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1.

電子ブック

EB
David A. Hopwood, D. A. Hopwood
出版情報: Elsevier ScienceDirect Books , 2009
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Contributors
Preface
Volumes in Series
Polyketides / Section I:
Introduction to Polyketide Biosynthesis / Kira J. Weissman1:
Introduction
Acknowledgment
References
Structural Enzymology of Polyketide Synthases / Shiou-Chuan (Sheryl) Tsai ; Brian Douglas Ames2:
Fatty Acid Synthase
Different Types of PKS and a Summary of Structural Work / 3:
Structural Enzymology of Individual Domains / 4:
Summary and Future Prospects / 5:
Acknowledgments
Fungal Type I Polyketide Synthases / Russell J. Cox ; Thomas J. Simpson
Partially Reducing PKSs: 6-MethylSalicylate Synthase
Nonreducing PKSs
Highly Reducing PKSs
NR/HR PKS Hybrid Systems: Zearalenone (ZAE1 and ZAE2)
Conclusions / 6:
Tandem Acyl Carrier Protein Domains in Polyunsaturated Fatty Acid Synthases / Hui Jiang ; Scott R. Rajski ; Ben Shen
Methods
Conclusion
Iterative Type I Polyketide Synthases for Enediyne Core Biosynthesis / Geoffrey P. Horsman ; Steven G. Van Lanen
The DEBS Paradigm for Type I Modular Polyketide Synthases and Beyond / Leonard Katz
DEBS and the Concept of a Module
Beyond the DEBS Paradigm
Formation and Characterization of Acyl Carrier Protein-Linked Polyketide Synthase Extender Units / Yolande A. Chan ; Michael G. Thomas7:
Overproduction and Purification of Recombinant Proteins
Formation and Characterization of Hydroxymalonyl-ACP and Aminomalonyl-ACP
Type I Polyketide Synthases That Require Discrete Acyltransferases / Yi-Qiang Cheng ; Jane M. Coughlin ; Si-Kyu Lim8:
The Enzymology of Polyether Biosynthesis / Tiangang Liu ; David E. Cane ; Zixin Deng9:
Genetic Mining and Functional Analysis of Genes Specific to Polyether Biosynthetic Pathways
Premonensin, the Parent Unsaturated Monensin Polyketide
Epoxidases MonCl, NigCl, and NanO
Epoxide Hydrolases MonBI/BII, NigBI/BII, NanI, and Lsd19
NanE, a Polyether-Specific Thioesterase
Assay of Polyether Thioesterase Activity
Transcriptional Analysis of the Nanchangmycin Biosynthetic Pathway Genes
Enzymology of the Polyenes Pimaricin and Candicidin Biosynthesis / Juan F. Martin ; Jesus F. Aparicio10:
Pimaricin as a Prototype of Small Polyenes: Discovery and Properties
Pimaricin Biosynthesis in S. natalensis
Regulation of Pimaricin Biosynthesis
Candicidin: A Prototype of "Aromatic" Polyenes
The Candicidin/FR-008 Gene Cluster
Biosynthesis of PABA: The pabAB and pabC Genes
The Polyketide Synthases
Monooxygenase Genes: Modifications of the Polyketide Chain
Transporter Genes
Genes Related to Mycosamine Biosynthesis / 11:
Regulatory Genes / 12:
Phosphate Represses Expression of the pabAB Gene / 13:
Future Perspectives / 14:
Genetic Analysis of Nystatin and Amphotericin Biosynthesis / Sergey Zotchev ; Patrick Caffrey
Gene Inactivation and Replacement in the Nystatin Producer Streptomyces noursei
Gene Inactivation and Replacement in the Amphotericin Producer Streptomyces nodosus
Production, Purification, and Characterization of Novel Amphotericin- and Nystatin-Related Polyenes
Polyketide Versatility in the Biosynthesis of Complex Mycobacterial Cell Wall Lipids / Tarun Chopra ; Rajesh S. Gokhale
Acetate and Propionate Feeding Studies
Genome Sequencing and Identification of Polyketide Synthases
Mycobacterial Polyketide Synthases
Techniques to Characterize PKS Enzymes
Genetic Engineering to Produce Polyketide Analogues / Christopher D. Reeves ; Eduardo Rodriguez
AT Domain Replacement to Alter a-Carbon Substitution
Procedure for Engineering AT Replacements in the Chromosome
Engineering b-Carbon Processing
Engineering when only a Single Crossover Event is Possible
Heterologous Expression of Engineered PKS Genes
Chemobiosynthesis
Mutasynthesis
Gene Knockouts to Obtain Analogues
Design and Synthesis of Pathway Genes for Polyketide Biosynthesis / Salvador Peiru ; Hugo Gramajo ; Hugo G. Menzella
Redesign of PKS Genes to Accommodate Unique Restriction Sites Flanking Individual Components and for Efficient Expression in E. coli
Validation of Synthetic PKS Gene Design
A Rapid Assay to Identify Productive Combinations of PKS Modules
Assembly of Larger Polyketide Synthases Using Information Gained with the Bimodular Assay
Design and Construction of Synthetic Operons for the Expression of Sugar Pathway Genes
Heterologous Production of Polyketides in Bacteria / 15:
General Considerations for the Heterologous Expression of Polyketide Pathways
S. coelicolor as a Model System for Heterologous Expression of Polyketides
Procedure for the Heterologous Production of Polyketides in S. coelicolor
System Improvements for the Heterologous Production of Polyketides in Streptomyces spp
Recent Developments for the Production of Polyketides in Nonactinomycete Bacteria
In Vitro Analysis of Type II Polyketide Synthase / Wenjun Zhang ; Yi Tang16:
Expression and Purification of Type II PKSs
In Vitro Activity Assays
Bacterial Fatty Acid Synthesis and its Relationships with Polyketide Synthetic Pathways / John E. Cronan ; Jacob Thomas17:
Bacterial Fatty Acids
Acyl Carrier Protein, the Key Component of Bacterial Fatty Acid Synthesis
Overview of the Reactions of Fatty Acid Biosynthesis
The Initiation Steps of Fatty Acid Synthesis
The Enzymes of the Fatty Acid Elongation Cycle
Unsaturated Fatty Acid Synthesis in E. coli
The Abundant Exceptions to the E. coli Fatty Acid Synthesis Paradigm
Relationships between Fatty Acid Synthesis and Polyketide Synthesis
Methods for Study of Bacterial Fatty Acid Synthesis
Aminocoumarins / Section II:
Aminocoumarins: Mutasynthesis, Chemoenzymatic Synthesis, and Metabolic Engineering / Lutz Heide18:
Generation of Integrative Cosmids and Heterologous Expression of Novobiocin, Clorobiocin, and Coumermycin A1 Gene Clusters
Generation of Single and or Multiple Deletions in the Integrative Cosmids
Mutasynthetic Generation of New Aminocoumarin Antibiotics
In Vitro Amide Synthetase Assays for the Identification of Suitable Ring A Analogues for Mutasynthesis
Use of Various Amide Synthetase Genes for Expanding Mutasynthesis Product Range
Generation of Substrates for Chemoenzymatic Synthesis
Chemoenzymatic Synthesis of New Clorobiocin Analogues
Generation of New Aminocoumarin Antibiotics by Metabolic Engineering
Carbohydrates / Section III:
Enzymology of Aminoglycoside Biosynthesis-Deduction from Gene Clusters / Udo F. Wehmeier ; Wolfgang Piepersberg19:
Some Key Enzymes in the Biosyntheses of Aminoglycoside Antibiotics
Acarbose and Related Metabolites
Biosynthetic Enzymes for the Aminoglycosides Butirosin and Neomycin / Fumitaka Kudo ; Tadashi Eguchi20:
General Method to Investigate Functions of the Biosynthetic Enzymes for Aminoglycosides
Neamine Biosynthetic Enzymes (Enzymes 1
Contributors
Preface
Volumes in Series
2.

