The Protein protocols handbook

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The Protein protocols handbook

edited by John M. Walker

Humana, c2002

2nd ed

  • : hbk
  • : pbk

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Includes bibliographical references and index

Description and Table of Contents

Volume

: hbk ISBN 9780896039407

Description

This greatly enhanced second edition introduces 60 critically important new chapters dealing with topics and techniques that have emerged since the first edition, as well as significantly updating the remaining articles. The new chapters cover many rapidly developing areas, particularly the application of mass spectrometry in protein characterization, as well as the now well-established 2-D PAGE technique in proteomics. The section on glycoprotein analysis has also been significantly expanded, and methods for the production of single-chain and phage-displayed antibodies have been added to the section on antibodies. Each readily reproducible method follows the highly praised format of the "Methods in Molecular Biology" series, offering a concise summary of its basic theory, a complete materials list, a step-by-step protocol for its successful execution, and extensive notes on avoiding pitfalls and on modifying the method to function within your own experimental circumstances.

Table of Contents

Part I: Quantitation of Proteins. Protein Determination by UV Absorption, Alastair Aitken and Michele P. Learmonth. The Lowry Method for Protein Quantitation, Jakob H. Waterborg. The Bicinchoninic Acid (BCA) Assay for Protein Quantitation, John M. Walker. The Bradford Method for Protein Quantitation, Nick J. Kruger. Ultrafast Protein Determinations Using Microwave Enhancement, Robert E. Akins and Rocky S. Tuan. The Nitric Acid Methods for Protein Estimation in Biological Samples, S.A. Boerner, Y.K. Lee, S.H. Kaufmann, and Keith C. Bible. Quantitation of Tryptophan in Proteins, Alastair A, Aitken and Michele P. Learmonth. Flow Cytometric Quantitation of Cellular Proteins, Thomas D. Friedrich, F. Andrew Ray, Judith A. Laffin, and John M. Lehman. Kinetic Silver Staining of Proteins, Douglas D. Root and Kuan Wang. Part II: Electrophoresis of Proteins and Peptides and Detection in Gels. Nondenaturing Polyacrylamide Gel Electrophoresis of Proteins, John M. Walker. SDS Polyacrylamide Gel Electrophoresis of Proteins, John M. Walker. Gradient SDS Polyacrylamide Gel Electrophoresis of Proteins, John M. Walker. SDS-Polyacrylamide Gel Electrophoresis of Peptides, Ralph C. Judd. Identification of Nucleic Acid Binding Proteins Using Nondenaturing SDS-PAGE, Robert E. Aitkens and Rocky S. Tuan. Cetyltrimethylammonium Bromide Discontinuous Gel Electrophoresis of Proteins: M-Based Separation of Proteins with Retained Native Activity, Robert E. Aitkens and Rocky S. Tuan. Acetic-Acid-Urea Polyacrylamide Gel Electrophoresis of Basic Proteins, Jakob H. Waterborg. Acid-Urea-Triton Polyacrylamide Gel Electrophoresis of Histones, Jakob H. Waterborg. Isoelectric Focusing of Proteins in Ultra-Thin Polyacrylamide Gels, John M. Walker. Protein Solubility in 2D Electrophoresis: Basic Principles and Issues, Thierry Rabilloud. Preparation of Protein Samples from Mouse and Human Tissues