close
1.

電子ブック
ＥＢ
1. Laboratory methods in enzymology : DNA
Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2013
所蔵情報: loading…
2.

電子ブック
ＥＢ
2. Methods in Enzymology, Vol. 530: Laboratory Methods in Enzymology: RNA
Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2013
所蔵情報: loading…
3.

電子ブック
ＥＢ
3. Translation Initiation: Cell Biology, High-throughput and Chemical-based Approaches : Cell Biology, High-throughput and Chemical-based Approaches
Jon; Lorsch, Jon Lorsch, Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2007
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Purification of FLAG-Tagged Eukaryotic Initiation Factor 2B Complexes, Subcomplexes, and Fragments from Saccharomyces cerevisiae / Sarah S. Mohammad-Qureshi ; Raphael Haddad ; Karren S. Palmer ; Jonathan P. Richardson ; Edith Gomez ; Graham D. Pavitt1：
Introduction
Plasmid Vectors and Yeast Strains Used / 2：
Expression and Purification of elF2B / 3：
Functional Analysis of Purified Proteins / 4：
Conclusions / 5：
Acknowledgments
References
In Vivo Deletion Analysis of the Architecture of a Multiprotein Complex of Translation Initiation Factors / Klaus H. Nielsen ; Leos Valasek
Ni[superscript 2+] Affinity Purification of elF3 Using a Polyhistidine Tag
Deletion/Mutational Analysis of elF3 Subunits and Ni[superscript 2+] Affinity Purification of Their Subcomplexes
elF3 Purification Using Other Epitope Tags
CAM (Clustered-30-Alanine Mutagenesis)
An Approach to Studying the Localization and Dynamics of Eukaryotic Translation Factors in Live Yeast Cells / Susan G. Campbell ; Mark P. Ashe
Yeast Strains and Growth Conditions
Application of Live Cell Imaging
Additional In Vivo Techniques
In Vitro and Tissue Culture Methods for Analysis of Translation Initiation on the Endoplasmic Reticulum / Samuel B. Stephens ; Christopher V. Nicchitta
Background
Methods
Analysis of Protein Synthesis Initiation on ER Membrane-Bound Ribosomes of Tissue Culture Cells
Velocity Sedimentation
Mammalian Stress Granules and Processing Bodies / Nancy Kedersha ; Paul Anderson
Detection and Identification of SGs and PBs
Immunostaining Protocol
Stimuli for the Induction of SGs and PBs
Transfection-lnduced SGs
Induction of PBs / 6：
Methods to Analyze MicroRNA-mediated Control of mRNA Translation / Jennifer L. Clancy ; Marco Nousch ; David T. Humphreys ; Belinda J. Westman ; Traude H. Beilharz ; Thomas Preiss7：
Systems to Measure miR-Mediated Repression
Detection of miR-Mediated Changes in mRNA Stability
Measurement of miR Target mRNA Deadenylation
Measuring the Distribution of miRNP Components in Polysome Profiles
Localization of miRNP Components to P-Bodies
Concluding Remarks
Methods for Studying Signal-Dependent Regulation of Translation Factor Activity / Xuemin Wang ; Christopher G. Proud
Introduction to Signaling Pathways and the Control of Translation Factors
Experimental Protocols
Analysis of the Phosphorylation States of Translation Factors and Signaling Components - Overview
Assays for Specific Protein Kinases
Assays for Initiation Factor Function
Analysis of mRNA Translation in Cultured Hippocampal Neurons / Yi-Shuian Huang ; Joel D. Richter8：
Materials and Reagents for Primary Neuron Culture
RNA Transfection and Reporter Assays
shRNA Design and Lenti-shRNA Virus Production
shRNA Knockdown of CPEB3 in Cultured Neurons
Synaptoneurosome Isolation and [superscript 35]S-met/cys Labeling
UV-Crosslinking, Immunoprecipitation of an RNA-Binding Protein, CPEB3
Detecting Ribosomal Association with the 5[prime] Leader of mRNAs by Ribosome Density Mapping (RDM) / Naama Eldad ; Yoav Arava9：
General Concept
Genome-Wide Analysis of mRNA Polysomal Profiles with Spotted DNA Microarrays / Daniel Melamed10：
Experimental Designs
