Serpin structure and evolution:
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Amsterdam ; Heidelberg [u.a.]
Elsevier, Acad. Press
2011
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
501 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XLVIII, 502 S., [6] Bl. Ill., graph. Darst. 24 cm |
| ISBN: | 9780123859501 0123859506 |
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Datensatz im Suchindex
| _version_ | 1804148719748120576 |
|---|---|
| adam_text | Titel: Serpin structure and evolution
Autor: Whisstock, James C.
Jahr: 2011
Contents
Contributors xi
Preface xvii
Volumes in Series xix
1. Intracellular Production of Recombinant Serpins in Yeast 1
Dion Kaiserman, Corinne Hitchen, Vita Levina, Stephen P. Bottomley,
and Phillip I. Bird
1. Introduction 1
2. Selection of Strain and Expression Plasmid 2
3. Growth of Yeast 3
4. Transformation of Yeast 4
5. Screening Transformants 4
6. Large-Scale Growth and Induction 5
7. Lysis 6
8. Purification 7
9. Assessing Serpin Activity and Removing Inactive Forms 9
10. Production of Polymerogenic Serpins 10
References 12
2. Production of Recombinant Serpins in Escherichia coli 13
Mary C. Pearce and Lisa D. Cabrita
1. Introduction 14
2. Experimental Procedures for the Production of Serpins in f. coli 20
3. Some Common Variations Used for Expression of Other Serpins 21
4. Preparation of AT from Inclusion Bodies 23
5. Preparation of Soluble AT 24
References 27
3. Isolation and Characterization of the Nuclear Serpin MENT 29
Sergei Grigoryev and Sheena McGowan
1. Introduction 30
2. Purification of the MENT Protein 31
3. Protease Inhibition/Serpin Activity 34
vi Contents
4. MENT Interaction with DNA and Chromatin In Vitro 36
5. Analysis of MENT Association with Native Chromatin In Situ 42
Acknowledgments 46
References 46
4. Solving Serpin Crystal Structures 49
Randy J. Read, Aiwu Zhou, and Penelope E. Stein
1. Introduction 50
2. Protein Production and Purification 50
3. Modifications to Aid Crystallization 51
4. Crystallization 51
5. Experimental Phasing 52
6. Molecular Replacement 53
7. Phase Improvement by Density Modification 57
8. Refinement and Validation 58
References 59
5. Crystallography of Serpins and Serpin Complexes 63
M. A. Dunstone and James C. Whisstock
1. Introduction 64
2. First Glimpses of Serpin Structures 64
3. The Serpin-Enzyme Complex 64
4. The Michaelis Complex 76
5. Conformational Control of Serpins-Antithrombin and Heparin 77
6. Nonconventional Serpin Complexes 77
7. Conformational Change and the Formation of the Latent Conformation 78
8. Abnormal Conformational Change-The 5-Form 79
9. Serpin Polymers 79
10. Crystallization of Serpins and Serpin Complexes 81
11. Conclusions 82
References 82
6. Serpins as Hormone Carriers: Modulation of Release 89
Robin Carrell, Xiaoqiang Oj, and Aiwu Zhou
1. Serpins and Allosteric Modulation 89
2. Hormone Carriage-TBG and CBG 90
3. Temperature Response: A Protein Thermocouple 95
4. Angiotensinogen and Its Interaction with Renin 96
Acknowledgments 100
References 101
Contents vii
7. Serpin-Glycosaminoglycan Interactions 105
Chantelle M. Rein, Umesh R. Desai, and Frank C. Church
1. Quantitative Methods 106
2. Qualitative Methods 121
3. Animal Models 127
Acknowledgments 131
References 131
8. Targeting Serpins in High-Throughput and Structure-Based
Drug Design 139
Yi-Pin Chang, Ravi Mahadeva, Anathe 0. M. Patschull, Irene Nobeli,
Ugo I. Ekeowa, Adam R. McKay, Konstantinos Thalassinos, James A. Irving,
Imran Haq, Mun Peak Nyon, John Christodoulou, Adriana Ordóñez,
Elena Miranda, and Bibek Gooptu
1. Introduction 140
2. Targeting the s4A Site with Peptides in a Pathogenic Variant of
xi-ant¡trypsin 142
3. Computational Approaches 148
4. In vitro Screening of Small Molecules 155
5. Mammalian Cell Models and Beyond 166