for 2-D Electrophoresis, Joachim Klose. Radiolabelling of Eukaryotic Cells and Subsequent Preparation for 2-D, Nick Bizios. Two-Dimensional PAGE Using Carrier Ampholyte pH Gradients in the First Dimension, Patricia Gravel. Casting Immobilized pH Gradients, Elisabetta Gianazza. Nonequilibrium pH Gel Electrophoresis, Mary Lopez. Difference Gel Electrophoresis, Mustafa Unlu. Comparing 2-D Electrophoresis Gels Across Internet Databases, Peter F. Lemkin. Immunoblotting of 2-DE Separated Proteins, Barbara Magi, Luca Bini, Sabrina Liberatori, Roberto Raggiarchi, and Vitaliano Pallini. Quantification of Radiolabeled Proteins in Polyacrylamide Gels, Wayne R. Springer. Quantification of Proteins on Polyacrylamide Gels, Bryan J. Smith. Rapid and Sensitive Staining of Unfixed Proteins in Polyacrylamide Gels with Nile Red, John-Ramon Daban. Zinc Reverse Staining Technique, Carlos Fernandez-Patron. Protein Staining with Calconcarboxylic Acid in Polyacrylamide Gels, Jung-Kap Choi. Detection of Proteins in Polyacrylamide Gels by Silver Staining, Michael J. Dunn. Protein Detection on Polyacrylamide Gels and on Electroblots Using Transition Metal Chelate Stains, Wayne F. Patton. Detection of Proteins in Polyacrylamide Gels by Fluorescent Staining, Michael J. Dunn. Detection of Proteins and Sialogycoproteins in Polyacrylamide Gels Using Eosin X Stain, Fan Lin and Gary Wise. Electroelution of Proteins from Polyacrylamide Gels, Paul Jeno. Autoradiography and Fluorography of Acrylamide Gels, Antonella Circolo. Part III: Blotting and Detection of Proteins. Protein Blotting by Electroblotting, Robin Thorpe. Protein Blotting by the Semidry Method, Patricia Gravel. Protein Blotting by the Capillary Method, John M. Walker. Protein Blotting of Basic Proteins Resolved on Acid-Urea-Trinton-Polyacrylamide Gels, Genevieve P. Delcuve and James R. Davie. Alkaline Phosphatase Labeling of IgG Antibody, G. Brian Wisdom. b-Galactosidase Labeling of IgG Antibody, G. Brian Wisdom . Horseradish Peroxidase Labeling of IgG Antibody, G. Brian Wisdom. Digoxigenin (DIG) Labeling of IgG Antibody, G. Brian Wisdom. Conjugation of Fluorochromes to Antibodies, Su-Yau Mao. Coupling of Antibodies with Biotin, Rosaria P. Haugland. Preparation of Avidin Conjugates, Rosaria P. Haugland and M.K. Bhalgat. MDPF Staining of Proteins on Western Blots, F. Alba and Joan-Ramon Daban. Cooper Iodided Staining of Proteins and its Silver Enhancement, Douglas D. Root and Kuan Wang. Detection of Proteins on Blots Using Direct Blue 71, Hee-Youn Hong, Gyurng-Soo Yoo, and Jung-Kap Choi. Protein Staining and Immunodetection Using Immunogold, Susan J. Fowler. Detection of Polypeptides on Immunoblots Using Enzyme Conjugated or Radiolabeled Secondary Ligands, Nicholas J. Kruger. Avidin- or Streptavidin-Biotin as a Highly Sensitive Method to Stain Total Proteins on Membranes, Kenneth E. Santora, Stefanie A. Nielson, Kristi A. Lewis, and William J. LaRochelle. Detection of Protein on Blots Using Chemifluorescence, Catherine C. Copse and Susan J. Fowler. Quantification of Proteins on Western Blots using ECL, J. Dickinson and Susan J. Fowler. Reutilization of Western Blots After Chemiluminescent Detection or Autoradiography, Scott Kaufmann. Part IV: Chemical Modification of Proteins