Data Acquisition and Analysis
Synthesis of Anti-Reverse Cap Analogs (ARCAs) and their Applications in mRNA Transtation and Stability / Ewa Grudzien-Nogalska ; Janusz Stepinski ; Jacek Jemielity ; Joanna Zuberek ; Ryszard Stolarski ; Robert E. Rhoads ; Edward Darzynkiewicz11：
Chemical Synthesis
In Vitro and In Vivo Assays
Binding Affinity of ARCAs for elF4E
Incorporation of ARCAs into RNA by In Vitro Transcription
Properties of ARCAs and ARCA-Capped mRNAs in Cell-Free Translation Systems
Properties of ARCA-Capped mRNAs in Mammalian Cells
Methods for Identifying Compounds that Specifically Target Translation / Letizia Brandi ; Attilio Fabbretti ; Pohl Milon ; Marcello Carotti ; Cynthia L. Pon ; Claudio O. Gualerzi12：
Materials Required
Methods and Tests
Identifying Small Molecule Inhibitors of Eukaryotic Translation Initiation / Regina Cencic ; Francis Robert ; Jerry Pelletier13：
A Reverse Chemical Genetic Assay Probing elF4E:elF4G and elF4A:efF4G Interactions
A Forward Chemical Genetic Screen to Identify Inhibitors of Eukaryotic Translation
Characterization of Inhibitors of Translation Identified in Chemical Genetic Screens
Discussion and Concluding Remarks
Isolation and Identification of Eukaryotic Initiation Factor 4A as a Molecular Target for the Marine Natural Product Pateamine A / Woon-Kai Low ; Yongjun Dang ; Tilman Schneider-Poetsch ; Zonggao Shi ; Nam Song Choi ; Robert M. Rzasa ; Helene A. Shea ; Shukun Li ; Kaapjoo Park ; Gil Ma ; Daniel Romo ; Jun O. Liu14：
Total Synthesis of Pateamine A
Synthesis of Derivatives of Pateamine A and Structure Activity Relationship Studies
Structural Analysis of PatA Leading to DMDA-PatA and Viable Positions for Derivatization
Synthesis of a Bioactive Biotin-Pateamine A (B-PatA) Conjugate
Affinity Pull-Down of PatA-Binding Proteins
Identification of PatA-Binding Proteins
Author Index
Subject Index
Contributors
Preface
Volumes in Series
4.

電子ブック
ＥＢ
4. Translation Initiation: Reconstituted Systems and Biophysical Methods : Reconstituted Systems and Biophysical Methods
Jon; Lorsch, Jon Lorsch, Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2007
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Transient Kinetics, Fluorescence, and FRET in Studies of Initiation of Translation in Bacteria / Pohl Milon ; Andrey L. Konevega ; Frank Peske ; Attilio Fabbretti ; Claudio O. Gualerzi ; Marina V. Rodnina1：
Introduction
Experimental Outline / 2：
Materials / 3：
Experimental Procedures / 4：
Rapid Kinetic Measurements / 5：
Quench-Flow Measurements / 6：
GTPase Activity / 7：
Dipeptide Formation / 8：
Applications of the Method / 9：
Binding of fMet-tRNA to the 30S Subunit / 10：
FRET to IF3 / 11：
Nucleotide Binding to IF2 / 12：
Subunit Joining / 13：
Acknowledgments
References
Binding of mRNA to the Bacterial Translation Initiation Complex / Sean M. Studer ; Simpson Joseph
Real-Time Dynamics of Ribosome-Ligand Interaction by Time-Resolved Chemical Probing Methods / Anna Maria Giuliodori ; Cynthia L. Pon
General Strategy
Time-Resolved Chemical Probing with DMS
Time-Resolved Probing with ONOOK
Time-Resolved Chemical Probing with Fe(II)-EDTA
Overexpression and Purification of Mammalian Mitochondrial Translational Initiation Factor 2 and Initiation Factor 3 / Domenick G. Grasso ; Brooke E. Christian ; Angela Spencer ; Linda L. Spremulli
Assays for IF2[subscript MT] and IF3[subscript MT]
Purification of His-Tagged IF2[subscript MT]
Purification of His-Tagged IF3[subscript MT]
In Vitro Studies of Archaeal Translational Initiation / Dario Benelli ; Paola Londei
Preparation of S. solfataricus Cellular Extracts, Ribosomes, and Other Cellular Fractions
In Vitro Translation of Archaeal mRNAs at High Temperature
Ribosome/mRNA Interaction
Initiation Factors
