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. | ||
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*'''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]]. | ||
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 helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</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>. Another example | 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 helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</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>. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures. | ||
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<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Secondary Structures of Sample Proteins'''<scene name='Secondary_structure/1dtg_ss/6'> (Initial scene)</scene></center></td></tr></table> | |||
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==How Jmol Determines Secondary Structure== | ==How Jmol Determines Secondary Structure== | ||
===From PDB files=== | ===From PDB files=== | ||
