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Fe-S cluster enzymes part A / edited by Sheilla S. David

Front Cover -- Fe-S Cluster Enzymes Part A -- Copyright -- Contents -- Contributors -- Preface -- Chapter One: Genetic, Biochemical, and Biophysical Methods for Studying Fe-S Proteins and Their Assembly -- 1. Fe-S Cluster Biology -- 2. Genetic Approaches and Strategies -- 2.1. Genetic Selection and/... Full description

PPN (Catalogue-ID): 897544617
Personen: David, Sheila S. [HerausgeberIn]
Format: eBook eBook
Language: English
Published: Cambridge, MA, Elsevier, Academic Press, [2017]
©2017
Edition: First edition
Series: Methods in enzymology (volume 595)
Basisklassifikation: 35.74
Subjects:

Eisen-Schwefel-Proteide

Formangabe: Aufsatzsammlung
Physical Description: 1 Online-Ressource (xv, 425 Seiten), Illustrationen, Diagramme.
ISBN: 978-0-12-811938-9

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490 1 |a Methods in enzymology  |v volume 595 
520 |a Front Cover -- Fe-S Cluster Enzymes Part A -- Copyright -- Contents -- Contributors -- Preface -- Chapter One: Genetic, Biochemical, and Biophysical Methods for Studying Fe-S Proteins and Their Assembly -- 1. Fe-S Cluster Biology -- 2. Genetic Approaches and Strategies -- 2.1. Genetic Selection and/or Screens Based on Fe-S Biogenesis Defects -- 2.2. The Use of Conditional Alleles -- 2.3. Genetic Approaches to Investigate Functional Redundancy -- 2.4. Suppressor-Based Strategies -- 2.5. trans-Dominant Mutations -- 2.6. E. coli Strains of Particular Interest for Fe-S Cluster Biogenesis Studies -- 2.6.1. The eSUF and eISC Strains -- 2.6.2. The Hpx Strain -- 2.6.3. The Iron-Minus Strain -- 2.7. Construction of Frataxin Models -- 3. Biochemistry of Fe-S Clusters -- 3.1. Purification of Fe-S Cluster-Containing Proteins -- 3.2. Characterization of Fe-S Proteins -- 4. Spectroscopy of Fe-S Proteins -- 4.1. UV-Visible Absorption Spectroscopy -- 4.2. Mössbauer Spectroscopy -- 4.3. Electronic Paramagnetic Resonance Spectroscopy -- 4.4. Hyperfine Sublevel Correlation Spectroscopy -- 4.5. Raman Resonance Spectroscopy -- 4.6. Circular Dichroism -- 4.7. Nuclear Magnetic Resonance Spectroscopy -- Acknowledgments -- References -- Chapter Two: De Novo Design of Iron-Sulfur Proteins -- 1. Introduction -- 2. [4Fe-4S] -- 3. [3Fe-4S] Clusters -- 4. [2Fe-2S] Clusters -- 5. [Fe8S7] Clusters -- 6. Protocols -- 6.1. Diiron Hexacarbonyl Cluster Incorporation Into Peptide (Roy et al., 2012) -- 6.2. [4Fe-4S] Cluster Incorporation Into Peptide -- 6.3. EPR [4Fe-4S] Sample Preparation -- 6.4. Hydrogen Production With Diiron Hexacarbonyl -- 6.5. Electrochemical Measurements -- References -- Chapter Three: In Vitro Studies of Cellular Iron-Sulfur Cluster Biosynthesis, Trafficking, and Transport -- 1. Introduction 
520 |a 2. Preparation of Fe-S Clusters and Kinetic Determination of Fe-S Cluster Transfer Reactions -- 2.1. Na6[Fe2S2](GS)4 Synthesis -- 2.1.1. Equipment -- 2.1.2. Buffers and Reagents -- 2.1.3. Procedure -- 2.1.4. Notes -- 2.2. Cluster Uptake and Protein-Protein Transfer Reactions -- 2.2.1. Equipment -- 2.2.2. Buffers and Reagents -- 2.2.3. Procedure -- 2.2.4. Notes -- 2.3. Glutathione Extraction -- 2.3.1. Equipment -- 2.3.2. Buffers and Reagents -- 2.3.3. Procedure -- 2.3.4. Notes -- 3. Fe-S Cluster Stimulation and Transport in Liposome Assays -- 3.1. ATPase Stimulation Assays -- 3.1.1. Equipment -- 3.1.2. Buffers and Reagents -- 