Nuclear Magnetic Resonance (NMR)

Biophysical Journal Teaching Article

Teaching High-Resolution Nuclear Magnetic Resonance to graduate Students in Biophysics
Laura Lerner and David A. Horita
Biophys. J. 65(6): 2692-2697 (1993) (pdf version ~157 K)

Volume Contents

• Introduction (David Gorenstein)
• Chapter 1: Fundamentals of NMR (Tom James) - [download pdf file ~1137 K]
• Chapter 2: Introduction to Theory and Practice of 2D NMR (J. Evans)
• Chapter 3: High Resolution NMR of Peptides and Proteins (J. Evans)
• Chapter 4: Solid-State NMR (J. Evans)
• Chapter 5: 2D NOESY of Proteins (J. Evans)
• Chapter 6: Homonuclear 3D NMR (Rob Kaptein)
• Chapter 7: A Pictorial Representation of Product-Operator Formalism: Non-Classical Vector Diagrams for Multidimensional NMR (David Donne and David Gorenstein) - [download pdf file ~2840 K]
• Chapter 8: NMR Relaxation Theory (T. Farrar)
• Chapter 9: Electron-nucleus interactions and its biophysical consequences (Ivano Bertini and Claudio Luchinat) - [download pdf file ~518 K]
• Chapter 10: Paramagnetic effects in proteins (Ivano Bertini and Claudio Luchinat)
• Chapter 11: NMR of paramagnetic proteins (Ivano Bertini and Claudio Luchinat) - [download pdf file ~355 K]
• Chapter 12: NMR of Nucleic Acids (David Wemmer)
• Chapter 13: Structural Refinement Using Homonuclear NMR (Bruce Luxon, Tom James)
• Chapter 14: Multidimensional Heteronuclear NMR of Proteins (G. Marius Clore, Angela Gronenborn)
• Chapter 15: Protein Sequential Assignment Strategies (Flemming Poulsen, Mogens Kjaer)
• Chapter 16: Quality of NMR Derived Structures (Tom James)
• Chapter 17: NMR of Membrane Proteins (S. Opella)
• Chapter 18: NMR of Protein-Nucleic Acid Complexes (G. M. Clore, A. Gronenborn)
• Chapter 19: NMR of Protein-Ligand Interactions (G. K. Roberts)
• Chapter 20: Magnetic Resonance Imaging (Joan Dawson and Paul Lauterbur)
• Chapter 21: NMR of Quadrupolar Nuclei (Gil Navon)
• Chapter 22: Dynamical Process in Biomolecules (B. D. Nageswara Rao and Steven D. Landy)
• Chapter 23: Multinuclear NMR of RNA (E. Nikonowicz)
• Chapter 24: Fluorine NMR ( J. T. Gerig) - [download pdf file ~275 K]
• Chapter 25: ³¹P NMR in Nucleic Acids (D. G. Gorenstein)
• Chapter 26: NMR Software (B. Luxon)

CHAPTERS

• Introduction (David Gorenstein)
  
  
• Chapter 1: Fundamentals of NMR
  Tom James
  (pdf version ~1137 K)

  1.2 Magnetic Resonance

  Nuclear Spins

  The Resonance Phenomenon

  Sensitivity and the Boltzmann Equation

  Magnetization

  1.3 The Nuclear Magnetic Resonance Experiment

  Pulsed NMR

  Fourier Transform Nuclear Magnetic Resonance

  1.4 Relaxation

  Basis

  Causes

  Measurements

  1.5 Other NMR Parameters

  General Features of the Nuclear Magnetic Resonance Spectrum

  Chemical Shift

  Spin-spin Coupling (Splitting)

  Linewidth

  Peak Intensity

  1.6 Nuclear Overhauser Effect

  1.7 Chemical Exchange

  [Return to Index]

• Chapter 2: Introduction to Theory and Practice of 2D NMR (J. Evans)
  [Return to Index]

