Relating Structure to Function - BioQUEST



Molecule Informatics Portfolio

Structure Determines Function

Learning Objectives

Students should be able to:

Access and interpret structural data about a protein of interest and its homologs

Develop a portfolio of data about the structure and function of their proteins

Serve as an expert source of information when the class encounters this molecule within the class curriculum.

EMBI Molecule of the Month Archive



PDB Molecule of the Month Home Page



Consurf (Overlay of Protein Structures)



Background Instruction

Assume proteins have been introduced.

Tutorial on protein structure (primary, secondary, etc.)

Tutorial visualizing protein structure in its many representations using a small peptide example in class

physical model building in class using of some representation of a small peptide with

different amino acids such as a model kit. (Make sure they discover the side chains as

charms on a bracelet and that side chains interact in a folded protein.)

tutorial on visualizing structures (Chime) on ball and stick, ribbon diagrams and space filling (change display, etc.) visualizing protein structures starting with ball and stick and tracing N terminus to C terminus.An easy way to do this is to complete the following tutorial: Exercise 5 called Protein Secondary Structure on the Essential Biochemistry website.(Students will need to download Chime to complete this exercise. The tutorial guides them through the download. Chime does not run well with Explorer so use another Browser when you download Chime.)



Lab Activity A: Protein Retrieval and Visualization of Myoglobin

i. Use the Protein Data Bank (PDB) to find Myoglobin

ii. Explain where the data come from that gets deposited in the Protein Data Bank

iii. Obtain the primary amino acid sequence of Myoglobin (FASTA) via PDB

iv. Determine how many amino acids are in myoglobin, how many histidines are present

and at what positions, which amino acids are at the N and C terminus, which

amino acid is the first in the myoglobin protein chain?

vi. Download Protein Workshop and view Myoglobin. Learn to zoom in and turn the molecule.

vii. Find the N and C terminus (click on proposed end and watch display on lower left)

viii. Find the Histidines in Myoglobin that make close contact with the Heme small molecule?

Molecule Informatics Portfolio

1st Assignment

Teams select name of protein out of a hat (in class) which they will study for the term.

a) Retrieve and save your protein amino acid sequence and structure using PDB or EMBI

Interpro in digital and printed format. This is the beginning of your Molecule Portfolio.

Be sure to write down the identifier labels such as a PDB ID number.

b) Where did the researchers physically obtain this protein for study (which organism)?

c) Write a description of the primary (how many aa?), secondary, tertiary, and quaternary

(if any) structure(s) of your protein. Identify the amino acids at the N and C termini.

d) save a digital copy of the image and be prepared to show it at any time in the semester.

2nd Assignment

Identify and categorize the biological role of your protein ( i.e. immune function, cytoskeleton, etc.)

(Use sources other than your textbook for this.)

3rd Assignment

Where does this molecule appear in your textbook? Looking at the lecture schedule, at what point in the term would you expect that the class would be discussing your molecule?

4th Assignment

Define the following terms: homolog, ortholog, paralog, protein family, and protein motif.

Look for homologs of your protein in the PDB from other organisms.

Obtain the primary sequences (FASTA) of each protein and keep track of which proteins you are studying by using PDB identifier labels. Save them as text files on your desktop.

5th Assignment

Before the 5th assignment, students can complete Lab Activity B to learn new tools.

Research your own protein using lab activity B as a guide.

Lab Activity B: Study Myoglobin in Biology Workbench to Perform A Multiple Sequence Alignment (CLUSTAL W) and Create an Unrooted Tree

Go to PDB and download 3-5 myoglobin sequences from different source organisms to text files.

One file per source.

Register for a Biology Workbench account and login.

Create a new session. Hit Run.

Go to Protein Tools. Hit Run.

Add new protein sequence by Browsing and Uploading the text file to Biology Workbench. Hit Run and Label sequence by source and SAVE. Repeat until all files are uploaded.

Check boxes of sequences to be aligned.

Do a ClustalW Multiple Sequence Alignment to see the similarities of the primary sequence. Hit Run.

Save the unrooted tree. Copy and paste the sequence alignment to Word or Powerpoint.

Look at the Consensus Key. Describe what this means in the myoglobin alignment.

Consensus key (see documentation for details)

* - single, fully conserved residue

: - conservation of strong groups

. - conservation of weak groups

- no consensus

Which proteins are most closely related? Support your answer with specific data.

Save the CLUSTALW alignment to your desktop in MSF format as a text file in case you want to use it to look at the similarities in your protein structures.

Extension: 6th Assignment (Structure Overlay)

This tool will allow you to display the structures of all of your homologous proteins to see where they might be similar and different.

You need a Multiple Sequence Alignment (like CLUSTALW) already saved to your desktop (as in Lab Activity B). It should be saved as a text file.

Go to to overlap the structures of your proteins from different organisms. To do this, you need one of the PDB identifiers of one of your proteins. Enter it on the Consurf site. On the same page, you will add a

User Provided Sequence Alignment in the box entitled add your own MSA file. Do this by browsing and uploading the text file of the alignment from your desktop. Submit your query and wait for the results. View the structural overlay. You can manipulate this structural overlay if you view it within the Swiss-PDB Viewer (if you have previously downloaded the program).

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