the protein protocols handbook

CHAIT• The Rockefeller University, New York, NY JUNG-KAP CHOI• College of Pharmacy, Chonnam National University, Kwangju, Korea PHILIPP CHRISTEN•Biochemisches Institut der Universität Zü

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The Protein Protocols Handbook

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Printed in the United States of America 10 9 8 7 6 5 4 3 2 1

Library of Congress Cataloging in Publication Data

The Protein Protocols Handbook: Second Edition / edited by John M Walker.

p cm.

ISBN 0-89603-940-4 (HB); 0-89603-941-2 (PB)

Includes bibliographical references and index.

1 Proteins Analysis Laboratory manuals I Walker, John M.,

1948-Qp551 P697512 2002

572'.6 dc21

2001039829

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v

The Protein Protocols Handbook, Second Edition aims to provide a cross-section of

analytical techniques commonly used for proteins and peptides, thus providing abenchtop manual and guide for those who are new to the protein chemistry laboratoryand 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™ 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 ofthe book is to provide experimentalists with a full account of the practical steps necessaryfor carrying out each protocol successfully, the Methods section contains detailed step-by-step descriptions of every protocol that should result in the successful execution ofeach method The Notes section complements the Methods material by indicating howbest 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 theprotocol

Since the first edition of this book was published in 1996 there have, of course, beensignificant developments in the field of protein chemistry Hence, for this second edition

I have introduced 60 chapters/protocols not present in the first edition, significantlyupdated a number of chapters remaining from the first edition, and increased the overalllength of the book from 144 to 164 chapters The new chapters particularly reflect theconsiderable developments in the use of mass spectrometry in protein characterization.Recognition of the now well-established central role of 2-D PAGE in proteomics hasresulted in an expansion of chapters on this subject, and I have also included a number

of new techniques for staining and analyzing protein blots The section on glycoproteinanalysis has been significantly expanded, and aspects of single chain antibodies andphage-displayed antibodies have been introduced in the section on antibodies

We each, of course, have our own favorite, commonly used methods, be it a gelsystem, gel-staining method, blotting method, and so on; I’m sure you will find yourshere However, I have, as before, also described alternatives for some of these tech-niques; though they may not be superior to the methods you commonly use, they maynevertheless be more appropriate in a particular situation Only by knowing the range oftechniques that are available to you, and the strengths and limitations of these techniques,will you be able to choose the method that best suits your purpose Good luck in yourprotein analysis!

John M Walker

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Preface v

Contributors xix

PART I: QUANTITATION OF PROTEINS

1 Protein Determination by UV Absorption

Alastair Aitken and Michèle P Learmonth 3

2 The Lowry Method for Protein Quantitation

5 Ultrafast Protein Determinations Using Microwave Enhancement

Robert E Akins and Rocky S Tuan 23

6 The Nitric Acid Method for Protein Estimation in Biological Samples

Scott A Boerner, Yean Kit Lee, Scott H Kaufmann,

and Keith C Bible 31

7 Quantitation of Tryptophan in Proteins

8 Flow Cytometric Quantitation of Cellular Proteins

Thomas D Friedrich, F Andrew Ray, Judith A Laffin,

and John M Lehman 45

9 Kinetic Silver Staining of Proteins

Douglas D Root and Kuan Wang 51

PART II: ELECTROPHORESIS OF PROTEINS AND PEPTIDES AND DETECTION IN GELS

10 Nondenaturing Polyacrylamide Gel Electrophoresis of Proteins

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viii Contents

14 Identification of Nucleic Acid Binding Proteins Using NondenaturingSodium Decyl Sulfate Polyacrylamide Gel Electrophoresis

(SDecS-Page)

15 Cetyltrimethylammonium Bromide Discontinuous Gel Electrophoresis

of Proteins: Mr-Based Separation of Proteins with Retained

Native Activity

16 Acetic–Acid–Urea Polyacrylamide Gel Electrophoresis of Basic Proteins

19 Protein Solubility in Two-Dimensional Electrophoresis:

Basic Principles and Issues

25 Difference Gel Electrophoresis

Mustafa Ünlü and Jonathan Minden 185

26 Comparing 2-D Electrophoretic Gels Across Internet Databases

Peter F Lemkin and Gregory C Thornwall 197

27 Immunoblotting of 2-D Electrophoresis Separated Proteins

Barbara Magi, Luca Bini, Sabrina Liberatori,

Roberto Raggiaschi, and Vitaliano Pallini 215

28 Quantification of Radiolabeled Proteins in Polyacrylamide Gels

Wayne R Springer 231

29 Quantification of Proteins on Polyacrylamide Gels

Bryan John Smith 237

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32 Protein Staining with Calconcarboxylic Acid in Polyacrylamide Gels

Jung-Kap Choi, Hee-Youn Hong, and Gyurng-Soo Yoo 259

33 Detection of Proteins in Polyacrylamide Gels by Silver Staining

Michael J Dunn 265

34 Background-Free Protein Detection in Polyacrylamide Gels

and on Electroblots Using Transition Metal Chelate Stains

Wayne F Patton 273

35 Detection of Proteins in Polyacrylamide Gels by Fluorescent Staining

Michael J Dunn 287

36 Detection of Proteins and Sialoglycoproteins in Polyacrylamide

Gels Using Eosin Y Stain

Fan Lin and Gary E Wise 295

37 Electroelution of Proteins from Polyacrylamide Gels

Paul Jenö and Martin Horst 299

38 Autoradiography and Fluorography of Acrylamide Gels

Antonella Circolo and Sunita Gulati 307

PART III: BLOTTING AND DETECTION METHODS

39 Protein Blotting by Electroblotting

Mark Page and Robin Thorpe 317

40 Protein Blotting by the Semidry Method

Geneviève P Delcuve and James R Davie 337

43 Alkaline Phosphatase Labeling of IgG Antibody

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47 Conjugation of Fluorochromes to Antibodies

Su-Yau Mao 351

48 Coupling of Antibodies with Biotin

Rosaria P Haugland and Wendy W You 355

49 Preparation of Avidin Conjugates

Rosaria P Haugland and Mahesh K Bhalgat 365

50 MDPF Staining of Proteins on Western Blots

F Javier Alba and Joan-Ramon Daban 375

51 Copper Iodide Staining of Proteins and Its Silver Enhancement

Douglas D Root and Kuan Wang 381

52 Detection of Proteins on Blots Using Direct Blue 71

Hee-Youn Hong, Gyurng-Soo Yoo, and Jung-Kap Choi 387

53 Protein Staining and Immunodetection Using Immunogold

Susan J Fowler 393

54 Detection of Polypeptides on Immunoblots Using Enzyme-Conjugated

or Radiolabeled Secondary Ligands

Nicholas J Kruger 405

55 Utilization of Avidin- or Streptavidin-Biotin as a Highly Sensitive

Method to Stain Total Proteins on Membranes

Kenneth E Santora, Stefanie A Nelson, Kristi A Lewis,

and William J LaRochelle 415

56 Detection of Protein on Western Blots Using Chemifluorescence

Catherine Copse and Susan J Fowler 421

57 Quantification of Proteins on Western Blots using ECL

Joanne Dickinson and Susan J Fowler 429

58 Reutilization of Western Blots After Chemiluminescent

Detection or Autoradiography

Scott H Kaufmann 439

PART IV: CHEMICAL MODIFICATION OF PROTEINS

AND PEPTIDE PRODUCTION AND PURIFICATION

59 Carboxymethylation of Cysteine Using Iodoacetamide/Iodoacetic Acid

60 Performic Acid Oxidation

61 Succinylation of Proteins

62 Pyridylethylation of Cysteine Residues

Malcolm Ward 461

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63 Side Chain Selective Chemical Modifications of Proteins

