| Contributors |
| Preface |
| Volumes in Series |
| Nitric Oxide-Metabolising and Detoxifying Enzymes / Section I： |
| Structural Studies on Flavodiiron Proteins / Joao B. Vicente ; Maria Armenia Carrondo ; Miguel Teixeira ; Carlos Frazao1： |
| Introduction |
| Crystallization of Flavodiiron Proteins / 2： |
| Diffraction Data Collection, Structure Determination, and Refinement / 3： |
| Overall Description of Structures / 4： |
| Conclusion / 5： |
| References |
| Biochemical, Spectroscopic, and Thermodynamic Properties of Flavodiiron Proteins / Marta C. Justino ; Vera L. Goncalves ; Ligia M. Saraiva |
| Cloning of Genes Encoding Flavodiiron Proteins and Their Truncated Domains |
| Production and Purification of Recombinant Flavodiiron Proteins |
| Biochemical Characterization of Flavodiiron Proteins |
| Spectroscopic Properties |
| Redox Properties / 6： |
| Conclusions / 7： |
| Acknowledgments |
| Kinetic Characterization of the Escherichia coli Nitric Oxide Reductase Flavorubredoxin / Francesca M. Scandurra ; Elena Forte ; Maurizio Brunori ; Paolo Sarti ; Alessandro Giuffre |
| Amperometric Measurements |
| Spectroscopic Measurements |
| 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 |
| Measurement of Cytochrome c Nitrite Reductase-Dependent Consumption of Nitric Oxide in Whole Cells |
| Growth of E. coli Optimized for Cytochrome c Nitrite Reductase Production for Use in Enzyme Purification |
| Purification of Cytochrome c Nitrite Reductase |
| Assaying the Cytochrome c Nitrite Reductase |
| Crystallization of E. coli Cytochrome c Nitrite Reductase |
| Concluding Remarks |
| The Respiratory Nitric Oxide Reductase (NorBC) from Paracoccus denitrificans / Sarah J. Field ; Faye H. Thorndycroft ; Andrey D. Matorin ; Nicholas J. Watmough |
| Purification of Native NorBC from Paracoccus denitrificans |
| Purification of Recombinant NorBC |
| Amperometric Assays of NO Consumption |
| Pseudoazurin as an Electron Donor in Assays of NorBC |
| Preparation of NOR for Spectroscopic Investigation |
| Electron Paramagnetic Resonance Spectroscopy |
| Redox-Controlled Dinitrosyl Formation at the Diiron-Oxo Center of NorA / Rainer Cramm ; Katja Strube8： |
| Genetic Context and Expression of the NorA Gene in R. eutropha |
| Purification of NorA |
| Disulfide Bridges in NorA |
| Iron Analysis and Preparation of Apo-NorA |
| Interconversion of Redox Forms of NorA |
| Generation of NorA-DNIC In Vitro |
| Preparation of NorA-DNIC Formed In Vivo |
| Quantification of NO from NorA-DNIC / 9： |
| Outlook / 10： |
| Purification and Functional Analysis of Fungal Nitric Oxide Reductase Cytochrome P450nor / Li Zhang ; Hirofumi Shoun |
| Screening of P450nor Activity |
| Gas Analysis |
| Purification of P450nor |
| Nitric Oxide Reductase Activity Assay |
| Protein Sequencing |
| Isolation of cDNA |
| Subcellular Fractionation of T. cutaneum |
| Site-Directed Mutagenesis |
| Expression of Recombinant Proteins |
| Purification of Recombinant Proteins / 11： |
| Titration of NAD Analogs / 12： |
| Stopped-Flow Rapid Scan Analysis / 13： |
| Other Analysis / 14： |
| 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. Cooper15： |
| Evaluation of Current Techniques for Measuring pNO, pO[subscript 2], and K[subscript M] (O[subscript 2]) |
| Nitric Oxide Donor Compounds |
| Nitric Oxide Kinetics |
| Oxygen Kinetics |
| Optical Detection of Enzyme Intermediates in the Presence of Oxygen and NO |
| Appendices |
| Sensor Proteins / Section II： |
| Cloning, Expression, and Purification of the N-terminal Heme-Binding Domain of Globin-Coupled Sensors / Jennifer A. Saito ; Tracey Allen K. Freitas ; Maqsudul Alam |
