AninditaVarshneya BIOL368 Week 9: Difference between revisions

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* Use the [https://ppopen.informatik.tu-muenchen.de/ Predict Protein Server] to analyze the V3 region of Subject 4, Visit 1-1
* Use the [https://ppopen.informatik.tu-muenchen.de/ Predict Protein Server] to analyze the V3 region of Subject 4, Visit 1-1
** Copy and paste their sequence from the [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php Bedrock HIV Problem Space] into PPS
** Copy and paste their sequence from the [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php Bedrock HIV Problem Space] into PPS
** Information provided here includes summary data of the sequence (length, aligned proteins, matched PDB structures) and amino acid composition. The UniProt website provides much more information about the sequence, but the PredictProtein server more visual representations of similar information.
*** I appreciate that the PredictProtein server also explains how they collect certain data.
*** The PredictProtein server seems to now have as much information as the Uniprot website.
* Download the HIV Protein Structure from [https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=8099 Kwong et al. (1998) structure 1GC1.]
** Open the protein on [https://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D software site] that is available on the computers in the lab.
** N and C termini can be found be selecting the first and last amino acid for each of the 4 chains. They are the yellow highlighted ends of each protein in the model.
** The secondary structures are shown below, but I run out of time in class to compare them with the results presented by Markham et al.
===Conclusion===
===Conclusion===
===Data and Files===
===Data and Files===

Revision as of 16:55, 25 October 2016

Electronic Lab Notebook

Purpose

Methods and Results

  • Convert DNA sequence of subject 4 during visit one into a protein sequence using NCBI ORF Finder
    • The frame without the stop codon is the true open reading frame.
    • My translated protein sequence: E V V I R S E N F T N N A K I I I V Q L N E S V E I N C T R P N N N T R K S I H I G P G R A F Y T T G D I I G D I R Q A Y C N I S R A E W N N T L K H I V I K L R E H F G N K T I V F N H S S
    • Markham et al. protein sequence: EVVIRSENFTNNAKIIIVQLNKSVEINCTRPNNNTIRRIPIGPGRAFYTTGRIGDIRPAHCNISRTKWNNALKLIVNKLREQFRNKTIIFNQSS
  • Learn more the gp120 protein using UniProt Knowledgebase (UniProt KB)
    • Searching "HIV gp120" returned 206,278 results
    • I selected the entry with the accession number: P04578
    • The types of information provided include:
      • Function, Names and Taxonomy, Subcellular location, Pathology/Biotechnology, PTM/Processing, Interaction, Structure, Family and Domains, Sequence, Cross-references, Entry information, Similar proteins, and other miscellaneous information.
  • Use the Predict Protein Server to analyze the V3 region of Subject 4, Visit 1-1
    • Copy and paste their sequence from the Bedrock HIV Problem Space into PPS
    • Information provided here includes summary data of the sequence (length, aligned proteins, matched PDB structures) and amino acid composition. The UniProt website provides much more information about the sequence, but the PredictProtein server more visual representations of similar information.
      • I appreciate that the PredictProtein server also explains how they collect certain data.
      • The PredictProtein server seems to now have as much information as the Uniprot website.
  • Download the HIV Protein Structure from Kwong et al. (1998) structure 1GC1.
    • Open the protein on Cn3D software site that is available on the computers in the lab.
    • N and C termini can be found be selecting the first and last amino acid for each of the 4 chains. They are the yellow highlighted ends of each protein in the model.
    • The secondary structures are shown below, but I run out of time in class to compare them with the results presented by Markham et al.

Conclusion

Data and Files

Defining the Research Project

Acknowledgements

References

Other Links

User Page: Anindita Varshneya

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

Weekly Assignments Individual Journal Assignments Shared Journal Assignments

SURP 2015

Links: Electronic Lab Notebook

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