and Peptide Production and Purification. Carboxymethylation of Cysteine Using Iodoacetamide/Iodoacetic Acid, Alastair Aitken. Performic Acid Oxidation, Alastair Aitken. Succinylation of Protein, Alastair Aitken. Pyridylethylation of Cystenine Residues, Malcolm Ward. Side-Chain Selective Chemical Modifications of Proteins, Dan S. Tawfik. Nitration of Tyrosines, Dan S. Tawfik. Ethoxyformylation of Histidine, Dan S. Tawfik. Modification of Arginine Side Chains with p-Hydroxyphenylglyoxal, Dan S. Tawfik. Amidination of Carboxyl Groups, Dan S. Tawfik. Amidination of Lysine Side Chains, Dan S. Tawfik. Modification of Tryptophan with 2-Hydroxy-5 Nitrogenzylbromide, Dan S. Tawfik. Modification of Sulhydryl Groups with DTNB, Dan S. Tawfik. Chemical Cleavage of Proteins at Methionyl-X Peptide Bonds., Bryan J. Smith. Chemical Cleavage of Proteins at Trypotophanyl-X Peptide Bonds, Bryan J. Smith. Chemical Cleavage of Proteins at Aspartyl-X Peptide Bonds, Bryan J. Smith. Chemical Cleavage of Proteins at Cysteinyl-X Peptide Bonds, Bryan J. Smith. Chemical Cleavage of Proteins at Asparaginyl-Glycyl Peptide Bonds, Bryan J. Smith. Enzymatic Digestion of Proteins in Solution and in SDS Polyacrylamide Gels , Kathryn L. Stone. Enzymatic Digestion of Proteins on PVDF Membranes, Joseph Fernandez and Sheenah Mische. Reverse Phase HPLC Separation of Enzymatic Digests of Proteins, Kathryn L. Stone. Part V: Protein/Peptide Characterization. Peptide Mapping by two-Dimensional Thin-Layer Electrophoresis-Thin-Layer Chromatography, Ralph C. Judd. Peptide Mapping by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis, Ralph C. Judd. Peptide Mapping by High-Performance Liquid Chromatography, Ralph C. Judd. Production of Protein Hydrolysates Using Enzymes, John M. Walker and Patricia J. Sweeney. Amino Acid Analysis by Pre-Column Derivatization, Philipp Christen, Molecular Weight Estimation for Native Proteins Using High-Performance Size Exclusion Chromatography, G. Brent Irvine. Detection of Disulfide-Linked Peptides by HPLC, Alastair Aitken and Michele P. Learmonth. Detection of Disulfide-Linked Peptides by Mass Spectrometry, Alastair Aitken and Michele P. Learmonth. Diagonal Electrophoresis for Detection of Disulfide-Bridges, Alastair Aitken and Michele P. Learmonth. Estimation of Disulfide Bonds Using Ellman's Reagent, Alastair Aitken and Michele P. Learmonth. Quantitation of Cysteine Residues and Disulfide Bonds by Electrophoresis, Alastair Aitken and Michele P. Learmonth. Analyzing Protein Phosphorylation John Colyer x 91 Mass Spectrometric Analysis of Protein Phosphorylation Debora Bonefant, Thierry Mini, and Paul Jeno x 92 Identification of Proteins Modified by Protein Carboxyl Methyltransferase Darin J. Weber and Philip N. McFadden x 93 Analysis of Protein Palmitoylation Morag A. Grassie and Graeme Milligan x 94 Incorporation of Radiolabeled Prenyl Alcohols and Their Analogs into Mammalian Cell Proteins: A Useful Tool for Studying Protein Prenylation Alberto Corsini x 95 The Metabolic Labelling and Analysis of Isoprenylated Proteins Douglas Andres, Dean Crick, Brian Finlin, and Charles Waechter x 96 Two-Dimensional Phosphopeptide mapping Steven F. Dowdy x 97 Detection and Characterization of Protein Mutations by Mass Spectrometry