Biochem 800 – Practical Nuclear Magnetic Resonance Theory.
Every fall semester, Dr. Milo Westler, Director of NMRFAM, teaches Biochem 800 – Practical Nuclear Magnetic Resonance Theory (2 credits) at UW-Madison on Tuesdays and Thursdays at 11:00am in Room 2221 in the DeLuca Biochemical Sciences Building. Scope of the course includes study of multipulsed, multinuclear, and multidimensional NMR spectroscopy, emphasis on the vector and product, and operator formalisms for the analysis of modern pulse sequences. Course format is lecture and discussion and grades will be based on participation and problem sets. Topics to be covered: The Vector Paradigm; Coherence and Magnetization; Radio Frequency (Rf) Excitation; Chemical Shifts; Signal Detection; Fourier Transformation; Coherence Transfer Pathways and Phase Cycling; Pulsed Field Gradients; Scalar Coupling; Product Operator Formalism; Coherence Transfer; Isotope Directed Editing; Two-Dimensional NMR; Multi (>2)-Dimensional NMR; 1H, 13C, and 15N Triple Resonance 3D and 4D NMR; Pulse Concatenation and Sequence Optimization; Relaxation. Prerequisites are introductory NMR (e.g., organic chemistry), basic trigonometry, elementary physics, and physical chemistry.
Biochem 801 – Biochemical Applications of Nuclear Magnetic Resonance.
Every spring semester, Professor John Markley and a team of scientists from NMRFAM teach Biochem 801 – Biochemical Applications of Nuclear Magnetic Resonance (2 credits) This course consists of lectures surveying current solution-state nuclear magnetic resonance techniques used in biochemical research; the emphasis is on how data are acquired and on practical applications. Prerequisite: Consent of instructor. Sample Syllabus.
18 October 2016
Integrative NMR for biomolecular research. NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page (http://pine.nmrfam.wisc.edu/download_packages.html), and detailed instructions are available from the Integrative NMR Video Tutorial page (http://pine.nmrfam.wisc.edu/integrative.html). Continue reading at PubMed.
21 November 2014
A small angle X-ray scattering (SAXS) instrument, Bruker-AXS Nanostar, have been installed and is operational. A Bruker-Axs Nanostar with a rotating anode source is now installed (funding obtained from NIH-shared instrumentation, Professor Sam Butcher, PI, UW-Madison Department of Biochemistry). The system resides in NMRFAM and is available to users of the facility. More information about the system is at Bruker’s website.
Several documents on the use of the instrument and SAXS data analysis are available.
- NMRFAM SAXS Manual for Data Processing and Modeling (by Jordan Burke & Jameson Bothe)
- NanoStar Script Guide
- SAXS Trapezoid Integration (MS Office XML Spreadsheet)
- SAXS Temperature script
21 November 2014
NMRFAM-SPARKY is a recently updated version of SPARKY (https://www.cgl.ucsf.edu/home/sparky) that supports user-defined enhancements. We have used these capabilities to develop new tools in support of packages generated at NMRFAM for automated protein assignment and structure determination. The added features support:
(1) interfacing with servers offering new technologies,
(2) tools for data visualization and verification, and
(3) new protocols for maximizing the efficiency of NMR data analysis. In NMRFAM-SPARKY, we have refined these SPARKY enhancements through their use in our annual workshops by participants with varying experience in protein NMR spectroscopy.
15 February 2013
Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy. ADAPT-nuclear magnetic resonance (ADAPT-NMR) offers an automated approach to the concurrent acquisition and processing of protein NMR data with the goal of complete backbone and side chain assignments. What the approach lacks is a useful graphical interface for reviewing results and for searching for missing peaks that may have prevented assignments or led to incorrect assignments. Because most of the data ADAPT-NMR collects are 2D tilted planes used to find peaks in 3D spectra, it would be helpful to have a tool that reconstructs the 3D spectra. Continue reading at PubMed
1 October 2012
PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis. PACSY (Protein structure And Chemical Shift NMR spectroscopy) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. Continue reading at PubMed
1 April 2012
RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts. The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency, and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Continue reading at PubMed