
Protein NMR Spectroscopy : Practical Techniques and Applications.
Başlık:
Protein NMR Spectroscopy : Practical Techniques and Applications.
Yazar:
Roberts, Gordon.
ISBN:
9781119972013
Yazar Ek Girişi:
Basım Bilgisi:
1st ed.
Fiziksel Tanımlama:
1 online resource (380 pages)
İçerik:
Protein NMR Spectroscopy: Practical Techniques and Applications -- Contents -- List of Contributors -- Introduction -- References -- 1 Sample Preparation, Data Collection and Processing -- 1.1 Introduction -- 1.2 Sample Preparation -- 1.2.1 Initial Considerations -- 1.2.2 Additives -- 1.2.3 Sample Conditions -- 1.2.4 Special Cases -- 1.2.5 NMR Sample Tubes -- 1.2.5.1 3 mm Tubes -- 1.3 Data Collection -- 1.3.1 Locking -- 1.3.2 Tuning -- 1.3.3 Shimming -- 1.3.4 Calibrating Pulses -- 1.3.5 Acquisition Parameters -- 1.3.6 Fast Acquisition Methods -- 1.4 Data Processing -- References -- 2 Isotope Labelling -- 2.1 Introduction -- 2.2 Production Methods for Isotopically Labelled Proteins -- 2.2.1 Recombinant Protein Expression in Living Organisms -- 2.2.1.1 Escherichia coli -- 2.2.1.2 Yeast Cells -- 2.2.1.3 Other Host Cells -- 2.2.2 Cell-Free Synthesis -- Protocol 1: Preparation of the Amino Acid Free S30 Extract -- Protocol 2: Cell-Free Reaction on a Small Scale -- 2.3 Uniform Isotope Labelling of Proteins -- 2.3.1 Uniform 15N Labelling -- 2.3.2 Uniform 13C, 15N Labelling -- 2.3.3 2H Labelling -- 2.4 Selective Isotope Labelling of Proteins -- 2.4.1 Amino Acid Type-Selective Labelling -- 2.4.2 Reverse Labelling -- 2.4.3 Stereo-Selective Labelling -- 2.5 Segmental Labelling -- 2.6 SAIL Methods -- 2.6.1 Concept of SAIL -- 2.6.2 Practical Procedure for the SAIL Method -- Protocol 3: Production of SAIL Proteins by the E. coli Cell-Free Method -- 2.6.3 Residue-Selective SAIL Method -- Protocol 4: Optimisation of the Amount of SAIL Amino Acids for the Production of Calmodulin Selectively Labelled by SAIL Phenylalanine -- 2.7 Concluding Remarks -- Acknowledgements -- References -- 3 Resonance Assignments -- 3.1 Introduction -- 3.2 Resonance Assignment of Unlabelled Proteins -- 3.2.1 Spin System Assignments -- 3.2.2 Sequence-Specific Assignments.
3.2.3 Possible Difficulties -- 3.3 15N-Edited Experiments -- 3.4 Triple Resonance -- 3.4.1 3D Triple Resonance -- 3.4.1.1 Identification of Spin Systems -- 3.4.1.2 Sequential Assignment -- 3.4.1.3 Proline Residues -- 3.4.2 4D Triple Resonance -- 3.4.3 Computer-Assisted Backbone Assignments -- 3.4.4 Unstructured Proteins -- 3.4.5 Large Proteins -- 3.5 Side-Chain Assignments -- References -- 4 Measurement of Structural Restraints -- 4.1 Introduction -- 4.2 NOE-Based Distance Restraints -- 4.2.1 Physical Background -- 4.2.2 NMR Experiments for Measuring the NOE -- 4.2.3 Set-up of NOESY Experiments -- 4.2.3.1 Estimation of T2s -- Recipe 4.1: 1-1 Echo Experiment -- Recipe 4.2: Set-up of Optimal Acquisition Times -- Recipe 4.3: Set-up of a 3D 15N-Edited NOESY Experiment (Figure 4.2a) -- Recipe 4.4: Set-up of a 3D 13C-Edited NOESY Experiment -- 4.2.4 Deriving Structural Information from NOE Cross-peaks -- Recipe 4.5: Extraction of Distances Using Classes -- Recipe 4.6: Extraction of Distances Using the Two-Spin Approximation -- 4.2.5 Information Content of NOE Restraints -- 4.3 Dihedral Restraints Derived from J-Couplings -- 4.3.1 Physical Background -- 4.3.2 NMR Experiments for Measuring J-Couplings -- Recipe 4.7: E.COSY Experiment -- Recipe 4.8: Quantitative J-Correlation -- 4.3.3 Deriving Structural Information from J-Couplings -- 4.4 Hydrogen Bond Restraints -- 4.4.1 NMR H-Bond Observables -- 4.4.2 Detection of N-H∙∙∙O=C H-Bonds in Proteins -- Recipe 4.9: Setting up a Long-Range HNCO Experiment for H-Bond Detection -- 4.5 Orientational Restraints -- 4.5.1 Physical Background -- 4.5.1.1 Dipolar Couplings in Anisotropic Solution -- 4.5.1.2 The Alignment Tensor -- 4.5.1.3 Chemical Shifts in Anisotropic Solution -- 4.5.2 Alignment Methods -- 4.5.2.1 Intrinsic Molecular Alignment -- 4.5.2.2 Indirect Alignment by External Media.