Yoshinao Wada x 98 Peptide sequencing by Nanoelectrospray Tendem Mass Spectrometry Ole Norregaard Jensen x 99 MALDI Mass Spectrometry for Protein Identification Using Peptide and Fragment Ion Masses Paul Courchesne and Scott D. Patterson x 100 Protein Ladder Sequencing Brian T. Chait x 101 Sequence Analysis with WinGene/WinPep Lars Hennig x 101 Sequence Analysis with WinGene/WinPep Lars Hennig x 102 Isolation of Proteins Cross-Linked to DNA by Cisplatin Virginia A. Spencer and James R. Davie x 103 Isolation of Proteins Cross-Linked to DNA by Formaldehyde Virginia A. Spencer and James R. Davie x Part VI : Glycoproteins 104 Detection of Glycoproteins in Gels and Blots Nicolle H. Packer, Malcolm Ball, Peter L. Devine, and Wayne, F. Patton x 105 Staining of Glycoproteins/Proteoglycans on SDS-Gels Holger J. Moller x 106 Identification of Glycoproteins on Nitrocellulose Membranes Using Lectin Blotting Patricia Gravel x 107 A Lectin-Binding Assay for the Rapid Characterization of the Glycosylation of Purified Glycoproteins Mohammad T. Goodarzi, Angeliki Fontinopoulou, and Graham A. Turner x 108 Chemical Methods of Analysis of Glycoproteins Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 109 Monosaccharide Analysis by HPAEC Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 110 Monosaccharide Analysis by GC Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 111 Determination of Monosaccharide Linkage and Substitution Patterns by GC,MS Methylation Analysis Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 112 Sialic Acid Analysis by HPAEC-PAD Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 113 Chemical Release of O-Linked Oligosaccharide Chains Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 114 O-Linked Oligosaccharide Profiling by HPLC Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 115 O-Linked Oligosaccharide Profiling by HPLC Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 116 Release of N-Linked Oligosaccharide Chains by Hydrazinolysis T. Mizuochoi and Elizabeth F. Hounsell x 117 Enzymatic Release of O- and N-Linked Oligosaccharide Chains Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 118 N-Linked Oligosaccharide Profiling by HPLC on Porous Graphitized Carbon (PGC) Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 119 N-Linked Oligosaccharide Profiling by HPLC on Porous Graphitized Carbon (PGC) Elizabeth F. Hounsell, Michael J. Davies, and Kevin D. Smith x 120 N-Linked Oligosaccharide Profiling by HPAEC-PAD Michael Weitzhandler x 121 Microassay Analysis of Protein Glycosylation Nicky K.C. Wong x 122 Polyacrylamide Gel Electrophoresis of Fluorophore-Labeled Carbohydrates from Glycoproteins Brian K. Brandley, John C. Klock, and Christopher M. Star x 123 HPLC Analysis of Fluorescently Labelled Glycans Tony Merry x 124 Glycoprofiling Purified Glycoproteins using Surface Plasmon Resonance Angeliki Fotinopoulou and G.A. Turner x Sequencing Heparan Sulphate Saccharides Jeremy E. Turnbull x 126 Analysis of Glycoprotein Heterogeneity by CE and Mass Spectrometry Andrew D. Hooker and David C. James x 127 Affinity Chromatography of Oligosaccharides and Glycopeptides with Immobilized Lectins Kazuo Yamamoto x Part VII : Antibody Production 128 Antibody Production Robert Burns