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<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 1 - Protein structure''' ==
<StructureSection load="HORF6.pdb" size="500" color="white" frame="true" align="right" caption="hORF6 (PDB ID=1PRX)" />


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It can help to see the  
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_3/1'>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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'''Q6: How many α-helices are there in this protein?'''
'''Q7: How many α-helices are there in this protein?'''


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'''Q7: How many β-strands make up the β-sheet?'''
'''Q8: How many β-strands make up the β-sheet?'''


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'''Q8: Is the topology of the β-sheet parallel, anti-parallel or mixed?'''
'''Q9: Is the topology of the β-sheet parallel, anti-parallel or mixed?'''


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Use the Henderson-Hasselbach equation to answer the questions below.  
Use the Henderson-Hasselbach equation to answer the questions below.  
(The p<i>K</i><sub>a</sub> of the –SH group of free cysteine is 8.5. The cytosol of human cells is normally at pH 7.3. The p<i>K</i><sub>a</sub> of the active site cysteine in a 1-Cys Prx enzyme has been measured at 6.0.)
(The p<i>K</i><sub>a</sub> of the –SH group of free cysteine is 8.35. The cytosol of human cells is normally at pH 7.35 The p<i>K</i><sub>a</sub> of the active site cysteine in a 1-Cys Prx enzyme has been measured at 6.2.)


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'''Q9: What would be the % ionization of the –SH group of free cysteine in the cytosol?'''
'''Q10: What would be the % ionization of the –SH group of free cysteine in the cytosol?'''
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'''Q10: What would be the % ionization of the –SH group of the Prx active site cysteine in the cytosol?'''
'''Q11: What would be the % ionization of the –SH group of the Prx active site cysteine in the cytosol?'''
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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.
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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'''Q11: Which residues have side chains close to Cys47? (Hint: try mousing over each of the displayed sidechains to identify them.)'''
'''Q12: Give the name and residue number for each of the amino acid residues that have side chains within 4Å of the sulfur atom in Cys47. (Hint: try mousing over each of the displayed sidechains to identify them.)'''


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'''Q12: What feature of the local environment around Cys74 might stabilize the existence of a thiolate ion?'''
'''Q13: What feature of the local environment around Cys47 might stabilize the existence of a thiolate ion?'''


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