Ryan N. Willhite Week 9

Week 9 Work Day

 * Notes/brainstorming


 * 1) Bedrock
 * Retrieving sequences from those compared in HIV Evolution Project.
 * Amino acid sequences instead of nucleic
 * Viewing subjects 5,6,7,10, and 13.


 * 1) 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.


 * Questions


 * 1) ORFing allows one to go from DNA sequences to proteins sequences.
 * www.ncbi.nlm.nih.gov/gorf/gorf.html


 * 1) Possible experiments and tools
 * ProtParam
 * 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



Comments/Notes

 * 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.

ProtParam

 * 1) Compare Subjects 5/6/7/10
 * 2) www.expasy.org/tools/#primary
 * 3) ProtParam tools
 * 4) Entered amino acid sequences

Results

 * 1) Subject 5


 * [[Image:Subject5.png]]


 * 1) Subject 6


 * [[Image:Subject6.png]]


 * 1) Subject  7


 * [[Image:Subject7.png]]


 * 1) Subject 10


 * [[Image:Subject10.png]]

Comments

 * 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.

Paper/ppt

 * 1) Paper1 pmid=18215327

[[Media:Hivproteinstructure.ppt|Powerpoint]]