電子ブック

EB
William S. Allison, Anne Neville Murphy, Immo E. Scheffler
出版情報: Elsevier ScienceDirect Books , 2009
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Electron Transport Complexes / Part A:
Visualizing functional flexibility by three dimensional electron microscopy: reconstructing Complex I of the mitochondrial respiratory chain / M. Radermacher1:
Electron tomography of the mitochondrion / T. Frey ; G. Perkins ; M. Sun2:
Mid-IR vibrational studies of complex I / D. Marshall ; P. Rich3:
Electron transfer in respiratory complexes resolved by an ultra-fast freeze-quench approach / N. Belevich ; M. Verkhovsky4:
Use of ruthenium photooxidation techniques to study electron transfer in the cytochrome bc1 complex / F. Millett ; B. Durham ; C. Yu ; L. Yu5:
Use of ruthenium photoreduction techniques to study electron transfer in cytochrome oxidase / R. Gennis6:
Mass spectrometric characterization of subunits of electron transfer complexes that are encoded in the mitochondrial genome / J. Carroll ; J. Walker7:
The assembly of respiratory chain complexes studied by GFP-tagged subunits, L. Nijtmans / 8:
Two-dimensional native electrophoresis for functional assays of mitochondrial complexes / W. Wittig ; H. Schägger9:
Reliable assay for complex I in human blood lymphocytes and skin fibroblasts / L. Elly ; A. de Wit ; W. Sluiter10:
Purification of the cytochrome c reductase/cytochrome c oxidase supercomplex of yeast mitochondria / E. Boekema ; H. Braun11:
Supercomplex organization of the yeast mitochondrial respiratory chain complexes and the ADP/ATP carrier proteins / R. Stuart12:
Role of cysteine desulfurase Nfs1 in human mitochondrial Fe-S protein biogenesis / O. Stehling ; R. Lill13:
Identification and properties of the novel 2Fe-2S center in the outer membrane protein, mitoNEET / S. Wiley ; M. Rardin ; J. Dixon14:
Nucleotide-dependent iron-sulfur cluster biogenesis in mitochondria / D. Pain15:
Preparation of samples for EPR and Mössbauer spectroscopy of intact Saccharomyces cerrevisiae mitochondria / J. Garber-Morales ; R. Miao ; G. Holmes-Hampton ; P. Lindahl16:
Fluorescence correlation spectroscopy to probe mitochondrial mobility and intramatrix protein diffusion / P. Willems ; W. Koopman17:
Characterization of alternative complex I of Plasmodium falciparum mitochondria / N. Fisher ; A. J. Warman ; S. Ward ; G. Biagini18:
Analysis of respiratory chain complex assembly using radiolabeled nuclear- and mitochondrial-encoded subunits / M. McKenzie ; M. Lazarou ; M. Ryan19:
Reactive Oxygen Species / Part B:
Measuring redox changes to mitochondrial protein thiols using Redox DIGE / T. Hurd ; K. Lilley ; M. Murphy20:
Measuring the effects of Hepatitis C proteins on mitochondrial electron transport and production of reactive oxygen species / S. Weinman21:
Paraquat induced production of reactive oxygen species in brain mitochondria / D. Drechsel ; M. Patel22:
The uptake and interactions of the redox cycler paraquat with mitochondria / H. Cocheme23:
Superoxide production by rat brain and skeletal muscle mitochondria / W. Kunz24:
Quantitation, localization, and tissue specificities of mitochondrial reactive oxygen species production / C. Mathews25:
The reaction mechanisms of electron transfer and superoxide generation in the cytochrome nc1 complex / D. Xia ; S. Yang ; Y. Yin26:
Measurement of superoxide formation by mitochondrial complex I of Yarrowia lipolytica / S. Dröse ; A. Galkin ; U. Brandt27:
An improved method for introducing point mutations into the mitochondrial cytochrme b gene to facilitate studying the role of cytochrome b in the formation of reactive oxygen species / B. Trumpower28:
Electron Transport Complexes / Part A:
Visualizing functional flexibility by three dimensional electron microscopy: reconstructing Complex I of the mitochondrial respiratory chain / M. Radermacher1:
Electron tomography of the mitochondrion / T. Frey ; G. Perkins ; M. Sun2:
3.