4.5.3 Measurements and Data Analysis -- 4.5.4 Determination of the Alignment Tensor -- 4.5.4.1 Degeneracy of Solutions -- 4.5.4.2 Prediction of the Alignment Tensor from the Structure -- 4.5.5 RDCs in Structure Validation -- 4.5.5.1 Q-Factor -- 4.5.6 RDCs in Structure Determination -- 4.5.6.1 Structure Refinement -- 4.5.6.2 Domain Orientation -- 4.5.6.3 De Novo Structure Determination -- 4.5.7 Conclusion -- 4.6 Chemical Shift Structural Restraints -- 4.6.1 Origin of Chemical Shifts and Its Relation to Protein Structure -- 4.6.2 Obtaining Chemical Shifts -- 4.6.3 Backbone Dihedral Angle Restraints from Chemical Shifts (TALOS) -- Recipe 4.10: Using the TALOS+ Program (for details see http://spin.niddk.nih.gov/bax/ software/TALOS+/) -- 4.6.4 Protein Structure Determination from Chemical Shifts (CS-Rosetta) -- Recipe 4.11: CS-Rosetta Structure Calculation -- 4.7 Solution Scattering Restraints -- 4.7.1 Physical Background -- 4.7.2 Shape Reconstructions from Solution Scattering Data -- 4.7.3 Use of SAXS in High-Resolution Structure Determination -- 4.7.4 Sample Preparation -- 4.7.5 Data Collection -- 4.7.6 Data Processing and Initial Analysis -- Acknowledgement -- References -- 5 Calculation of Structures from NMR Restraints -- 5.1 Introduction -- 5.2 Historical Development -- 5.3 Structure Calculation Algorithms -- 5.3.1 Molecular Dynamics Simulation versus NMR Structure Calculation -- 5.3.2 Potential Energy - Target Function -- 5.3.3 Torsion Angle Dynamics -- 5.3.3.1 Tree Structure -- 5.3.3.2 Kinetic Energy -- 5.3.3.3 Forces = Torques =− Gradient of the Target Function -- 5.3.3.4 Equations of Motion -- 5.3.3.5 Torsional Accelerations -- 5.3.3.6 Time Step -- 5.3.4 Simulated Annealing -- Protocol for Simulated Annealing -- 5.4 Automated NOE Assignment -- 5.4.1 Ambiguity of Chemical Shift Based NOESY Assignment -- 5.4.2 Ambiguous Distance Restraints.