71 Chemical Cleavage of Proteins at Methionyl-X Peptide Bonds

72 Chemical Cleavage of Proteins at Tryptophanyl-X Peptide Bonds

73 Chemical Cleavage of Proteins at Aspartyl-X Peptide Bonds

74 Chemical Cleavage of Proteins at Cysteinyl-X Peptide Bonds

75 Chemical Cleavage of Proteins at Asparaginyl-Glycyl Peptide Bonds

76 Enzymatic Digestion of Proteins in Solution and in SDS

Polyacrylamide Gels

Kathryn L Stone and Kenneth R Williams 511

77 Enzymatic Digestion of Membrane-Bound Proteins for Peptide

Mapping and Internal Sequence Analysis

Joseph Fernandez and Sheenah Mische 523

78 Reverse Phase HPLC Separation of Enzymatic Digests of Proteins

Kathryn L Stone and Kenneth R Williams 533

PART V: PROTEIN/PEPTIDE CHARACTERIZATION

79 Peptide Mapping by Two-Dimensional Thin-Layer

Electrophoresis–Thin-Layer Chromatography

Ralph C Judd 543

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80 Peptide Mapping by Sodium Dodecyl Sulfate-Polyacrylamide

Gel Electrophoresis

81 Peptide Mapping by High-Performance Liquid Chromatography

82 Production of Protein Hydrolysates Using Enzymes

John M Walker and Patricia J Sweeney 563

83 Amino Acid Analysis by Precolumn Derivatization with Dinitrophenyl-5-L-Alanine Amide (Marfey's Reagent)

1-Fluoro-2,4-Sunil Kochhar, Barbara Mouratou, and Philipp Christen 567

84 Molecular Weight Estimation for Native Proteins Using

High-Performance Size-Exclusion Chromatography

G Brent Irvine 573

85 Detection of Disulfide-Linked Peptides by HPLC

86 Detection of Disulfide-Linked Peptides by Mass Spectrometry

87 Diagonal Electrophoresis for Detecting Disulfide Bridges

88 Estimation of Disulfide Bonds Using Ellman's Reagent

89 Quantitation of Cysteine Residues and Disulfide Bonds

by Electrophoresis

90 Analyzing Protein Phosphorylation

John Colyer 603

91 Mass Spectrometric Analysis of Protein Phosphorylation

Débora BoneNfant, Thierry Mini, and Paul Jenö 609

92 Identification of Proteins Modified by Protein

(D-Aspartyl/L-Isoaspartyl) Carboxyl Methyltransferase

Darin J Weber and Philip N McFadden 623

93 Analysis of Protein Palmitoylation

Morag A Grassie and Graeme Milligan 633

94 Incorporation of Radiolabeled Prenyl Alcohols and Their Analogs

into Mammalian Cell Proteins: A Useful Tool for Studying

Protein Prenylation

Alberto Corsini, Christopher C Farnsworth, Paul McGeady, Michael

H Gelb, and John A Glomset 641

95 The Metabolic Labeling and Analysis of Isoprenylated Proteins

Douglas A Andres, Dean C Crick, Brian S Finlin,

and Charles J Waechter 657

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96 2-D Phosphopeptide Mapping

Hikaru Nagahara, Robert R Latek, Sergi A Ezhevsky,

and Steven F Dowdy, 673

97 Detection and Characterization of Protein Mutations

by Mass Spectrometry

Yoshinao Wada 681

98 Peptide Sequencing by Nanoelectrospray Tandem Mass Spectrometry

Ole Nørregaard Jensen and Matthias Wilm 693

99 Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

for Protein Identification Using Peptide and Fragmention Masses

Paul L Courchesne and Scott D Patterson 711

100 Protein Ladder Sequencing

Rong Wang and Brian T Chait 733

101 Sequence Analysis with WinGene/WinPep

Lars Hennig 741

102 Isolation of Proteins Cross-linked to DNA by Cisplatin

Virginia A Spencer and James R Davie 747

103 Isolation of Proteins Cross-linked to DNA by Formaldehyde

Virginia A Spencer and James R Davie 753

PART VI : GLYCOPROTEINS

104 Detection of Glycoproteins in Gels and Blots

Nicolle H Packer, Malcolm S Ball, Peter L Devine,

and Wayne F Patton 761

105 Staining of Glycoproteins/Proteoglycans in SDS-Gels

Holger J Møller and Jørgen H Poulsen 773

106 Identification of Glycoproteins on Nitrocellulose Membranes

Using Lectin Blotting

Patricia Gravel 779

107 A Lectin-Binding Assay for the Rapid Characterization

of the Glycosylation of Purified Glycoproteins

Mohammad T Goodarzi, Angeliki Fotinopoulou,

and Graham A Turner 795

108 Chemical Methods of Analysis of Glycoproteins

Elizabeth F Hounsell, Michael J Davies, and Kevin D Smith 803

109 Monosaccharide Analysis by HPAEC

110 Monosaccharide Analysis by Gas Chromatography (GC)

111 Determination of Monosaccharide Linkage and Substitution

Patterns by GC-MS Methylation Analysis

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xiv Contents

112 Sialic Acid Analysis by HPAEC-PAD

113 Chemical Release of O-Linked Oligosaccharide Chains

114 O-Linked Oligosaccharide Profiling by HPLC

115 O-Linked Oligosaccharide Profiling by HPAEC-PAD

116 Release of N-Linked Oligosaccharide Chains by Hydrazinolysis

Tsuguo Mizuochi and Elizabeth F Hounsell 823

117 Enzymatic Release of O- and N-Linked Oligosaccharide Chains

118 N-Linked Oligosaccharide Profiling by HPLC on Porous

Graphitized Carbon (PGC)

Elizabeth F Hounsell, Michael J Davies, and Kevin D Smith 829

119 N-Linked Oligosaccharide Profiling by HPAEC-PAD

120 HPAEC-PAD Analysis of Monosaccharides Released by

Exoglycosidase Digestion Using the CarboPac MA1 Column

Michael Weitzhandler Jeffrey Rohrer, James R Thayer,

and Nebojsa Avdalovic 833

121 Microassay Analyses of Protein Glycosylation

Nicky K.C Wong, Nnennaya Kanu, Natasha Thandrayen,

Geert Jan Rademaker, Christopher I Baldwin,

David V Renouf, and Elizabeth F Hounsell 841

122 Polyacrylamide Gel Electrophoresis of Fluorophore-Labeled

Carbohydrates from Glycoproteins

Brian K Brandley, John C Klock, and Christopher M Starr 851

123 HPLC Analysis of Fluorescently Labeled Glycans

Tony Merry 865

124 Glycoprofiling Purified Glycoproteins Using Surface Plasmon Resonance

Angeliki Fotinopoulou and Graham A Turner 885

125 Sequencing Heparan Sulfate Saccharides

Jeremy E Turnbull 893

126 Analysis of Glycoprotein Heterogeneity by Capillary Electrophoresis and Mass Spectrometry

Andrew D Hooker and David C James 905

127 Affinity Chromatography of Oligosaccharides and Glycopeptides

with Immobilized Lectins

Kazuo Yamamoto, Tsutomu Tsuji, and Toshiaki Osawa 917

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PART VII : ANTIBODY TECHNIQUES