x 129 Production of Antibodies Using Proteins in Gel Bands Sally Ann Amero, Tharappel C. James, and Sarah C.R. Elgin x 130 Raising Highly Specific Polyclonal Antibodies Using Biocompatible Support Bound Antigens Monique Diano and Andre Le Bivic x 131 Production of Antisera Using Peptide Conjugates Thomas E. Adrian x 132 The Chloramine T Method for Radiolabeling Protein Graham S. Bailey x 133 The Lactoperoxidase Method for Radiolabeling Protein Graham S. Bailey x 134 The Bolton and Hunter Method for Radiolabeling Protein Graham S. Bailey x 135 Preparation of I125 Labelled Peptides and Proteins With High Specific Activity Using Iodogen J. Michael Conlon x 136 Purification and Assessment of Quality of Radioiodinated Protein Graham S. Bailey x 137 Purification of IgG by Precipitation with Sodium Sulfate or Ammonium Sulfate Mark Page and Robin Thorpe x 138 Purification of IgG Using Caprylic Acid Mark Page and Robin Thorpe x 139 Purification of IgG Using DEAE-Sepharose Chromatography Mark Page and Robin Thorpe x 140 Purification of IgG Using Ion-Exchange HPLC Mark Page and Robin Thorpe 141 Purification of IgG by Precipitation with Polyethylene Glycol (PEG) Mark Page and Robin Thorpe x 142 Purification of IgG Using protein A or Protein G Mark Page and Robin Thorpe x 143 Purification of IgG Using Size Exclusion High Performance Liquid Chromatography Carl Dolman Robin Thorpe x 144 Purification of IgG Using Affinity Chromatography on Antigen-Ligand Columns Mark Page and Robin Thorpe x 145 Purification of IgG Using Thiophilic Chromatography Mark Page and Robin Thorpe x 146 Analysis of IgG Fractions by Electrophoresis Mark Page and Robin Thorpe x 147 Purification of Immunoglobulin Y (IgY) from Chicken Eggs C.R. Bird and Robin Thorpe x 148 Affinity Purification of Immunoglobulins Using PAM (Protein A Mimetic) Giorgio Fassina x 149 Detection of Serological Cross Reactions by Western Cross Blotting Josef Thalhammer x 150 Bacterial Expression, Purification, and Characterization of Single-Chain Antibodies Sergey M. Kipriyanovx 151 Enzymatic Digestion of Monoclonal Antibodies Sarah M. Andrew x 152 How to make Bispecific Antibodies Ruth R. French x 153 Phage Display: Biopanning on Purified Proteins and Proteins Expressed in Whole Cell Membranes George Ehrlich, Wolfgang Berthold, and Pascal Bailon x 154 Screening of Phage Displayed Antibody Libraries Martin Welschof x 155 Antigen Measurements Using ELISA William Jordan x 156 Enhanced Chemiluminescence Immunoassay Richard A.W. Scott x 157 Immunoprecipitation Kari Johansen x Part VIII: Monoclonal antibodies 158 Immunogen Preparation and Immunization Procedures for Rats and Mice Mark Page and Robin Thorpe x 159 Hybridoma Production Mark Page and Robin Thorpe x 160 Screening Hybridoma Culture Supernatants Using Solid-Phase Radiobinding Assay Mark Page and Robin Thorpe x 161 Screening Hybridoma Culture Supernatants Using ELISA Mark Page and Robin Thorpe x 162 Growth and Purification of Murine Monoclonal Antibodies Mark Page and Robin Thorpe x 163 Affinity Purification Techniques for Monoclonal Antibodies Mark Page and Robin Thorpe x 164 A Rapid Method for Generating Large Numbers of High-Affinity Monoclonal Antibodies from a Single Mouse N. Man and Glenn E. Morris x Index
Volume