| Bioinformatic Search of Globin-Coupled Sensors |
| Functional Analysis of Globin-Coupled Sensors |
| 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 |
| Assays |
| 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 |
| Production of 4Fe-FNR Protein |
| Determination of Iron and Acid-Labile Sulfide Content of FNR |
| UV-Visible Absorbance Spectra of FNR |
| Cluster Reaction with Nitric Oxide and Oxygen |
| Purification of 2Fe-FNR |
| Detection of Other Reaction Products |
| Genome-Wide Identification of Binding Sites for the Nitric Oxide-Sensitive Transcriptional Regulator NsrR / Sam Efromovich ; David Grainger ; Diane Bodenmiller ; Stephen Spiro |
| Strain Construction |
| Reference and Control Samples |
| Culture Conditions |
| Immunoprecipitation of DNA Targets Associated with NsrR |
| DNA Labeling, Microarray Hybridization, and Processing |
| Visualization and Analysis of DNA Microarray Data |
| A New Statistical Methodology for Treatment of Chip-on-Chip Data |
| Characterization of the Nitric Oxide-Reactive Transcriptional Activator NorR / Benoit D'Autreaux ; Nick Tucker ; Ray Dixon |
| Measurement of NorR Activity In Vivo |
| Measurement of Transcriptional Activation by NorR In Vitro |
| Detection of the Ferrous-Nitrosyl Form of NorR by In Vivo Electron Paramagnetic Resonance (EPR) |
| In Vitro Reconstitution of the Iron Center in NorR |
| Measurement of NO Affinity |
| Standardization of the NO Electrode |
| Determination of NorRFe(NO) K[subscript d] |
| Acknowledgment |
| Advanced Spectroscopic Methods / Section III： |
| 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 |
| Hemoglobin Superfamily: An Overview |
| Microbial Hemoglobins |
| Resonance Raman Spectroscopy: Applications in Hemeproteins |
| Structures and Functions of Microbial Hemoglobins |
| Closing Remarks |
| 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 |
| Electron Paramagnetic Resonance in a Nutshell |
| EPR Studies of NO-Ligated Globins |
| EPR Studies of Ferric globins |
| Spin-Labeling Heme Proteins |
| Future Challenges and Possibilities |
| 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 Mozzarelli16： |
| Oxygen-Binding Curves to Heme Proteins |
| Determination of OBCs for Hemoglobin in Solution |
| Determination of K[subscript 1] for Hemoglobin in Solution in the Absence of Allosteric Effectors |
| Determination of OBCs for T State Hemoglobin Gels in the Absence and Presence of Allosteric Effectors |
| Determination of OBCs for T State Hemoglobin Crystals |
| Determination of OBCs for Hemocyanin in Solution and in Silica Gels |
| Characterization of Ligand Migration Mechanisms inside Hemoglobins from the Analysis of Geminate Rebinding Kinetics / Stefania Abbruzzetti ; Elena Grandi ; Cristiano Viappiani17： |
| Principles of Nanosecond Laser Flash Photolysis |
| Basic Experimental Layouts |
| Encapsulation of Hbs in Silica Gels |
| Enhancement of Geminate Rebinding and Advantages of Gel Encapsulation |
| Extraction of Kinetic Information |
| Ligand Dynamics in Heme Proteins Observed by Fourier Transform Infrared Spectroscopy at Cryogenic Temperatures / Karin Nienhaus ; G. Ulrich Nienhaus18： |
| Materials |
| Fourier Transform Infrared Cryospectroscopy |
| Low-Temperature FTIR Spectroscopy on NO-Ligated Heme Proteins |
| Time-Resolved X-Ray Crystallography of Heme Proteins / Vukica Srajer ; William E. Royer, Jr.19： |
| Experiment |
| Data Processing and Analysis |
| A Case Study: Scapharca Dimeric Hemoglobin |
| Structural Dynamics of Myoglobin / M. Brunori ; D. Bourgeois ; B. Vallone20： |
| Background |
| Crystallographic Studies of Myoglobin States |
| Experimental Approaches |