Functional Analyses of Recombinant S. solfataricus IFS
Interaction of Initiation Factors with Ribosomal Subunits
IF/tRNA[subscript i superscript Met] Interaction
Interaction of [[superscript 35]S]Met-tRNA[subscript i superscript Met] with Ribosomes
Translational G-Proteins
Reconstitution of Yeast Translation Initiation / Michael G. Acker ; Sarah E. Kolitz ; Sarah F. Mltchell ; Jagpreet S. Nanda ; Jon Lorsch
Large-Scale Lysis of S. cerevisiae Cells
Purification of 40S and 60S Ribosomal Subunits from S. cerevisiae
Ribosome Quality Analysis (Identity Gel)
Purification of His-Tagged eIF2 from S. cerevisiae
Purification of His-Tagged eIF3 from S. cerevisiae
Overexpression and Purification of Yeast eIF1, eIF1A, and eIF5 from E. coli
Overexpression and Purification of Yeast eIF1A in E. coli
Overexpression and Purification of Yeast eIF5B in E. coli
Purification of Yeast Methionyl-tRNA Synthetase (YMETRS) from S. cerevisiae
RNA Synthesis and Purification
Charging tRNA[subscript iMet] with Methionine
Filter Binding Assay to Monitor Ternary Complex Formation
Benchtop eIF2 GTPase Assay / 14：
43S/80S Complex Gel Shift Assay / 15：
Solutions / 16：
Assembly and Analysis of Eukaryotic Translation Initiation Complexes / Andrey V. Pisarev ; Anett Unbehaun ; Christopher U. T. Hellen ; Tatyana V. Pestova
Chemicals, Enzymes, and Biological Materials
Purification of 40S and 60S Ribosomal Subunits
Purification of Native eIF3 and eIF4F
Purification of Native eIF2, eIF5, and eIF5B
Expression in E. coli and Purification of Recombinant eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, and eIF5B
Preparation and Aminoacylation of Initiator tRNA
Assembly of 48S and 80S Initiation Complexes on [beta]-Globin mRNA
Resolution of Translation Initiation Complexes by Sucrose Density Gradient Centrifugation
Toe Printing Analysis of Ribosomal Complexes
Site-Directed UV Cross-Linking of mRNA in Initiation Complexes
Directed Hydroxyl Radical Probing to Localize Initiation Factors on the 40S Subunit
Reconstitution of Mammalian 48S Ribosomal Translation Initiation Complex / Romit Majumdar ; Jayanta Chaudhuri ; Umadas Maitra
Reagents
Buffers
General Methods
Reconstitution of the 48S Ribosomal Complex
Remarks
Biophysical Approach to Studies of Cap-eIF4E Interaction by Synthetic Cap Analogs / Anna Niedzwiecka ; Janusz Stepinski ; Jan M. Antosiewicz ; Edward Darzynkiewicz ; Ryszard Stolarski
Syntheses and Purification of Cap Analogs
Binding of the Cap Analogs to eIF4E by Fluorescence Titration Experiments
Application of Microcalorimetry to Studying eIF4E-Cap Interaction
Stopped-Flow Fluorescence Studies of Binding Cap Analogs to eIF4E
Biophysical Studies of the Translation Initiation Pathway with Immobilized mRNA Analogs / John E. G. McCarthy ; Steven Marsden ; Tobias von der Haar
Generation of RNAs
Protocol 1: 3[prime]-End Biotinylation of a Transcript by Use of Poly(A) Polymerase
Protocol 2: Introduction of Aldehyde Groups by Oxidation of the mRNA 3[prime]-End
Protocol 3: Thiolation at the mRNA 5[prime]-End by Use of Polynucleotide Kinase
Protection-Based Assays to Measure Aminoacyl-tRNA Binding to Translation Initiation Factors / Yves Mechulam ; Laurent Guillon ; Laure Yatime ; Sylvain Blanquet ; Emmanuelle Schmitt
Purification of Overproduced Initiator tRNA
Preparation of Methionylated tRNA
Protection Assay
Conclusion
NMR Methods for Studying Protein-Protein Interactions Involved in Translation Initiation / Assen Marintchev ; Dominique Frueh ; Gerhard Wagner
Types of Interactions in Translation from the Perspective of K[subscript D] and Lifetime of the Complex
NMR Methods for Studying Protein Interactions in Translation
Descriptions of NMR Methods
Special Cases
Summary
