Advanced Structural Biology Courses
The Structural Biology Program offers a vibrant array of advanced courses relevant to Structural Biology as typified by the following examples below. Students should consult the GBS Course list for a complete listing.
Principles of Membrane Protein Structure and Function
Course Masters: Drs. Aller, Bjornsti and DeLucas
This course is designed to familiarize students with the latest experimental techniques used to express, purify, characterize and crystallize integral membrane proteins (IMPs). Students will examine the structure/function relationships for different integral membrane protein families including G-protein coupled receptors (GPCRs), ion channels, transporters and IMPs involved in signal transduction. The interaction of several of these IMPs with other proteins or small molecule agonists/antagonists will be reviewed, focusing on the structure-function aspects of these interactions
Course Masters: Drs. Dokland, Prevelige, Saad and Walter
This course will focus on the use of X-ray crystallography, Cryo-Electron microscopy and Image Reconstruction, NMR, and Mass Spectrometry to obtain structures of biological macromolecules. Each component will be taught separately (Drs Walter, Dokland, Saad and Prevelige, respectively). Each module will focus on insuring the student has a basic understanding of the essential principles of the technique and its practical application. Examples will be drawn from virology, bacteriology, cell biology and immunology. Students will be actively involved through assigned problem sets and in class discussion. The material in this course will be targeted towards second year graduate students and non-specialists. This course will be every other year.
Course Masters: Prevelige, Saad, Walter, Dokland
This course will dissect viral life-cycles with an emphasis on the structural basis for each step. Since each step solves a biological problem it will be organized by the steps of the lifecycle rather than by families of viruses. In this way, commonalities and differences will be most apparent. The source material will be both current and classic primary literature. Student involvement will take the form of reading, presenting, and discussing those papers. This course is intended for graduate students in their 3 or greater year. While the Hybrid Techniques course is not a prerequisite it is highly recommended. This course will alternate with the Hybrid Techniques course.
Course Master: N. Rama Krishna:
The main purpose of this course is to provide fundamental understanding (physics) to graduate students who want to utilize NMR spectroscopy as a major tool in their structural biology research. Students with elementary Quantum Mechanics background will gain the optimum benefit from this course. The course is offered every two years. This course covers basic NMR Theory and Concepts (Nuclear Spin-1/2, Bloch Equations, FT-NMR, Rotating Frame, Various Relaxation Mechanisms, Chemical shits, J couplings, etc), Density Matrix Theory, Product Operator Description of 2D- and 3D-NMR, Nuclear Overhauser Effect, Conformational Exchange, Solomon-McConnel equations, Residual Dipolar Couplings, NMR spectra of Amino acids, Peptides and Proteins, Solvent Suppression Methods, Random Coil Chemical shifts, 2D-NMR methods for assignments and structure calculations of peptides and small proteins, 3D/4D-NMR methods for assignment and structure studies of large proteins, CYANA Structure-Refinement calculations, NMR of nucleic acids, Protein Dynamics, and study of Protein-Ligand complexes including applications in drug design (STD-NMR, trNOESY, SAR-by-NMR and ILOE).
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Course Master: N. Rama Krishna
The main purpose of this Course is to make students feel comfortable with the operation of the state-of-the-art NMR spectrometers. At the conclusion of the course, students should feel encouraged to incorporate NMR spectroscopy in their research programs on a regular basis (course is offered annually). This is a hands-on instruction to students about putting the sample in the magnet, tuning the probe, magnet shimming, deuterium lock, pulse calibration, setting up 1D/2D/3D-NMR experiments, and data processing using Topspin software. The students will utilize gramicidin-S and 15N/13C-calmodulin as a test samples. They are also encouraged to bring their own samples from their mentor’s laboratories. We will utilize the 500 MHz and 600 MHz NMR spectrometers for this workshop, with two students at each spectrometer, taking turns in learning the operation. Course limited to 8 students maximum (i.e., four students in the morning sessions and four students in the afternoon sessions). (6-week Course, with 6 Hrs/week for each student)
Course Masters: Drs. Champion Deivanayagam and Larry DeLucas
Students participating in this course will acquire a sufficient understanding of the theoretical and experimental aspects of protein crystallography to enable them to crystallize proteins, collect X-ray diffraction data, and determine and refine protein structures using molecular replacement and isomorphous replacement phase determination methods. Students will learn a variety of experimental techniques including automated nano-crystallization, crystal harvesting and cryo-preparation, data collection via in-house and synchrotron X-ray diffraction as well as becoming familiar with the latest structure determination software and hands on training in solving molecular replacement structures and ab-initio phasing. (course is offered every two years).
Course Master: Dr. Yuhua Song
The BME 580 course introduces students to computational structural biology. Graduate students are taught molecular modeling principles and applications. Throughout the course, students are offered hands-on exercises in molecular modeling tools and software.
Course Masters: Drs Barnes and Renfrow
Students participating in this course become familiar with standard analysis of proteins and protein mixtures by analytical mass spectrometry. This includes the analysis of recombinant and native isolations of proteins including the analysis of post translational modifications. The first month of the course will focus on the fundamentals of mass spectrometry and protein analysis and will be open to first year students. The second and third months of the course is followed by an applications section for students who have completed their first year course requirements. Included topics throughout the course include, sample preparation, mass spectrometry instrumentation, mass spectral interpretation, proteomic experimentation, database searching, analysis of protein modifications, targeted analysis of proteins in complex mixtures, and structural techniques in mass spectrometry.
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