BICM 88900
 Protein NMR Spectroscopy, Fall, 2018

This is a course that is aimed at biochemists/biophysicists/structural biologists interested in the use of solution NMR methodology to determine the structures of small to medium sized proteins.  The course includes a brief introduction to the theoretical methods used to describe standard NMR experiments, a detailed description of the application of these experiments to obtain resonance assignments and structural constraints in isotope-labeled proteins and finally the use of NMR-determined constraints to obtain three-dimensional structures. The course will also include hands-on workshops in resonance assignment and structure calculations utilizing common software. The last few lectures of the course will cover advanced topics that include, but are not limited to, the use of constraints from residual dipolar couplings, paramagnetic relaxation enhancement and chemical shifts to complement traditional methodology to obtain high-resolution structures of proteins and protein complexes.
Prerequisites: Two semesters of Biochemistry are required. Some knowledge of quantum mechanics (perhaps as part of a Physical Chemistry class) is encouraged. A background in NMR theory (e.g. Columbia G6270 – NMR Spectroscopy of Macromolecules offered at the NYSBC), while not required, will be very helpful in getting the most out of the course.
All course notes will be available from the following site:
http://www.nysbc.net/twiki/bin/view/Main/ProteinNmrCourse
Students should pre-register here: http://www.nysbc.net/twiki/register.html
Note that access is allowed only from computers that have an IP address belonging to a NYSBC partner institution.

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LECTURE DATE TOPIC INSTRUCTOR
1 8/30 Organizational Meeting Ronnie Ghose
2a 9/6 Introduction to modern NMR – the basics Mike Goger
2b 9/6 Features of NMR spectra: Classical representation of the NMR experiment Mike Goger
3a 9/13 Quantum mechanics of spin Ronnie Ghose
3b 9/13 Semi-classical theory of NMR - the density operator Ronnie Ghose
4a 9/20 Product operators and applications Ronnie Ghose
4b 9/20 Fourier transform NMR Ronnie Ghose
5a 9/27 Protein NMR - the HSQC experiment and variants Shibani Bhattacharya
5b 9/27 Triple-resonance experiments Shibani Bhattacharya
6a 10/4 Assignment of backbone resonances Shibani Bhattacharya
6b 10/4 Assignment of sidechain resonances  Shibani Bhattacharya
7a 10/11 NMR data processing and assignment using NMRViewJ/NMRFx - I Bruce Johnson
7b 10/11 NMR data processing and assignment using NMRViewJ/NMRFx - II Bruce Johnson
8a 10/18 Generation of constraints for structure calculations - I Ronnie Ghose
8b 10/18 Generation of constraints for structure calculations - II Ronnie Ghose
9a 10/25 Structure calculations using XPLOR-NIH - I Charles Schwieters
9b 10/25 Structure calculations using XPLOR-NIH - II Charles Schwieters
10a 11/1 NMR relaxation and dynamics - I Art Palmer 
10b 11/1 NMR relaxation and dynamics - II Art Palmer 
11a 11/8 Isotope labeling strategies Kevin Gardner
11b 11/8 Small molecule screening Kevin Gardner
12a 11/15 Accuracy and precision of NMR structures Ronnie Ghose
12b 11/15 Intrinsically disordered proteins David Cowburn
13a 11/29 Chemical shifts  Paul Robustelli
13b 11/29 Non-linear sampling techniques Jeff Hoch
14a 12/6 Hybrid approaches - I Kevin Gardner
14b 12/6 Hybrid approaches - II Kevin Gardner

 

TIME AND PLACE
New York Structural Biology Center, Room A-11 on Thursdays from 2-5 PM.

GRADING
Take-home mid-term - 50%
Final presentation - 50%

ANNOUNCEMENTS
Course related announcements will be posted here.