Structural Methods for Studying IRES Function / Jeffrey S. Kieft ; David A. Costantino ; Megan E. Filbin ; John Hammond ; Jennifer S. Pfingsten
Methods
Conclusions
Biophysical and Biochemical Investigations of dsRNA-Activated Kinase PKR / Sean A. McKenna ; Darrin A. Lindhout ; Takashi Shimoike ; Joseph D. Puglisi
Expression and Purification of PKR
RNA Synthesis
Phosphorylation Assays
Measuring RNA-Protein Stabilities
Monitoring the Association State of PKR
NMR Spectroscopy
In Vitro Translation Assays
Expression and Purification of Recombinant Wheat Translation Initiation Factors eIF1, eIF1A, eIF4A, eIF4B, eIF4F, eIF(ISO)4F, and eIF5 / Laura K. Mayberry ; Michael D. Dennis ; M. Leah Allen ; Kelley Ruud Nitka ; Patricia A. Murphy ; Lara Campbell ; Karen S. Browning
Procedures
Results
In Vitro Reconstitution and Biochemical Characterization of Translation Initiation by Internal Ribosomal Entry / Victoria G. Kolupaeva ; Sylvain de Breyne
Plasmids
Purification of Factors and Ribosomes
Preparation of IRES-Containing mRNA and Aminoacylated Initiator tRNA
Strategies for Identification of Viral IRESs
Assays for 48S Complex Formation in Cell-Free Extracts: Sucrose Density Gradient Centrifugation
Assays for 48S Complex Formation in Cell-Free Extracts: Toe Printing
Identification of the Minimum Set of Factors Required for 48S Complex Formation
Reconstitution of 48S Complex Formation on Type 2 Picornavirus IRESs
Toe Printing to Map Stable Interactions of the IRES with Components of the Translation Apparatus
Mapping Interactions of the IRES with Components of the Translation Apparatus by Chemical and Enzymatic Footprinting
Directed Hydroxyl Radical Cleavage
Author Index
Subject Index
Contributors
Preface
Volumes in Series
5.

電子ブック
ＥＢ
5. Translation Initiation: Extract Systems and Molecular Genetics
Jon; Lorsch, Jon Lorsch, Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2007
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Use of Reticulocyte Lysates for Mechanistic Studies of Eukaryotic Translation Initiation / William C. Merrick ; Diane Barth-Baus1：
Introduction
Materials / 2：
Methods / 3：
Translation of an mRNA to Yield a Radioactive Product / 4：
Quantitation of Reaction Products / 5：
Optimization of Translations / 6：
Reporter Proteins for Translation / 7：
Experimental Use of Nuclease-Treated Lysates / 8：
References
Studying Translational Control in Drosophila Cell-Free Systems / Fatima Gebauer ; Matthias W. Hentze
Preparation of Ovary Extracts
Preparation of Embryo Extracts
The Translation Assay
Acknowledgments
Use of In Vitro Translation Extract Depleted in Specific Initiation Factors for the Investigation of Translational Regulation / Daniel R. Gallie
Factors Involved in Translation Initiation
Experimental Methods to Generate and Use Fractionated Translation Extracts
A Highly Efficient and Robust In Vitro Translation System for Expression of Picornavirus and Hepatitis C Virus RNA Genomes / Yuri V. Svitkin ; Nahum Sonenberg
Cell-Free Model for EMCV Replication
Materials for Cell-Free Synthesis of EMCV
Methods for Cell-Free Synthesis of EMCV
In Vitro Translation of HCV RNA
Materials for In Vitro Translation of HCV RNA
Methods and Applications of In Vitro Translation of HCV RNA
Perspectives and Future Applications
A Practical Approach to Isolate 48S Complexes: Affinity Purification and Analyses / Nicolas Locker ; Peter J. Lukavsky
Design of Strepto-Tagged mRNAs for Affinity Purification of 48S Complexes
Affinity Purification of 48S Complexes
Analysis of the Purified 48S Complexes
Functional Analysis of the Purified 48S Complexes
Conclusion
Yeast Phenotypic Assays on Translational Control / Bumjun Lee ; Tsuyoshi Udagawa ; Chingakham Ranjit Singh ; Katsura Asano
Quantitative Yeast Growth Assay
Use of FOA to Assay Lethal Mutations and Perform Plasmid Shuffling