128 Antibody Production

Robert Burns 935

129 Production of Antibodies Using Proteins in Gel Bands

Sally Ann Amero, Tharappel C James, and Sarah C.R Elgin 941

130 Raising Highly Specific Polyclonal Antibodies Using Biocompatible Support-Bound Antigens

Monique Diano and André Le Bivic 945

131 Production of Antisera Using Peptide Conjugates

135 Preparation of 125I Labeled Peptides and Proteins with High

Specific Activity Using IODO-GEN

Mark Page and Robin Thorpe 983

138 Purification of IgG Using Caprylic Acid

139 Purification of IgG Using DEAE-Sepharose Chromatography

140 Purification of IgG Using Ion-Exchange HPLC

Carl Dolman, Mark Page, and Robin Thorpe 989

141 Purification of IgG by Precipitation with Polyethylene Glycol (PEG)

142 Purification of IgG Using Protein A or Protein G

143 Analysis and Purification of IgG Using Size-Exclusion High

Performance Liquid Chromatography (SE-HPLC)

Carl Dolman and Robin Thorpe 995

144 Purification of IgG Using Affinity Chromatography

on Antigen-Ligand Columns

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145 Purification of IgG Using Thiophilic Chromatography

Mark Page and Robin Thorpe 1003

146 Analysis of IgG Fractions by Electrophoresis

147 Purification of Immunoglobulin Y (IgY) from Chicken Eggs

Christopher R Bird and Robin Thorpe 1009

148 Affinity Purification of Immunoglobulins Using Protein A

Mimetic (PAM)

Giorgio Fassina, Giovanna Palombo, Antonio Verdoliva,

and Menotti Ruvo 1013

149 Detection of Serological Cross-Reactions by Western Cross-Blotting

Peter Hammerl, Arnulf Hartl, Johannes Freund,

and Josef Thalhamer 1025

150 Bacterial Expression, Purification, and Characterization

153 Phage Display: Biopanning on Purified Proteins and Proteins

Expressed in Whole Cell Membranes

George K Ehrlich, Wolfgang Berthold, and Pascal Bailon 1059

154 Screening of Phage Displayed Antibody Libraries

Heinz Dörsam, Michael Braunagel, Christian Kleist,

Daniel Moynet, and Martin Welschof 1073

155 Antigen Measurements Using ELISA

William Jordan 1083

156 Enhanced Chemiluminescence Immunoassay

Richard A.W Stott 1089

157 Immunoprecipitation

Kari Johansen and Lennart Svensson 1097

PART VIII: MONOCLONAL ANTIBODIES

158 Immunogen Preparation and Immunization Procedures

for Rats and Mice

159 Hybridoma Production

160 Screening Hybridoma Culture Supernatants Using Solid-Phase

Radiobinding Assay

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161 Screening Hybridoma Culture Supernatants Using ELISA

162 Growth and Purification of Murine Monoclonal Antibodies

163 Affinity Purification Techniques for Monoclonal Antibodies

Alexander Schwarz 1121

164 A Rapid Method for Generating Large Numbers of High-Affinity

Monoclonal Antibodies from a Single Mouse

Nguyen Thi Man and Glenn E Morris 1129

Index 1139

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SARAH M ANDREW• Chester College of Higher Education, UK

NEBOJSA AVDALOVIC•Dionex Corporation, Life Science Research Group,

Sunnyvale, CA

GRAHAM S BAILEY•Department of Biological Sciences, University of Essex, Colchester, UK

PASCAL BAILON• Department of Pharmaceutical and Analytical R & D,

Hoffmann-LaRoche Inc., Nutley, NJ

MALCOLM S BALL• Co-operative Research Centre for Eye Research Technology, Sydney, Australia

SALVADOR BARTOLOMÉ•Departament de Bioquímica i Biologia Molecular,

Universität Autònoma de Barcelona, Bellaterra (Barcelona), Spain

ANTONIO BERMÚDEZ• Departament de Bioquímica i Biologia Molecular, Universität Autònoma de Barcelona, Bellaterra (Barcelona), Spain

WOLFGANG BERTHOLD• Division of Biopharmaceutical Sciences, IDEC

Pharmaceuticals Corp., San Diego, CA

MAHESH K BHALGAT• Molecular Probes, Inc., Eugene, OR

KEITH C BIBLE• Division of Medical Oncology, Mayo Clinic, Rochester, MN

LUCA BINI• Department of Molecular Biology, University of Siena, Italy

CHRISTOPHER R BIRD•Division of Immunobiology, National Institute for Biological Standards and Control, Potters Bar, UK

NICK BIZIOS• AGI Dermatics, Freeport, NY

SCOTT A BOERNER• Division of Medical Oncology, Mayo Clinic, Rochester, MN

DÉBORA BONENFANT• Department of Biochemistry, Biozentrum der Universität Basel, Switzerland

BRIAN K BRANDLEY• Glyko Inc., Navato, CA

MICHAEL BRAUNAGEL• Affitech, Oslo, Norway

xix

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ROBERT BURNS•Antibody Unit, Scottish Agricultural Science Agency, Edinburgh, UK

FRANCA CASAGRANDA• CSIRO Division of Biomolecular Engineering, Victoria, Australia; Present address: European Molecular Biology Laboratory,

Heidelberg, Germany

BRIAN T CHAIT• The Rockefeller University, New York, NY

JUNG-KAP CHOI• College of Pharmacy, Chonnam National University, Kwangju, Korea

PHILIPP CHRISTEN•Biochemisches Institut der Universität Zürich, Switzerland

ANTONELLA CIRCOLO•Maxwell Finland Lab for Infectious Diseases, Boston, MA

JOHN COLYER• Department of Biochemistry & Molecular Biology, University

of Leeds, UK

J MICHAEL CONLON• Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE

CATHERINE COPSE• Amersham Biosciences, Amersham, UK

ALBERTO CORSINI• Department of Pharmacological Sciences, University

of Milan, Italy

PAUL L COURCHESNE• Amgen Inc., Thousand Oaks, CA

DEAN C CRICK• Department of Biochemistry, University of Kentucky, Lexington, KY

JOAN-RAMON DABAN• Departament de Bioquímica i Biologia Molecular, Universität Autònoma de Barcelona, Bellaterra (Barcelona), Spain

JAMES R DAVIE• Manitoba Institute of Cell Biology, Winnipeg, Canada

GENEVIÈVE P DELCUVE•Manitoba Institute of Cell Biology, Winnipeg, Canada

PETER L DEVINE• Proteome Systems Ltd., Sydney, Australia

MONIQUE DIANO• IBDM, Faculté des Sciences de Luminy, Marseille, France

JOANNE DICKINSON• Amersham Biosciences, Amersham Labs, UK

CARL DOLMAN• Division of Immunobiology, National Institute for Biological

Standards and Control, Potters Bar, UK

HEINZ DÖRSAM• German Cancer Research Center, Heidelberg, Germany

STEVEN F DOWDY• University of California Medical Center, San Francisco, CA

MICHAEL J DUNN• Department of Neuroscience, Institute of Psychiatry,

De Crespigny Park, London, UK

GEORGE K EHRLICH• Department of Pharmaceutical and Analytical R & D,

Hoffman-LaRoche Inc., Nutley, NJ

SARAH C R ELGIN• Department of Biology, Washington University in St Louis, MO

SERGEI A EZHEVSKY• Howard Hughes Medical Institute, Washington University School of Medicine, St Louis, MO

