Isotope labeling of biomolecules - applications
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| Format: | Elektronisch E-Book |
| Sprache: | English |
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Cambridge, MA
Academic Press
2016
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| Ausgabe: | First edition |
| Schriftenreihe: | Methods in enzymology
volume 566 |
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Datensatz im Suchindex
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| adam_text | Titel: Isotope labeling of biomolecules - applications
Autor: Kelman, Zvi
Jahr: 2016
CONTENTS
Contributors xi
Preface xv
Section I
Nuclear Magnetic Resonance Spectroscopy
1. Application of Natural Isotopic Abundance nH-13C- and
^-^N-Correlated Two-Dimensional NMR for Evaluation
of the Structure of Protein Therapeutics 3
Luke W. Arbogast, Robert G. Brinson, and John P. Marino
1. Introduction 4
2. Preparation of Protein Therapeutic Samples 6
3. Acquisition of 2D Spectra 9
4. Processing 2D-Correlated Spectra 20
5. Comparative Analysis of 2D-Correlated Spectra 23
6. Perspectives 31
Acknowledgments 31
References 32
2. A Semiautomated Assignment Protocol for Methyl
Group Side Chains in Large Proteins 35
Jonggul Kim, Yingjie Wang, Geoffrey Li, and Gianluigi Veglia
1. Introduction 36
2. Labeling of Side Chain Methyl Groups for Large Proteins 37
3. Methyl Labeling Protocol for the cAMP-Dependent Protein Kinase A 39
4. Semiautomated Methyl-Group Resonance Assignment Strategies 44
5. Semiautomated Assignment Protocol Using FLAMEnGO 2.0 46
6. Conclusions and Perspectives 54
Acknowledgments 54
References 54
3.19F-Site-Specific-Labeled Nucleotides for Nucleic
Acid Structural Analysis by NMR 59
Lincoln G. Scott and Mirko Hennig
1. Introduction 60
2. General Enzymatic Synthesis of 2F-ATP, 5F-CTP, and 5F-UTP 61
vi
Contents
3. Stability of Modified RNA 64
4. Diagnostics of 19F-Chemical Shifts 66
5. NMR-Assignment Strategies for Fluoro-Modified RNA 68
6. Coupling Measurements in Fluoro-Modified RNA 74
7. Solvent-Induced Isotope Shifts 77
8. Ligand-lnduced Chemical Shift Changes 79
9. Conclusion and Remarks 82
Acknowledgments 83
References 83
4. Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene
as a NMR Assignment Tool and Probe of
Homopyrimidine/Homopurine Tract Structural Dynamics 89
Robert G. Brinson, Jennifer T. Miller, Jason D. Kahn,
Stuart FJ. Le Grice, and John P. Marino
1. Introduction 90
2. Preparation of dF-Substituted Oligonucleotides for NMR Analysis 93
3. NMR Methods 95
4. dF as an NMR Assignment Tool 96
5. Structural and Dynamic Perturbations Observed by dF Substitution 102
6. Conclusions 108
Acknowledgments 109
References 109
Section II
Scattering Techniques
5. Biomolecular Deuteration for Neutron Structural
Biology and Dynamics 113
Michael Haertlein, Martine Moulin, Juliette M. Devos, Valerie Laux,
Orla Dunne, and V. Trevor Forsyth
1. The Motivation for Macromolecular Deuteration Approaches 114
2. Concepts of In Vivo Deuteration 124
3. Levels of Specificity in Deuterium Labeling 140
4. Conclusion and Perspective 146
Acknowledgments 148
References 149
Contents
vii
6. Deuterium Labeling Together with Contrast Variation
Small-Angle Neutron Scattering Suggests How
Skp Captures and Releases Unfolded Outer Membrane Proteins 159
Nathan R. Zaccai, Clifford W. Sandlin, James T. Hoopes, Joseph E. Curtis,
Patrick J. Fleming, Karen G. Fleming, and Susan Krueger
1. Introduction 160
2. SANS from Biological Molecules in Solution 163
3. Materials and Methods 171
4. Results 179
5. Discussion 201
6. Conclusions 204
Acknowledgments 205
References 205
7. Deuteration in Biological Neutron Reflectometry 211
Frank Heinrich
1. Introduction 212
2. Experimental Methods 216
3. Data Analysis 220
4. Conclusion 226
5. Acknowledgments 226
References 227
8. Deuterium Labeling Strategies for Creating Contrast
in Structure-Function Studies of Model Bacterial Outer
Membranes Using Neutron Reflectometry 231
Anton P. Le Brun, Luke A. Clifton, Stephen A. Holt, Peter J. Holden,
and Jeremy H. Lakey
1. Introduction 232
2. Brief Introduction to Neutron Reflectometry and Data Analysis 234
3. Isolation of Deuterated LPS from Rough Strains of Escherichia coli 239
4. Formation of Rough LPS Monolayers at the Air-Liquid Interface 242
