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Pocket Guide to Biomolecular NMR


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Table of Contents

1 Atomic Bells and Frequency Finders 1.1 Chemical Choirs 1.2 Essentials of Electromagnetism 1.3 Electromagnetic Microsensors 1.4 Frequency Finders Mathematical Sidebar 1.1: Fourier Transform 1.5 Basics of one-dimensional NMR Mathematical Sidebar 1.2 Converting Hz to PPM References 2 Bonded Bells and Two-Dimensional Spectra 2.1 Introduction to Coupling 2.2 Bonded Bells: J-Coupling Mathematical Sidebar 2.1: Karplus Equation 2.3 NMR Maps: Two-Dimensional Spectra Mathematical Sidebar 2.2 Why 12C and 14N atoms are so shy? 2.4 The 1H-15N HSQC: Our Bread and Butter 2.5 Hidden Notes: Creating Two-Dimensional Spectra References 3 Neighboring Bells and Structure Bundles 3.1 Bumping Bells: Dipole-Dipole Coupling Mathematical Sidebar 3.1: Dipole-dipole Coupling 3.2 Atomic Meter Stick: the NOE 3.3 Into "Three-D" 3.4 Adult "Connect-the-Dots:" HNCA 3.5 Putting the Pieces Together: A Quick Review 3.6 Wet Noodles and Proteins Bundles: Building a Three-Dimensional Structure References 4 Relaxation Theory Part One: Silencing of the Bells 4.1 Nothing Rings Forever: Two Paths to Relax 4.2 Relaxation: Ticket to the Protein Prom Mathematical Sidebar 4.1: Boltzmann Distribution 4.3 Oh-My, How Your Field Fluctuates 4.4 Blowing Off Steam and Returning to Equilibrium: T1 Mathematical Sidebar 4.2: T1 Relaxation 4.5 Loosing Lock-Step : Coherence and T2 Mathematical Sidebar 4.3: T2 Relaxation and Spin Echo References 5 Relaxation Theory Part Two: Moving Atoms and Changing Notes 5.1 Keeping the Terms Straight 5.2 NMR Dynamics in a Nutshell: The Rules of Exchange 5.3 Two States, One Peak: Atoms in the Fast Lane of Exchange 5.4 Two States, Two Peaks: Atoms in the Slow Lane of Exchange 5.5 Two States, One Strange Peak: Atoms in Intermediate Exchange 5.6 Tumbling Together: Rotational Correlation Time ( c) 5.7 Summary References 6 Protein Dynamics 6.1 Dynamics Analysis by NMR: Multli-Channel Metronomes, Not a GPS 6.2 Elegant Simplicity: Lipari and Szabo Throw Out the Models 6.3 Wagging Tails and Wiggling Bottoms: Local versus Global Motion 6.4 Measuring Fast Motion: Model Free Analysis Mathematical Sidebar 6.1: Correlation Functions and Model Free 6.5 Changing Directions on the Track: Refocusing Pulses 6.6 Measuring Intermediate Motion: CPMG Relaxation Dispersion Analysis 6.7 Measuring Slow Motion: Z-Exchange Spectroscopy 6.8 Measuring Motion Summary References

About the Author

Currently an Assistant Editor for the journal Cell, Michaeleen Doucleff obtained her PhD in Chemistry from the University of California, Berkeley while working in the lab of David E. Wemmer. Doucleff then became a Nancy Nossal postdoctoral fellow at the National Institute's of Health in the lab of G. Marius Clore. Throughout her career, she has used NMR spectroscopy and X-ray crystallography to characterize the structure and dynamics of transcription factors and their interaction with DNA. Mary Hatcher-Skeers is a Professor of Chemistry in the Joint Science Dept. of Claremont McKenna, Pitzer and Scripps Colleges in Claremont CA. She teaches General Chemistry, Biochemistry, Physical Chemistry and NMR Spectroscopy. Hatcher-Skeers received her PhD in Chemistry from the University of Washington while working in the lab of Gary Drobny. She was then a NIH Post-Doctoral Fellow in the labs of Judith Herzfeld at Brandeis University and Robert Griffin at MIT. Professor Hatcher-Skeers' research uses solid-state and solution NMR spectroscopy to investigate the role of DNA structure and dynamics in protein and drug binding. She has trained over 70 undergraduates in her research lab, a number who have gone on to graduate programs in chemistry and biochemistry. Nicole Crane, Ph.D. is currently a Scientist at the Naval Medical Research Center in Silver Spring, MD where she is establishing the Regenerative Medicine Department's Advanced Imaging Program. Her research focuses on development and utilization of spectroscopic techniques to improve understanding of the wound healing process, particularly in traumatic acute wounds, as well as identifying and quantifying transplant-associated ischemia and reperfusion injury. Her experience as an applied spectroscopist includes applications in forensics, pharmaceuticals, and biomedicine. Dr. Crane has published over fifteen peer-reviewed publications and presented at numerous regional and national scientific meetings. She is also an inventor on two US patents.

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