17 Jun 2014

Exploring Proteins as Ligands using the Protein Data Bank

In-Class Activity

Submitted by Elizabeth Jamieson, Smith College

This in class activity is designed to introduce students to how amino acid side chains can coordinate metal ions in proteins.  It guides students through the exploration of several metal binding sites in proteins using the Ligand Explorer program on the Protein Data Bank (PDB) website.  Essentially, it is a way for them to use the PDB to “discover” the information generally presented on this topic in the introductory chapters of bioinorganic textbooks.  At the end it asks students to think about Hard Soft Acid Base theory and to see how that can be applied to the binding of metals in proteins.  I’ve also posted a separate document with this activity that highlights several additional web based resources for examining the structure of metals in proteins if anyone wants to explore this topic further.

Learning Goals: 

By doing this in class activity, a student will be able to:

•Identify which amino acid side chains are likely to coordinate to metal ions and recognize their different coordination modes

•Use Java based programs on the Protein Data Bank to explore the metal coordination environment in proteins

•Apply Hard Soft Acid Base theory to explain the metal ion specificity in proteins

Implementation Notes: 

I have been thinking about making a learning object like this for some time, but finally put it together in time for the 2014 TUES workshop on the Bioinorganic Applications of Coordination Chemistry.  In my bioinorganic elective and my advanced inorganic class, I always cover this topic with students, but always thought it would be better to have a more “active learning” type of activity for them to do.  We will test this activity at the workshop, and I hope to implement it in class next time I teach this topic. 

I envision using this LO with students who have some knowledge of coordination chemistry and have been introduced to the basics of protein structure.  I have been using the Bertini, Gray, Stiefel, and Valentine Biological Inorganic Chemistry:  Structure and Reactivity textbook the past couple of times I’ve taught bioinorganic, so have referenced that text in this LO.  However, it could easily be adapted to a similar section of a different text.

The section of the LO on post-translational modifications was put in specfically to provide some background on one of the papers presented at the 2014 workshop.  It is a topic that I cover in my biochemistry and bioinorganic class, but this is something that could easily be skipped if you prefer by just deleting item 8 in the worksheet. 

In the past when I have had the students use the PDB, some have had issues getting the Java based programs to work on their computers.  Usually at least half of the class can get it to work, so I will sometimes have students partner with each other for PDB based activities if this is the case.  I have included links to the Java troubleshooting pages on the PDB website to assist with these technical issues. 


Time Required: 
I would estimate that students would need at least 30 min to do this exercise, and, more realistically it would probably take them closer to 45 min.
Evaluation Methods: 

I have not yet been able to assess this LO, but imagine one could ask questions on a problem set or exam related to how amino acids bind to metals and/or Hard Soft Acid Base theory.  See the related activities suggested above for ideas. 


Evaluation Results: 

No results to report at this time.

Creative Commons License: 
Creative Commons Licence


The students in my Bioinorganic Chemistry course worked on this LO this past week and absolutely loved it. The class is populated mostly by students who are biology majors and who have not had a separate course in Inorganic Chemistry. They saw how their predictions about which amino acids might be good ligands for transition metals matched the various examples. They also made the connection between these results and HSAB theory.

A couple comments and some minor adjustments I made were:

1. The prep says that when using Ligand Explorer “the amino acids that are involved in metal binding are highlighted” on the top of the screen. We found that that only happened if you clicked on the one-letter code for one of the ligating amino acids first.

2. Lowering the threshold metal interaction to 2.8A got rid of the apparent bidentate ligation by glutamic acid. This might not be a concern for more experienced students.

3. With superoxide dismutase (2SOD), highlighting both metals (in the “Choose a Ligand to Analyze” shift-click whichever metal is not currently highlighted) allows students to see the bridging histidine quite nicely. Some had missed that the same His was ligated to both metals when looking at the metals separately.

4. The answer key seems to emphasize distinguishing between the two nitrogen atoms in histidine. If this is expected of students, then perhaps a question about that as part of question 1 (which amino acid side chains are expected to be able to serve as a ligand for a transition metal ion). Of course, the instructor could choose to not emphasize this distinction.

A great L.O. that I will plan on using again in the future!

The VIPEr community supports respectful and voluntary sharing. Click here for a description of our default Creative Commons license.