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.
This is a literature discussion based on a 2018 Inorganic Chemistry paper from the Lehnert group titled “Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases“(DOI: 10.1021/acs.inorgchem.7b02333).
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.
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.
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 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).
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:
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
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!).