CHRISTOPHER C FARNSWORTH• Department of Protein Chemistry, IMMUNEX

Corporation, Seattle, WA

GIORGIO FASSINA• Biopharmaceuticals, Tecnogen SCPA, Parco Scientifico, Piana

di Monte Verna (CE), Italy

JOSEPH FERNANDEZ• Protein/DNA Technology Center, Rockefeller University, NY

CARLOS FERNANDEZ-PATRON• Department of Biochemistry, University

of Alberta, Edmonton, Canada

BRIAN S FINLIN• Department of Biochemistry, University of Kentucky, Lexington, KY

ANGELIKI FOTINOPOULOU• Department of Clinical Biochemistry, The Medical School, University of Newcastle, Newcastle upon Tyne, UK

SUSAN J FOWLER• Amersham Biosciences, Amersham, UK

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RUTH R FRENCH• Lymphoma Research Unit, Tenovus Research Laboratory,

Southhampton General Hospital, UK

THOMAS D FRIEDRICH• Center for Immunology and Microbial Disease, Albany Medical College, NY

JOHANNES FREUND•Institute of Chemistry and Biochemistry, Immunology Group, University of Salzburg, Austria

MICHAEL H GELB• Departments of Chemistry and Biochemistry, University

of Washington, Seattle, WA

ELISABETTA GIANAZZA• Istituto di Scienze Farmacologiche, Universita di Milano, Italy

JOHN A GLOMSET• Howard Hughes Medical Institute, University of Washington, Seattle, WA

MOHAMMAD T GOODARZI•Department of Clinical Biochemistry, The Medical School, University of Newcastle, New Castle upon Tyne, UK

MORAG A GRASSIE• Department of Biochemistry & Molecular Biology, Institute

of Biomedical and Life Sciences, University of Glasgow, UK

PATRICIA GRAVEL• Triskel Integrated Services, Geneva, Switzerland

SUNITA GULATI•Maxwell Finland Lab for Infectious Diseases, Boston, MA

PETER HAMMERL•Institute of Chemistry and Biochemistry, Immunology Group, University of Salzburg, Austria

ARNULF HARTL•Institute of Chemistry and Biochemistry, Immunology Group, University of Salzburg, Austria

ROSARIA P HAUGLAND• Molecular Probes Inc., Eugene, OR

LARS HENNIG• Swiss Federal Institute of Technology, Zürich, Switzerland

HEE-YOUN HONG• College of Pharmacy, Chonnam National University,

Kwangju, Korea

ANDREW HOOKER• Sittingbourne Research Centre, Pfizer Ltd, Analytical Research and Development (Biologics), Sittingbourne, UK

MARTIN HORST• STRATEC Medical, Oberdorf, Switzerland

ELIZABETH F HOUNSELL• School of Biological and Chemical Sciences, Birkbeck University of London, UK

G BRENT IRVINE• School of Biology and Biochemistry, Queen’s University

of Belfast, UK

DAVID C JAMES• Sittingbourne Research Centre, Pfizer Ltd, Analytical Research and Development (Biologics), Sittingbourne, UK

THARAPPEL C JAMES• Dublin, Ireland

PAUL JENÖ• Department of Biochemistry, Biozentrum der Universität

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SERGEY M KIPRIYANOV• Affimed Therapeutics AG, Ladenburg, Germany

CHRISTIAN KLEIST• Institute for Immunology, Heidelberg, Germany

JOACHIM KLOSE• Institut für Humangenetik Charité, Humboldt-Universität,

Berlin, Germany.

SUNIL KOCHHAR•Nestlé Research Center, Lausanne, Switzerland

NICHOLAS J KRUGER• Department of Plant Sciences, University of Oxford, UK

JUDITH A LAFFIN• Department of Microbiology, Immunology, and Molecular

Genetics, The Albany Medical College, Albany, NY

WILLIAM J LAROCHELLE• Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institute of Health, Bethesda, MD

ROBERT R LATEK• Howard Hughes Medical Institute, Washington University School

ANDRÉ LE BIVIC• IBDM, Faculté des Sciences de Luminy, Marseille, France

YEAN KIT LEE• Division of Medical Oncology, Mayo Clinic, Rochester, MN

PETER LEMKIN• LECB/NCI-FCRDC, Frederick, MD

KRISTI A LEWIS• Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institute of Health, Bethesda, MD

SABRINA LIBERATORI• Department of Molecular Biology, University of Siena, Italy

FAN LIN• Department of Pathology, Temple University Hospital, Philadelphia, PA

Mary F Lopez• Proteome Systems, Woburn, MA

BARBARA MAGI• Department of Molecular Biology, University of Siena, Italy

NGUYEN THI MAN• MRIC, North East Wales Institute, Deeside, Clwyd, UK

SU-YAU MAO• Department of Immunology and Molecular Genetics, Medimmune Inc., Gaithersburg, MD

PHILIP N MCFADDEN• Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR

PAUL MCGEADY• Department of Chemistry, Clark Atlanta University, Georgia

TONY MERRY• Department of Biochemistry, The Glycobiology Institute, University

of Oxford, UK

GRAEME MILLIGAN• Department of Biochemistry & Molecular Biology, Institute

of Biomedical and Life Sciences, University of Glasgow, UK

JONATHAN MINDEN• Millennium Pharmaceuticals, Cambridge, MA

THIERRY MINI• Department of Biochemistry, Biozentrum der Universität

Basel, Switzerland

SHEENAH M MISCHE• Protein/DNA Technology Center, Rockefeller University, NY

HOLGER J MØLLER• Department of Clinical Biochemistry, Aarhus University

Hospital, Amtssygehuset, Aarhus, Denmark

GLENN E MORRIS• MRIC, North East Wales Institute, Wrexhäm, UK

BARBARA MOURATOU•Biochemisches Institut der Universität Zürich, Switzerland

DANIEL MOYNET• INSERM, Bordeaux Cedex, France

HIKARU NAGAHARA• Howard Hughes Medical Institute, Washington University School of Medicine, St Louis, MO

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STEFANIE A NELSON• Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institute of Health, Bethesda, MD

TOSHIAKI OSAWA• Yakult Central Institute for Microbiology Research, Tokyo, Japan

NICOLLE PACKER• Proteome Systems Ltd., Sydney, Australia

MARK PAGE• Apovia Inc., San Diego, CA

VITALIANO PALLINI• Department of Molecular Biology, University of Siena, Italy

GIOVANNA PALOMBO• Biopharmaceuticals, Tecnogen SCPA, Parco Scientifico, Piana

SCOTT D PATTERSON• Celera Genomics, Rockville, MD

WAYNE F PATTON• Molecular Probes Inc., Eugene, OR

JERGEN H POULSEN• Department of Clinical Biochemistry, Aarhus University Hospital, Amtssygehuset, Aarhus, Denmark

THIERRY RABILLOUD• DBMS/BECP, CEA-Grenoble, Grenoble, France

ROBERTO RAGGIASCHI• Department of Molecular Biology, University of Siena, Italy

MENOTTI RUVO• Biopharmaceuticals, Tecnogen SCPA, Parco Scientifico, Piana di Monte Verna (CE), Italy