: pbk ISBN 9780896039414

Description

The Protein Protocols Handbook, Second Edition aims to provide a cross-section of analytical techniques commonly used for proteins and peptides, thus providing a benchtop manual and guide for those who are new to the protein chemistry laboratory and for those more established workers who wish to use a technique for the first time. All chapters are written in the same format as that used in the Methods in Molecular Biology(TM) series. Each chapter opens with a description of the basic theory behind the method being described. The Materials section lists all the chemicals, reagents, buffers, and other materials necessary for carrying out the protocol. Since the principal goal of the book is to provide experimentalists with a full account of the practical steps necessary for carrying out each protocol successfully, the Methods section contains detailed st- by-step descriptions of every protocol that should result in the successful execution of each method. The Notes section complements the Methods material by indicating how best to deal with any problem or difficulty that may arise when using a given technique, and how to go about making the widest variety of modifications or alterations to the protocol. Since the first edition of this book was published in 1996 there have, of course, been significant developments in the field of protein chemistry.

Table of Contents

Part I. Quantitation of Proteins 1 Protein Determination by UV Absorption Alastair Aitken and Michele P. Learmonth 2 The Lowry Method for Protein Quantitation Jakob H. Waterborg 3 The Bicinchoninic Acid (BCA) Assay for Protein Quantitation John M. Walker 4 The Bradford Method for Protein Quantitation Nicholas J. Kruger 5 Ultrafast Protein Determinations Using Microwave Enhancement Robert E. Akins and Rocky S. Tuan 6 The Nitric Acid Method for Protein Estimation in Biological Samples Scott A. Boerner, Yean Kit Lee, Scott H. Kaufmann, and Keith C. Bible 7 Quantitation of Tryptophan in Proteins Alastair Aitken and Michele P. Learmonth 8 Flow Cytometric Quantitation of Cellular Proteins Thomas D. Friedrich, F. Andrew Ray, Judith A. Laffin, and John M. Lehman 9 Kinetic Silver Staining of Proteins Douglas D. Root and Kuan Wang Part II. Electrophoresis of Proteins and Peptides and Detection in Gels 10 Nondenaturing Polyacrylamide Gel Electrophoresis of Proteins John M. Walker 11 SDS Polyacrylamide Gel Electrophoresis of Proteins John M. Walker 12 Gradient SDS Polyacrylamide Gel Electrophoresis of Proteins John M. Walker 13 SDS-Polyacrylamide Gel Electrophoresis of Peptides Ralph C. Judd 14 Identification of Nucleic Acid Binding Proteins Using Nondenaturing Sodium Decyl Sulfate Polyacrylamide Gel Electrophoresis (SDecS-Page) Robert E. Akins and Rocky S. Tuan 15 Cetyltrimethylammonium Bromide Discontinuous Gel Electrophoresis of Proteins: Mr-Based Separation of Proteins with Retained Native Activity Robert E. Akins and Rocky S. Tuan 16 Acetic-Acid-Urea Polyacrylamide Gel Electrophoresis of Basic Proteins Jakob H. Waterborg 17 Acid-Urea-Triton Polyacrylamide Gel Electrophoresis of Histones Jakob H. Waterborg 18 Isoelectric Focusing of Proteins in Ultra-Thin Polyacrylamide Gels John M.Walker 19 Protein Solubility in Two-Dimensional Electrophoresis: Basic Principles and Issues Thierry Rabilloud 20 Preparation of Protein Samples from Mouse and Human Tissues for 2-D Electrophoresis Joachim Klose 21 Radiolabeling of Eukaryotic Cells and Subsequent Preparation for 2-D Electrophoresis Nick Bizios 22 Two-Dimensional Polyacrylamide Gel Electrophoresis Using Carrier Ampholyte pH Gradients in the First Dimension Patricia Gravel 23 Casting Immobilized pH Gradients (IPGs) Elisabetta Gianazza 24 Nonequilibrium pH Gel Electrophoresis (NEPHGE) Mary F. Lopez 25 Difference Gel Electrophoresis Mustafa Unlu and Jonathan Minden 26 Comparing 2-D Electrophoretic Gels Across Internet Databases Peter F. Lemkin and Gregory C. Thornwall 27 Immunoblotting of 2-D Electrophoresis Separated Proteins Barbara Magi, Luca Bini, Sabrina Liberatori, Roberto Raggiaschi, and Vitaliano Pallini 28 Quantification of Radiolabeled Proteins in Polyacrylamide Gels Wayne R. Springer 29 Quantification of Proteins on Polyacrylamide Gels Bryan John Smith 30 Rapid and Sensitive Staining of Unfixed Proteins in Polyacrylamide Gels with Nile Red Joan-Ramon Daban, Salvador Bartolome, Antonio Bermudez, and F. Javier Alba 31 Zinc-Reverse Staining Technique Carlos Fernandez-Patron 32 Protein Staining with Calconcarboxylic Acid in Polyacrylamide Gels Jung-Kap Choi, Hee-Youn Hong, and Gyurng-Soo Yoo 33 Detection of Proteins in Polyacrylamide Gels by Silver Staining Michael J. Dunn 34 Protein Detection on Polyacrylamide Gels and Electroblots Using Transition Metal Chelate Stains Wayne F. Patton 35 Detection of Proteins in Polyacrylamide Gels by Fluorescent Staining Michael J. Dunn 36 Detection of Proteins and Sialoglycoproteins in Polyacrylamide Gels Using Eosin Y Stain Fan Lin and Gary E. Wise 37 Electroelution of

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