User:J. Shaun Lott/BIOSCI 203: Difference between revisions

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On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>

==Your Heading Here (maybe something like 'Structure')==

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

</StructureSection>On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>

The [http://www.rcsb.org/pdb/explore/explore.do?structureId=1PRX protein][http://www.proteopedia.org/wiki/index.php/1prx structure] we will be looking at in this part of the lab is the N-terminal domain of the human 1-Cys peroxidase enzyme [http://www.nature.com.ezproxy.auckland.ac.nz/nsmb/journal/v5/n5/abs/nsb0598-400.html hORF6]. Click

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It can help to see the

<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/3'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/2'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram. If we view the bonds in the protein in stick format, showing just the <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds_3/2'>backbone atoms</scene>, we can easily see the backbone H-bond patterns that are distinctive for α-helices and β-sheets.

<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/3'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/2'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram.

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~~<applet load="HORF6.pdb" size="500" color="white" frame="true" align="left" caption="Active site of hORF6 (PDB ID=1PRX)" />~~

Now let’s look more closely at the hORF structure to see if we can identify what local features of the protein structure may influence the ability of the active site cysteine to ionize.

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-On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>
+==Your Heading Here (maybe something like 'Structure')==
+<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
+Anything in this section will appear adjacent to the 3D structure and will be scrollable.
+</StructureSection>On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>
 The [http://www.rcsb.org/pdb/explore/explore.do?structureId=1PRX protein][http://www.proteopedia.org/wiki/index.php/1prx structure] we will be looking at in this part of the lab is the N-terminal domain of the human 1-Cys peroxidase enzyme [http://www.nature.com.ezproxy.auckland.ac.nz/nsmb/journal/v5/n5/abs/nsb0598-400.html hORF6]. Click
@@ Line 16: / Line 21: @@
 It can help to see the
-<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/3'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a  <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/2'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram. If we view the bonds in the protein in stick format, showing just the <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds_3/2'>backbone atoms</scene>, we can easily see the backbone H-bond patterns that are distinctive for α-helices and β-sheets.
+<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/3'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a  <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/2'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram.
@@ Line 47: / Line 52: @@
 ----
-<applet load="HORF6.pdb" size="500" color="white" frame="true" align="left" caption="Active site of hORF6 (PDB ID=1PRX)" />
 Now let’s look more closely at the hORF structure to see if we can identify what local features of the protein structure may influence the ability of the active site cysteine to ionize.