Jordan T. Detamore Week 9: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(fix bullets) |
(fix bullets) |
||
| Line 5: | Line 5: | ||
#Convert one of your DNA sequences into protein sequences using either the [https://www.ncbi.nlm.nih.gov/orffinder/ NCBI Open Reading Frame Finder] or the [http://web.expasy.org/translate/ ExPASY Translate tool]. | #Convert one of your DNA sequences into protein sequences using either the [https://www.ncbi.nlm.nih.gov/orffinder/ NCBI Open Reading Frame Finder] or the [http://web.expasy.org/translate/ ExPASY Translate tool]. | ||
#* How do you know which of the six frames is the correct reading frame (without looking up the answer)? | #* How do you know which of the six frames is the correct reading frame (without looking up the answer)? | ||
**It is the only sequence that does not have a stop codon. No stop codon should be present because this is the middle segment of a protein sequence. | #**It is the only sequence that does not have a stop codon. No stop codon should be present because this is the middle segment of a protein sequence. | ||
#* Once you answered the question above, you can check your answer and obtain the rest of the protein sequences from the [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php BEDROCK HIV Problem Space]. | #* Once you answered the question above, you can check your answer and obtain the rest of the protein sequences from the [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php BEDROCK HIV Problem Space]. | ||
# Find out what is already known about the HIV gp120 envelope protein in the [http://www.uniprot.org UniProt Knowledgebase (UniProt KB)]. UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases. | # Find out what is already known about the HIV gp120 envelope protein in the [http://www.uniprot.org UniProt Knowledgebase (UniProt KB)]. UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases. | ||
Revision as of 16:22, 25 October 2016
Electronic Notebook
Defining HIV Structure Research Project
HIV Structure In-Class Activity
- Purpose
- Convert one of your DNA sequences into protein sequences using either the NCBI Open Reading Frame Finder or the ExPASY Translate tool.
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- It is the only sequence that does not have a stop codon. No stop codon should be present because this is the middle segment of a protein sequence.
- Once you answered the question above, you can check your answer and obtain the rest of the protein sequences from the BEDROCK HIV Problem Space.
- How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgebase (UniProt KB). UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases.
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- 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?
- 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?
- Download the structure file for the paper we read in journal club from the NCBI Structure Database.
- Kwong et al. (1998) structure 1GC1.
- You may also be interested in these other structures from related gp120 structure articles:
- These files can be opened with the Cn3D software site that is installed on the computers in the lab (this software is free, so you can download it and use it at home, too.) Alternately, you may choose to use the Star Biochem program to do this portion of your work. Answer the following:
- Find the N-terminus and C-terminus of each polypeptide tertiary structure.
- Locate all the secondary structure elements. Do these match the predictions made by the PredictProtein server?
- Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.
- Conclusion
Acknowledgements
References
Useful links
LMU Seaver College of Science and Engineering
