Globins and other nitric oxide-reactive proteins / edited by Robert K. Poole.

Format:

Book

Contributor:

Poole, Robert K.

Series:

Methods in enzymology ; v. 436-437.

Methods in enzymology ; v. 436-437

Language:

English

Subjects (All):

Globin.

Proteins.

Physical Description:

volumes : illustrations (some color) ; 24 cm.

Place of Publication:

San Diego, Calif. : Academic, 2008-

Contents:

Section I Nitric Oxide-Metabolising and Detoxifying Enzymes 1

1 Structural Studies on Flavodiiron Proteins / Joao B. Vicente, Maria Armenia Carrondo, Miguel Teixeira, Carlos Frazao 3

2 Crystallization of Flavodiiron Proteins 4

3 Diffraction Data Collection, Structure Determination, and Refinement 7

4 Overall Description of Structures 8

2 Biochemical, Spectroscopic, and Thermodynamic Properties of Flavodiiron Proteins / Joao B. Vicente, Marta C. Justino, Vera L. Goncalves, Ligia M. Saraiva, Miguel Teixeira 21

2 Cloning of Genes Encoding Flavodiiron Proteins and Their Truncated Domains 24

3 Production and Purification of Recombinant Flavodiiron Proteins 25

4 Biochemical Characterization of Flavodiiron Proteins 26

5 Spectroscopic Properties 29

6 Redox Properties 32

3 Kinetic Characterization of the Escherichia coli Nitric Oxide Reductase Flavorubredoxin / Joao B. Vicente, Francesca M. Scandurra, Elena Forte, Maurizio Brunori, Paolo Sarti, Miguel Teixeira, Alessandro Giuffre 47

2 Amperometric Measurements 49

3 Spectroscopic Measurements 51

4 Escherichia coli Cytochrome c Nitrite Reductase NrfA / Thomas A. Clarke, Paul C. Mills, Susie R. Poock, Julea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D. Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A. G. Soderberg, Stephen Spiro|cJessica Van Wonderen, David J. Richardson 63

2 Measurement of Cytochrome c Nitrite Reductase-Dependent Consumption of Nitric Oxide in Whole Cells 66

3 Growth of E. coli Optimized for Cytochrome c Nitrite Reductase Production for Use in Enzyme Purification 66

4 Purification of Cytochrome c Nitrite Reductase 68

5 Assaying the Cytochrome c Nitrite Reductase 69

6 Crystallization of E. coli Cytochrome c Nitrite Reductase 73

5 The Respiratory Nitric Oxide Reductase (NorBC) from Paracoccus denitrificans / Sarah J. Field, Faye H. Thorndycroft, Andrey D. Matorin, David J. Richardson, Nicholas J. Watmough 79

2 Purification of Native NorBC from Paracoccus denitrificans 82

3 Purification of Recombinant NorBC 85

4 Amperometric Assays of NO Consumption 86

5 Pseudoazurin as an Electron Donor in Assays of NorBC 88

6 Preparation of NOR for Spectroscopic Investigation 91

7 Electron Paramagnetic Resonance Spectroscopy 96

6 Redox-Controlled Dinitrosyl Formation at the Diiron-Oxo Center of NorA / Rainer Cramm, Katja Strube 103

2 Genetic Context and Expression of the NorA Gene in R. eutropha 105

3 Purification of NorA 106

4 Disulfide Bridges in NorA 107

5 Iron Analysis and Preparation of Apo-NorA 108

6 Interconversion of Redox Forms of NorA 109

7 Generation of NorA-DNIC In Vitro 111

8 Preparation of NorA-DNIC Formed In Vivo 113

9 Quantification of NO from NorA-DNIC 113

10 Outlook 114

7 Purification and Functional Analysis of Fungal Nitric Oxide Reductase Cytochrome P450nor / Li Zhang, Hirofumi Shoun 117