• Chapter 3: High Resolution NMR of Peptides and Proteins (J. Evans)
  [Return to Index]

• Chapter 4: Solid-State NMR (J. Evans)
  [Return to Index]

• Chapter 5: 2D NOESY of Proteins (J. Evans)
  [Return to Index]

• Chapter 6: Homonuclear 3D NMR (Rob Kaptein)
  [Return to Index]

• Chapter 7: A Pictorial Representation of Product-Operator Formalism: Non-Classical Vector Diagrams for Multidimensional NMR
  David Donne and David Gorenstein
  (pdf version ~2840 K)
  

  7.1 Introductions

  7.2 Non-Classical Pictoral Representation of Base Operations

  The Product operator formalism

  Essence of the classical vector model

  Derivation of one-spin vectors

  Derivation of two-spin vectors

  7.3 Graphical Description of Time Evolution

  Chemical shift evolution

  Scalar coupling evolution

  Effects of pulses

  Vector representation of three-spin systems

  7.4 Application of the Non-Classical Vector Model

  Coherence transfer: the 2D COSY experiment

  Origin of diagonal peaks
  Origin of cross peaks
  Phase properties of COSY peaks
  The unobservable coherence
  

  Multiple-quantum coherence spectroscopy

  The INADEQUATE experiment The immportance of phose cycling The DEPT experiment

  Sensitivity enhancement in multidimensional NMR

  Sensitivity enhancement and quadrature detection The original HSQC experiment The sensitivity-enhanced HSQC experiment

  7.5 Conclusion

  [Return to Index]

• Chapter 8: NMR Relaxation Theory (T. Farrar)
  [Return to Index]

• Chapter 9: Electron-nucleus interactions and its biophysical consequences
  Ivano Bertini and Claudio Luchinat
  (pdf version ~518 K)

  9.1 Basic electron spin properties

  Differences and analogies between electron and nuclear spins

  Electron-nucleus dipolar and contact interactions

  9.2 Electron-nucleus interactions seen from the nucleus

  The shifts

  Nuclear relaxation

  9.3 Gains and losses from the NMR viewpoint

  9.4 Solvent relaxometry

  9.5 Paramagnetic ions as probes

  Shift reagents

  Relaxation reagents

  Contrast agents in MRI

  9.6 Magnetic coupled systems

  [Return to Index]

• Chapter 10: Paramagnetic effects in proteins (Ivano Bertini and Claudio Luchinat)

  10.1 Nature of the paramagnetic center

  10.2 Effects on protein nuclei

  10.3 Effects on solvent nuclei

  10.4 Paramagnetic molecules-biomolecules interactions

  Shift reagents

  Relaxation reagents

  Contrast agents

  10.5 Relaxometry

  10.6 Polymetallic systems

  [Return to Index]

• Chapter 11: NMR of paramagnetic proteins
  Ivano Bertini and Claudio Luchinat
  (pdf version ~355 K)

  11.1 NMR as a spectroscopic tool

  Signal detection and assignment

  Information on the magnetic susceptibility tensor

  Spin density delocalization

  11.2 NMR as a structural tool

  Contact shifts as structural constraints

  MCPCSs as constraints

  Nuclear relaxation enhancement-based constraints

  11.3 Perspectives in NMR of paramagnetic molecules

  [Return to Index]

• Chapter 12: NMR of Nucleic Acids (David Wemmer)
  [Return to Index]

• Chapter 13: Structural Refinement Using Homonuclear NMR (Bruce Luxon, Tom James)
  [Return to Index]

• Chapter 14: Multidimensional Heteronuclear NMR of Proteins (G. Marius Clore, Angela Gronenborn)
  [Return to Index]

• Chapter 15: Protein Sequential Assignment Strategies (Flemming Poulsen, Mogens Kjaer)

