Nitric Oxide: Chemical and Analytical Methods / Section I: |
The Chemistry of Nitric Oxide and Related Species / Martin H. HughesChapter 1: |
Delivery of nitric oxide for analysis of the function of cytochrome / c. Lindsay J. Cole ; Wilhelmina M. Huston ; James W.B. MoirChapter 2: |
The preparation and purification of NO gas and the use of NO releasers / Chapter 3: |
The application of NO donors and other agents of nitrosative stress in biological systems / Rubina G. Aga ; Martin N. Hughes |
The Chemistry of Peroxynitrite Implications for Biological Activity / Sara Goldstein ; Gabor Mereacute;nyiChapter 4: |
Nitric Oxide (NO) Selective Electrodes / Ian R. Davies ; Xueji ZhangChapter 5: |
NO, N2O and O2 Reaction Kinetics: Scope and Limitations of the / Clark Electrode L.A.M. Pouvreau ; M. J. F. Strampraad ; S. Van Berloo ; J. H. Kattenberg ; S. de VriesChapter 6: |
Chemiluminescence quantification of Nitric oxide and its derivatives in liquid samples / Jay R. Laver ; Tacirc;nia M. Stevanin ; Robert C. ReadChapter 7: |
Bacterial and Archaeal Hemoglobins / Section II: |
Interactions of nitric oxide with hemoglobin: from microbes to man / Michael Angelo ; Alfred Hausladen ; Jonathan S. StamlerChapter 8: |
Expression and purification of / E. coli Hmp Robert K. PooleChapter 9: |
Alberto Boffi / Chapter 10: |
Liacute;gia M. Saraiva / Chapter 11: |
Paul R. Gardner / Chapter 12: |
Alessandra Bonamore / Chapter 13: |
Assessment of Biotechnologically Relevant Characteristics of Heterologous Hemoglobins in Escherichia coli / Pauli T. Kallio ; Christian J. T. Bollinger ; Taija Koskenkorva ; Alexander D. FreyChapter 14: |
Guo-Qiang CHEN / Chapter 15: |
Robert K. Poole / Chapter 16: |
Martino Bolognesi / Chapter 17: |
Paolo Visca / Chapter 18: |
Other Hemoglobins / Section III: |
Kirsten Mees / Laurent Coger ; Christophe Lechauve ; Michael C. Marden ; Alexandra Pesce ; Martino Bolognesi ; Luc MoneesChapter 19: |
Measurement of distal histidine coordination equilibrium and kinetics in hexacoordinate hemoglobins / Benoit J. Smagghe ; Puspita Halder ; Mark S. HargroveChapter 20: |
Purification of Class 1 Plant Hemoglobins and Examination of their Functional Properties / Abir U. Igamberdiev ; Robert D. HillChapter 21: |
Use of in silico (computer) methods to predict and analyze the tertiary structure of plant hemoglobins / Sabarinathan Kuttalingam Gopalasubramaniam ; Veroacute;nica Garrocho-Villegas ; Genoveva Bustos Rivera ; Nina Pastor ; Rauacute;l Arredondo-PeterChapter 22: |
A Self-induction Method to Produce High Quantities of Recombinant Functional Flavo-Leghemoglobin Reductase / Estibaliz Urarte ; Intilde;igo Auzmendi ; Selene Rol ; Idoia Ariz ; Pedro Aparicio-Tejo ; Jose F. MoranChapter 23: |
Spectroscopic and crystallographic characterization of bis-histidyl adducts in tetrameric hemoglobins / Alessandro Vergara ; Luigi VitaglianoChapter 24: |
Contributors |
Preface |
Volumes in Series |
Nitric Oxide-Metabolising and Detoxifying Enzymes |
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 |
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 |
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 ; 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-Jensen30: |
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 ; Inigo Auzmendi ; Cesar Arrese-Igor ; Esther M. Gonzalez31: |
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 |