電子ブック

EB
John N. Abelson, Tom W. Muir
出版情報: Elsevier ScienceDirect Books , 2009
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(Tentative)
Protein Engineering with the Traceless Staudinger Ligation / Ronald T. Raines ; Annie Tam1:
Mechanistic studies of RNR using unnatural amino acids and semisynthesis / Joann Stubbe2:
Using Expressed Protein Ligation to Probe the Substrate Specificity of Lantibiotic Synthetases / Wilfred van der Donk ; Xingang Zhang3:
Protein Phosphorylation by Semisynthesis: From Paper to Practice / Phlip A. Cole,Lawrence M. Szewczuk ; Mary Katherine Tarrant4:
Mechanistic studies of semisynthetic ion channels / Francis Valiyaveetil5:
Semi-synthesis of proteins using split inteins / Henning D. Mootz ; Christina Ludwig ; Joachim Zettler ; Daniel Garbe6:
Segmental Isotopic Labeling of Proteins for Nuclear Magnetic Resonance / David Cowburn ; Dongsheng Liu ; Rong Xu7:
Use of intein-mediated protein ligation strategies for the fabrication of functional protein arrays / Shao Q Yao ; Souvik Chattopadhaya ; Farhana B. Abu Bakar8:
Expressed Protein Ligation for Metalloprotein Design and Engineering / Yi Lu ; Kenneth Clark9:
(Tentative)
Protein Engineering with the Traceless Staudinger Ligation / Ronald T. Raines ; Annie Tam1:
Mechanistic studies of RNR using unnatural amino acids and semisynthesis / Joann Stubbe2:
4.