Assay of Dominant Negative Mutants, Foreign Proteins, or Phenotypic Suppression by Overexpression
Assay of Stringency in Start Codon Selection
Assay of Translation Initiation Activities with GCN4 as Reporter
Polysome Profiling
Localization and Characterization of Protein-Protein Interaction Sites
The Use of Two-Hybrid Assay to Identify Protein-Protein Interaction Sites
GST Pull-Down Assay
Site-Directed Mutagenesis to Study Protein-Protein Interactions
Co-IP Assay
In Vivo Stabilization of Preinitiation Complexes by Formaldehyde Cross-Linking / Leos Valasek ; Bela Szamecz ; Alan G. Hinnebusch ; Klaus H. Nielsen
Rationale Behind the Choice of HCHO as a Stabiiization Agent
Whole Cell Extract Preparation and WCE Fractionation
Analysis of Fractionated Preinitiation Complexes
Special Considerations and the Resedimentation Protocol
Final Remarks
Molecular Genetic Structure-Function Analysis of Translation Initiation Factor elF5B / Byung-Sik Shin ; Thomas E. Dever9：
Future Directions
The Use of Fungal In Vitro Systems for Studying Translational Regulation / Cheng Wu ; Nadia Amrani ; Allan Jacobson ; Matthew S. Sachs10：
Methods and Discussion
Summary
Investigating Translation Initiation Using Drosophila Molecular Genetics / Gritta Tettweilerd Paul Lasko11：
P-Elements
Perspectives and Conclusions
Important Sources for Drosophila Protocols
Drosophila Stock Centers
Analysis of RNA:Protein Interactions In Vivo: Identification of RNA-Binding Partners of Nuclear Factor 90 / Andrew M. Parrott ; Melissa R. Walsh ; Michael B. Mathews12：
Expression of Epitope-Tagged Proteins
RNP Immunoprecipitation (RIP) Assay
Identification of Unknown RNAs by PCR Amplification and Sequencing
Acknowledgment
Approaches for Analyzing the Differential Activities and Functions of elF4E Family Members / Robert E. Rhoads ; Tzvetanka D. Dinkova ; Rosemary Jagus13：
In Silico Detection and Analysis of elF4E Family Members
Assessing Differential Cap-Binding Properties of elF4E Family Members
Expression of elF4E Family Members
Assessing elF4E Family Members in Translation Systems
Protein-Protein Interaction Assays as a Means to Differentiate Functions of elF4E Family Members
Global Microarray Studies of Polysomal mRNA Distribution
Tethered Function Assays: An Adaptable Approach to Study RNA Regulatory Proteins / Jeff Coller ; Marv Wickens14：
Introduction and Rationale
The Basic Design of the Tethered function Assay
The Tether
The Reporter mRNA
A Priori Considerations about the Logic of the Assay
Important Controls
Examples of the Tethered Function Assay in the Literature
Prospects
Analysis of Ribosomal Shunting During Translation Initiation in Eulkaryotic mRNAs / Vincent P. Mauro ; Stephen A. Chappell ; John Dresios15：
Defining the Site or Sites of Ribosomal Recruitment
Experimental Approaches to Determine Which Segments of an mRNA Are Shunted
Identification of Ribosomal Shunt Sites
Determining Whether Putative Shunt Sites Bind to Ribosomal Subunits
Assessing mRNA-rRNA Base Pairing in Yeast
Assessing Ribosomal Shunting Mediated by mRNA-rRNA Base Pairing Interactions
Considerations in Using the Mouse-Yeast Hybrid mRNA System
Author Index
Subject Index
Contributors
Preface
Volumes in Series
6.

電子ブック
ＥＢ
6. Methods in Enzymology, Vol. 533: Laboratory Methods in Enzymology: Cell, Lipid and Carbohydrate
Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2013
所蔵情報: loading…
7.

電子ブック
ＥＢ
7. Methods in Enzymology, Vol. 536: Laboratory Methods in Enzymology: Protein, Part A
Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2014
所蔵情報: loading…
8.

電子ブック
ＥＢ
8. Laboratory Methods in Enzymology : Protein Part B
Jon Lorsch
出版情報: Elsevier ScienceDirect Books , Academic Press, 2014
所蔵情報: loading…
9.