5. Modeling Monolayers of Rc-LPS from Neutron Reflectometry Data 244
6. Forming Asymmetric Bilayers Using Phospholipids and Rough LPS 246
7. Final Remarks 249
Acknowledgments 250
References 250
viii Contents
9. Essential Strategies for Revealing Nanoscale Protein
Dynamics by Neutron Spin Echo Spectroscopy 253
David J.E. Callaway and Zimei Bu
1. Introduction 254
2. Essentials for Determining Nanoscale Protein Internal Motion 255
3. Preparation of Partially Deuterated Protein Samples for NSE Experiments 265
4. Summary 268
References 268
Section III
Mass Spectrometry
10. Method for the Determination of 1SN Incorporation
Percentage in Labeled Peptides and Proteins 273
Eric L. Kilpatrick
1. Introduction 274
2. Materials 275
3. Background 275
4. Trypsin Digestion 276
5. Mass Spectrometry 279
6. Program Description 281
7. Results 285
8. Conclusions 287
References 288
11.QconCAT: Internal Standard for Protein Quantification 289
Kerry Bauer Scott, lllarion V. Turko, and Karen W. Phinney
1. Introduction 290
2. QconCAT Design 292
3. Expression and Purification of QconCAT 294
4. Characterization 297
5. Application of QconCAT 300
References 301
12. Production, Purification, and Characterization of 1SN-Labeled
DNA Repair Proteins as Internal Standards for Mass
Spectrometric Measurements 305
Prasad T. Reddy, Pawel Jaruga, Bryant C. Nelson, Mark S. Lowenthal,
Ann-Sofie Jemth, Olga Loseva, Erdem Coskun, Thomas Helleday,
and Miral Dizdaroglu
1. Introduction
306
Contents
ix
2. Materials and Methods 310
3. Production and Purification of E. coli 15N-Fpg Protein 311
4. Production and Purification of 15N-hOGG1 314
5. Production and Purification of ,sN-hNEIL1 315
6. Production and Purification of ,sN-hAPE1 317
7. Production and Purification of lsN-hMTH1 318
8. Mass Spectrometric Analysis of 1SN-Labeled Proteins 320
9. Applications to the Measurement of DNA Repair Proteins 321
10. Conclusions 326
Acknowledgments 326
References 327
Section IV
Hydrogen-Deuterium Exchange Mass Spectrometry
13. Hydrogen Exchange Mass Spectrometry 335
Leland Mayne
1. Introduction 336
2. HX Mechanism 336
3. Experimental Considerations—Exchange Labeling 338
4. Experimental Considerations—MS Measurement 345
5. Mass Spectrometer Instrument Considerations 347
6. Data Analysis 348
7. Conclusion 354
References 355
14. Mapping Protein-Ligand Interactions with Proteolytic
Fragmentation, Hydrogen/Deuterium Exchange-Mass
Spectrometry 357
Elyssia S. Gallagher and Jeffrey W. Hudgens
1. Introduction 358
2. H/D Exchange Theory 359
3. The HDX-MS Experiment 368
4. Interpreting HDX-MS Data to Determine Protein-Ligand Interaction Maps 388
Disclaimer 395
References 397
15. Isotope Labeling of Biomolecules: Structural Analysis
of Viruses by HDX-MS 405
Miklos Guttman and Kelly K. Lee
1. Introduction 406
2. Methods 411
x Contents
3. Example HDX-MS Experiment with Bovine Ribonudease A 419
Acknowledgments 421
References 421
Author Index
Subject Index
427
453
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| series | Methods in enzymology |
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| spellingShingle | Isotope labeling of biomolecules - applications Methods in enzymology Biomolekül (DE-588)4135124-1 gnd Isotopenmarkierung (DE-588)4176811-5 gnd Biochemische Methode (DE-588)4319880-6 gnd |
| subject_GND | (DE-588)4135124-1 (DE-588)4176811-5 (DE-588)4319880-6 (DE-588)4143413-4 |
| title | Isotope labeling of biomolecules - applications |
| title_auth | Isotope labeling of biomolecules - applications |
| title_exact_search | Isotope labeling of biomolecules - applications |
| title_full | Isotope labeling of biomolecules - applications edited by Zvi Kelman |
| title_fullStr | Isotope labeling of biomolecules - applications edited by Zvi Kelman |
| title_full_unstemmed | Isotope labeling of biomolecules - applications edited by Zvi Kelman |
| title_short | Isotope labeling of biomolecules - applications |
| title_sort | isotope labeling of biomolecules applications |
| topic | Biomolekül (DE-588)4135124-1 gnd Isotopenmarkierung (DE-588)4176811-5 gnd Biochemische Methode (DE-588)4319880-6 gnd |
| topic_facet | Biomolekül Isotopenmarkierung Biochemische Methode Aufsatzsammlung |
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