Matthew K. Oki Individual Journal 9

Week 9 Individual Journal

Methods & Results

1. Convert DNA Sequences to protein sequences in ExPASY Translate tool
   • Below is an example of the output of the DNA to protein sequence conversion. They are separated into six reading frames.

1. • How do you know which of the six frames is the correct reading frame (without looking up the answer)?
     • We knew the correct reading frame was the one that had a sequence with no stop codon in the entire frame.
2. Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgebase (UniProt KB).
   • If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
     • There are 206,278 results
   • Entry P04578 was looked up and observed. What types of information are provided about this protein?
     • Function, taxonomy, location on the subcellular level, pathology, processing, interaction, family and domain, sequence, cross-references, and miscellaneous information are all provided on this protein page.
3. PredictProtein server was used to analyze only the V3 region of the Markham et al. (1998) sequences.
   • • An amino acid sequence from Markham et al. (1998) was placed in the database and analyzed.
   • How does this information relate to what is stored in the UniProt database?
     • This was an interesting figure because it described possible binding sites, bond locations, and secondary structure locations. It also links back to the UniProt database for certain target alignments.
4. Protein Structure from Kwong et al. (1998) was downloaded and opened in Cn3D software site. The picture of the result is posted below

• Find the N-terminus and C-terminus of each polypeptide tertiary structure.
  • Each terminus of each polypeptide was found by looking for the ends of each polypeptide. By using the coloring shortcuts, this process of finding the ends was sped up.
• Locate all the secondary structure elements. Does this match the predictions made by the PredictProtein server?
  • The PredictProtein server gave us a prediction of two helices and six beta sheets. This was seen exactly in the Cn3D program rendering of the Kwong et al. (1998) structure.
• Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.

Data & Files

• There were no data and files used in this project.

Scientific Conclusion

The different programs used during this weeks project allowed me to gain a different perspective on protein sequences as a whole. The ExPASY Translate tool allowed us to change DNA sequence into a protein sequence in a matter of seconds. Here, the importance of reading frames was shown.

Defining Our Research Project

• Our Question:
• Our Prediction:
• Which subjects, visits, and clones will you use to answer your question?

Acknowledgments

• I would like to thank my partner, William P. Fuchs, for the assistance on this week's project, both in assistance on the structure program methods in class and completion of the our project idea outside of class.
• I would also like to thank Kam D. Dahlquist, Ph.D. for providing the instructions and information for this assignment both in class and on this document: BIOL368/F16:Week 9.
• Even though I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
• Matthew K. Oki 21:38, 25 October 2016 (EDT):

References

1. BIOL368/F16:Week 9
2. ExPASY Translate tool
3. UniProt Knowledgebase (UniProt KB)
4. PredictProtein server
5. Cn3D software site
6. Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568

Class Homework Links

Weekly Assignments

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 14 Week 15

Individual Journals

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 14 Week 15

Class Journals

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 14 Week 15

Other Links

My Home Page: Matthew K. Oki

Class Home Page: Bioinformatics Home Page

My Paper Resume: Matthew K. Oki Resume