電子ブック
ＥＢ
9. Translation Initiation: Cell Biology, High-throughput and Chemical-based Approaches : Cell Biology, High-throughput and Chemical-based Approaches
Jon; Lorsch, Jon Lorsch, Jon Lorsch
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2007
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Purification of FLAG-Tagged Eukaryotic Initiation Factor 2B Complexes, Subcomplexes, and Fragments from Saccharomyces cerevisiae / Sarah S. Mohammad-Qureshi ; Raphael Haddad ; Karren S. Palmer ; Jonathan P. Richardson ; Edith Gomez ; Graham D. Pavitt1：
Introduction
Plasmid Vectors and Yeast Strains Used / 2：
Expression and Purification of elF2B / 3：
Functional Analysis of Purified Proteins / 4：
Conclusions / 5：
Acknowledgments
References
In Vivo Deletion Analysis of the Architecture of a Multiprotein Complex of Translation Initiation Factors / Klaus H. Nielsen ; Leos Valasek
Ni[superscript 2+] Affinity Purification of elF3 Using a Polyhistidine Tag
Deletion/Mutational Analysis of elF3 Subunits and Ni[superscript 2+] Affinity Purification of Their Subcomplexes
elF3 Purification Using Other Epitope Tags
CAM (Clustered-30-Alanine Mutagenesis)
An Approach to Studying the Localization and Dynamics of Eukaryotic Translation Factors in Live Yeast Cells / Susan G. Campbell ; Mark P. Ashe
Yeast Strains and Growth Conditions
Application of Live Cell Imaging
Additional In Vivo Techniques
In Vitro and Tissue Culture Methods for Analysis of Translation Initiation on the Endoplasmic Reticulum / Samuel B. Stephens ; Christopher V. Nicchitta
Background
Methods
Analysis of Protein Synthesis Initiation on ER Membrane-Bound Ribosomes of Tissue Culture Cells
Velocity Sedimentation
Mammalian Stress Granules and Processing Bodies / Nancy Kedersha ; Paul Anderson
Detection and Identification of SGs and PBs
Immunostaining Protocol
Stimuli for the Induction of SGs and PBs
Transfection-lnduced SGs
Induction of PBs / 6：
Methods to Analyze MicroRNA-mediated Control of mRNA Translation / Jennifer L. Clancy ; Marco Nousch ; David T. Humphreys ; Belinda J. Westman ; Traude H. Beilharz ; Thomas Preiss7：
Systems to Measure miR-Mediated Repression
Detection of miR-Mediated Changes in mRNA Stability
Measurement of miR Target mRNA Deadenylation
Measuring the Distribution of miRNP Components in Polysome Profiles
Localization of miRNP Components to P-Bodies
Concluding Remarks
Methods for Studying Signal-Dependent Regulation of Translation Factor Activity / Xuemin Wang ; Christopher G. Proud
Introduction to Signaling Pathways and the Control of Translation Factors
Experimental Protocols
Analysis of the Phosphorylation States of Translation Factors and Signaling Components - Overview
Assays for Specific Protein Kinases
Assays for Initiation Factor Function
Analysis of mRNA Translation in Cultured Hippocampal Neurons / Yi-Shuian Huang ; Joel D. Richter8：
Materials and Reagents for Primary Neuron Culture
RNA Transfection and Reporter Assays
shRNA Design and Lenti-shRNA Virus Production
shRNA Knockdown of CPEB3 in Cultured Neurons
Synaptoneurosome Isolation and [superscript 35]S-met/cys Labeling
UV-Crosslinking, Immunoprecipitation of an RNA-Binding Protein, CPEB3
Detecting Ribosomal Association with the 5[prime] Leader of mRNAs by Ribosome Density Mapping (RDM) / Naama Eldad ; Yoav Arava9：
General Concept
Genome-Wide Analysis of mRNA Polysomal Profiles with Spotted DNA Microarrays / Daniel Melamed10：
Experimental Designs
Data Acquisition and Analysis
Synthesis of Anti-Reverse Cap Analogs (ARCAs) and their Applications in mRNA Transtation and Stability / Ewa Grudzien-Nogalska ; Janusz Stepinski ; Jacek Jemielity ; Joanna Zuberek ; Ryszard Stolarski ; Robert E. Rhoads ; Edward Darzynkiewicz11：
Chemical Synthesis
In Vitro and In Vivo Assays
Binding Affinity of ARCAs for elF4E
Incorporation of ARCAs into RNA by In Vitro Transcription
Properties of ARCAs and ARCA-Capped mRNAs in Cell-Free Translation Systems
Properties of ARCA-Capped mRNAs in Mammalian Cells
Methods for Identifying Compounds that Specifically Target Translation / Letizia Brandi ; Attilio Fabbretti ; Pohl Milon ; Marcello Carotti ; Cynthia L. Pon ; Claudio O. Gualerzi12：
Materials Required
Methods and Tests
Identifying Small Molecule Inhibitors of Eukaryotic Translation Initiation / Regina Cencic ; Francis Robert ; Jerry Pelletier13：
A Reverse Chemical Genetic Assay Probing elF4E:elF4G and elF4A:efF4G Interactions
A Forward Chemical Genetic Screen to Identify Inhibitors of Eukaryotic Translation
Characterization of Inhibitors of Translation Identified in Chemical Genetic Screens
Discussion and Concluding Remarks
Isolation and Identification of Eukaryotic Initiation Factor 4A as a Molecular Target for the Marine Natural Product Pateamine A / Woon-Kai Low ; Yongjun Dang ; Tilman Schneider-Poetsch ; Zonggao Shi ; Nam Song Choi ; Robert M. Rzasa ; Helene A. Shea ; Shukun Li ; Kaapjoo Park ; Gil Ma ; Daniel Romo ; Jun O. Liu14：
Total Synthesis of Pateamine A
Synthesis of Derivatives of Pateamine A and Structure Activity Relationship Studies
Structural Analysis of PatA Leading to DMDA-PatA and Viable Positions for Derivatization
Synthesis of a Bioactive Biotin-Pateamine A (B-PatA) Conjugate
Affinity Pull-Down of PatA-Binding Proteins
Identification of PatA-Binding Proteins
Author Index
Subject Index
Contributors
Preface
Volumes in Series
10.

