• We need two reports( CASE STUDY); each report should have THE BELOW pages.
• Title for first report: AVPR2 (4 PAGES DOUBLE SPACE)
• Title for second report: CHRNA1 (6 PAGES BOUBLE SPACE ) THIS IS FOR TONY
• Firstly: write the introduction and you should include THE WHAT IS THE PROTEIN OF THE SEQUENCES ABOVE AND THEIR FUNCTIONS.
• PLZ NOTE THAT THE BELOW INSTRUCTION CONTAIN GUIDE FOR PREVIOUS PRACTICE EXERSIZE THE IMPORTANCE HERE TO USE THE BELOW LINKS WITH THE SAME STEPS BCZ OF INFO ORGANISATION
• ANOTHER NOTE IS TO USE THE DOWNLOADABLE PICTURE OF YOUR RESULT AND EXPLAIN IT IN DETAILS

• Secondly: Information to find out includes protein domains, secondary structure, tertiary structure, level of conservation, & range of species with this protein. However there may be further bits of information that you determine which can also be included.
• These are exercises how can you find the protein domains, secondary structure, tertiary structure, level of conservation, & range of species with this protein.

#-Find the conserved Domains for two protein sequences by using these steps:

Go to http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi and paste in your protein sequence.

What conserved domains are present in your sequence?

PFAM

Go to http://pfam.xfam.org/  and paste in your protein sequence.

What conserved domains are present in your sequence? Do you have both PFAM-A and PFAM –B domains? How do these results compare with the previous?

 Protein Secondary Structure

Go to Softberry Proteins secondary structure page http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=propt

There are a number of software tools here. Try these out on your protein sequence.

3-D protein structure

Go to PDB http://www.rcsb.org/pdb/home/home.do#Subcategory-search_sequences  , and paste in your protein sequence.

Other tools are available – take a look at CN3D

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Protein Structure

Exercise – 3D structures

you can find the structure of the two proteins in these two databases.

http://www.ncbi.nlm.nih.gov/structure

http://www.pdb.org/pdb/home/home.do

Look for secondary structure, and 3D structure

Secondary structure prediction

Take the sequence for the protein you just looked at, and run it through 2 or more of the following secondary structure tools. You may also wish to try the test sequences that some of these sites have.

How does the prediction compare to the structure

http://bioinf.cs.ucl.ac.uk/psipred/

http://www.compbio.dundee.ac.uk/jpred4/index.html

http://expasy.org/resources/search/keywords:secondary%20structure%20prediction

http://www.predictprotein.org/

3D prediction

http://predictioncenter.org/

This is a link to the servers that can predict protein structure. Try running your protein sequence through one of these (note it may not run in the time available, but can be looked later) http://www.predictioncenter.org/index.cgi?page=links

 ** TMMA – Multiple Sequence Alignment

 In this exercise we are going to look at the conservation of sequence in rhodopsin and related sequences. Rhodopsin is the visual pigment in the eye, and is  member of the G-Protein Coupled Receptor (GPCR)/seven transmembrane domain (7TM) protein superfamily.

• Find the human rhodopsin protein sequence – Accession no NP_000530  in Genbank, at NCBI
• Find related sequences by using BLASTP, and selecting homo sapiens in Organism box
• Run BLASTP. IN your results you should see a range of related human proteins.
• Select a range of sequences using the check boxes, and download the sequences
• Go to Clustal omega http://www.ebi.ac.uk/Tools/msa/clustalo/ and paste in your protein sequences
• Carry out the alignment, and look at the result. Have you included enough sequences? If not repeat using additional sequences.
• Repeat the BLASTP search, but this time in the organism box, select primates, then check the exclude box
• In the BLASTP results you should see rhodopsin from a range of species. Download sequences from as diverse a range of species as you can.
• Run CLUSTAL Omega on the different rhodopsin sequences you have collected
• What does this tell you about the conservation of rhodopsin?

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