電子ブック

EB
Daniel Herschlag
出版情報: Elsevier ScienceDirect Books , Elsevier Science & Technology, 2009
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Contributors
Preface
Volumes in Series
Chemical and Functional Probing of RNA Structure, Interactions, and Folding / Section I:
Nucleotide Analog Interference Mapping / Ian T. Suydam ; Scott A. Strobel1:
Introduction
Materials and Reagents / 2:
Methods / 3:
Properties of Analogs / 4:
Nucleotide Analog Interference Suppression / 5:
Conclusions / 6:
References
Hydroxyl-Radical Footprinting to Probe Equilibrium Changes in RNA Tertiary Structure / Inna Shcherbakova ; Somdeb Mitra
Sample Preparation
Equilibrium òOH Footprinting Based on Peroxidative Fenton Chemistry
Equilibrium òOH Footprinting Based on Oxidative Fenton Chemistry
Cleavage Product Separation
Quantitation of the Changes in the Reactivity and Data Analysis
Acknowledgments / 7:
Rapid Quantification and Analysis of Kinetic òOH Radical Footprinting Data Using SAFA / Katrina Simmons ; Joshua S. Martin ; Alain Laederach
Using SAFA
Data Normalization
Data Visualization
Conclusion
Acknowledgment
High-Throughput SHAPE and Hydroxyl Radical Analysis of RNA Structure and Ribonucleoprotein Assembly / Jennifer L. McGinnis ; Caia D. S. Duncan ; Kevin M. Weeks
Theory
Practice
Examples and Interpretation
Perspectives and Conclusion
Metal Ion-Based RNA Cleavage as a Structural Probe / Marcello Forconi ; Daniel Herschlag
Mechanisms of Metal Ion-Based Cleavage of Nucleic Acids
Metal Ion-Based Cleavage of RNA as a Structural Probe
Protocols
2'-Amino-Modified Ribonucleotides as Probes for Local Interactions Within RNA / James L. Hougland ; Joseph A. Piccirilli
2'-Amino-2'-Deoxynucleotide Synthesis and Incorporation
2'-Amino-2'-Deoxynucleotides as Sites for Covalent Modification
General Strategy for Investigating 2'-Hydroxyl Interactions Using 2'-Deoxy and 2'-Aminonucleotides
Studies of RNA Catalysis Using 2'-Amino-2'-Deoxynucleotides
Using 2'-Aminonucleotides to Investigate RNA Structure and Function: Case Studies
RNA Crosslinking Methods / Michael E. Harris ; Eric L Christian
Synthesis of Modified RNA Crosslinking Substrates
Generation of Crosslinked RNAs
Mapping of Crosslinked Nucleotides
Assessing the Validity of Crosslinking Data
Chemical Probing of RNA and RNA/Protein Complexes / Zhili Xu ; Gloria M. Culver8:
Materials
Handling of the Chemicals
Optimization of the Chemical Probing Reactions
Procedure of Chemical Probing
RNA Extraction
Normalization of the RNA Sample
Primer Extension Analysis
Data Evaluation / 9:
Summary / 10:
RNA Folding During Transcription: Protocols and Studies / Terrence N. Wong ; Tao Pan
Protocol 1: Determination of Transcriptional Pause Sites
Protocol 2: Structural Mapping of Paused Complexes
Protocol 3: Cotranscriptional RNA Folding as Measured via Oligohybridization
Protocol 4: Cotranscriptional RNA Folding Measured via P RNA Catalytic Activity
Protocol 5: The Folding of Self-Cleaving RNAs During Transcription
Additional Methodologies
Cotranscriptional Folding Studies from our Laboratory
Catalytic Activity as a Probe of Native RNA Folding / Yaqi Wan ; David Mitchell III ; Rick Russell
Preliminary Measurements of Catalytic Reaction
Following RNA Folding by Continuous Activity Assay
Following RNA Folding by Discontinuous Activity Assay
Other Applications of Catalytic Activity as a Probe of Folding
Probing RNA Structure Within Living Cells / Andreas Liebeg ; Christina Waldsich11:
Experimental Procedure
Application
Limitations
Structural Analysis of RNA in Living Cells by In Vivo Synchrotron X-Ray Footprinting / Tadepalli Adilakshmi ; Sarah F. C. Soper ; Sarah A. Woodson12:
Beamline Setup for In Vivo Footprinting
Preparation of Samples
Exposure of Cells to X-Ray Beam
Isolation of Total RNA from Irradiated Cells
Primer Extension
Analysis of X-Ray Footprinting Experiments
Results on E. coli RNAs
Future of Footprinting
Determination of Intracellular RNA Folding Rates Using Self-Cleaving RNAs / Peter Y. Watson ; Martha J. Fedor13:
Using RNA Turnover Rates as a "Clock" for Measuring RNA Assembly Kinetics
Applications
Identifying Metal Ion Interactions in RNA / Section II:
Separation of RNA Phosphorothioate Oligonucleotides by HPLC / John K. Frederiksen14:
Introduction: Phosphorothioate Oligonucleotides and the Need for Separation
HPLC Separation of Phosphorothioate Diastereomers
Materials and Methods
Examples of Phosphorothioate Oligonucleotide Separations
Use of Phosphorothioates to Identify Sites of Metal-Ion Binding in RNA / 15:
Use of Phosphorothioate-Containing Ribozymes to Identify Sites of Metal-Ion Binding
EPR Methods to Study Specific Metal-Ion Binding Sites in RNA / Laura Hunsicker-Wang ; Matthew Vogt ; Victoria J. DeRose16:
ENDOR Spectroscopy to Identify Metal Ligands
ESEEM Spectroscopy
RNA Thermodynamics / Section III:
Optical Melting Measurements of Nucleic Acid Thermodynamics / Susan J. Schroeder ; Douglas H. Turner17:
Instrumentation
Calibrations
Brief Theory of Optical Melting Experiments
Two-State Assumption
Experimental Design
Data Interpretation
Error Analysis
Analyzing RNA and DNA Folding Using Temperature Gradient Gel Electrophoresis (TGGE) with Application to In Vitro Selections / Durga M. Chadalavada ; Philip C. Bevilacqua18:
Temperature Gradient Gel Electrophoresis
Experimental Design and Application of TGGE to RNA and DNA
Studying RNA-DNA and RNA-Protein Interactions by Isothermal Titration Calorimetry / Andrew L. Feig19:
Required Materials
Sample Considerations and Preparation
Cleaning the Sample Cell and Titration Syringe
Collecting Titration Data
Data Processing and Analysis
Special Considerations
Author Index
Subject Index
Contributors
Preface
Volumes in Series
5.