電子ブック
ＥＢ
10. Translation Initiation: Reconstituted Systems and Biophysical Methods : Reconstituted Systems and Biophysical Methods
Jon; Lorsch, Jon Lorsch, Jon Lorsch
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2007
所蔵情報: loading…
目次情報: 続きを見る
Contributors
Preface
Volumes in Series
Transient Kinetics, Fluorescence, and FRET in Studies of Initiation of Translation in Bacteria / Pohl Milon ; Andrey L. Konevega ; Frank Peske ; Attilio Fabbretti ; Claudio O. Gualerzi ; Marina V. Rodnina1：
Introduction
Experimental Outline / 2：
Materials / 3：
Experimental Procedures / 4：
Rapid Kinetic Measurements / 5：
Quench-Flow Measurements / 6：
GTPase Activity / 7：
Dipeptide Formation / 8：
Applications of the Method / 9：
Binding of fMet-tRNA to the 30S Subunit / 10：
FRET to IF3 / 11：
Nucleotide Binding to IF2 / 12：
Subunit Joining / 13：
Acknowledgments
References
Binding of mRNA to the Bacterial Translation Initiation Complex / Sean M. Studer ; Simpson Joseph
Real-Time Dynamics of Ribosome-Ligand Interaction by Time-Resolved Chemical Probing Methods / Anna Maria Giuliodori ; Cynthia L. Pon
General Strategy
Time-Resolved Chemical Probing with DMS
Time-Resolved Probing with ONOOK
Time-Resolved Chemical Probing with Fe(II)-EDTA
Overexpression and Purification of Mammalian Mitochondrial Translational Initiation Factor 2 and Initiation Factor 3 / Domenick G. Grasso ; Brooke E. Christian ; Angela Spencer ; Linda L. Spremulli
Assays for IF2[subscript MT] and IF3[subscript MT]
Purification of His-Tagged IF2[subscript MT]
Purification of His-Tagged IF3[subscript MT]
In Vitro Studies of Archaeal Translational Initiation / Dario Benelli ; Paola Londei
Preparation of S. solfataricus Cellular Extracts, Ribosomes, and Other Cellular Fractions
In Vitro Translation of Archaeal mRNAs at High Temperature
Ribosome/mRNA Interaction
Initiation Factors
Functional Analyses of Recombinant S. solfataricus IFS
Interaction of Initiation Factors with Ribosomal Subunits
IF/tRNA[subscript i superscript Met] Interaction
Interaction of [[superscript 35]S]Met-tRNA[subscript i superscript Met] with Ribosomes
Translational G-Proteins
Reconstitution of Yeast Translation Initiation / Michael G. Acker ; Sarah E. Kolitz ; Sarah F. Mltchell ; Jagpreet S. Nanda ; Jon Lorsch
Large-Scale Lysis of S. cerevisiae Cells
Purification of 40S and 60S Ribosomal Subunits from S. cerevisiae
Ribosome Quality Analysis (Identity Gel)
Purification of His-Tagged eIF2 from S. cerevisiae
Purification of His-Tagged eIF3 from S. cerevisiae
Overexpression and Purification of Yeast eIF1, eIF1A, and eIF5 from E. coli
Overexpression and Purification of Yeast eIF1A in E. coli
Overexpression and Purification of Yeast eIF5B in E. coli
Purification of Yeast Methionyl-tRNA Synthetase (YMETRS) from S. cerevisiae
RNA Synthesis and Purification
Charging tRNA[subscript iMet] with Methionine
Filter Binding Assay to Monitor Ternary Complex Formation
Benchtop eIF2 GTPase Assay / 14：
43S/80S Complex Gel Shift Assay / 15：
Solutions / 16：
Assembly and Analysis of Eukaryotic Translation Initiation Complexes / Andrey V. Pisarev ; Anett Unbehaun ; Christopher U. T. Hellen ; Tatyana V. Pestova
Chemicals, Enzymes, and Biological Materials
Purification of 40S and 60S Ribosomal Subunits
Purification of Native eIF3 and eIF4F
Purification of Native eIF2, eIF5, and eIF5B
Expression in E. coli and Purification of Recombinant eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, and eIF5B
Preparation and Aminoacylation of Initiator tRNA
Assembly of 48S and 80S Initiation Complexes on [beta]-Globin mRNA
Resolution of Translation Initiation Complexes by Sucrose Density Gradient Centrifugation
