Chris Rhodes Week 6

Star Biochem: Questions and Answers

The specific methods used in this experiment are detailed here

Star Biochem Site -> Start: Star Biochem will download and open on the computer -> Samples -> DNA glycolase hOGG1 w/DNA

1. Can you identify the DNA and the HOGG! protein in the structure? Where is the DNA segment? -> The DNA is circled in black and the Protein structure is circled in Red
2. Identify the name and sequence number of one the amino acids that contains a sulfur atom. Is the sulfur atom in the backbone or sidechain? :[CYS] 241:A SG #2406, Sidechain
3. List the 13 amino acids numbered 105-117: Threonine, Leucine, Alanine, Glutamine, Leucine, Tyrosine, Histidine, Histidine, Tryptophan, Glycine, Serine, Valine, Aspartic Acid
4. Are there helices, sheets, or coils present in hOGG1? What secondary structure do amino acids 105-117 fold into?-> Yes shown below, pink represents helices, yellow represents sheets, and blue represents coils. 105-117 Fold in a helix
5. Are the negatively charged amino acids located on the inside or outside of the protein? What does this suggest about the environment the protein is in? The negatively charged amino acids are the on the outside of the protein structure indicating that the protein will most likely make hydrogen bonds meaning its environment is hydrophilic.
6. How many base pairs can you count within the double helix? How many base pairs are unpaired? Is the oxidized guanine paired or unpaired? -> 14 base pairs, only 1 is unpaired, the oxidized guanine is the unpaired base, its position is shown here ->
   • Note: Adjusting the size sliders in the nucleic acid tab caused the program to freeze. The values and screenshots taken for the above question were created through the use of size and transparency sliders of the Proteins, Primary tab instead. Though not shown, the oxidized guanine was found on the outside of the DNA double helix and imbedded in the hOGG1 protein complex. This suggests that hGGO1 is capable of detecting any damaged base pairs that cause the base to flip to the outside of the double helix backbone.
7. Is helix 1 or 16 more likely to recognize damaged guanine bases? -> Given the positions of helix 1, 16 and the oxidized guanine shown below, it would seem that helix 16 is far more likely to recognize the oxidized guanine. Helix 16 is within a reasonable proximity to the oxidized guanine where as helix 1 is located at the outer edge of the protein complex and most likely serves only a structural purpose.
   • By visualizing the two helices based on their side chain interactions we can see that helix 16 is actually interacting with the oxidized guanine where as, again, helix 1's position removes any possibility of direct interaction.
   • Note: Again, since adjusting the nucleic acid sliders caused the program to freeze the screenshots taken used only the Protein Primary tab sliders.

CN3D: Questions and Answers

Cn3D can be downloaded here

The DNA Glycosylase hOGG1 structure file can be found here To download click the "Download Cn3D" button on the page.

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