User:J. Shaun Lott/BIOSCI 203: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
{{Template:Protected page banner}} | {{Template:Protected page banner}} | ||
<applet load="HORF6.pdb" size="500" color="white" frame="true" align="right" caption="hORF6" /> | <applet load="HORF6.pdb" size="500" color="white" frame="true" align="right" caption="hORF6 (PDB ID=1PRX)" /> | ||
== '''BIOSCI 203 Lab 2 - Protein structure''' == | == '''BIOSCI 203 Lab 2 - Protein structure''' == | ||
| Line 10: | Line 10: | ||
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 ==> | 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 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 | 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 | ||
<scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>here</scene> for an 'all atoms' view of the protein. This will show us all the atoms (except for the hydrogens) coloured by the 'CPK' colour scheme we talked about in lectures - blue for nitrogen atoms, red for oxygen atoms, grey for carbon atoms and yellow for sulfur atoms. Pretty hard to see what's going on, isn't it? | <scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>here</scene> for an 'all atoms' view of the protein. This will show us all the atoms (except for the hydrogens) coloured by the 'CPK' colour scheme we talked about in lectures - blue for nitrogen atoms, red for oxygen atoms, grey for carbon atoms and yellow for sulfur atoms. Pretty hard to see what's going on, isn't it? | ||
| Line 46: | Line 46: | ||
---- | ---- | ||
<applet load="HORF6.pdb" size="500" color="white" frame="true" align="left" caption="Active site" /> | <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. | 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. | ||