Toe Printing Analysis of Ribosomal Complexes
Site-Directed UV Cross-Linking of mRNA in Initiation Complexes
Directed Hydroxyl Radical Probing to Localize Initiation Factors on the 40S Subunit
Reconstitution of Mammalian 48S Ribosomal Translation Initiation Complex / Romit Majumdar ; Jayanta Chaudhuri ; Umadas Maitra
Reagents
Buffers
General Methods
Reconstitution of the 48S Ribosomal Complex
Remarks
Biophysical Approach to Studies of Cap-eIF4E Interaction by Synthetic Cap Analogs / Anna Niedzwiecka ; Janusz Stepinski ; Jan M. Antosiewicz ; Edward Darzynkiewicz ; Ryszard Stolarski
Syntheses and Purification of Cap Analogs
Binding of the Cap Analogs to eIF4E by Fluorescence Titration Experiments
Application of Microcalorimetry to Studying eIF4E-Cap Interaction
Stopped-Flow Fluorescence Studies of Binding Cap Analogs to eIF4E
Biophysical Studies of the Translation Initiation Pathway with Immobilized mRNA Analogs / John E. G. McCarthy ; Steven Marsden ; Tobias von der Haar
Generation of RNAs
Protocol 1: 3[prime]-End Biotinylation of a Transcript by Use of Poly(A) Polymerase
Protocol 2: Introduction of Aldehyde Groups by Oxidation of the mRNA 3[prime]-End
Protocol 3: Thiolation at the mRNA 5[prime]-End by Use of Polynucleotide Kinase
Protection-Based Assays to Measure Aminoacyl-tRNA Binding to Translation Initiation Factors / Yves Mechulam ; Laurent Guillon ; Laure Yatime ; Sylvain Blanquet ; Emmanuelle Schmitt
Purification of Overproduced Initiator tRNA
Preparation of Methionylated tRNA
Protection Assay
Conclusion
NMR Methods for Studying Protein-Protein Interactions Involved in Translation Initiation / Assen Marintchev ; Dominique Frueh ; Gerhard Wagner
Types of Interactions in Translation from the Perspective of K[subscript D] and Lifetime of the Complex
NMR Methods for Studying Protein Interactions in Translation
Descriptions of NMR Methods
Special Cases
Summary
Structural Methods for Studying IRES Function / Jeffrey S. Kieft ; David A. Costantino ; Megan E. Filbin ; John Hammond ; Jennifer S. Pfingsten
Methods
Conclusions
Biophysical and Biochemical Investigations of dsRNA-Activated Kinase PKR / Sean A. McKenna ; Darrin A. Lindhout ; Takashi Shimoike ; Joseph D. Puglisi
Expression and Purification of PKR
RNA Synthesis
Phosphorylation Assays
Measuring RNA-Protein Stabilities
Monitoring the Association State of PKR
NMR Spectroscopy
In Vitro Translation Assays
Expression and Purification of Recombinant Wheat Translation Initiation Factors eIF1, eIF1A, eIF4A, eIF4B, eIF4F, eIF(ISO)4F, and eIF5 / Laura K. Mayberry ; Michael D. Dennis ; M. Leah Allen ; Kelley Ruud Nitka ; Patricia A. Murphy ; Lara Campbell ; Karen S. Browning
Procedures
Results
In Vitro Reconstitution and Biochemical Characterization of Translation Initiation by Internal Ribosomal Entry / Victoria G. Kolupaeva ; Sylvain de Breyne
Plasmids
Purification of Factors and Ribosomes
Preparation of IRES-Containing mRNA and Aminoacylated Initiator tRNA
Strategies for Identification of Viral IRESs
Assays for 48S Complex Formation in Cell-Free Extracts: Sucrose Density Gradient Centrifugation
Assays for 48S Complex Formation in Cell-Free Extracts: Toe Printing
Identification of the Minimum Set of Factors Required for 48S Complex Formation
Reconstitution of 48S Complex Formation on Type 2 Picornavirus IRESs
Toe Printing to Map Stable Interactions of the IRES with Components of the Translation Apparatus
Mapping Interactions of the IRES with Components of the Translation Apparatus by Chemical and Enzymatic Footprinting
Directed Hydroxyl Radical Cleavage
Author Index
Subject Index
Contributors
Preface
Volumes in Series
文献の複写および貸借の依頼を行う
 文献複写・貸借依頼