Ryan N. Willhite Week 9
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Week 9 Work Day
- Retrieving sequences from those compared in HIV Evolution Project.
- Amino acid sequences instead of nucleic
- Viewing subjects 5,6,7,10, and 13.
- Utilizing Protein tools on workbench in order to upload these sequences.
- After uploading, doing a multiple sequence alignment to compare
- Comparisons include: (6-13, 6-5, 13-5, 7-10, 7-5, 10-5)
- If time and interesting data, comparisions will be made between all subjects to cover all areas.
- If enough time, time points will also be looked at in the most interesting of all these sequences in order to determine the changes in structure atthree different time points.
- ORFing allows one to go from DNA sequences to proteins sequences.
- Possible experiments and tools
- Predict the physico-chemical properties of a protein
- Scan Prosite
- analyzing post translational modifications
- retrieving a 3D structure
- Overall, since the DNA sequences failed to give any significant evidence perhaps protein confirmations and information can help provide more information on the categorization of progression.
Mutliple Sequence Alignment Results
- Comparison of Subject 6 and 13
- Comparison of Subject 6 and 5
- Comparison of Subject 13 and 5
- Comparison of Subject 6 and 7
- The trees helped give a visual as the to similarities and differences between these moderate and non- progressors.
- As seen above the non- progressors were quite different than those of the moderate progressors.
- Two moderates being compared were very similar in sequences
- This may suggest that looking at protein sequences are a more efficient way of categorizing.
- This leads to a curiosity in structure
- Structures between moderate subjects such as subject 7. subject 6, and subject 5
- With results suggesting 7 maybe more like a rapid progressor than moderate progressors, these structures will b viewed as well
- Subject 7/10 will be compared, with hopefully similarities that can potentially put 7 in the rapid progressor category according to a similarity in structure.
- Compare Subjects 5/6/7/10
- ProtParam tools
- Entered amino acid sequences
- Subject 5
- Subject 6
- Subject 7
- Subject 10
- The highest percent of amino acids found in the moderates 5,6, and 7 is (Ile)
- THe highest percent of amino acids found in the rapid 10 to compare is (Asn)
- Looking at these compositions along with protein structure seems to be a more efficient way of categorizing progression. The difference in amino acid composition suggests a role in type of progression.
- Paper1 pmid=18215327