2 Screening of P450nor Activity 119

3 Gas Analysis 119

4 Purification of P450nor 120

5 Nitric Oxide Reductase Activity Assay 121

6 Protein Sequencing 122

7 Isolation of cDNA 123

8 Subcellular Fractionation of T. cutaneum 124

9 Site-Directed Mutagenesis 125

10 Expression of Recombinant Proteins 126

11 Purification of Recombinant Proteins 127

12 Titration of NAD Analogs 128

13 Stopped-Flow Rapid Scan Analysis 130

14 Other Analysis 131

8 A Quantitative Approach to Nitric Oxide Inhibition of Terminal Oxidases of the Respiratory Chain / Maria G. Mason, Rebecca S. Holladay, Peter Nicholls, Mark Shepherd, Chris E. Cooper 135

2 Evaluation of Current Techniques for Measuring pNO, pO[subscript 2], and K[subscript M] (O[subscript 2]) 137

3 Nitric Oxide Donor Compounds 138

4 Nitric Oxide Kinetics 139

5 Oxygen Kinetics 149

6 Optical Detection of Enzyme Intermediates in the Presence of Oxygen and NO 151

Section II Sensor Proteins 161

9 Cloning, Expression, and Purification of the N-terminal Heme-Binding Domain of Globin-Coupled Sensors / Jennifer A. Saito, Tracey Allen K. Freitas, Maqsudul Alam 163

2 Bioinformatic Search of Globin-Coupled Sensors 164

3 Functional Analysis of Globin-Coupled Sensors 166

10 Oxygen-Sensing Histidine-Protein Kinases: Assays of Ligand Binding and Turnover of Response-Regulator Substrates / Marie-Alda Gilles-Gonzalez, Gonzalo Gonzalez, Eduardo Henrique Silva Sousa, Jason Tuckerman 173

2 Assays 175

11 Reactions of Nitric Oxide and Oxygen with the Regulator of Fumarate and Nitrate Reduction, a Global Transcriptional Regulator, during Anaerobic Growth of Escherichia coli / Jason C. Crack, Nick E. Le Brun, Andrew J. Thomson, Jeffrey Green, Adrian J. Jervis 191

2 Production of 4Fe-FNR Protein 194

3 Determination of Iron and Acid-Labile Sulfide Content of FNR 197

4 UV-Visible Absorbance Spectra of FNR 198

5 Cluster Reaction with Nitric Oxide and Oxygen 198

6 Purification of 2Fe-FNR 204

7 Detection of Other Reaction Products 204

12 Genome-Wide Identification of Binding Sites for the Nitric Oxide-Sensitive Transcriptional Regulator NsrR / Sam Efromovich, David Grainger, Diane Bodenmiller, Stephen Spiro 211

2 Strain Construction 214

3 Reference and Control Samples 216

4 Culture Conditions 217

5 Immunoprecipitation of DNA Targets Associated with NsrR 218

6 DNA Labeling, Microarray Hybridization, and Processing 219

7 Visualization and Analysis of DNA Microarray Data 220

8 A New Statistical Methodology for Treatment of Chip-on-Chip Data 222

13 Characterization of the Nitric Oxide-Reactive Transcriptional Activator NorR / Benoit D'Autreaux, Nick Tucker, Stephen Spiro, Ray Dixon 235

2 Measurement of NorR Activity In Vivo 237

3 Measurement of Transcriptional Activation by NorR In Vitro 238

4 Detection of the Ferrous-Nitrosyl Form of NorR by In Vivo Electron Paramagnetic Resonance (EPR) 240

5 In Vitro Reconstitution of the Iron Center in NorR 242

6 Measurement of NO Affinity 243

7 Standardization of the NO Electrode 246

8 Determination of NorRFe(NO) K[subscript d] 247

Section III Advanced Spectroscopic Methods 253

14 Hemoglobins from Mycobacterium tuberculosis and Campylobacter jejuni: A Comparative Study with Resonance Raman Spectroscopy / Changyuan Lu, Tsuyoshi Egawa, Masahiro Mukai, Robert K.

