Secondary structure: Difference between revisions
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<applet load='1dtg' size='400' frame='true' align='right' caption=' | <applet load='1dtg' size='400' frame='true' align='right' caption='' scene='Cartoon_backbone_representation/1dtg_ss/1'/> | ||
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]] for a particular secondary structure the values for phi and psi are located at a particular area of the plot. There are three important second structures - helix, β-pleated sheets and turns, and there are several variations of each one of them. 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 has a standard of coloring them <font color=#FF0080>alpha helix</font>, <font color=#A00080>3<sub>10</sub> helix</font> and <font color=#600080>pi helix</font> as shown in [[Helices in Proteins]]. 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]]. 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 on the right of a human transferrin n-lobe mutant (PDB code [[1dtg]]) is shown in cartoon backbone representation to highlight its secondary structure, with alpha-helices in magenta and beta-sheets in yellow. Another example is <scene name='Secondary_structure/Gly_phosphyl/1'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]). (When Proteopedia is upgraded to run in Jmol ver. 12, other types of helices in addition to α-helices as well as a large number of β-turns will be shown in these two examples.) | 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]] for a particular secondary structure the values for phi and psi are located at a particular area of the plot. There are three important second structures - helix, β-pleated sheets and turns, and there are several variations of each one of them. 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 has a standard of coloring them <font color=#FF0080>alpha helix</font>, <font color=#A00080>3<sub>10</sub> helix</font> and <font color=#600080>pi helix</font> as shown in [[Helices in Proteins]]. 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]]. 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 on the right of a human transferrin n-lobe mutant (PDB code [[1dtg]]) is shown in cartoon backbone representation to highlight its secondary structure, with alpha-helices in magenta and beta-sheets in yellow. Another example is <scene name='Secondary_structure/Gly_phosphyl/1'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]). (When Proteopedia is upgraded to run in Jmol ver. 12, other types of helices in addition to α-helices as well as a large number of β-turns will be shown in these two examples.) | ||
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<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Secondary Structures of Examples'''<scene name='Cartoon_backbone_representation/1dtg_ss/1'> (Initial scene)</scene></center></td></tr></table> | |||
== External Links == | == External Links == | ||
For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | ||
Revision as of 19:17, 15 February 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 for a particular secondary structure the values for phi and psi are located at a particular area of the plot. There are three important second structures - helix, β-pleated sheets and turns, and there are several variations of each one of them. 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 has a standard of coloring them alpha helix, 310 helix and pi helix as shown in Helices in Proteins. 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. 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 on the right of a human transferrin n-lobe mutant (PDB code 1dtg) is shown in cartoon backbone representation to highlight its secondary structure, with alpha-helices in magenta and beta-sheets in yellow. Another example is (PDB code 1abb). (When Proteopedia is upgraded to run in Jmol ver. 12, other types of helices in addition to α-helices as well as a large number of β-turns will be shown in these two examples.)
External LinksExternal Links
For more information, see Wikipedia's page on secondary structure.