  15.1 Introduction to sequential assignment of proteins

  15.2 Recognition of amino acid residues in protein NMR spectra

  ¹H NMR spectroscopy

  ¹H and ¹⁵N NMR spectroscopy

  ¹H, ¹³C and ¹⁵N NMR spectroscopy

  15.3 Sequential assignment

  ¹H- NMR spectroscopy using NOESY

  ¹H and ¹⁵N NMR spectroscopy using NOESY

  ¹H, ¹³C and ¹⁵N NMR spectroscopy using correlation spectroscopy

  15.4 Assignment in theory and practice

  15.5 Assignment using computers

  [Return to Index]

• Chapter 16: Quality of NMR Derived Structures (Tom James)

  16.1 Introduction

  16.2 Factors Influencing Structural Accuracy

  16.3 Criteria for Assessing Quality of Structures Derived Using NMR Data

  [Return to Index]

• Chapter 17: NMR of Membrane Proteins (S. Opella)
  [Return to Index]

• Chapter 18: NMR of Protein-Nucleic Acid Complexes (G. M. Clore, A. Gronenborn)
  [Return to Index]

• Chapter 19: NMR of Protein-Ligand Interactions (G. K. Roberts)

  19.1 Introduction

  Information on protein-ligand interactions available from NMR

  Importance of exchange

  Experimental strategies

  19.2 Exchange effects on NMR spectra in the context of ligand binding

  Basic characteristics of fast, intermediate and slow exchange

  Analysis of spectra

  Fast exchange
  Moderately fast and intermediate exchange
  Slow exchange

  19.3 Examples - direct observation of the complex

  Use of isotope labelling to distinguish protein and ligand resonances

  Intermolecular NOEs - identification of contact residues

  Intramolecular NOEs - ligand conformation

  Chemical shifts - charge states

  Dynamics

  19.4 Examples - observation of averaged signals

  Transferred NOEs - intramolecular and intermolecular

  Qualitative analysis
  Quantitative analysis

  Paramagnetic relaxation

  Chemical shifts and determination of equilibrium constants

  Problems of averaging - interpretation of averaged parameters

  19.5 Summary

  19.6 References

  [Return to Index]

• Chapter 20: Magnetic Resonance Imaging (Joan Dawson and Paul Lauterbur)
  [Return to Index]

• Chapter 21: NMR of Quadrupolar Nuclei (Gil Navon)
  [Return to Index]

• Chapter 22: Dynamical Process in Biomolecules (B. D. Nageswara Rao and Steven D. Landy) Dynamic NMR Processes in Biomolecules B. D. Nageswara Rao and S. B. Landy

  22.1 Introduction

  1.1 Dynamical nature of macromolecular complexes

  1.2 Effect of exchange on NMR spectra 1.2.1 Lineshapes 1.2.2 Relaxation parameters

  1.3 Quantitative analysis of exchange effects 1.3.1 Preview 1.3.2 Organization of the chapter

  22.2 Mathematical formulation of exchange effects using generalized Bloch matrices

  2.1 Lineshapes

  2.2 Spin-lattice relaxation rates

  2.3 Nuclear Overhauser Effect (NOE)

  22.3 Computation of lineshapes

  3.1 Simple lines, Bloch equations

  3.2 Spin multiplets, density matrix methods

  3.3 Procedure for simulating spectra

  3.4 Examples

  22.4 Spin-lattice relaxation in paramagnetic complexes

  4.1 Effects of lifetimes, experimental strategies

  4.2 Relaxation effects in equilibrium

  4.3 Experimental examples

  22.5 Exchange effects in NOE experiments

  5.1 Transferrred NOE (TRNOE)

  5.1.1 Fast exchange between bound and free states 5.1.2 Slow exchange between bound and free states 5.1.3 Multiple binding sites

  5.2 Methods of analysis

  5.2.1 Initial-slope method 5.2.2 Relaxation-matrix method 5.2.3 Errors in derived distances

  5.3 Examples

  22.6 Problems

  6.1 Elementary problems

  6.2 Advanced problems

  
  [Return to Index]

• Chapter 23: Multinuclear NMR of RNA (E. Nikonowicz)