電子ブック

EB
Richard R Burgess, Richard Burgess, Murray P. Deutscher
出版情報: Elsevier ScienceDirect Books , Elsevier Science, 2009
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Why Purify Enzymes? / Murray Deutscher ; Arthur Kornberg
Developing Purification Procedures / Section I:
Strategies and Considerations for Protein Purifications / Stuart Linn
Use of Bioinformatics in Planning a Protein Purification / Richard R. Burgess
Preparing A Purification Summary Table
General Methods for Handling Proteins and Enzymes / Section II:
Setting Up A Laboratory / Murray P. Deutscher
Buffers: Principle and Practice / Vincent S. Stoll ; John S. Blanchard
Measurement of Enzyme Activity / T. K. Harris ; M. M. Keshwani
Quantitation of Protein / James E. Noble ; Marc J. A. Bailey
Concentration of Proteins and Removal of Solutes / Jonathan K. Romero ; David R. H. Evans ; Matthew Westoby
Maintaining Protein Stability
Recombinant Protein Expression and Purification / Section III:
Selecting an Appropriate Method for Expressing a Recombinant Protein / William H. Brondyk
Bacterial Systems for Production of Heterologous Proteins / Frank R. Collart ; Ashley M. Frank ; Sarah Zerbs
Expression in the Yeast Pichia Pastoris / James M. Cregg ; Ilya Tolstorukov ; Anasua Kusari ; Jay Sunga ; Knut Madden ; Thomas Chappell
Baculovirus-Insect Cell Expression Systems / Donald L. Jarvis
Recombinant Protein Production By Transient Gene Transfer Into Mammalian Cells / Sabine Geisse ; Cornelia Fux
Tagging For Protein Expression / Arun Malhotra
Refolding of Solubilized Inclusion Body Proteins
Preparation of Extracts and Subcellular Fractionation / Section IV:
Advances In Preparation of Biological Extracts for Protein Purification / Anthony C. Grabski
Isolation of Subcellular Organelles and Structures / Jörg Von Hagen ; Uwe Michelsen
Purification Procedures: Bulk Methods / Section V:
Protein Precipitation Techniques
Affi-Gel Blue for Nucleic Acid Removal and Early Enrichment of Nucleotide Binding Proteins
Purification Procedures: Chromatographic Methods / Section VI:
Ion Exchange Chromatography / Alois Jungbauer ; Rainer Hahn
Gel Filtration / Earle Stellwagen
Protein Chromatography on Hydroxyapatite Columns / Larry J. Cummings ; Mark A. Snyder ; Kimberly Brisack
Theory and Use of Hydrophobic Interaction Chromatography in Protein Purification Applications / Justin T. Mccue
Purification Procedures: Affininty Methods / Section VII:
Affinity Chromatography: General Methods / Marjeta Urh ; Dan Simpson ; Kate Zhao
Immobilized-Metal Affinity Chromatography (IMAC) / Frank Schäfer* Helena Block ; Barbara Maertens ; Anne Spriestersbach ; Nicole Brinker ; Jan Kubicek ; Roland Fabis And Jörg Labahn
Identification, Production, and Use of Polyol-Responsive Monoclonal Antibodies for Immunoaffinity Chromatography / Nancy E. Thompson ; Katherine M. Foley ; Elizabeth S. Stalder ; And Richard R. Burgess
Purification Procedures: Electrophoretic Methods / Section VIII:
One-Dimensional Gel Electrophoresis / David E. Garfin
Protein Analysis Using High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis and Isoelectric Focusing / Friedman
Protein Gel Staining Methods: An Introduction And Overview / Thomas H. Steinberg
Elution of Proteins From Gels
Immunodetection By Protein Blotting Performing and Optimizing Western Blots With An Emphasis on Chemiluminescent Detection / Alice Alegria-Schaffer ; Krishna Vattem ; Andrew Lodge
Purification Procedures: Membrane Proteins And Glycoproteins / Section IX:
Detergents: An Overview / Dirk Linke
Purification of Membrane Proteins / Sue-Hwa Lin ; Guido Guidotti
Purification of Recombinant G-Protein-Coupled Receptors / Reinhard Grisshammer
Cell-Free Translation Of Integral Membrane Proteins Into Unilamelar Liposomes / Michael A. Goren ; Akira Nozawa ; Shin-Ichi Makino ; Russell L. Wrobel ; Brian G. Fox
Characterization of Purified Proteins / Section X:
Determination of Protein Purity / David G. Rhodes ; Thomas M. Laue
Determination of Size, Molecular Weight, and Presence of Subunits / Robert E. Bossio
Identification and Quantification of Protein Posttranslational Modifications / Andrew Link
Parallel Methods For Expression And Purification / Scott A. Lesley
Techniques To Isolate O2-Sensitive Proteins: [4Fe-4S]-FNR As An Example / Aixin Yan ; Patricia J. Kiley
Rethinking Your Purification Procedure
Important But Little Known (Or Forgotten) Artifacts in Protein Biochemistry
Why Purify Enzymes? / Murray Deutscher ; Arthur Kornberg
Developing Purification Procedures / Section I:
Strategies and Considerations for Protein Purifications / Stuart Linn
6.