Poole, Syun-Ru Yeh 255

1 Hemoglobin Superfamily: An Overview 256

2 Microbial Hemoglobins 257

3 Resonance Raman Spectroscopy: Applications in Hemeproteins 258

4 Structures and Functions of Microbial Hemoglobins 266

15 The Power of Using Continuous-Wave and Pulsed Electron Paramagnetic Resonance Methods for the Structure Analysis of Ferric Forms and Nitric Oxide-Ligated Ferrous Forms of Globins / Sabine Van Doorslaer, Filip Desmet 287

2 Electron Paramagnetic Resonance in a Nutshell 289

3 EPR Studies of NO-Ligated Globins 295

4 EPR Studies of Ferric globins 301

5 Spin-Labeling Heme Proteins 304

6 Future Challenges and Possibilities 305

16 Oxygen Binding to Heme Proteins in Solution, Encapsulated in Silica Gels, and in the Crystalline State / Luca Ronda, Stefano Bruno, Serena Faggiano, Stefano Bettati, Andrea Mozzarelli 311

1 Oxygen-Binding Curves to Heme Proteins 313

2 Determination of OBCs for Hemoglobin in Solution 316

3 Determination of K[subscript 1] for Hemoglobin in Solution in the Absence of Allosteric Effectors 318

4 Determination of OBCs for T State Hemoglobin Gels in the Absence and Presence of Allosteric Effectors 318

5 Determination of OBCs for T State Hemoglobin Crystals 320

6 Determination of OBCs for Hemocyanin in Solution and in Silica Gels 323

17 Characterization of Ligand Migration Mechanisms inside Hemoglobins from the Analysis of Geminate Rebinding Kinetics / Stefania Abbruzzetti, Stefano Bruno, Serena Faggiano, Luca Ronda, Elena Grandi, Andrea Mozzarelli, Cristiano Viappiani 329

2 Principles of Nanosecond Laser Flash Photolysis 330

3 Basic Experimental Layouts 331

4 Encapsulation of Hbs in Silica Gels 335

5 Enhancement of Geminate Rebinding and Advantages of Gel Encapsulation 336

6 Extraction of Kinetic Information 337

18 Ligand Dynamics in Heme Proteins Observed by Fourier Transform Infrared Spectroscopy at Cryogenic Temperatures / Karin Nienhaus, G. Ulrich Nienhaus 347

2 Materials 349

3 Fourier Transform Infrared Cryospectroscopy 353

4 Low-Temperature FTIR Spectroscopy on NO-Ligated Heme Proteins 365

19 Time-Resolved X-Ray Crystallography of Heme Proteins / Vukica Srajer, William E. Royer, Jr. 379

2 Experiment 381

3 Data Processing and Analysis 385

4 A Case Study: Scapharca Dimeric Hemoglobin 388

20 Structural Dynamics of Myoglobin / M. Brunori, D. Bourgeois, B. Vallone 397

2 Crystallographic Studies of Myoglobin States 399

3 Experimental Approaches 400

21 Use of the Conjugate Peak Refinement Algorithm for Identification of Ligand-Binding Pathways in Globins / Stephen D. Golden, Kenneth W. Olsen 417

2 Exploration of Oxygen-Binding Pathways in Myoglobin 418

3 Theoretical Models 419

4 Potential Energy Function 420

5 Transition Pathways 421

6 Methods 425

7 Results 429

22 Finding Gas Migration Pathways in Proteins Using Implicit Ligand Sampling / Jordi Cohen, Kenneth W. Olsen, Klaus Schulten 439

2 Methods 442

3 Example Calculation: Truncated Hemoglobin (trHb) from Paramecium caudatum 446

23 Identification of Ligand-Binding Pathways in Truncated Hemoglobins Using Locally Enhanced Sampling Molecular Dynamics / Stephen D. Golden, Kenneth W. Olsen 459

2 Molecular Dynamics 462

3 Locally Enhanced Sampling Molecular Dynamics 465

4 Methods 466

5 Results 468

24 Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation / Marcelo A. Marti, Luciana Capece, Axel Bidon-Chanal, Alejandro Crespo, Victor Guallar, F. Javier Luque, Dario A. Estrin 477

2 Molecular Dynamics (MD) Methods 479

3 Quantum Mechanical-Molecular Mechanical Methods 485

5 Ligand Migration Profiles from MSMD and PELE Simulations: Exploring Ligand Entry Pathways in M. tuberculosis trHbN 490

25 Microbial Responses to Nitric Oxide and Nitrosative Stress: Growth, "Omic," and Physiological Methods / Steven T. Pullan, Claire E. Monk, Lucy Lee, Robert K. Poole 499

