Getting To Know Your Protein

Exercise 3

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?

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

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?

II. Search for telomerase structures. Do you find a telomerase protein structure?

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 (you will first need to download them from http://www.rcsb.org ). (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 (you will first need to download them from http://www.rcsb.org ) 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.