電子ブック

EB
Daniel J. Klionsky
出版情報: Elsevier ScienceDirect Books , 2009
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LC3-based assay for monitoring autophagy / Shunsuke Kimura ; Naonobu Fujita ; Takeshi Noda ; Tamotsu YoshimoriChapter 1:
Analysis of autophagy using GFP-LC3 transgenic mice / Noboru MizushimaChapter 2:
Photoactivatable GFP / Jennifer Lippincott-Schwartz ; Dale HaileyChapter 3:
Assaying for autophagic protein degradation / Fred MeijerChapter 4:
Sequestration assays for mammalian autophagy / Per O. SeglenChapter 5:
Incorporation of monodansylcadaverine (MDC) as an assay to assess autophagy induction and monitoring fusion with a degradative compartment / Maria Isabel ColomboChapter 6:
The GST-BHMT assay and related assays for autophagy / Carol A. Mercer ; Patrick B. DennisChapter 7:
Redox and autophagy-ROS as an indicator for autophagic activity / Ruth Scherz-Shouval ; Zvulun ElazarChapter 8:
FACS analysis of autophagy / Elena Shvets ; Ephraim FassChapter 9:
Electron microscopy in mammals / PSivi YlS-Anttila ; Eeva-Liisa EskelinenChapter 10:
Monitoring mTOR activity / Ken InokiChapter 11:
Using p62 as a marker for autophagy / Terje JohansenChapter 12:
Cytosolic LC3 ratio as a quantitative index of macroautophagy / Motoni Kadowaki ; Md. Razaul KarimChapter 13:
Pexophagy in mammalian cells / Junji Ezaki ; Takashi Ueno ; Eiki Kominami ; Masaaki KomatsuChapter 14:
Mitophagy in mammalian cells / Ji Zhang ; Paul A. NeyChapter 15:
Quantification of WIPI-1/Atg18 puncta formation for assessing mammalian autophagy / Tassula Proikas-Cezanne ; Simon G. PfistererChapter 16:
Correlative light and electron microscopy (CLEM) using GFP-LC3 and other autophagosome markers / Sharon Tooze ; Minoo RaziChapter 17:
Nanotechnology assays for autophagy / Oleksandr SeleverstovChapter 18:
Photoconvertible KAEDA-LC3 for monitoring autophagic flux / Christoph Goemans ; Aviva TolkovskyChapter 19:
Methods to monitor Chaperone-mediated autophagy / Ana Maria Cuervo ; Susmita KaushikChapter 20:
Autophagy in response to Salmonella enterica serovar Typhimurium infection / Cheryl Birmingham ; John BrumellChapter 21:
Monitoring autophagy during Mycobacterium tuberculosis infection / Vojo DereticChapter 22:
Shigella, Listeria and Streptococcus induction of autophagy / Michinaga Ogawa ; Yuko Yoshikawa ; Ichiro Nakagawa ; Chihiro Sasakawa ; Trinad ChakrabortyChapter 23:
Measuring the impact of infection on autophagy in macrophages / Jean-Francois Dubuisson ; Brenda Byrne ; Michele SwansonChapter 24:
LC3-based assay for monitoring autophagy / Shunsuke Kimura ; Naonobu Fujita ; Takeshi Noda ; Tamotsu YoshimoriChapter 1:
Analysis of autophagy using GFP-LC3 transgenic mice / Noboru MizushimaChapter 2:
Photoactivatable GFP / Jennifer Lippincott-Schwartz ; Dale HaileyChapter 3:
7.

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EB
Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , 2009
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Contributors
Preface
Volumes in Series
Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1:
Introduction
Estimation of Phase Response Curves / 2:
Specific Applications / 3:
Discussion / 4:
Acknowledgments / Appendix I:
References
Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard
Biochemical Conventions and Calculations
Application to Physiological Systems
Acknowledgment
Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke
Decomposition of Sensor Errors
Measures of Average Glycemia and Deviation from Target
Risk and Variability Assessment
Measures and Plots of System Stability / 5:
Time-Series-Based Prediction of Future BG Values / 6:
Conclusions / 7:
Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger
Methodology
Job Submission
Results
Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels
The Chemical Master Equation
The Stochastic Simulation Algorithm
The Tau-Leaping Method
Measurement of Simulation Error
Software and Two Numerical Experiments
Conclusion
Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse
Types of Biological Data and Their Acquisition
Analysis in the Time Domain
Analysis in the Frequency Domain
Time/Frequency Analysis and the Wavelet Transform
Signal Conditioning
Strength and Regularity of a Signal
A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8:
Computational Design of Surface Charge-Charge Interactions
Experimental Verification of Computational Predictions
Closing Remarks
Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen
Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region
Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces
Locating the Boundary of the Smallest Multidimensional Confidence Region
Finding the Minimum and Maximum of the Prediction Model over the Confidence Region
An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation
95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation
Appendix
Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9:
Calculating the pH Dependence of Protein Characteristics
Setting up and Running a pKa/ Calculation
Analyzing the Results of a pKa/ Calculation
How Reliable Are Calculated pKa/ Values?
Predicting pH Activity Profiles
Decomposition Analysis
Predicting Protein Stability Profiles
Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles
Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10:
Review of Least Squares
Experiment Design Using Vprior/-Numerical Illustrations
Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11:
Conceptual Overview of Model Evaluation and Comparison
Model Comparison Methods
Model Comparison at Work: Choosing between Protein Folding Models
Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12:
Course Description
Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13:
Extracting Melting Curves from Raw Fluorescence
Methods Used for Clustering and Classifying Melting Curves by Genotype
Methods Used for Modeling Melting Curves
Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14:
Early Attempts to Identify and Characterize Pulsatile Hormone Release
Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection
Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts
Limitations and Subsequent Improvements in Deconvolution Procedures
Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model
Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy
Evaluation of Coupled Systems
Evaluation of Hormonal Networks with Feedback Interactions
Future Directions
AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15:
Methods
Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16:
Author Index
Subject Index
Contributors
Preface
Volumes in Series
8.

