Fall 2023, Wednesday 5:30-8:30 pm, 221 Brown Lab (computer classroom)
Prof. Brian Bahnson
312A Drake Hall
research office phone: 302-831-0786
email: bahnson@udel.edu
office hours: by appointment
class website: https://sites.udel.edu/chem645
Outline of course
The course will begin with an overview of structural biology, including how X-ray crystallography, NMR spectroscopy, cryo EM, AlphaFold, homology modeling and other techniques are used to solve structures and develop models of macromolecules. Then representative classes of proteins will be discussed in terms of how the protein’s structure relates to its function. This class is meant for both people directly interested in structural biology, as well as those that plan to collaborate with structural biologists.
X-ray crystallography vs. NMR spectroscopy – Each method has advantages and disadvantages. Also each technique supplies different information. Topics that will be covered include: crystal growth and sample preparation, data collection and instrumentation, methods to obtain phases or obtain NMR distance restraints, model building and model refinement. Next we’ll go through a homology modeling assignment. Your in class presentations and final projects will bring other related topics into our discussion. Examples of information about structure and dynamics from other methods include: cryo EM, CD, mass spec, fluorescence, genomics, structure prediction, protein folding, can structure be predicted ab initio? Modeling the dynamics of protein motion – molecular dynamics, potential energy functions, energy minimization, functional role of proteins in biological systems- enzymes, transporters, ion channels, energy transducers, signal transduction, molecular motors, structural scaffolds, gene expression, etc…
Useful texts
“Introduction to Proteins Structure, Function, and Motion, Second Edition” by Amit Kessel and Nir Ben-Tal, Second Edition, CRC Press (2018)
“Crystallography Made Crystal Clear” by Gale Rhodes, Third Edition, Academic Press (2006)
Review articles and primary literature will be used extensively.
You should have and refer to a biochemistry textbook. If you don’t have a text, I would recommend the free version of the textbook titled “Biochemistry Free For All”, which can be download here:
www.davincipress.com/
available to borrow short term from my office.
“Introduction to Protein Structure” by Branden & Tooze, Second Edition (1999).
“Protein Structure and Function” by Gregory A. Petsko and Dagmar Ringe, Sinauer Associates, Inc. (2003)
“Nuclear Magnetic Resonance” by P. J. Hore (Oxford Chemistry Primers, 32) (1995).
“Crystallization of Biological Macromolecules” by Alexander McPherson, Cold Spring Harbor Laboratory Press (1999)
“Practical Protein Crystallography”, by Dunan E. McRee, AcademicPress (1993)
“Protein NMR Spectroscopy: Principles and Practice”, by John Cavanagh, Academic Press (1996)
“X-Ray Structure Determination: A Practical Guide”, 2nd Edition by George H. Stout, Lyle H. Jensen, John Wiley & Sons (1989)
and many others…
Grade breakdown
Midterm exam – 20% – in class
Homology modeling assignment – 20% – will be problem set based and will utilize the primary literature, the world wide web, and your laptops. You will be encouraged and instructed in how to load much of the software (freeware) on your own computers.
Research Paper Discussions – 20% – our 2nd half of the semester will be devoted to in depth discussion of primary literature on selected topics of your choosing. You will each be assigned a portion of the topic to lead the discussion from.
Final Exam – 20% – take home assigned day of class and due during finals week.
Class participation – 20%
Course prerequisites
Introductory biochemistry class, such as CHEM 527 or 641
Course objectives
The course presents a theoretical and practical overview of structural biology, including how X-ray crystallography, NMR spectroscopy, cryo EM, AlphaFold, homology modeling and other techniques are used to solve or model structure of macromolecules. Representative proteins discussed in terms of how each protein’s structure relates to its function. This class is meant for both people directly interested in structural biology, as well as those that plan to collaborate with structural biologists. Students will improve their abilities to read, understand and critically discuss primary literature related to structural biology. Students will likewise improve presentation skills, working with fellow students on joint tasks, and develop skills using computers to aid in structural biology pursuits.
Use of Artificial Intelligence Tools
For assignments, such as the homology modeling assignment and the take home final, you will be allowed to use AI tools such as ChatGPT so long as you explicitly cite and acknowledge the use of these tools.
Departmental learning objectives
This course meets departmental learning objectives 1, 3, 4, 5, 8, 9 and 10.