6. Conclusion 168
References 169
9. Development of Inhibitors of Plasminogen Activator lnhibitor-1 177
Shih-Hon Li and Daniel A. Lawrence
1. Introduction 178
2. Serpins as Drug Targets 179
3. Development of PAI-1 Inhibitors 184
4. Concluding Remarks 200
References 200
10. Bioinformatic Approaches for the Identification of Serpin Genes
with Multiple Reactive Site Loop Coding Exons 209
Stefan Borner and Hermann Ragg
1. Introduction 210
2. Procedure for Identification of Serpin Genes with mRSL
Cassette Exons 211
3. Conclusion 219
Acknowledgment 220
References 220
viü Contents
11. Methods to Measure the Kinetics of Protease Inhibition
by Serpins 223
Anita J. Horvath, Bernadine G. C. Lu, Robert N. Pike,
and Stephen P. Bottomley
1. Introduction 223
2. Determining the Rate of Protease Inhibition (/c0) 226
3. Efficiency of the Serpin Inhibitory Reaction 230
Acknowledgments 233
References 233
12. Predicting Serpin/Protease Interactions 237
Jiangning Song, Antony Y. Matthews, Cyril F. Reboul, Dion Kaiserman,
Robert N. Pike, Phillip I. Bird, and James C. Whisstock
1. Introduction 238
2. Phage Display Methods 242
3. Sequence Analysis Methods 256
4. Concluding Remarks and Perspective 269
Acknowledgments 270
References 270
13. Ammo-Terminal Oriented Mass Spectrometry of Substrates
(ATOMS): N-Terminal Sequencing of Proteins and Proteolytic
Cleavage Sites by Quantitative Mass Spectrometry 275
Alain Doucet and Christopher M. Overall
1. Introduction 276
2. Overview of ATOMS 277
3. Control Experiment to Determine the Ratio Cutoff and Identify
Natural N-Termini, Basal Proteolytic Products, and Outliers 281
4. Limited Proteolytic Processing of the Target Protein by the Test
Protease In Vitro 282
5. Isotopic Labeling and Tryptic Digestion 283
6. Identification of Peptides by Liquid Chromatography-Tandem Mass
Spectrometry 286
7. Mass Spectrometry Data Analysis 287
8. Discussion: Measuring the Effect of Protease Inhibitors on the
Generation of Proteolytic Fragments 291
Acknowledgments 292
References 292
Contents ix
14. Computational Methods for Studying Serpin Conformational
Change and Structural Plasticity 295
Itamar Kass, Cyril F. Reboul, and Ashley M. Buckle
1. Introduction 296
2. Local to Global Dynamics Simulations 299
3. Pushing the Limits-Improving Conformational Sampling 304
4. I Know Where to Go-Directed Simulations 307
5. Nondynamical Methods 308
6. Software 309
7. Force Fields 311
8. Hardware 313
9. Case Study 314
10. Outlook 316
References 319
15. Probing Serpin Conformational Change Using Mass
Spectrometry and Related Methods 325
Yuko Tsutsui, Anindya Sarkar, and Patrick L. Wintrode
1. Introduction 326
2. Applications of HXMS 331
3. Determination of Thermodynamic Stability Using Hydrogen-
Deuterium Exchange Combined with Mass Spectrometry 336
4. Functional Unfolding During the Native -* Cleaved Transition 343
5. Investigating the Polymerization Pathway and Polymer Structure
of arAT by HXMS and Ion Mobility MS 344
6. Future Prospects 348
References 348
16. Determining Serpin Conformational Distributions with Single
Molecule Fluorescence 351
Nicole Mushero and Anne Gershenson
1. Introduction 353
2. Labeling Serpins and Proteases with Fluorophores 354
3. Overview of Single Molecule Fluorescence Techniques 355
4. Serpin Polymerization 358
5. Conformational Distributions of Protease-Serpin Complexes 368
6. Conclusions and Future Directions 373
Acknowledgments 373
References 374
x Contents
17. Serpin Polymerization In Vitro 379
James A. Huntington and Masayuki Yamasaki
1. Introduction 380
2. Methods of Inducing Polymerization 383
3. Kinetics of Polymerization 395
4. Effect of Mutations and Drugs on Polymerization 402
5. Mechanisms of Polymerization 408
6. Conclusions 415
Acknowledgments 416