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EB
David A. Hopwood, D. A. Hopwood
出版情報: Elsevier ScienceDirect Books , 2009
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Overview articles / Part 1:
Introduction - chemical classes of complex natural products and overview of their biosynthesis
Discovery of novel natural products
Trans-modification of intermediates on the assembly line in PKS, FAS and NRPS biosynthesis
Post-assembly line modifications, including glycosylation
Cloning and analysis of natural product pathways
In silico prediction of pathways from DNA sequence
Mass spectrometric analysis of PKS and NRPS biosynthetic intermediates
Synthetic probes for PKS and NRPS biochemistry
Directed evolution of natural products
Expression in a heterologous host
Pathway-specific and global regulation of antibiotic biosynthesis
Regulation of antibiotic production by bacterial hormones
Peptides / Part 2:
Non-ribosomally-synthesised peptides Overview of NRPSs, and mechanistic and structural studies / A:
Siderophores Cephamycins and clavulanic acid
Glycopeptides
Lipopeptides
Precursor
Biosynthesis
Ribosomally synthesised peptides / B:
Lantibiotic biosynthesis and engineering of novel compounds
Cyclic peptides from marine bacteria
Overview articles / Part 1:
Introduction - chemical classes of complex natural products and overview of their biosynthesis
Discovery of novel natural products
9.

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EB
Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , 2009
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Contributors
Preface
Volumes in Series
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics / Jad Walters ; Sara L. Milam ; A. Clay Clark1:
Introduction
Equilibrium Unfolding / 2:
Measuring Folding Kinetics / 3:
References
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory / Keith D. Connaghan-Jones ; David L. Bain
Assessing Protein Functional and Structural Homogeneity
Dissecting Linked Assembly Reactions
Analysis and Dissection of Natural Promoters / 4:
Measuring the Energetics of Coactivator Recruitment / 5:
Correlation to Biological Function / 6:
Conclusions and Future Directions / 7:
Acknowledgments
General Principles / Dan Grilley ; Ana Maria Soto ; David E. Draper
Ion-Binding Properties of HQS
Preparation of Solutions and Reagents
Instrumentation and Data Collection Protocols
Data Analysis
Controls and Further Considerations
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models / Tural Aksel ; Doug Barrick
Historical Overview of Ising Models and Motivation for the Present Review
Linear Repeat Proteins and Their Connection to Linear Ising Models
Formulating a Homopolymer Partition Function and the Zipper Approximation
Matrix Approach: Homopolymers
Matrix Approach: Heteropolymers
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding
Matrix Homopolymer Analysis of Consensus TPR Folding
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding / 8:
Summary and Future Directions / 9:
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials / Ernesto Freire ; Arne Schön ; Adrian Velazquez-Campoy
The Binding Polynomial
Microscopic Constants and Cooperativity
Independent or Cooperative Binding?
Analysis of ITC Data Using Binding Polynomials
A Typical Case: Macromolecule with Two Ligand-Binding Sites
Data Interpretation
An Experimental Example
Experimental Situations from the Literature / 10:
Macromolecule with Three Ligand-Binding Sites / 11:
Conclusions / 12:
Appendix
Acknowledgment
Kinetic and Equilibrium Analysis of the Myosin ATPase / Enrique M. De La Cruz ; E. Michael Ostap
Reagents and Equipment Used for all Assays
Steady-State ATPase Activity of Myosin
Steady-State Measurement of Actomyosin Binding Affinities
Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions
Kinetic Simulations
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin / Jo M. Holt ; Gary K. Ackers
Cooperativity and Intrinsic Binding
The Macroscopic Binding Isotherm
The Hill Coefficient
Microscopic Cooperativity in Hemoglobin
Summary
Methods for Measuring the Thermodynamic Stability of Membrane Proteins / Heedeok Hong ; Nathan H. Joh ; James U. Bowie ; Lukas K. Tamm
Two Classes of Membrane Proteins
Methods for Measuring Transmembrane Domain Oligomer Stability
Methods for Measuring Multipass ?-helical Membrane Protein Stability
Methods to Study the Stability of ?-barrel Membrane Proteins
A Few Salient Results on Forces that Stabilize Membrane Proteins
Conclusion and Outlook
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands / Gregory Benison ; Elisar Barbar
NMR Methodology
Monomer-dimer Equilibrium Coupled to Electrostatics
Dimerization is Coupled to Ligand Binding
Folding is Coupled to Binding
Allostery in LC8
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry / Michael T. Henzl
Practical Aspects of Data Collection
Illustrative Global ITC Analyses of Divalent Ion Binding
Conclusion
Energetic Profiling of Protein Folds / Jason Vertrees ; James O. Wrabl ; Vincent J. Hilser
Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics
Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble
Principal Components Analysis of Energetic Profile Space
Energetic Profiles are Conserved Between Homologous Proteins
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm
CE Algorithm Described for Structure Coordinates
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation / Juyang Huang
Materials and Methods
Result and Discussion
Concluding Remarks
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding / Nathan A. Siegfried ; Philip C. Bevilacqua13:
Folding Cooperativity Defined
Thermodynamic Boxes: Design, Implementation, and Interpretation
Thermodynamic Cubes: Design, Implementation, and Interpretation
Examples of Cooperativity in RNA
Measuring Thermodynamic Parameters by UV Melting
The Thermodynamics of Virus Capsid Assembly / Sarah Katen ; Adam Zlotnick14:
The Structural Basis of Capsid Stability
Analysis of Capsid Stability
Applications of Thermodynamic Evaluation of Virus Capsid Stability
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems / John J. Correia ; Walter F. Stafford15:
Methods
Simulation and Analysis of Dimerization
Kinetically Mediated Dimerization
A Stepwise Approach
Final Thoughts
Author Index
Subject Index
Contributors
Preface
Volumes in Series
10.