F ANDREW RAY • Department of Biology, Hartwick College, Oneonta, NY

JEFFREY ROHRER• Dionex Corporation, Life Science Research Group, Sunnyvale, CA

DOUGLAS D ROOT• Department of Biological Sciences, University of North Texas, Denton, TX

KENNETH E SANTORA• Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institute of Health, Bethesda, MD

ALEXANDER SCHWARZ• Biosphere Medical Inc., Rockland, MA

BRYAN JOHN SMITH• Celltech, R&D, Slough, UK

VIRGINIA SPENCER• Manitoba Institute of Cell Biology, Manitoba, Canada

WAYNE R SPRINGER• VA San Diego Healthcare System, CA

CHRISTOPHER M STARR• Glyko Inc., Novato, CA

KATHRYN L STONE• Yale Cancer Center Mass Spectrometry Resource and W M Keck Foundation Biotechnology Resource Laboratory, New Haven, CT

RICHARD A W STOTT• Department of Clinical Chemistry, Doncaster Royal

Infirmary, South Yorkshire, UK

LENNART SVENSSON• Department of Virology, Swedish Institute For Infectious Disease Control, Sweden

PATRICIA J SWEENEY• School of Natural Sciences, Hatfield Polytechnic, University

of Hertfordshire, UK

DAN S TAWFIK• Department of Biological Chemistry, the Weizman Institute

of Science, Rehovot, Israel

JOSEPH THALHAMER• Institute of Chemistry and Biochemistry, Immunology Group, University of Salzburg, Austria

JAMES R THAYER• Dionex Corporation, Life Science Research Group, Sunnyvale, CA

GEORGE C THORNWALL• LECB/NCI-FCRDC, Frederick, MD

ROBIN THORPE• Division of Immunobiology, National Institute for Biological

Standards and Control, Potters Bar, UK

TSUTOMU TSUJI• Hoshi Pharmaceutical College, Tokyo, Japan

ROCKY S TUAN• Department of Orthopaedic Surgery, Thomas Jefferson University Philadelphia, PA

Trang 22

JEREMY E TURNBULL• School of Biosciences, University of Birmingham, UK

GRAHAM A TURNER• Department of Clinical Biochemistry, The Medical School, University of Newcastle, New Castle upon Tyne, UK

MUSTAFAÜNLÜ• Millennium Pharmaceuticals, Cambridge, MA

ANTONIO VERDOLIVA• Biopharmaceuticals, Tecnogen SCPA, Parco Scientifico, Piana

YOSHINAO WADA• Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan

CHARLES J WAECHTER• Department of Biochemistry, University of Kentucky,

JOHN M WALKER•Department of Biosciences, University of Hertfordshire, School

of Natural Sciences, Hatfield, UK

MALCOLM WARD•Proteome Sciences plc, Kings College, London, UK

JAKOB H WATERBORG• Cell Biology & Biophysics, University

of Missouri-Kansas City, Kansas City, MO

DARIN J WEBER• Department of Biochemistry and Biophysics, Oregon State

University, Corvallis, OR

MICHAEL WEITZHANDLER• Dionex Corporation, Life Science Research Group, Sunnyvale, CA

MARTIN WELSCHOF• Axaron Bioscience AG, Heidelberg, Germany

MATTHIAS WILM• Department of Biochemistry and Molecular Biology, Odense University, Denmark

JOHN F K WILSHIRE• CSIRO Division of Biomolecular Engineering, Victoria, Australia

G BRIAN WISDOM• School of Biology and Biochemistry, The Queen’s University, Medical Biology Centre, Belfast, UK

GARY E WISE• Department of Anatomy & Cell Biology, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA

KENNETH R WILLIAMS• Yale Cancer Center Mass Spectrometry Resource and W M Keck Foundation Biotechnology Resource Laboratory, New Haven, CT

NICKY K C WONG• Department of Biochemistry, University of Hong Kong,

Pokfulam, Hong Kong

KAZUO YAMAMOTO• Department of Integrated Biosciences, Graduate School

of Frontier Sciences, University of Tokyo, Japan

GYURNG-SOO YOO• College of Pharmacy, Chonnam National University,

Kwangju, Korea

WENDY W YOU• Department of Biochemistry and Biophysics, Oregon State

University, Corvallis, OR

Trang 23

UV Absorption 1

P ART I

QUANTITATION OF PROTEINS

Trang 24

UV Absorption 3

1

3

Protein Determination by UV Absorption

Alastair Aitken and Michèle P Learmonth

1 Introduction

1.1 Near UV Absorbance (280 nm)

Quantitation of the amount of protein in a solution is possible in a simple eter Absorption of radiation in the near UV by proteins depends on the Tyr and Trpcontent (and to a very small extent on the amount of Phe and disulfide bonds) There-

spectrom-fore the A280 varies greatly between different proteins (for a 1 mg/mL solution, from 0

up to 4 [for some tyrosine-rich wool proteins], although most values are in the

range 0.5–1.5 [1]) The advantages of this method are that it is simple, and the sample

is recoverable The method has some disadvantages, including interference from otherchromophores, and the specific absorption value for a given protein must be deter-mined The extinction of nucleic acid in the 280-nm region may be as much as 10 timesthat of protein at their same wavelength, and hence, a few percent of nucleic acid cangreatly influence the absorption

1.2 Far UV Absorbance

The peptide bond absorbs strongly in the far UV with a maximum at about 190 nm.This very strong absorption of proteins at these wavelengths has been used in proteindetermination Because of the difficulties caused by absorption by oxygen and the lowoutput of conventional spectrophotometers at this wavelength, measurements are moreconveniently made at 205 nm, where the absorbance is about half that at 190 nm Mostproteins have extinction coefficients at 205 nm for a 1 mg/mL solution of 30–35 and

between 20 and 24 at 210 nm (2).

Various side chains, including those of Trp, Phe, Tyr, His, Cys, Met, and Arg (in

that descending order), make contributions to the A205(3).

The advantages of this method include simplicity and sensitivity As in the method

outlined in Subheading 3.1 the sample is recoverable and in addition there is little

variation in response between different proteins, permitting near-absolute tion of protein Disadvantages of this method include the necessity for accurate calibra-tion of the spectrophotometer in the far UV Many buffers and other components, such

determina-as heme or pyridoxal groups, absorb strongly in this region

From: The Protein Protocols Handbook, 2nd Edition Edited by: J M Walker © Humana Press Inc., Totowa, NJ

Trang 25

4 Aitken and Learmonth

2 Materials

1 0.1 M K2SO4 (pH 7.0)

2 5 mM potassium phosphate buffer, pH 7.0.

