Chris Rhodes Week 6: Difference between revisions
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[http://mit.edu/star/biochem/ Star Biochem Site] -> Start: Star Biochem will download and open on the computer -> Samples -> DNA glycolase hOGG1 w/DNA | [http://mit.edu/star/biochem/ Star Biochem Site] -> Start: Star Biochem will download and open on the computer -> Samples -> DNA glycolase hOGG1 w/DNA | ||
#Can you identify the DNA and the | #Can you identify the DNA and the hOGG1 protein in the structure? Where is the DNA segment? -> The DNA is circled in black and the Protein structure is circled in Red [[Image:CHR_Image1_20111005.png]] | ||
#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 | #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 | ||
#List the 13 amino acids numbered 105-117: Threonine, Leucine, Alanine, Glutamine, Leucine, Tyrosine, Histidine, Histidine, Tryptophan, Glycine, Serine, Valine, Aspartic Acid | #List the 13 amino acids numbered 105-117: Threonine, Leucine, Alanine, Glutamine, Leucine, Tyrosine, Histidine, Histidine, Tryptophan, Glycine, Serine, Valine, Aspartic Acid | ||
# 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. [[Image:CHR_Image_20111005.png]] [[Image:CHR_Image3_20111005.png]] 105-117 Fold in a helix | # 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. [[Image:CHR_Image_20111005.png]] [[Image:CHR_Image3_20111005.png]] 105-117 Fold in a helix | ||
#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? | #Are the negatively charged or acidic amino acids located on the inside or outside of the protein? What does this suggest about the environment the protein is found 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.[[Image:CHR_Image4_20111005.png]] | ||
# 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 below [[Image:CHR_Image5_20111005.png]] | # 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 below [[Image:CHR_Image5_20111005.png]] | ||
#*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. | #*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. | ||
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The DNA Glycosylase hOGG1 structure file can be found [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=71948 here] To download click the "View Structure" button on the page. | The DNA Glycosylase hOGG1 structure file can be found [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=71948 here] To download click the "View Structure" button on the page. | ||
#Is this structure Tertiary or Quaternary? -> Since the projection shows not only the protein structure but also the heme groups incorporated in the protein it is showing interaction of subunits and is therefore a Quaternary structure. | |||
#How many domains does DNA glycosylase? Explain. -> DNA Glycosylase seems to have 4 domains. The Cn3D program provides a list of the four different domains and allows you to highlight each individual domain shown below [[Image:CHR_Image1_20111007.png]] | |||
#Can you view the same things in the structure using this program as you did when you were using Star Biochem? -> Using Cn3D does allow you to see most of the same things as you can see in Star Biochem such as Hydrophobicity, Ball and Stick, and Space Filling models however usually in less detail. In some respects, Cn3D is easier to use than Star Biochem as it allows for easier visualization of the domains, protein sequences, and, through the use of the domain sequence panel, the individual proteins that fall into a chosen category.Cn3D also allows you to highlight and visualize select amino acids in the protein without having to make the rest of the protein structure invisible as Star Biochem requires. Cn3D however, does not offer as much versatility as Star Biochem and is not as capable of performing more detailed alterations and selections of amino acids by their characteristics or categories. All in all I would say that Cn3D is an easy to use program for the basic visualization of a protein's structure and characteristics and would be well suited to beginners or those that only require simple analysis, while Star Biochem is more complex and difficult to navigate but provides a more advanced and versatile tool capable of more detailed and more specific visualizations of a protein and it's characteristics, which would be more suited to advanced users who require the vast list of analytical tools that Star Biochem offers. | |||
#This is the closest I could get to a similar image between Cn3D and Star Biochem. It was based off of the structure of the protein circled in red in the rendering used in Question 1 of the Star Biochem exercise. I used the outer side chains as improvised points of reference and rendered the Cn3D image in Ball and Stick format to be more similar to the Star Biochem layout though it is still difficult to see the similarities due to the absence of the DNA strand in the Cn3D image file. [[Image:CHR_Image2_20111007.png]][[Image:CHR_Image3_20111007.png]] | |||