  23.1 Introduction to labeled RNA

  Isotopic enrichment of RNA
  Resonance assignment strategy

  23.2 Characteristics of the heteronuclear spectrum of RNA

  Scalar couplings in RNA nucleotides
  Chemical shifts of the ¹³C, ¹⁵N, and ³¹P spectra

  23.3 Resonance assignment using isotopically enriched RNAs

  Scalar correlation strategies
  Ribose ring correlations: HCCH-COSY and HCCH-TOCSY experiments
  Intra-nucleotide base-to-ribose correlations: HsCsNbCbHb and long range ¹⁵N-¹H HSQC
  Correlations through the phosphate backbone: HETCOR and HCP
  Intra-base correlations between exchangeable and non-exchangeable protons
  Through-space correlation strategies
  Intra- and inter-residue correlations via non-exchangeable protons: ¹³C-edited 3D NOESY experiment
  Exchangeable ¹H resonance assignment: ¹⁵N-edited 3D NOESY experiment

  23.4 Extracting structural information from labeled RNA molecules

  ¹³C/¹⁵N-edited NOESY

  Heteronuclear edited COSY for 3JHH

  Backbone torsion angles from 3JCP

  23.5 Dynamic information from heteronuclear relaxation

  [Return to Index]

• Chapter 24:
  Fluorine NMR
  J. T. Gerig
  (pdf version ~275 K)

  24.1 Introduction

  Fluorine in chemistry and biochemistry

  NMR in biochemistry

  Fluorine NMR in biochemistry

  Fluorine containing biological materials

  Fluorine containing proteins

  24.2 Fluorine chemical shifts in biological systems

  Fluorine referensing

  Factors affecting fluorine shielding in biological systems

  Fluorine chemical shift changes in biological systems

  H₂O/D₂O solvent sensitivity

  Theoretical considerations of fluorine shielding in biological systems

  24.3 Fluorine relaxation in biological systems

  Fluorine relaxation by dipole-dipole mechanism

  Fluorine relaxation through cheical shift anisotropy

  24.4 Practical consideration

  24.5 Some Samples

  Fluorine NMR as an analytical tool

  Fluorine NMR studies of ligand-receptor complexes

  Protein denaturation

  The role of specific amino acids in protein function

  Structural mobility

  Effects of fluorine on structure and dynamics in biological systems

  Summary

  References

  [Return to Index]

• Chapter 25: ³¹P NMR in Nucleic Acids (D. G. Gorenstein)

  25.0 Introduction

  25.1 Phosphorus-31 Chemical Shifts

  Introduction and Basic Principles

  Theoretical ³¹P Chemical Shift Calculations and Empirical Observations

  Bond Angle Effects

  Stereoelectronic Effects on ³¹P Chemical Shifts

  Extrinsic and Other Effects on ³¹P Chemical Shifts

  25.2 Assignment of ³¹P Signals of Oligonucleotides

  25.3 ³¹P Heteronuclear Coupling Constants

  25.4 ³¹P Melting Curves

  25.5 ³¹P NMR of Polynucleic Acids

  25.6 ³¹P NMR of DNA-Drug Complexes

  25.7 Sequence-Specific Variation in ¹³P Chemical Shifts and Coupling Constants

  ³¹P Chemical Shifts as a Function of Sequence and Position

  Conformation and Dynamics of the Phosphate Ester Backbone

  Origin of Sequence-specific Variations in Torsional Angles and Coupling Constants

  Comparison of the Phosphate Backbone Torsional Angle Variations from NMR and X-ray Crystal Structures

  Correlation of Local Helical Geometry with Backbone Conformation

  25.8 ³¹P NMR of Protein-DNA Complexes

  25.9 Conclusions

  [Return to Index]

• Chapter 26: NMR Software (B. Luxon)
  [Return to Index]

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  © 1999, Biophysical Society

  Last updated 1/19/99
  Carol Gross cgross@biosci.umn.edu