3.1.3. Procedure -- 3.1.4. Notes -- 3.2. Liposome Synthesis and Protein Incorporation -- 3.2.1. Equipment -- 3.2.2. Buffers and Reagents -- 3.2.3. Procedure -- 3.2.4. Notes -- 3.3. Cluster Transfer Monitored by Tiron Assay and Flow Cytometry -- 3.3.1. Equipment -- 3.3.2. Buffers and Reagents -- 3.3.3. Procedure -- 3.3.4. Notes -- 4. Summary and Conclusions -- References -- Chapter Four: Combined Biochemical, Biophysical, and Cellular Methods to Study Fe-S Cluster Transfer and Cytosolic Aconit ... -- 1. Introduction -- 2. In Vitro Fe-S Cluster Transfer From mNT to a Model Recipient -- 2.1. Purifications of mNT and FDX -- 2.1.1. Purification of H. sapiens Holo-mNT -- 2.1.2. Purification of E. coli Holo-FDX -- 2.1.3. Preparation of Apo-FDX -- 2.2. In Vitro Cluster Transfer Reaction Between Holo-mNT and Apo-FDX -- 2.2.1. UV-Visible Absorption Spectroscopy -- 2.2.2. Native PAGE -- 2.2.3. NMR Spectroscopy -- 3. Identification of a Physiological Recipient of the mNT Cluster -- 3.1. In Vitro Studies -- 3.1.1. In Vitro Cluster Transfer Reaction Between Holo-mNT and IRP1 -- 3.1.2. Measurement of Aconitase Activity -- 3.2. In Cellulo Studies -- 3.2.1. Effect of NO Challenge on Cytosolic Aconitase Activity -- 3.2.1.1. NO Challenge Assay 
520 |a 3.2.1.2. Preparation of Mitochondria-Enriched Fractions and Cytosolic Extracts -- 3.2.2. Involvement of mNT in the Fe-S Repair of Cytosolic Aconitase After Nitrosative Stress -- 3.3. Partner Protein Abundance in Mammalian Tissues -- 4. Conclusions -- References -- Chapter Five: Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria -- 1. Introduction -- 2. Multiprotein Complex Expression and Purification Strategies -- 2.1. DNA Constructs Used for Four-Protein Coexpression in E. coli -- 2.2. Purification of the Four-Protein Complex From E. coli -- 2.2.1. Equipment -- 2.2.2. Buffers and Reagents -- 2.2.3. Procedure -- 2.2.3.1. Programs for Affinity and Size-Exclusion Chromatography -- 2.2.3.1.1. Step 1: HiTrap Ni-Column -- 2.2.3.1.2. Steps 2 and 4: Sephacryl S-300 Column -- 2.2.3.1.3. Step 3: StrepTrap HP Column -- 2.2.3.2. SDS-PAGE Analysis of the Complex -- 2.2.3.2.1. Materials and Buffers -- 2.2.3.2.2. Procedure -- 2.3. Chemical Cross-Linking of the Complex -- 2.3.1. Materials and Buffers -- 2.3.2. Cross-Linking Procedure -- 3. Approaches to Biochemically Characterize the Purified Complex -- 3.1. Amino Acid Analysis to Define the Subunit Stoichiometry -- 3.2. Enzymatic Activity Assays -- 3.2.1. Cysteine Desulfurase Activity Assay -- 3.2.1.1. Equipment -- 3.2.1.2. Buffers and Solutions -- 3.2.1.3. Procedure -- 3.2.2. Fe-S Cluster Assembly Assay (Adapted From Kondapalli, Kok, Dancis, Layer et al., 2006) -- 3.2.2.1. Equipment -- 3.2.2.2. Buffers and Solutions -- 3.2.2.3. Procedure -- 4. Approaches to Define the Structure of the Complex -- 4.1. Dynamic Light Scattering -- 4.1.1. Equipment -- 4.1.2. Procedure -- 4.2. Comparative Size-Exclusion Chromatography -- 4.2.1. Proteins -- 4.2.2. Procedure -- 4.3. Electron Microscopy -- 4.3.1. Grid Preparation and Negative Staining of Purified Complex 
