Courtney L. Merriam Week 9: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(→‎References: added websites to use)
(updated methods)
Line 13: Line 13:
#*
#*
===HIV Structure In-class Activity===
===HIV Structure In-class Activity===
*Convert your DNA sequences into protein sequences.
#Convert your DNA sequences into protein sequence using [https://www.ncbi.nlm.nih.gov/orffinder/ NCBI Open Reading Frame Finder]
*How do you know which of the six frames is the correct reading frame?
#*How do you know which of the six frames is the correct reading frame?
**
#**
*Once you have done one example, you can obtain the rest of the protein sequences from the BEDROCK HIV Problem Space.
#*Once you have done one example, you can obtain the rest of the protein sequences from the [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php BEDROCK HIV Problem Space].  
*Perform a multiple sequence alignment on the protein sequences.
#Find out what is already known about the HIV gp120 envelope protein in the [http://www.uniprot.org UniProt Knowledgeable (UniProt KB)] .  
*#Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
##If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
*#*
##*
*#How do you account for this?
##Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120.
*#*
##What types of information are provided about this protein in this database entry?
*Which of the procedures from the Week 8 Assignment that you ran on the entire gp120 sequence are applicable to the V3 fragment you are working with now?
##*
**
#We are going to use the [https://ppopen.informatik.tu-muenchen.de/ PredictProtein server] to analyze just the V3 region from Markham et al. (1998).
*#How are they applicable?
#*Paste one of the amino acid sequences from Markham et al. (1998) into the input field and submit.
*#*
#*Explore the types of information provided. How does this information relate to what is stored in the UniProt database?
*In particular, you should perform the secondary structure prediction on the V3 fragment.
#**
*Download the structure file for the paper we read in journal club from the NCBI Structure Database and answer the following:
#Download the structure file for the paper we read in journal club from the [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar NCBI Structure Database] 
*#Find the N-terminus and C-terminus of each polypeptide tertiary structure.
#The files can be opened with the [http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D software site]. Answer the following:
*#Locate all the secondary structure elements. Do these match the predictions made above?
##Find the N-terminus and C-terminus of each polypeptide tertiary structure.
*#*
##Locate all the secondary structure elements. Do these match the predictions made above?
*#Locate the V3 region and figure out the location of the sequences from the alignment in the structure.
##*
*#Analyze whether the amino acid changes that you see in the multiple sequence alignment would affect the 3D structure and explain why you think this.
##Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.
*#*
*Instead of using Cn3D or StarBiochem to do this, you could use the program ConSurf.


==Data and Files==
==Data and Files==
Line 55: Line 53:
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar NCBI Structure Database]  
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=Structure&itool=toolbar NCBI Structure Database]  


[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D software site]


{{Courtney L. Merriam}}
{{Courtney L. Merriam}}

Revision as of 14:03, 25 October 2016

Purpose

The purpose of this experiment was to

Methods and Results

Defining Your HIV Structure Research Project

  1. What is your question?
  2. Make a prediction about the answer to your question before you begin your analysis.
  3. Which subjects, visits, and clones will you use to answer your question?
  4. Justify why you chose the subjects, visits, and clones you did.

HIV Structure In-class Activity

  1. Convert your DNA sequences into protein sequence using NCBI Open Reading Frame Finder
    • How do you know which of the six frames is the correct reading frame?
    • Once you have done one example, you can obtain the rest of the protein sequences from the BEDROCK HIV Problem Space.
  2. Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgeable (UniProt KB) .
    1. If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
    2. Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120.
    3. What types of information are provided about this protein in this database entry?
  3. We are going to use the PredictProtein server to analyze just the V3 region from Markham et al. (1998).
    • Paste one of the amino acid sequences from Markham et al. (1998) into the input field and submit.
    • Explore the types of information provided. How does this information relate to what is stored in the UniProt database?
  4. Download the structure file for the paper we read in journal club from the NCBI Structure Database
  5. The files can be opened with the Cn3D software site. Answer the following:
    1. Find the N-terminus and C-terminus of each polypeptide tertiary structure.
    2. Locate all the secondary structure elements. Do these match the predictions made above?
    3. Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.

Data and Files

No files or data was used for this assignment.

Conclusion

Acknowledgments

I collaborated with Avery Vernon-Moore and [[User:]] in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

NCBI Open Reading Frame Finder

BEDROCK HIV Problem Space

UniProt Knowledgebase (UniProt KB)

PredictProtein server

NCBI Structure Database

Cn3D software site

Useful Links

Courtney L. Merriam

Clas Page: Bioinformatics Laboratory

Weekly Assignments Individual Journal Assignments Shared Journal Assignments
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Courtney_L._Merriam_Week_9&oldid=961207"