| Use of the Conjugate Peak Refinement Algorithm for Identification of Ligand-Binding Pathways in Globins / Stephen D. Golden ; Kenneth W. Olsen21： |
| Exploration of Oxygen-Binding Pathways in Myoglobin |
| Theoretical Models |
| Potential Energy Function |
| Transition Pathways |
| Methods |
| Results |
| Finding Gas Migration Pathways in Proteins Using Implicit Ligand Sampling / Jordi Cohen ; Klaus Schulten22： |
| Example Calculation: Truncated Hemoglobin (trHb) from Paramecium caudatum |
| Discussion |
| Identification of Ligand-Binding Pathways in Truncated Hemoglobins Using Locally Enhanced Sampling Molecular Dynamics / 23： |
| Molecular Dynamics |
| Locally Enhanced Sampling Molecular Dynamics |
| 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. Estrin24： |
| Molecular Dynamics (MD) Methods |
| Quantum Mechanical-Molecular Mechanical Methods |
| Illustrative Examples |
| Ligand Migration Profiles from MSMD and PELE Simulations: Exploring Ligand Entry Pathways in M. tuberculosis trHbN |
| Microbial Responses to Nitric Oxide and Nitrosative Stress: Growth, "Omic," and Physiological Methods / Steven T. Pullan ; Claire E. Monk ; Lucy Lee25： |
| Nitric Oxide, NO-Releasing Agents, and Nitrosating Agents |
| Illustrative Results from Applications of These Methods |
| 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. Fang26： |
| NO.-Dependent Antimicrobial Actions of Murine Macrophages |
| NO.-Dependent Antimicrobial Actions of Human Macrophages |
| NO.-dependent Antimicrobial Actions in Laboratory Mice |
| Measuring Nitric Oxide Metabolism in the Pathogen Neisseria meningitidis / Melanie J. Thomson ; Tania M. Stevanin ; James W. B. Moir27： |
| Safety Aspects of Handling N. meningitidis in the Laboratory |
| Metabolism of Neisseria sp. |
| Experimental Approaches to Analyzing Nitrogen Metabolism Relevant to NO |
| Simultaneous Measurement of Oxygen and NO during Pure Culture of N. meningitidis |
| Measurement of NO Production/Disappearance in Tissue Culture Using Human Monocyte-Derived Macrophages |
| 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. Barroso28： |
| Determination of L-Arginine-Dependent NOS Activity by Ozone Chemiluminescence in Plant Tissues |
| Assay of GSNOR Activity |
| Localization of S-Nitrosothiols and S-Nitrosoglutathione in Plant Tissues by Confocal Laser-Scanning Microscopy (CLSM) |
| Methods for Nitric Oxide Detection during Plant-Pathogen Interactions / E. Vandelle ; M. Delledonne29： |
| Nitric Oxide Detection by Mass Spectrometry |
| Nitric Oxide Detection by Laser Photoacoustic Spectroscopy |
| Nitric Oxide Detection by Chemiluminescence |
| Nitric Oxide Detection by Hemoglobin Conversion |
| Nitric Oxide Detection by Electron Paramagnetic Resonance (EPR) Spin Trap |
| Nitric Oxide Detection Using Diaminofluoresceins |
| 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. Hill30： |
| Measuring Hemoglobin-Dependent NO Scavenging |
| Techniques for Determination of Subcellular Localization of Plant Hemoglobins |
| Imaging of Hemoglobin-Dependent NO Scavenging in Arabidopsis Plants |
| Engineering of GLB1-GFP/GLB2-GFP Constructs and Microscopic Analysis of A. thaliana Plants Expressing GFP-Tagged Hemoglobin |
| 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. Moran31： |
| Immunodetection of Nitrated Proteins: Metal-Mediated Tyrosine Nitration of BSA |
| Tyrosine Nitration of Purified Recombinant Vu_FeSOD Affects its Enzymatic Activity |
| Tyrosine Nitration in Vu_FeSOD can be Estimated Using Antibodies Against 3-Nitrotyrosine |
| SIN-1-Dependent Vu_FeSOD Nitration can be Detected by the Loss of Enzymatic Activity |
| Author Index |
| Subject Index |
ＥＢ
