BIOL368/F14:Chloe Jones Week 8

Working with Protein Sequences In-class Activity

Chapter 4: Reading a SWISS-PROT entry

Source: Bioinformatics for Dummies pp.110-123

• Using the database UniProt KB which has two subsections: Swis-Prot and TrEMBL.

1. If you search on the keywords "HIV" and "gp120", how many results do you get?
   • 180,227 results.

General Information about the entry

• Entry name: 9HIV1
• Primary Accession Number :Q75760
• Secondary Accession Numbers :N/A
• Intergrated into Swiss-Prot on :November 1, 1996
• Sequence was last modified on : November 1, 1996
• Annotations were last modified on : October 1, 2014

Name and origin of the protein

• Protein name:Envelope glycoprotein gp160
• Synonyms:N/A
• Gene name:Env
• From:Homo sapiens (Human) [TaxID: 9606] TaxID:9606
• Taxonomy: Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Primate lentivirus group

References

• Number of references:9

The comments :?? The cross references :172

• ENA, European Nucleotide Archive (more information possibly)

Keyword

• Apoptosis, fushion of virus membrane with host membrane, host-virus interaction, viral attachment to host cell, viral immunoevasion, Viral penetration into host cytoplasm, virus entry into host cell

Chapter 5: ORFing your DNA sequence

Source: Bioinformatics for Dummies pp.146-147

• Fasta format of Envelope glycoprotein gp160 obtained from UniProt KB was placed in the in the imput box of ORF Finder(Open Reading Frame Finder). 6 parallel horizontal bars were present with integers correlating to the reading frame.
• Putting in DNA sequences: Subject 1 visit 1, clone 1:
• The protein with the open reading frame was in the ORF Finder database was projected to be #2, or #3. Looking at the exPASy database 5’3” Frame 3 had an open reading frame with no stop codons interrupting /truncating the lengh of the DNA.
• Apoptosis, fushion of virus membrane with host membrane, host-virus interaction, viral attachment to host cell, viral immunoevasion, Viral penetration into host cytoplasm, virus entry into host cell

The features Media***

Chapter 6:Working with a single protein sequence

Source: Bioinformatics for Dummies pp.159-195

Predicting the main physico-chemical properties of a protein

• Used the program ExPasy ProtParam for computation of physcial and chemical parameters of a given protein
• Imput the Swiss-Prot/TrEMBL accession number Q75760. Then click compute parameters button >Submit
  • Corresponds to the HIV gp120 sequence that was used for the crystal structure for the Huang et al. (2005) paper.
  • Can also enter raw sequence
• Save the file
• media ***

Interpreting ProtParam results

• Used ExPasy ProtParam for data.

Molecular Weight: 96160.4 Daltons Extinction Coefficients:

• assuming all pairs of Cys residues form cystines= 184145M1cm1
• assuming all Cys residues are reduced= 182770 M1cm1
• ~Tell you how much light (visible or invisible) your protein absorbs at a certain wavelength.

Instability

• • instability index (II) is computed to be 37.91
  • classifies the protein as stable

Half-Life

• The estimated half-life is:
  • 30 hours (mammalian reticulocytes, in vitro)
  • >20 hours (yeast, in vivo)
  • >10 hours (Escherichia coli, in vivo)

Digesting a protein in a computer

• Used ExPasy Peptide Cutter
• Imput accession number: Q75760
• Program cuts protein at specific site