CHEM 86900 - Protein NMR Spectroscopy - Spring 2015

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 strongly 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.

CUNY Policy on Academic Integrity

January 29       
Organizational Meeting
Ronnie Ghose
February 5
Introduction to modern NMR – The basics
Introduction to modern NMR – Pulsed NMR                                              
Mike Goger


February 19 

Quantum mechanics of Spin                                                                  
The density operator
Ronnie Ghose                                                                                                  
February 26   
Product operators and applications                                                  
Multi-dimensional NMR
Ronnie Ghose                                                                                                
March 5         
Protein NMR Spectroscopy - HSQC and variants                           
Triple-resonance experiments and backbone assignments
Shibani Bhattacharya              
March 12
Triple-resonance experiments and sidechain assignments       
Shibani Bhattacharya

Introduction to resonance assignment approaches                                        
Kaushik Dutta

March 19
NMRview Workshop

Lecture Notes                                                                           
Bruce Johnson

March 26
Review of assignment procedures                                                     
Kaushik Dutta

Introduction to Structure Calculations                                                     
Kaushik Dutta

April 2 
Structure calculations using XPLOR-NIH
Lecture Notes
Tutorial dataset                                            
Charlers Schwieters

(due on or before 04/20/2015)
Data for Question 4
Data for Question 5


April 16
Review of structure calculations                                                           
Kaushik Dutta

Generation of structural constraints, Assessing NMR structures                                        
Ronnie Ghose

April 23   NO CLASS

April 30

Isotope labeling strategies for NMR                                                 
Kevin Gardner
Muchmore et. al. 1989
Gardner et. al. 1998
Ruschak et. al. 2010
May 7              
Using chemical shifts for structure determination                               
Paul Robustelli

May 14             
NMR relaxation and dynamics - Part 1
NMR relaxation and dynamics - Part 2                                                 
Art Palmer



All classes will be held at the New York Structural Biology Center from 1-4 PM in Room A-1.
The March 19 and April 2 workshops will be held at the CUNY Advanced Science Research Center (ASRC) from 10 AM - 4 PM. The room will be announced later.


Take-home Mid-term - 50%
Final presentation - 50%