Biomolecular NMR: Structure and Molecular Recognition

 

Nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for the interrogation of biomolecular structure and interactions at atomic resolution. Structural genomics efforts have produced refinements in the methodology for three-dimensional protein structure determination, such that new structures can be solved in a matter of weeks using increasingly automated processes. This course begins with a description of the quantum mechanical basis for multidimensional NMR using the product operator formalism. This powerful operator algebra rigorously predicts the propagation of the nuclear spin wavefunction under a time-independent Hamiltonian operator governing interactions between nuclear spins and between spins and static or transient magnetic fields, enabling the development of increasingly complex pulse sequences for multidimensional, multinuclear NMR measurements of biomolecules. Simple pulse sequences for magnetization transfer and isotope editing are described using product operators and combined into more complex two and three-dimensional pulse schemes for triple-resonance correlation of nuclei in proteins. Systematic application of these NMR methods to the sequence-specific assignment of isotopically-enriched proteins will then be linked to the interpretation of other types of NMR data (nuclear Overhauser effect; scalar and dipolar couplings) that report directly on tertiary structure. The balance of the course will consist of practical, hands-on training in basics of 2D/3D NMR data acquisition, processing and analysis, as well as interactive computer tutorials on the chemical shift assignment and 3-D structure determination processes. 

 

 

Contemporary X-ray Crystallography

 

X-ray crystallography is the main method for elucidating 3-dimensional structures of macromolecules and biomolecular complexes and is capable of revealing structural details at high resolutions (finer than 3.5 Å).  Powered by modern synchrotron-based light sources and state-of-the-art computer programs, contemporary crystallographic research has provided mechanistic insights into complex cellular functions such as gene transcription and translation.  While crystallographic computer programs are openly available, the use of these packages by biologists who do not have a theoretical comprehension of crystallography can be unproductive.  This course is designed to teach non-crystallographers the capability to intelligently use crystallographic programs that are often available in the form of bundled software.  Attendees will learn systematically the central theory behind the crystallographic tools in use today, and hence grow an appreciation of the physical process that takes place during an experiment to determine the structure of a protein or nucleic acid.  A central aim of this course is to generate stimulating discussions that will help the students to grasp the essence of macromolecular crystallography.

 

 

Special Topics in Biochemistry: Proteomics

 

This course is designed for graduate students who wish to acquire a better understanding of fundamental concepts of mass spectrometry-based proteomics. The lectures will cover protein/peptide separation techniques, protein mass spectrometry, biological applications including quantitative proteomics, protein modifications, interaction proteomics etc. The course also covers the interpretation of mass spectral data using various bioinformatics tools. If the students are interested in any specific topics that come under proteomics, we will try to include those in the lectures.