3 Nonionic detergent (0.01% Brij 35)

4 Guanidinium-HCl

5 0.2-µm Millipore (Watford, UK) filter

6 UV-visible spectrometer: The hydrogen lamp should be selected for maximum intensity

at the particular wavelength

7 Cuvets, quartz, for <215 nm

3 Methods

3.1 Estimation of Protein by Near UV Absorbance (280 nm)

1 A reliable spectrophotometer is necessary The protein solution must be diluted in the

buffer to a concentration that is well within the accurate range of the instrument (see

4 The value obtained will depend on the path length of the cuvet If not 1 cm, it must beadjusted by the appropriate factor The Beer-Lambert law states that:

whereε = extinction coefficient, c = concentration in mol/L and l = optical path length in

cm Therefore, if ε is known, measurement of A gives the concentration directly, ε isnormally quoted for a 1-cm path length

5 The actual value of UV absorbance for a given protein must be determined by some lute method, e.g., calculated from the amino acid composition, which can be determined

abso-by amino acid analysis (4) The UV absorbance for a protein is then calculated according

to the following formula:

A280 (1 mg/mL) = (5690nw + 1280ny + 120nc)/M (2)

where nw, ny, and nc are the numbers of Trp, Tyr, and Cys residues in the polypeptide of

mass M and 5690, 1280 and 120 are the respective extinction coefficients for these

resi-dues (see Note 5).

3.2 Estimation of Protein by Far UV Absorbance

1 The protein solution is diluted with a sodium chloride solution (0.9% w/v) until the

absor-bance at 215 nm is <1.5 (see Notes 1 and 6).

2 Alternatively, dilute the sample in another non-UV-absorbing buffer such as 0.1 M K2SO4,

containing 5 mM potassium phosphate buffer adjusted to pH 7.0 (see Note 6).

3 Measure the absorbances at the appropriate wavelengths (either A280 and A205, or A225 and

A215, depending on the formula to be applied), using a spectrometer fitted with a hydrogenlamp that is accurate at these wavelengths, using quartz cuvets filled with a volume ofsolution sufficient to cover the aperture through which the light beam passes (details in

Subheading 3.1.).

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UV Absorption 5

4 The A205 for a 1 mg/mL solution of protein (A2051 mg/mL) can be calculated within ±2%,

according to the empirical formula proposed by Scopes (2) (see Notes 7–10):

A2051 mg/mL = 27 + 120 (A280/A205) (3)

5 Alternatively, measurements may be made at longer wavelengths (5):

Protein concentration (µg/mL) = 144 (A215– A225) (4)The extinction at 225 nm is subtracted from that at 215 nm; the difference multiplied by

144 gives the protein concentration in the sample in µg/mL With a particular protein underspecific conditions accurate measurements of concentration to within 5 µg/L are possible

4 Notes

1 It is best to measure absorbances in the range 0.05–1.0 (between 10 and 90% of the dent radiation) At around 0.3 absorbance (50% absorption), the accuracy is greatest

inci-2 Bovine serum albumin is frequently used as a protein standard; 1 mg/mL has an A280 of 0.66

3 If the solution is turbid, the apparent A280 will be increased by light scattering Filtration(through a 0.2-µm Millipore filter) or clarification of the solution by centrifugation can becarried out For turbid solutions, a convenient approximate correction can be applied by

subtracting the A310 (proteins do not normally absorb at this wavelength unless they

con-tain particular chromophores) from the A280

4 At low concentrations, protein can be lost from solution by adsorption on the cuvet; thehigh ionic strength helps to prevent this Inclusion of a nonionic detergent (0.01% Brij 35)

in the buffer may also help to prevent these losses

5 The presence of nonprotein chromophores (e.g., heme, pyridoxal) can increase A280 Ifnucleic acids are present (which absorb strongly at 260 nm), the following formula can beapplied This gives an accurate estimate of the protein content by removing the contribu-

tion to absorbance by nucleotides at 280 nm, by measuring the A260 which is largely owing

to the latter (6).

Protein (mg/mL) = 1.55 A280– 0.76 A260 (5)Other formulae (using similar principles of absorbance differences) employed to deter-

mine protein in the possible presence of nucleic acids are the following (7,8):

Protein (mg/mL) = (A235– A280)/2.51 (6)

Protein (mg/mL) = 0.183 A230– 0.075.8 A260 (7)

6 Protein solutions obey Beer-Lambert’s Law at 215 nm provided the absorbance is <2.0

7 Strictly speaking, this value applies to the protein in 6 M guanidinium-HCl, but the value

in buffer is generally within 10% of this value, and the relative absorbances in dinium-HCl and buffer can be easily determined by parallel dilutions from a stock solution

guani-8 Sodium chloride, ammonium sulfate, borate, phosphate, and Tris do not interfere, whereas

0.1 M acetate, succinate, citrate, phthalate, and barbiturate show high absorption at 215 nm.

9 The absorption of proteins in the range 215–225 nm is practically independent of pHbetween pH values 4–8

10 The specific extinction coefficient of a number of proteins and peptides at 205 nm and

210 nm (3) has been determined The average extinction coefficient for a 1 mg/mL

solu-tion of 40 serum proteins at 210 nm is 20.5 ± 0.14 At this wavelength, a protein tration of 2 µg/mL gives A = 0.04 (5).

Trang 27

concen-6 Aitken and Learmonth

References

1 Kirschenbaum, D M (1975) Molar absorptivity and A1%/1 cm values for proteins at

selected wavelengths of the ultraviolet and visible regions Analyt Biochem 68, 465–484.

2 Scopes, R K (1974) Measurement of protein by spectrometry at 205 nm Analyt Biochem.

59, 277–282.

3 Goldfarb, A R., Saidel, L J., and Mosovich, E (1951) The ultraviolet absorption spectra

of proteins J Biol Chem 193, 397–404.

4 Gill, S C and von Hippel, P H (1989) Calculation of protein extinction coefficients from

amino acid sequence data Analyt Biochem 182, 319–326.

5 Waddell, W J (1956) A simple UV spectrophotometric method for the determination of

protein J Lab Clin Med 48, 311–314.

6 Layne, E (1957) Spectrophotornetric and turbidimetric methods for measuring proteins

Meth Enzymol 3, 447–454.

7 Whitaker, J R and Granum, P E (1980) An absolute method for protein determination

based on difference in absorbance at 235 and 280 nm Analyt Biochem 109, 156–159.

8 Kalb, V F and Bernlohr, R W (1977) A new spectrophotometric assay for protein in cell

extracts Analyt Biochem 82, 362–371.

Trang 28

The Lowry Method 7

(1) The procedure of Lowry et al (2) is no exception, but its sensitivity is moderately

constant from protein to protein, and it has been so widely used that Lowry proteinestimations are a completely acceptable alternative to a rigorous absolute determina-tion in almost all circumstances in which protein mixtures or crude extracts areinvolved

The method is based on both the Biuret reaction, in which the peptide bonds ofproteins react with copper under alkaline conditions to produce Cu+, which reacts withthe Folin reagent, and the Folin–Ciocalteau reaction, which is poorly understood but inessence phosphomolybdotungstate is reduced to heteropolymolybdenum blue by thecopper-catalyzed oxidation of aromatic amino acids The reactions result in a strongblue color, which depends partly on the tyrosine and tryptophan content The method issensitive down to about 0.01 mg of protein/mL, and is best used on solutions withconcentrations in the range 0.01–1.0 mg/mL of protein

2 Materials

1 Complex-forming reagent: Prepare immediately before use by mixing the following stocksolutions in the proportion 100:1:1 (by vol), respectively:

Solution A: 2% (w/v) Na2CO3 in distilled water

Solution B: 1% (w/v) CuSO4·5H2O in distilled water

Solution C: 2% (w/v) sodium potassium tartrate in distilled water

2 2 N NaOH.