5.4.3 Combined Automated NOE Assignment and Structure Calculation with CYANA -- 5.4.4 Network-Anchoring -- 5.4.5 Constraint Combination -- 5.4.6 Structure Calculation Cycles -- 5.5 Nonclassical Approaches -- 5.5.1 Assignment-Free Methods -- 5.5.2 Methods Based on Residual Dipolar Couplings -- 5.5.3 Chemical Shift-Based Structure Determination -- 5.6 Fully Automated Structure Analysis -- References -- 6 Paramagnetic Tools in Protein NMR -- 6.1 Introduction -- 6.2 Types of Restraints -- 6.2.1 Paramagnetic Dipolar Relaxation Enhancement -- 6.2.2 Other Types of Relaxation -- 6.2.3 Residual Dipolar Couplings -- 6.2.4 Contact and Pseudocontact Shifts -- 6.3 What Metals to Use? -- 6.4 Paramagnetic Probes -- 6.4.1 Substitution of Metals -- 6.4.2 Free Probes -- 6.4.3 Nitroxide Labels -- 6.4.4 Metal Binding Peptides -- 6.4.5 Synthetic Metal Chelating Tags -- Protocol for the Application of Paramagnetic NMR on Diamagnetic Proteins -- 6.5 Examples -- 6.5.1 Structure Determination of Paramagnetic Proteins -- 6.5.2 Structure Determination Using Artificial Paramagnets -- 6.5.3 Structures of Protein Complexes -- 6.5.4 Studying Dynamics with Paramagnetism -- 6.6 Conclusions and Perspective -- References -- 7 Structural and Dynamic Information on Ligand Binding -- 7.1 Introduction -- 7.2 Fundamentals of Exchange Effects on NMR Spectra -- 7.2.1 Definitions -- 7.2.2 Lineshape -- 7.2.3 Identification of the Exchange Regime -- 7.3 Measurement of Equilibrium and Rate Constants -- 7.3.1 Lineshape Analysis -- 7.3.1.1 Slow Exchange -- 7.3.1.2 Fast Exchange -- 7.3.2 Magnetisation Transfer Experiments -- 7.3.2.1 Saturation Transfer -- 7.3.2.2 Inversion Transfer -- 7.3.2.3 Two-Dimensional Exchange Spectroscopy -- 7.3.3 Relaxation Dispersion Experiments -- 7.4 Detecting Binding - NMR Screening.
7.4.1 Detecting Binding by Changes in Rotational and Translational Mobility of the Ligand -- 7.4.2 Detecting Binding by Magnetisation Transfer -- 7.4.2.1 Saturation Transfer Difference (STD) Spectroscopy -- 7.4.2.2 Water-LOGSY -- 7.5 Mechanistic Information -- 7.5.1 Problems of Fast Exchange -- 7.5.2 Identification of Kinetic Mechanisms -- 7.5.2.1 Slow Exchange -- 7.5.2.2 Fast Exchange -- 7.6 Structural Information -- 7.6.1 Ligand Conformation - the Transferred NOE -- 7.6.1.1 Exchange Rate -- 7.6.1.2 Contributions from Other Species -- 7.6.1.3 Spin Diffusion -- 7.6.1.4 Structure Calculation -- 7.6.2 Interligand Transferred NOEs -- 7.6.2.1 Two Ligands Bound Simultaneously -- 7.6.2.2 Competitive Ligands - INPHARMA -- 7.6.3 Ligand Conformation - Transferred Cross-Correlated Relaxation -- 7.6.4 Chemical Shift Mapping - Location of the Binding Site -- 7.6.5 Paramagnetic Relaxation Experiments -- 7.6.6 Isotope-Filtered and -Edited Experiments -- References -- 8 Macromolecular Complexes -- 8.1 Introduction -- 8.2 Spectral Simplification through Differential Isotope Labelling -- 8.3 Basic NMR Characterisation of Complexes -- Protocol for Protein-Protein Titrations -- 8.4 3D Structure Determination of Macromolecular Protein-Ligand Complexes -- 8.4.1 NOEs -- 8.4.2 Saturation Transfer -- 8.4.3 Residual Dipolar Couplings -- 8.4.4 Paramagnetic Relaxation Enhancements -- 8.4.5 Pseudo-Contact Shifts -- 8.4.6 Data-Driven Docking -- 8.4.7 Small Angle X-Ray Scattering (SAXS) -- 8.5 Literature Examples -- 8.5.1 Protein-Protein Interactions -- 8.5.2 Protein-DNA Interactions -- 8.5.3 Protein-RNA Interaction -- 8.5.3.1 Protein-dsRNA -- 8.5.3.2 Protein-ssRNA -- References -- 9 Studying Partially Folded and Intrinsically Disordered Proteins Using NMR Residual Dipolar Couplings -- 9.1 Introduction -- 9.2 Ensemble Descriptions of Unfolded Proteins.
9.3 Experimental Techniques for the Characterisation of IDPs.
Özet:
"This is a must for anyone interested in using solution NMR to study proteins. Summing Up: Highly recommended. Graduate students, researchers/faculty, and professionals/practitioners." (Choice, 1 April 2012).
Notlar:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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