles|phi and psi torsional angles]]. For this reason, on a [[Ramachandran Plots|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. | 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 3<sub>10</sub> 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 < | *'''Helices'''. [[Alpha helix]], pi helix and 3<sub>10</sub> 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 <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</span> and <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> 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]]. | *'''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]]. | *'''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]]. | ||
{{Clear}} | {{Clear}} | ||
<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center> | <table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center><scene name='Secondary_structure/1dtg_ss/6'> Initial scene</scene> '''for Secondary Structures of Sample Proteins''' </center></td></tr></table> | ||
{{Clear}} | {{Clear}} | ||
The structure of a human transferrin n-lobe mutant (PDB code [[1dtg]]) shows the presence of <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helices</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helices</span>, <span style="color:yellow;background-color:black;font-weight:bold;">beta-sheets</span>, and <span style="color:#6080FF;background-color:white;font-weight:bold;">beta-turns</span>. <jmol> | |||
<jmolLink> | |||
<script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt; | |||
set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein|as small spheres connected by sticks..."; | |||
delay 4.0; | |||
echo "Next hide all but the backbone atoms|keeping the connections shown..."; | |||
select protein and sidechain; | |||
var a = [1,2,3,4,5,6,7,8]; for(var i IN a) {color translucent @i; delay 0.4;}; | |||
delay 4.0; | |||
echo "The repeating patterns of the secondary structure|elements are starting to be noticeable."; | |||
delay 3.0; | |||
select protein; | |||
echo "To help with observing the patterns,|a tube tracing the backbone is revealed. "; | |||
var b = [0.01,0.05,0.1,0.2,0.3,0.4,0.45,0.5, 0.55]; for(var j IN b) {trace @j; delay 0.4;}; | |||
echo "And fade out the spheres and stick backbone.. "; | |||
var c = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var k IN c) {spacefill @k; wireframe @k; delay 0.4;}; | |||
wireframe off; spacefill off; | |||
echo "Finally fade in typical representation and|coloring of the secondary structure. "; | |||
color cartoon structure; | |||
var d = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var m IN d) { var n = 0.56 - m;cartoon @n; color cartoon translucent @n; trace @m; delay 0.4;}; | |||
trace off; delay 0.15; color cartoon translucent 0; cartoon on; | |||
</script> | |||
<text>A progression from all atoms to cartoon</text> | |||
</jmolLink> | |||
</jmol> illustrates the relationship of the protein backbone to the secondary structure representation. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures. | |||
==Displaying Secondary Structure== | |||
If you want a convenient, static view of the structurally-determined [[Secondary structure|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure''' will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right. The '''secondary structure''' will also be illustrated above the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank]. | |||
Many structures displayed on Proteopedia's PDB entry pages default to the cartoon view showing alpha helices and beta-sheets. If you need to see the secondary structure represented within the structure for any Proteopedia structure window, even or any [[Jmol]] view, ''click on the Jmol frank,'' and navigate the menu that comes up to first first ''Select'' --> ''All'' and then turn on the cartoons (''Style''--->''Scheme''--->''cartoon'') and then for added help color this cartoon representation by the scheme outlined in the next section below ( ''Color''--> ''Structures'''--> ''Cartoon'' ---> ''By Scheme'' -->''Secondary Structure'') . For advanced users, this is more easily accomplished by way of Jmol commands in the console, ''select all; cartoon on, color structure''. | |||
Alternatively, use [[Scene authoring tools|Proteopedia's Scene Authoring Tools]] to display a structure as ''cartoon'' by selecting ''cartoon'' on the representation tab and then the ''color by structure'' button under the color tab. | |||
==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]]): | ||
| Line 27: | Line 59: | ||
===Jmol's objective calculation=== | ===Jmol's objective calculation=== | ||
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. | 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 commands: <span style='background-color:yellow;'>select protein; calculate hbonds structure</span> | |||
< | and then clicking ''Run''.</blockquote> | ||
select protein; calculate structure | |||
</ | <blockquote> | ||
and then | 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> | ||
More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]]. | |||
== See Also == | == See Also == | ||
* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching) | |||
* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación) | |||
* [[Backbone representations]] explains backbone traces, smoothed traces, and ribbons ("cartoon" in JSmol). | |||
* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | * [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | ||
* [[Calculate structure]] | * [[Calculate structure]] | ||
* [[Membrane proteins]] | * [[Membrane proteins]] | ||
* [[Help:Color Keys]] | * [[Help:Color Keys]] | ||
* [[Basics of Protein Structure]] | |||
==External Resources== | ==External Resources== | ||
* [http://bioinf.cs.ucl.ac.uk/psipred/ 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. | * [http://bioinf.cs.ucl.ac.uk/psipred/ 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. | ||
Latest revision as of 12:10, 31 January 2020
|
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) shows the presence of alpha helices, 310 helices, beta-sheets, and beta-turns. illustrates the relationship of the protein backbone to the secondary structure representation. Another example, (PDB code 1abb), contains a pi helix in addition to the above structures.
Displaying Secondary StructureDisplaying Secondary Structure
If you want a convenient, static view of the structurally-determined secondary structure, or alternatively the secondary structure topology or wiring diagram, click on PDBsum below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the Contents listing on left side of the main PDBsum page. The secondary structure will be illustrated above the sequence in the main view with the secondary structure topology or wiring diagram accessible on the right. The secondary structure will also be illustrated above the sequence in the main view accessible under the Sequence tab at the Protein Data Bank.
Many structures displayed on Proteopedia's PDB entry pages default to the cartoon view showing alpha helices and beta-sheets. If you need to see the secondary structure represented within the structure for any Proteopedia structure window, even or any Jmol view, click on the Jmol frank, and navigate the menu that comes up to first first Select --> All and then turn on the cartoons (Style--->Scheme--->cartoon) and then for added help color this cartoon representation by the scheme outlined in the next section below ( Color--> Structures'--> Cartoon ---> By Scheme -->Secondary Structure) . For advanced users, this is more easily accomplished by way of Jmol commands in the console, select all; cartoon on, color structure.
Alternatively, use Proteopedia's Scene Authoring Tools to display a structure as cartoon by selecting cartoon on the representation tab and then the color by structure button under the color tab.
How Jmol Determines Secondary StructureHow Jmol Determines Secondary Structure
From PDB filesFrom 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 calculationJmol'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 commands: select protein; 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.
More detail on how calculate structure determines helices, strands and turns is at Calculate structure.
See AlsoSee Also
- Protein primary, secondary, tertiary and quaternary structure (slides for teaching)
- Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas (en formato de presentación)
- Backbone representations explains backbone traces, smoothed traces, and ribbons ("cartoon" in JSmol).
- Wikipedia's page on secondary structure.
- Calculate structure
- Membrane proteins
- Help:Color Keys
- Basics of Protein Structure
External ResourcesExternal 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.