# Which program would you prefer to use? -> As I mentioned in Question 3, the two programs have their own distinct advantages depending on what needs to be accomplished. The program that I would prefer to use would depend on the depth of analysis that is required for my experiment. If it is possible that I only need to visualize the general structure, domains, protein sequence, charge, or hydrophobicity then Cn3D would be far easier to use than would Star Biochem. However, if more detailed analysis or more complex visualizations were required then Star Biochem would be my program of choice as it offers more options and selection specificity than does Cn3D. | |||
==Links== | ==Links== | ||
{{Chris H. Rhodes}} | {{Chris H. Rhodes}} | ||
Latest revision as of 16:04, 7 October 2011
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
- Can you identify the DNA and the hOGG1 protein in the structure? Where is the DNA segment? -> The DNA is circled in black and the Protein structure is circled in Red
- 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
- List the 13 amino acids numbered 105-117: Threonine, Leucine, Alanine, Glutamine, Leucine, Tyrosine, Histidine, Histidine, Tryptophan, Glycine, Serine, Valine, Aspartic Acid
- 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 - Are the negatively charged or acidic amino acids located on the inside or outside of the protein? What does this suggest about the environment the protein is found 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.
- 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 below
- 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.
- 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.
- 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.
CN3D: Questions and Answers
Cn3D can be downloaded here
The DNA Glycosylase hOGG1 structure file can be found here To download click the "View Structure" button on the page.
- Is this structure Tertiary or Quaternary? -> Since the projection shows not only the protein structure but also the heme groups incorporated in the protein it is showing interaction of subunits and is therefore a Quaternary structure.
- How many domains does DNA glycosylase? Explain. -> DNA Glycosylase seems to have 4 domains. The Cn3D program provides a list of the four different domains and allows you to highlight each individual domain shown below
- Can you view the same things in the structure using this program as you did when you were using Star Biochem? -> Using Cn3D does allow you to see most of the same things as you can see in Star Biochem such as Hydrophobicity, Ball and Stick, and Space Filling models however usually in less detail. In some respects, Cn3D is easier to use than Star Biochem as it allows for easier visualization of the domains, protein sequences, and, through the use of the domain sequence panel, the individual proteins that fall into a chosen category.Cn3D also allows you to highlight and visualize select amino acids in the protein without having to make the rest of the protein structure invisible as Star Biochem requires. Cn3D however, does not offer as much versatility as Star Biochem and is not as capable of performing more detailed alterations and selections of amino acids by their characteristics or categories. All in all I would say that Cn3D is an easy to use program for the basic visualization of a protein's structure and characteristics and would be well suited to beginners or those that only require simple analysis, while Star Biochem is more complex and difficult to navigate but provides a more advanced and versatile tool capable of more detailed and more specific visualizations of a protein and it's characteristics, which would be more suited to advanced users who require the vast list of analytical tools that Star Biochem offers.
- This is the closest I could get to a similar image between Cn3D and Star Biochem. It was based off of the structure of the protein circled in red in the rendering used in Question 1 of the Star Biochem exercise. I used the outer side chains as improvised points of reference and rendered the Cn3D image in Ball and Stick format to be more similar to the Star Biochem layout though it is still difficult to see the similarities due to the absence of the DNA strand in the Cn3D image file.
- Which program would you prefer to use? -> As I mentioned in Question 3, the two programs have their own distinct advantages depending on what needs to be accomplished. The program that I would prefer to use would depend on the depth of analysis that is required for my experiment. If it is possible that I only need to visualize the general structure, domains, protein sequence, charge, or hydrophobicity then Cn3D would be far easier to use than would Star Biochem. However, if more detailed analysis or more complex visualizations were required then Star Biochem would be my program of choice as it offers more options and selection specificity than does Cn3D.
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