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Paper used

This research paper delves into utilizing Star Biochem to analyze the location and structure of the V3 loop region in a study on amino acid chains in HIV gp120 proteins. The methodology also involves BioWorkbench for multiple sequence alignments and examines the secondary structures of different chains. The results and discussions shed light on the insights gained from these analyses.

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Paper used

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Presentation Transcript

  1. Paper used authors

  2. outline • 1 • 2 • 3 • 4 • 5

  3. outline • 1 • 2 • 3 • 4 • 5

  4. outline • 1 • 2 • Usage of Star Biochem to Answer our Question • BioWorkbench used to create multiple sequence alignments • 5

  5. Usage of Star Biochem and to Answer our Question • Star Biochem was used to determine the location and structure of the V3 loop region • ProtParam was considered as a tool to use, however all the variable regions were determined to be coils so therefore was not necessary

  6. gp120 Secondary Structure Using Star Biochem Kwong et. al V3 region

  7. V3 region Secondary Structure Stanfield et. al 1F58 313-325 2F58 315-324 1NAK 312-323

  8. Stanfield et. al 2ndary Structure not useful in our examination of Markham data • Stanfield data composed of 12-14 amino acid chains • Markham data composed of 94-95 amino acid chains

  9. BioWorkbench used to create multiple sequence alignments • Each rapid progressor subject had a clone randomly chosen from their first and last visit • Control subjects had one clone randomly selected from last visit. • Each rapid progressor had their two sequences aligned • Control subjects were aligned with each other • All rapid progressor last visits were aligned with and without a control sequence

  10. ClustalW Multiple Sequence Alignment Results Single Subject Alignments Multiple Subject Alignments

  11. outline • 1 • 2 • 3 • 4 • 5

  12. outline • 1 • 2 • 3 • 4 • 5

  13. Background

  14. Question

  15. Methods/results

  16. Answers

  17. Discussion

  18. Further Questions

  19. Acknowledgements

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