Getting to Know the MetalPDB

Submitted by Anthony L. Fernandez / Merrimack College on Fri, 07/06/2018 - 11:29
Description

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures.

MetalPDB website

Submitted by Anthony L. Fernandez / Merrimack College on Wed, 05/16/2018 - 12:58
Description

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

Utilizing the PDB and HSAB theory to understand metal specificity in trafficking proteins

Submitted by EGunn / Simmons College on Thu, 07/17/2014 - 15:19
Description

This is an in-class PDB exercise based on the paper "Mechanisms Controlling the Cellular Metal Economy" by Gilston and O'Halloran. Students are asked to visualize the metal binding sites of several proteins discussed in the paper, highlighting unusual metal geometries. After identifying the amino acid residues involved in metal binding, students will discuss the bond structure in terms of HSAB theory. 

Literature Discussion of "Mechanisms Controlling the Cellular Metal Economy"

Submitted by Kyle Grice / DePaul University on Thu, 07/17/2014 - 15:07
Description

This is a literature discussion of a review by Tom O'Halloran (The link to the paper is included in the "Web Resources" below). The review covers concepts of metal content in cells, metal trasport, storage, and regulation. Its a good review to start a broader or deeper discussion about metals in biology. We have provided some questions to help guide the student discussion. These questions can be given to students prior to coming to class, and the answers can either be used for the in-class discussion and/or collected. 

The relevance of Transition Metal-Carbon Bonds in Biology and Chemistry

Submitted by Mwalimu / Russell Sage College on Tue, 07/15/2014 - 12:45
Description

The students will write a paper in which they analyze the Vitamin B12 co-enzyme from biological, chemical and biochemical perspectives, and will use the guided questions to help show the relevance of an organometallic chemistry experiment to real biochemical systems. This activity is based on a synthetic lab experiment that students would have performed on transition metal-carbon bonds in biology and chemistry (The lab experiment was adapted from third edition of “Inorganic Experiments” by Derek Woollins).

Learning Objects used at the 2014 VIPEr Workshop on Bioinorganic Chemistry

Submitted by Betsy Jamieson / Smith College on Wed, 06/25/2014 - 09:32

This collection highlights the learning objects used at the 2014 VIPEr workshop on the Bioinorganic Applications of Coordination Chemistry to introduce participants to the field of bioinorganic chemistry.   They provide essential background information on how metals bind to proteins as well as the techniques used in the research papers presented at the workshop.  A list of learning objects created at the workshop based on the current research of our expert speakers can be found at: 

Exploring Proteins as Ligands using the Protein Data Bank

Submitted by Betsy Jamieson / Smith College on Tue, 06/17/2014 - 15:23
Description

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 protei

Soluble Methane Monooxgenase Spectroscopy

Submitted by Gerard Rowe / University of South Carolina Aiken on Fri, 07/20/2012 - 09:37
Description

Determining the reactive intermediates in metalloenzymes is a very involved task, and requires drawing from many different spectroscopies and physical methods.  The facile activation and oxidation of methane to produce methanol is one of the "holy grails" of inorganic chemistry.  Strategies exist within materials science and organometallic chemistry to activate methane, but using the enzyme methane monooxygenase, nature is able to carry out this difficult reaction at ambient temperatures and pressures (and in water, too!).