2 Methods 504

3 Nitric Oxide, NO-Releasing Agents, and Nitrosating Agents 512

4 Illustrative Results from Applications of These Methods 514

26 Analysis of Nitric Oxide-Dependent Antimicrobial Actions in Macrophages and Mice / Andres Vazquez-Torres, Tania Stevanin, Jessica Jones-Carson, Margaret Castor, Robert C. Read, Ferric C. Fang 521

1 NO.-Dependent Antimicrobial Actions of Murine Macrophages 522

2 NO.-Dependent Antimicrobial Actions of Human Macrophages 528

3 NO.-dependent Antimicrobial Actions in Laboratory Mice 532

27 Measuring Nitric Oxide Metabolism in the Pathogen Neisseria meningitidis / Melanie J. Thomson, Tania M. Stevanin, James W. B. Moir 539

2 Safety Aspects of Handling N. meningitidis in the Laboratory 541

3 Metabolism of Neisseria sp. 541

4 Experimental Approaches to Analyzing Nitrogen Metabolism Relevant to NO 544

5 Simultaneous Measurement of Oxygen and NO during Pure Culture of N. meningitidis 547

6 Measurement of NO Production/Disappearance in Tissue Culture Using Human Monocyte-Derived Macrophages 555

28 Localization of S-Nitrosothiols and Assay of Nitric Oxide Synthase and S-Nitrosoglutathione Reductase Activity in Plants / Francisco J. Corpas, Alfonso Carreras, Francisco J. Esteban, Mounira Chaki, Raquel Valderrama, Luis A. Del Rio, Juan B. Barroso 561

2 Determination of L-Arginine-Dependent NOS Activity by Ozone Chemiluminescence in Plant Tissues 563

3 Assay of GSNOR Activity 566

4 Localization of S-Nitrosothiols and S-Nitrosoglutathione in Plant Tissues by Confocal Laser-Scanning Microscopy (CLSM) 567

29 Methods for Nitric Oxide Detection during Plant-Pathogen Interactions / E. Vandelle, M. Delledonne 575

2 Nitric Oxide Detection by Mass Spectrometry 577

3 Nitric Oxide Detection by Laser Photoacoustic Spectroscopy 579

4 Nitric Oxide Detection by Chemiluminescence 582

5 Nitric Oxide Detection by Hemoglobin Conversion 583

6 Nitric Oxide Detection by Electron Paramagnetic Resonance (EPR) Spin Trap 585

7 Nitric Oxide Detection Using Diaminofluoresceins 587

30 Bioimaging Techniques for Subcellular Localization of Plant Hemoglobins and Measurement of Hemoglobin-Dependent Nitric Oxide Scavenging In Planta / Kim H. Hebelstrup, Erik Ostergaard-Jensen, Robert D. Hill 595

2 Measuring Hemoglobin-Dependent NO Scavenging 596

3 Techniques for Determination of Subcellular Localization of Plant Hemoglobins 597

4 Imaging of Hemoglobin-Dependent NO Scavenging in Arabidopsis Plants 598

5 Engineering of GLB1-GFP/GLB2-GFP Constructs and Microscopic Analysis of A. thaliana Plants Expressing GFP-Tagged Hemoglobin 600

31 Use of Recombinant Iron-Superoxide Dismutase as A Marker of Nitrative Stress / Estibaliz Larrainzar, Estibaliz Urarte, Inigo Auzmendi, Idoia Ariz, Cesar Arrese-Igor, Esther M. Gonzalez, Jose F. Moran 605

2 Immunodetection of Nitrated Proteins: Metal-Mediated Tyrosine Nitration of BSA 608

3 Tyrosine Nitration of Purified Recombinant Vu_FeSOD Affects its Enzymatic Activity 610

4 Tyrosine Nitration in Vu_FeSOD can be Estimated Using Antibodies Against 3-Nitrotyrosine 612

5 SIN-1-Dependent Vu_FeSOD Nitration can be Detected by the Loss of Enzymatic Activity 612.

Notes:

Includes bibliographical references and indexes.

ISBN:

9780123742773

0123742773

9780123742780

OCLC:

191884323