Chris Rhodes Week 8

For today's lab we will working out of the Bioinformatics for Dummies 2nd edition book performing selected activities from Chapters 2, 4, 5, and 6 but modifying the protocols to apply to the current website formats and the use of HIV-1 gp120.

In Class Activities

Retrieving Protein Sequences

• The protein retrieved in this exercise is HIV-1 gp120. It was found by going to ExPASy and searching "HIV gp120 envelope protein" using the UniProtKB database, but verified independent gp120 protein could not be found. The gp120 protein sequence was instead taken from an entry of gp160 which contains the gp120 sqeuence. The UniProtKB entry of the gp160 protein used is found here and the sequence of the gp120 protein, shown as the highlighted residues within the gp160 protein sequence, is found here http://www.uniprot.org/blast/?about=P04578[33-511] -> This address couldn't be properly hyperlinked due to the [33-511] text causing problems with the linking format.
• The fasta form of the gp120 protein sequence was retrieved from the entry page and is shown here:

>sp|P04578|33-511
KLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISL
WDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSY
KLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVI
RSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLRE
QFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN

• From the list of gp160 proteins found when searching for gp120 in the first step 5 sequences were chosen to be used in the multiple retrieval exercise. The UniProt ID numbers of the 5 sequences are P04578, P03377, P03375, P35961, and P05877. From the options for downloading the sequences I chose the FASTA format, the txt version of the combined sequence FASTA file can be found here

Reading a Swiss-Prot Entry

• As with the first activity a UniProt verified gp120 protein could not be found so I will be working with the gp160 entry instead.
• The UniProt entry of the gp160 protein used can be found here
• The entry itself is very in-depth and contains a lot of information. Some of the major features of the entry include:
  • The protein name along with the names of the proteins that result from the cleavage of the original protein
  • The protein sequence, source organism, and in this case the viral host.
  • In-depth description of known functions and mechanisms of function.
  • Known Secondary Structure and ontologies
  • Details about protein domains, cellular location, additional miscellaneous information.

'ORFing your DNA sequence

• The NCBI ORF Finder can be found here
• The sequence used for this experiment is the fasta sequence of the gp120 protein displayed in the first activity
• The ORF's for the gp120 sequence were analyzed by placing the gp120 sequence ORF Finder box and pressing OrfFind
• The ORF Finder output for the gp120 sequence is shown here:

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