電子ブック

EB
William S. Allison, Anne Neville Murphy, Immo E. Scheffler
出版情報: Elsevier ScienceDirect Books , 2009
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Defining the Mitochondrial Proteome
Method to define the mammalian mitochondrial proteome / V. Mootha1:
Proteome Characterization of Mouse Brain Mitochondria Using Electrospray Ionization Tandem Mass Spectrometry / X.Fang ; C. S. Lee2:
Method to analyze tissue heterogeneity of the mammalian mitochondrial proteome / R. S. Balaban3:
Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data / D. Gaston, A. Tsausis ; A. Roger4:
MitoP2: the mitochondrial proteome database / H. Prokisch Post-Translational Modifications of Mitochondrial Proteins5:
Reversible protein acetylation in mitochondria / E. Verdin6:
Post-translational modifications of rat liver mitochondria outer membrane proteins' / C. L. Hoppel7:
Characterization of a novel ser/thr protein phosphatase in mitochondria / Y. Wang8:
Selective enrichment in phosphopeptides for the identification of phosphorylated mitochondrial proteins / R. Rizzuto ; G. Pocsfalvi9:
Isolation of Regulatory-competent, Phosphorylated Cytochrome c and Cytochrome c Oxidase / M. Hnttemann11:
Identification of tyrosine phosphorylated proteins by Src kinases in rat brain / M. Salvi12:
Detection of a mitochondrial kinase complex that mediates an ERK-dependent phosphorylation of mitochondrial protein in steroid biosynthesis / E. J. Podestß13:
Dual specific phosphatases 18 and 21 target to opposing sides of the mitochondrial inner membrane / J. Rardin ; J. E. Dixon14:
"Isolation and identification of palmitoylated proteins in mitochondria using a chemical biology approach L. G. Berthiaume Mitochondrial Dynamics / M. A. Kostiuk ; B. O. Keller15:
Mitochondrial fusion and movement using photoactivatable GFP / O. Shirihai16:
Regulation of mitochondrial fission and fusion by kinase and phosphatase activities. no title yet / S. Strack17:
Mitochondrial movement and synaptic function in Drosophila / T. L. Schwarz18:
The use of yeast and a novel biosensor to study mitochondrial ion transport, swelling, and mitophagy / R. J. Scheweyen19:
Complete Exchange of mtDNA's between Mouse Cells for Testing the Effects of mtDNA on Tumor Phenotypes / J. Hayashi Mitochondrial Function in Pancreatic Beta Cells20:
Coupling efficiency INS-1E cells / M. D. Brand ; C. Affourtit21:
Methods in the study of substrate-specific differences on mitochondrial function mediating insulin secretion from pancreatic beta cells / B. E. Corkey22:
Knocking down of UCP 2 in animal models of obesity / L. A.Velloso23:
Roles of the cytosolic and mitochondrial forms of the malic enzyme on insulin secretion / G. W. Cline24:
Altered regulation of the PINK1 locus as a link between type 2 diabetes and neurodegeneration / J. A. Timmons25:
Insulin secretion from pancreatic beta cells is affected deletion of the nicotinamide nucleotide transhydrogenase / R. D. Cox26:
Determination of oxidative capacity and mitochondrial function in insulin resistance and type 2 diabetes / G. Shulman et al27:
Mitochondrial ATP production rate / K. S. Nair28:
Defining the Mitochondrial Proteome
Method to define the mammalian mitochondrial proteome / V. Mootha1:
Proteome Characterization of Mouse Brain Mitochondria Using Electrospray Ionization Tandem Mass Spectrometry / X.Fang ; C. S. Lee2:
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