BIOL368/F14:Nicole Anguiano Week 6

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Star Biochem DNA Glycosylase Exercise

Methods and Results

  • First, I downloaded Star BioChem, and began following the instructions from the DNA Glycosylase Exercise worksheet.
  • I selected the “DNA glycosylase hOGG1 w/ DNA – H. sapiens (1EBM)” protein from the Samples > Select from Samples menu. I changed the size of the atoms from 20 to 100 to view the protein as a space-filling model.
hOGG1 space filling model. The DNA is easily visible.
Figure 1: The space-filling model of DNA Glycosylase. Note the smaller, less-visible DNA displayed as a ball and stick model.
  • Next, I pointed to a sulfur atom in the hOGG1 structure to obtain information about it.
A sulfur atom in hOGG1.
Figure 2: This sulfur atom is part of cysteine at position 241.
  • I selected View > View Specific Regions / Set Center of Rotation, then selected the amino acid in Figure 2. I moved the VDW Radius slider to 1 and unchecked the side-chain box. I observed that the sulfur atom disappeared. I checked the side-chain box and unchecked the backbone box. The sulfur atom remained. From there, I deduced that the Sulfur atom is a part of the side-chain.
The sulfur side-chain in hOGG1.
Figure 3: The position of the sulfur atom at amino acid 241. As the "backbone" box is unchecked and the atom is still visible, it can be deduced that it is in the side-chain.
  • I reset the structure by selecting Reset > Reset structure in the top menu, then scrolled down and found amino acids 105-117.
Number Amino Acid
105 Threonine (Thr)
106 Leucine (Leu)
107 Alanine (Ala)
108 Glutamine (Gln)
109 Leucine (Leu)
110 Tyrosine (Tyr)
111 Histidine (His)
112 Histidine (His)
113 Tryptophan (Trp)
114 Glycine (Gly)
115 Serine (Ser)
116 Valine (Val)
117 Aspartic Acid (Asp)
  • Table 1: The identity of amino acids number 105 to 117.
  • I clicked on the secondary tab and selected "all" to view all of the different structures (helices, coils, and sheets). I moved the Structures Size slider to the right to make them larger. I selected View > View Specific Regions / Set Center of Rotation, and selected amino acids 105 to 117 by clicking on amino acid 105, holding Shift, then clicking on amino acid 117. I moved the VDM Radius slider to 1 so that I could just see the selected amino acids.
An alpha helix created by amino acids 105-117.
Figure 4: The alpha helix formed by amino acids 105 to 117.

Questions

  1. The hOGG1 structure contains both DNA and protein. Can you differentiate between the DNA and protein components? How did you distinguish the DNA from the protein?
    • It is possible to differentiate between the DNA and protein components. The hOGG1 structure's proteins are displayed in the space-filling form, but the DNA is still visible in the ball and stick model (Fig. 1). Therefore, the DNA appears much smaller and thinner than the protein, making it easily distinguishable from the protein.
  2. hOGG1 contains multiple sulfur atoms.
    1. Identify the name and sequence number of one of the amino acids in the structure that contains a sulfur atom.
      • The sulfur atom in figure 2 is part of cysteine at position 241.
    2. Is the sulfur atom located in the backbone or in the side chain of the amino acid?
      • The sulfur atom is located in the side chain of the amino acid (Fig. 3).
  3. List the 13 amino acids numbered 105 through 117 in order.
    • See table 1.
  4. Within a protein chain, amino acids form local structures called secondary structures.
    1. Are helices, sheets or coils present in hOGG1? Describe the color that represents the secondary structures you observe.
      • Helices, sheets, and coils are all present in hOGG1. Helices are colored pink, sheets are colored yellow-orange, and coils are colored a darker blue-purple color.
    2. Amino acids 105 through 117 fold into one of the secondary structures. Which secondary structure do they fold into?
      • Amino acids 105-107 fold into an alpha helix (Fig. 4).

Cn3D Exercise

Methods and Results

Questions

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Nicole Anguiano
BIOL 368, Fall 2014

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