BIOL368/F14:Isabel Gonzaga Week 9

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HIV Structure Project

Defining Your HIV Structure Research Project

This research project will be completed in conjunction with Nicole Anguiano and Chloe Jones.

Question

How does the structure of the V3 protein region affect the HIV status (diagnosed, progressing or non-trending) of the patient?

Hypothesis

We hypothesize that diagnosed groups will express greater variability in the V3 region in their protein structure, in comparison to the non-trending groups. Initial comparisons show that diagnosed groups and progressing groups expressed greater genetic variability than non-trending groups. These changes may affect the third variable region, affecting the host's ability to adapt to the changes and generate sufficient immune response.

Subject Data

According to the BEDROCK HIV Sequence Data Table, I was able to determine which of the subjects used within my study actually developed aids. All 3 AIDS diagnosed were confirmed with the disease by their final visit. In the AIDS progressing groups, subjects developed AIDS within 1 year after their final visit. The Non-Trending groups all maintained high CD4 T Cell Counts above the threshold, even after the study was conducted. Sequences were for each visit and subject were chosen using a Random Integer Generator, to eliminate selection bias.


The following sequences was taken from the BEDROCK HIV Problem Space Database, from the Markham et al. (1998) study.
Table 1: Sequences analyzed

Group Subject Visit Sequences
AIDS Diagnosed 3


10


15		 1
6

1
6

1
4		 1, 2, 4
3, 4, 5

3, 6, 7
2, 4, 8

2, 3, 4
5, 8, 10
AIDS Progressing 7


8


14		 1
5

1
7

1
9		 2, 3, 9
2, 8, 9

1, 4, 5
1, 6, 7

2, 3, 4
9, 10, 11
No Trend 5


6


13		 1
5

1
9

1
5		 1, 3, 8
4, 5, 2

1, 2, 3
6, 7, 9

1, 3, 4
3, 5, 4



Protein sequences for each data set were taken from BEDROCK HIV Problem Space and converted to the following .txt files using word processor programs: [[Media:|AIDS Diagnosed Sequences]], AIDS Progressing Sequences, [[Media:|No Trend Sequences]].
DNA sequences for each data were also taken from BEDROCK HIV Problem Space and converted to the following .txt files: [[Media:|AIDS Diagnosed Sequences]], AIDS Progressing Sequences, [[Media:|No Trend Sequences]].

Multiple Sequence Alignment

ClustalW was performed for each group category from Visit 1 under the Biology Workbench Protein tools. Rootless phylogenetic trees were analyzed, and the multiple sequence alignment was conducted. This alignment was used to determine diversity within each category at each amino acid residue. ClustalW was also performed for each group category from the final visit.

Multiple Sequence alignment was also used to compare differences between amino acid sequences and DNA sequences. The DNA sequences for each clone was uploaded onto Biology Workbench under the 'nucleic tools' tab. ClustalW was performed for each group category three times: for visit 1, final visit and both visits combined.

There seem to be fewer differences between the amino acid sequences compared to the DNA sequences. This is likely due to the redundancy of the degenerate genetic code (ie. different combinations of DNA sequences form different codons that code for the same amino acid residue).

Analysis of V3 Structure

Huang et al. (2005) Structure 2B4C was uploaded onto StarBiochem. Images were developed by selecting various structural levels and adjusting size of atoms and groups.

Four polypeptide subunits were defined using the Quatenary structure methods:

  • Chain G (Yellow)
    • Residues: 84:G - 492:G
    • Amino end: Valine (position 84)
    • Carboxyl end: Glutamate (position 492)
  • Chain C (Light Pink)
    • Residues: 1:C - 175:C
    • Amino end: Lysine (position 1)
    • Carboxyl end: Valine (position 175)
  • Chain L (Green)
    • Residues: 1:L - 214:L
    • Amino end: Glutamate (position 1)
    • Carboxyl end: Cysteine (position 214)
  • Chain H (Dark Red)
    • Residues: 2:H - 216:H
    • Amino end: Glutamine (position 2)
    • Carboxyl end: Cysteine (position 216)

Secondary Structure Elements:

  • Beta Sheets: 22
  • Alpha Helices: 17
  • Random Coil: 84

V3 Region

  • Located between 296:G and 331:G
  • Sequence as follows:
    • C T R P N Q N T R L S I H I G P G R A F Y T T G E I I G D I R Q A H C

Weekly Assignments

Class Journals

Electronic Lab Notebook

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