3 Folin reagent (commercially available): Use at 1 N concentration.

4 Standards: Use a stock solution of standard protein (e.g., bovine serum albumin fraction V)containing 2 mg/mL protein in distilled water, stored frozen at –20°C Prepare standards

by diluting the stock solution with distilled water as follows:

Stock solution (µL) 0 2.5 5 12.5 25 50 125 250 500

Trang 29

8 Waterborg

3 Method

1 To 0.1 mL of sample or standard (see Notes 1–4), add 0.1 mL of 2 N NaOH Hydrolyze at

100°C for 10 min in a heating block or boiling water bath

2 Cool the hydrolysate to room temperature and add 1 mL of freshly mixed

complex-form-ing reagent Let the solution stand at room temperature for 10 min (see Notes 5 and 6).

3 Add 0.1 mL of Folin reagent, using a vortex mixer, and let the mixture stand at room

temperature for 30–60 min (do not exceed 60 min) (see Note 7).

4 Read the absorbance at 750 nm if the protein concentration was below 500 µg/mL or at

550 nm if the protein concentration was between 100 and 2000 µg/mL

5 Plot a standard curve of absorbance as a function of initial protein concentration and use it

to determine the unknown protein concentrations (see Notes 8–13).

4 Notes

1 If the sample is available as a precipitate, then dissolve the precipitate in 2 N NaOH and

hydrolyze as described in Subheading 3, step 1 Carry 0.2-mL aliquots of the hydrolyzate forward to Subheading 3, step 2.

2 Whole cells or other complex samples may need pretreatment, as described for the Burton

assay for DNA (3) For example, the perchloroacetic acid (PCA)/ethanol precipitate from

extraction I may be used directly for the Lowry assay, or the pellets remaining after the

PCA hydrolysis step (Subheading 3, step 3 of the Burton assay) may be used for Lowry.

In this latter case, both DNA and protein concentration may be obtained from the samesample

3 Peterson (4) has described a precipitation step that allows the separation of the protein

sample from interfering substances and also consequently concentrates the protein sample,allowing the determination of proteins in dilute solution Peterson’s precipitation step is

as follows:

a Add 0.1 mL of 0.15% deoxycholate to 1.0 mL of protein sample

b Vortex-mix, and stand at room temperature for 10 min

c Add 0.1 mL of 72% trichloroacetic acid (TCA), vortex-mix, and centrifuge at 1000–

3000g for 30 min.

d Decant the supernatant and treat the pellet as described in Note 1.

4 Detergents such as sodium dodecyl sulfate (SDS) are often present in protein

prepara-tions, added to solubilize membranes or remove interfering substances (5–7) Protein cipitation by TCA may require phosphotungstic acid (PTA) (6) for complete protein

pre-recovery:

a Add 0.2 mL of 30% (w/v) TCA and 6% (w/v) PTA to 1.0 mL of protein sample

b Vortex-mix, and stand at room temperature for 20 min

c Centrifuge at 2000g and 4°C for 30 min

d Decant the supernatant completely and treat the pellet as described in Note 1.

5 The reaction is very pH dependent, and it is therefore important to maintain the pH between

10 and 10.5 Therefore, take care when analyzing samples that are in strong buffer outsidethis range

6 The incubation period is not critical and can vary from 10 min to several hours withoutaffecting the final absorbance

7 The vortex-mixing step is critical for obtaining reproducible results The Folin reagent isreactive only for a short time under these alkaline conditions, being unstable in alkali, andgreat care should therefore be taken to ensure thorough mixing

8 The assay is not linear at higher concentrations Ensure that you are analyzing your sample

on the linear portion of the calibration curve

Trang 30

The Lowry Method 9

9 A set of standards is needed with each group of assays, preferably in duplicate Duplicate

or triplicate unknowns are recommended

10 One disadvantage of the Lowry method is the fact that a range of substances interfereswith this assay, including buffers, drugs, nucleic acids, and sugars (The effect of some ofthese agents is shown in Table 1 in Chapter 3.) In many cases, the effects of these agentscan be minimized by diluting them out, assuming that the protein concentration is suffi-ciently high to still be detected after dilution When interfering compounds are involved,

it is, of course, important to run an appropriate blank Interference caused by detergents,

sucrose, and EDTA can be eliminated by the addition of SDS (5) and a precipitation step (see Note 4).

11 Modifications to this basic assay have been reported that increase the sensitivity of thereaction If the Folin reagent is added in two portions, vortex-mixing between each addi-

tion, a 20% increase in sensitivity is achieved (8) The addition of dithiothreitol 3 min after the addition of the Folin reagent increases the sensitivity by 50% (9).

12 The amount of color produced in this assay by any given protein (or mixture of proteins)

is dependent on the amino acid composition of the protein(s) (see Introduction)

There-fore, two different proteins, each for example at concentrations of 1 mg/mL, can givedifferent color yields in this assay It must be appreciated, therefore, that using bovineserum albumin (BSA) (or any other protein for that matter) as a standard gives only anapproximate measure of the protein concentration The only time when this method gives

an absolute value for protein concentration is when the protein being analyzed is also used

to construct the standard curve The most accurate way to determine the concentration ofany protein solution is amino acid analysis

13 A means of speeding up this assay using raised temperatures (10) or a microwave oven

(see Chapter 5) has been described.

References

1 Sapan, C V., Lundblad, R L., and Price, N C (1999) Colorimetric protein assay

tech-niques Biotechnol Appl Biochem 29, 99–108.

2 Lowry, O H., Rosebrough, N J., Farr, A L., and Randall, R J (1951) Protein

measure-ment with the Folin phenol reagent J Biol Chem 193, 265–275.

3 Waterborg, J H and Matthews, H R (1984) The Burton assay for DNA, in Methods in Molecular Biology, Vol 2: Nucleic Acids (Walker, J M., ed.), Humana Press, Totowa, NJ,

pp 1–3

4 Peterson, G L (1983) Determination of total protein Methods Enzymol 91, 95–121.

5 Markwell, M.A.K., Haas, S M., Tolbert, N E., and Bieber, L L (1981) Protein

determi-nation in membrane and lipoprotein samples Methods Enzymol 72, 296–303.

6 Yeang, H Y., Yusof, F., and Abdullah, L (1998) Protein purification for the Lowry assay:acid precipitation of proteins in the presence of sodium dodecyl sulfate and other biologi-

cal detergents Analyt Biochem 265, 381–384.

7 Chang, Y C (1992) Efficient precipitation and accurate quantitation of

detergent-solubi-lized membrane proteins Analyt Biochem 205, 22–26.

8 Hess, H H., Lees, M B., and Derr, J E (1978) A linear Lowry-Folin assay for both

water-soluble and sodium dodecyl sulfate-solubilized proteins Analyt Biochem 85, 295–300.

9 Larson, E., Howlett, B., and Jagendorf, A (1986) Artificial reductant enhancement of the

Lowry method for protein determination Analyt Biochem 155, 243–248.

10 Shakir, F K., Audilet, D., Drake, A J., and Shakir, K M (1994) A rapid protein

determi-nation by modification of the Lowry procedure Analyt Biochem 216, 232–233.

