Application

BIOMOLECULAR NMR SPECTROSCOPY:analyzing complex biological mixtures (metabolomics) (5 credits)), 5 hp

 
40,1
2021
Method course
Spεr
10
2021-03-17
English
Celestine Chi
IMBIM
Husargatan 3
75123
2021-03-22; 2021-05-19 (w 12-20)
BMC
16 days, half time
 

Nuclear magnetic resonance (NMR) spectroscopy is a technique widely used in many science disciplines including physics, chemistry, medicine and life sciences. Researchers/students with background knowledge in chemistry and physics have an easy ride when it comes to mastering of the theoretical and practical knowledge of the technique. Students with medical and life science backgrounds are often at limbo with this technique. It is a long-standing problem of what is the best approach to teach this subject to students of medical and life science backgrounds. In this course, I focus on student learning by using active student participation1-4. Course evaluation and feedback from students in prior participation in the course revealed that emphasis should be made on exposing participants on more laboratory and practical aspects of the course. This is in agreement with the notion of active learning strategies.

Important to note that all lectures for this years course will be held online via zoom.

After completing the course, the student should be able to
• Describe the basic principles and operation of NMR instrumentation.
• Create a range of available NMR experiments needed to solve different structural problems (large biomolecules).
• Utilize and adapt different experimental setups to answer diverse biological questions with NMR spectroscopy.
• Describe sample requirements for a specific NMR experiments.
• Describe how NMR can be used to analyze different aspects of biomolecules.
Setup and run biological NMR experiments
• Use NMR to analyze complex complex biological samples (Metabolomics)

The aim of the course is to introduce the basics - both theory and practice - of NMR-spectroscopy of biomolecules. This includes:

• The principles of how to perform NMR measurements and structure elucidation.
• Nuclear Overhauser effect, polarization transfer, scalar and dipolar coupling, population and coherence transfer, chemical shift, NMR signal assignment and multidimensional NMR spectroscopy, isotope labelling and spectral editing strategies (e.g. HSQC, HMQC, TOCSY-HSQC, HNCO, HNCA, HNCACB, HCCH-TOCSY, NOESY),
• The basics of NMR structure calculation, including data collection, resonance assignment (ccpnmr and Topspin), collection of structural restraints and quality assessment.
• Strategies for structure determination of larger proteins (> 30 kDa) using specific labelling schemes and assignment.
• Strategies to extract dynamic information (T1, T2, hetNOE and order parameters) parameters.
• Basic design and implementation of an NMR experiment or pulse sequence.
• Using NMR to answer basic questions about protein-ligand interactions
• Monitoring post-translation modification in-live cells.
• NMR spectroscopy of nucleic acids and carbohydrates.
• Metabolic profiling of complex biological samples
• Using the structure calculation program CYANA.

English

ENTRY REQUIREMENT:
Either of the following will be sufficient: (1) 180 credits with 60 credits in chemistry, including 20 credits in biochemistry, or (2) 180 credits with 30 credits in chemistry and 30 credits in biology, including 20 credits in biochemistry, or (3) 180 credits within a related discipline.

Modules: Oral presentation (2 credit); Practicals (3 credits)
Assessment will be based on solving a practical exercise and on oral presentation. The grade will be pass or fail. To earn a pass, students will be required to complete the assignment of a 15-residue peptide (fragment from a larger protein), solve the structure and give an oral presentation.

M. H. Levitt, Second edition, Spin Dynamics – Basics of Nuclear Magnetic Resonance, Wiley, 2007.

J. Cavanagh, W. J. Fairbrother, A. G. Palmer III, and N. J. Skelton: Protein NMR Spectroscopy. Principles and Practice, Academic Press, 1996

Dr. Celestine Chi
Post docs and PhD students will assist in lab and practical exercises

Dr. Celestine N. Chi
Chi.celestine@imbim.uu.se

Show all courses 2021 »