References 417
18. The Serpinopathies: Studying Serpin Polymerization In Vivo 421
James A. Irving, Ugo I. Ekeowa, Didier Belorgey, Imran Haq, Bibek Gooptu,
Elena Miranda, Juan Pérez, Benoit D. Roussel, Adriana Ordóñez, Lucy
E. Dalton, Sally E. Thomas, Stefan J. Marciniak, Helen Parfrey, Edwin
R. Chilvers, Jeffrey H. Teckman, Sam Alam, Ravi Mahadeva, S. Tamir Rashid,
Ludovic Vallier, and David A. Lomas
1. Introduction to Serpin Polymers and the Serpinopathies-
David Lomas 423
2. Biophysical Techniques to Assess Serpin Polymers Formed
In Vivo- James Irving, Ugo Ekeowa, Didier Belorgey, and Imran Haq 424
3. Assessment of Serpin Polymers by Electron Microscopy-
Bibek Gooptu 428
4. Development of mAbs to Aberrant Conformers of arAntitrypsin
and Neuroserpin-Elena Miranda and Juan Pérez 436
5. Development of Cell Models to Assess the Polymerization of
Antitrypsin-Adriana Ordóñez 441
6. Development of Cell Models to Assess the Polymerization of
Neuroserpin-Elena Miranda, Juan Perez, and Benoit Roussel 443
7. Detection of the UPR and the OPR in the Serpinopathies-Lucy
Dalton, Sally Thomas, Benoit Roussel, and Stefan Marciniak 445
8. Characterization of the Interaction Between Serpin Polymers and
Neutrophils-Helen Parfrey and Edwin Chilvers 448
9. The Use of Transgenic Mice to Assess the Hepatic Consequences
of Serpin Polymerization. Jeff Teckman 451
10. The Use of Transgenic Mice to Assess the Pulmonary Consequences
of Serpin Polymerization-Sam Alam and Ravi Mahadeva 453
11. Characterization of Serpin Polymerization Using ¡PS to Generate
Hepatocyte-Like Cell Lines-Tamir Rashid and Ludovic Vallier 457
Acknowledgments 461
References 461
Author Index 467
Subject Index 493
|
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| discipline | Chemie / Pharmazie Biologie Medizin |
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| physical | XLVIII, 502 S., [6] Bl. Ill., graph. Darst. 24 cm |
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Serpin structure and evolution ed. by James C. Whisstock and Phillip I. Bird 1. ed. Amsterdam ; Heidelberg [u.a.] Elsevier, Acad. Press 2011 XLVIII, 502 S., [6] Bl. Ill., graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 501 Serpine (DE-588)4285093-9 gnd rswk-swf Strukturaufklärung (DE-588)4183788-5 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Serpine (DE-588)4285093-9 s Strukturaufklärung (DE-588)4183788-5 s DE-604 Methode (DE-588)4038971-6 s b DE-604 Whisstock, James C. edt Bird, Phillip I. Sonstige oth Methods in enzymology 501 (DE-604)BV000000938 501 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024655147&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Serpin structure and evolution Methods in enzymology Serpine (DE-588)4285093-9 gnd Strukturaufklärung (DE-588)4183788-5 gnd Methode (DE-588)4038971-6 gnd |
| subject_GND | (DE-588)4285093-9 (DE-588)4183788-5 (DE-588)4038971-6 (DE-588)4143413-4 |
| title | Serpin structure and evolution |
| title_auth | Serpin structure and evolution |
| title_exact_search | Serpin structure and evolution |
| title_full | Serpin structure and evolution ed. by James C. Whisstock and Phillip I. Bird |
| title_fullStr | Serpin structure and evolution ed. by James C. Whisstock and Phillip I. Bird |
| title_full_unstemmed | Serpin structure and evolution ed. by James C. Whisstock and Phillip I. Bird |
| title_short | Serpin structure and evolution |
| title_sort | serpin structure and evolution |
| topic | Serpine (DE-588)4285093-9 gnd Strukturaufklärung (DE-588)4183788-5 gnd Methode (DE-588)4038971-6 gnd |
| topic_facet | Serpine Strukturaufklärung Methode Aufsatzsammlung |
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| volume_link | (DE-604)BV000000938 |
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