Getting To Know Your Protein

Exercise 3 - Answers

Bioinformatics for Biologists 2005

In this exercise, you will be practicing how to use several different structure-related resources. You will approach the following tasks by using web-enabled tools to search structure databases and make predictions. Following these exercises, you will have the opportunity to use a structure visualization tool known as "Deep View". If you have any difficulties with the exercises, please ask for assistance.

Step 1 Search the PDB database

I. Goto the RCSB at http://www.rcsb.org/pdb. Search the database using the term "Protein Kinase". Do you find any relevant structures? You should find ~ 646 relevant structures.

II. Perform another search at the RCSB, this time, identify the protein that corresponds to the coordinates "1iep". This is the ABL kinase domain.

Step 2 Search NCBI's MMDB

I. Switch to NCBI's MMDB site at http://www.ncbi.nlm.nih.gov/Structure. Use this tool to search for "Protein Kinase". Do you get similar results as in Step 1? Yes, but more ~ 711 results.

II. Search for telomerase structures. Do you find a telomerase protein structure? No, they are all nucleotide (RNA) structures).

Step 3 Use the Dali Structure Family Database

I. Go to the Dali tool at http://www.ebi.ac.uk/dali. Specify that you want to perform an interactive search. Search for structure family members related to the 1iep coordinates, located on your desktop. (Note - the results of this job will be emailed to you about 45 min after you submit).

II. Align the 1iep.pdb and 3lck.pdb coordinates using the pairwise comparison.(Note - the results of this job will be emailed to you about 45 min after you submit).

Step 4 Predict a Secondary Structure

I. Use Jpred at http://www.compbio.dundee.ac.uk/~www-jpred/submit.html to predict the consensus secondary structure for the following sequence: (Note, it will take the server some time - wait for the Penguin to show up - you'll understand)

MAEAMDLGKDPNGPTHSSTLFVRDDGSSMSFYVRPSPAKRRLSTLILHGGGTVCRVQEPGAVLLAQ

PGEALAEASGDFISTQHILDCVERNERLELEAYRLGPASAADTGSEAKPGALAEGAAEPEPQRHAGRI

AFTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSLKDRYLKHLRGQEHKYLLGD

APVSPSSQKLKRKAEEDPEAADSGEPQNKRTPDLPEEEYVKEEIQENEEAVKKMLVEATREFEEVVV

DESPPDFEIHITMCDDDPPTPEEDSETQPDEE

II. View the HTML results of your query.

Step 5 Visualize a Protein Structure

I. Launch SPDV (Swiss-PDB Deep View Visualizer tool). Load the 1iep coordinates.

II. Practice rotating and translating the coordinates. Zoom in, zoom out.

III. Color positions 30-50 red.

IV. Render positions 60-120 as a ribbon.