520 |a 4.3.1.1. Equipment -- 4.3.1.2. Buffers and Solutions -- 4.3.1.3. Procedure -- 4.3.2. Transmission Electron Microscopy -- 4.3.2.1. Equipment -- 4.3.2.2. Procedure -- 4.4. Single-Particle Reconstruction -- 4.4.1. Equipment -- 4.4.2. Procedure (Adapted From the EMAN2 Tutorial http://blake.bcm.edu/emanwiki/eman2/tutorials) -- 4.5. Docking of Structures Into the EM Density Maps of the 3D Models -- 4.5.1. Procedure -- 4.6. MDFF for Docked Structures -- 4.6.1. Programs -- 4.6.2. Procedure -- 5. Approaches to Validate the Protein-Protein Interfaces of the Complex -- 5.1. Limited Proteolysis of Cross-Linked Complex and Tandem Mass Spectrometry Identification of Cross-Linked Peptides -- 5.1.1. Equipment -- 5.1.2. Buffers and Solutions -- 5.1.3. Procedure (Adapted From Ranatunga et al., 2016) -- 5.2. Analysis of Cross-Linked Peptides -- 5.2.1. Equipment -- 5.2.2. Programs -- 5.2.3. Procedure (Adapted From http://www.Stavrox.Com/Help.Php) -- 5.3. Analysis of Complex Interfaces -- 5.3.1. Equipment -- 5.3.2. Programs -- 5.3.3. Procedure -- Acknowledgments -- References -- Chapter Six: Fe-S Cluster Hsp70 Chaperones: The ATPase Cycle and Protein Interactions -- 1. Introduction -- 1.1. Substrate-Binding Cycle of Hsp70/J-Protein Chaperones -- 1.2. An Overview of Mitochondrial Iron-Sulfur Cluster Biogenesis -- 1.3. Complex Evolutionary History of Mitochondrial Hsp70s Involved in Fe-S Cluster Biogenesis -- 2. Hsc20-Isu Interaction -- 2.1. Glutathione-S-Transferase Pull-Down Assay -- 2.1.1. Equipment -- 2.1.2. Buffers and Reagents -- 2.1.3. Protein Preparations -- 2.1.4. Procedure -- 2.1.5. Notes -- 3. Hsp70/Hsc20-Isu-Binding Cycle -- 3.1. Hsp70-Isu Interaction -- 3.1.1. Detection of Ssq1-Isu Interaction Using GST Pull-Down Assay -- 3.2. ATPase Activity as a Measure of the Progression of the Hsp70/Hsc20-Isu Interaction Cycle -- 3.2.1. Equipment 
520 |a 3.2.2. Buffers and Reagents -- 3.2.3. Protein Preparations -- 3.2.4. Procedure -- 4. Concluding Remarks -- Acknowledgments -- References -- Chapter Seven: B. subtilis as a Model for Studying the Assembly of Fe-S Clusters in Gram-Positive Bacteria -- 1. Introduction -- 1.1. Sulfur-Activating Enzyme -- 1.2. Scaffold Protein as the Platform for the Synthesis of Fe-S Clusters -- 1.3. Transfer of Preformed Clusters to Final Acceptors -- 2. Fe-S Cluster Assembly in B. subtilis -- 3. Methods to Probe Individual Biosynthetic Steps in Fe-S Cluster Assembly -- 3.1. Cysteine Desulfurase Reactions -- 3.1.1. Ala-NDA Assay -- 3.1.2. Sulfide Assays -- 3.1.3. Sulfur Acceptors and Reducing Agents -- 3.2. Fe-S Cluster Assembly Reactions -- 3.3. Fe-S Cluster Transfer Reactions -- 4. Concluding Remarks -- Acknowledgment -- References -- Chapter Eight: Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases -- 1. Introduction to FeS Clusters -- 2. Crystallization of Hydrogenases -- 2.1. Introduction to Hydrogenases -- 2.2. Methods of Structural Characterization of [FeFe]-Hydrogenases -- 2.2.1. Structural Characterization of "Apo" Hydrogenases -- 2.2.2. Characterization of Oxygen Susceptibility in [FeFe]-Hydrogenases -- 2.2.3. X-Ray Damage-Free Structure of CpI Hydrogenase -- 2.2.4. Synthetic Reconstitution of the [FeFe]-Hydrogenase Active Site -- 2.3. Methods of Structural Characterization of [NiFe]-Hydrogenases -- 2.3.1. Background on [NiFe]-Hydrogenase Crystallization and Catalytic Cycle -- 2.3.2. Crystallization of [NiFe]-Hydrogenases With CO-Inhibition -- 2.3.3. Redox Poising of [NiFeSe]-Hydrogenase Crystals -- 2.3.4. Cryo-Electron Microscopy as a Structural Characterization Technique of Hydrogenases -- 2.3.5. Structural Characterization of a Group 4 [NiFe]-Hydrogenases 
520 |a 2.3.6. Gas Derivatization as a Tool to Probe Gas Channels in Hydrogenases Structures 
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