Trang 31

BCA for Protein Quantitation 11

11

3

The Bicinchoninic Acid (BCA) Assay

for Protein Quantitation

John M Walker

1 Introduction

The bicinchoninic acid (BCA) assay, first described by Smith et al (1) is similar to

the Lowry assay, since it also depends on the conversion of Cu2+ to Cu+ under alkaline

conditions (see Chapter 2) The Cu+ is then detected by reaction with BCA The twoassays are of similar sensitivity, but since BCA is stable under alkali conditions, thisassay has the advantage that it can be carried out as a one-step process compared to thetwo steps needed in the Lowry assay The reaction results in the development of anintense purple color with an absorbance maximum at 562 nm Since the production of

Cu+ in this assay is a function of protein concentration and incubation time, the proteincontent of unknown samples may be determined spectrophotometrically by compari-son with known protein standards A further advantage of the BCA assay is that it isgenerally more tolerant to the presence of compounds that interfere with the Lowryassay In particular it is not affected by a range of detergents and denaturing agentssuch as urea and guanidinium chloride, although it is more sensitive to the presence ofreducing sugars Both a standard assay (0.1–1.0 mg protein/mL) and a microassay(0.5–10µg protein/mL) are described

2 Materials

2.1 Standard Assay

1 Reagent A: sodium bicinchoninate (0.1 g), Na2CO3· H2O (2.0 g), sodium tartrate drate) (0.16 g), NaOH (0.4 g), NaHCO3 (0.95 g), made up to 100 mL If necessary, adjustthe pH to 11.25 with NaHCO3 or NaOH (see Note 1).

(dihy-2 Reagent B: CuSO4· 5H2O (0.4 g) in 10 mL of water (see Note 1).

3 Standard working reagent (SWR): Mix 100 vol of regent A with 2 vol of reagent B Thesolution is apple green in color and is stable at room temperature for 1 wk

2.2 Microassay

1 Reagent A: Na2CO3· H2O (0.8 g), NaOH (1.6 g), sodium tartrate (dihydrate) (1.6 g), made

up to 100 mL with water, and adjusted to pH 11.25 with 10 M NaOH.

2 Reagent B: BCA (4.0 g) in 100 mL of water

3 Reagent C: CuSO4· 5H2O (0.4 g) in 10 mL of water

Trang 32

1 To a 100-µL aqueous sample containing 10–100µg protein, add 2 mL of SWR Incubate

at 60°C for 30 min (see Note 2).

2 Cool the sample to room temperature, then measure the absorbance at 562 nm (see Note 3).

3 A calibration curve can be constructed using dilutions of a stock 1 mg/mL solution of

bovine serum albumin (BSA) (see Note 4).

Alterna-3 Following the heating step, the color developed is stable for at least 1 h

4 Note, that like the Lowry assay, response to the BCA assay is dependent on the amino acidcomposition of the protein, and therefore an absolute concentration of protein cannot bedetermined The BSA standard curve can only therefore be used to compare the relativeprotein concentration of similar protein solutions

5 Some reagents interfere with the BCA assay, but nothing like as many as with the Lowry

assay (see Table 1) The presence of lipids gives excessively high absorbances with this assay (2) Variations produced by buffers with sulfhydryl agents and detergents have been described (3).

6 Since the method relies on the use of Cu2+, the presence of chelating agents such as EDTAwill of course severely interfere with the method However, it may be possible to over-come such problems by diluting the sample as long as the protein concentration remainssufficiently high to be measurable Similarly, dilution may be a way of coping with any

agent that interferes with the assay (see Table 1) In each case it is of course necesary to

run an appropriate control sample to allow for any residual color development A cation of the assay has been described that overcomes lipid interference when measuring

modifi-lipoprotein protein content (4).

7 A modification of the BCA assay, utilizing a microwave oven, has been described that

allows protein determination in a matter of seconds (see Chapter 5).

8 A method has been described for eliminating interfering compounds such as thiols andreducing sugars in this assay Proteins are bound to nylon membranes and exhaustivelywashed to remove interfering compounds; then the BCA assay is carried out on the mem-

brane-bound protein (5).

Trang 33

BCA for Protein Quantitation 13

Table 1

Effect of Selected Potential Interfering Compounds a

BCA assay Lowry assay (µg BSA found) (µg BSA found)Water Interference Water InterferenceSample (50 µg BSA) blank blank blank blank

in the following corrected corrected corrected corrected

50µg BSA in water (reference) 50.00 — 50.00 —

0.2% Sodium azide 51.10 50.90 49.20 49.000.02% Sodium azide 51.10 51.00 49.50 49.60

10.0% Ammonium sulfate 16.00 12.00 Precipitated

3.0% Ammonium sulfate 44.90 42.00 21.20 21.4010.0% Ammonium sulfate, pH 11 48.10 45.20 32.60 32.80

2.0 M Sodium acetate, pH 5.5 35.50 34.50 5.40 3.30

0.2 M Sodium acetate, pH 5.5 50.80 50.40 47.50 47.60

1.0 M Sodium phosphate 37.10 36.20 7.30 5.30

0.1 M Sodium phosphate 50.80 50.40 46.60 46.60

0.1 M Cesium bicarbonate 49.50 49.70 Precipitated

a Reproduced from ref 1 with permission from Academic Press Inc.

Trang 34

14 Walker

9 A comparison of the BCA, Lowry and Bradford assays for analyzing gylcosylated and

non-glycosylated proteins have been made (6) Significant differences wee observed

between the assays for non-glycosylated proteins with the BCA assay giving results est to those from amino acid analysis Glycosylated proteins were underestimated by theBradford the method and overestimated by the BCA and Lowry methods The resultssuggest a potential interference of protein glycosylation with colorimetric assays

clos-10 A modification of this assay for analysis complex samples, which involves removing

con-taminants from the protein precipitate with 1 M HCl has been reported (7).

References

1 Smith, P K., Krohn, R I., Hermanson, G T., Mallia, A K., Gartner, F H., Provenzano,

M D., Fujimoto, E K., Goeke, N M., Olson, B J., and Klenk, D C (1985) Measurement

of protein using bicinchoninic acid Analyt Biochem 150, 76–85.

2 Kessler, R J and Fanestil, D D (1986) Interference by lipids in the determination of

protein using bicinchoninic acid Analyt Biochem 159, 138–142.

3 Hill, H D and Straka, J G (1988) Protein determination using bicinchoninic acid in the

presence of sulfhydryl reagents Analyt Biochem 170, 203–208.

4 Morton, R E and Evans, T A (1992) Modification of the BCA protein assay to

elimi-nate lipid interference in determining lipoprotein protein content Analyt Biochem 204,

332–334

5 Gates, R E (1991) Elimination of interfering substances in the presence of detergent in

the bicinchoninic acid protein assay Analyt Biochem 196, 290–295.

6 Fountoulakis, M., Juranville, J F., and Manneberg, M (1992) Comparison of the coomassiebrilliant blue, bicinchoninic acid and lowry quantitation assays, using nonglycosylated and

glycosylated proteins J Biochem Biophys Meth 24, 265–274.

7 Schoel, B., Welzel, M., and Kaufmann, S H E (1995) Quantification of protein in dilute

and complex samples–modification of the bicinchoninic acid assay J Biochem Biophys.

Meth 30, 199–206.

Trang 35

The Bradford Method 15

A rapid and accurate method for the estimation of protein concentration is essential

in many fields of protein study An assay originally described by Bradford (1) has

become the preferred method for quantifying protein in many laboratories This nique is simpler, faster, and more sensitive than the Lowry method Moreover, whencompared with the Lowry method, it is subject to less interference by common rea-

tech-gents and nonprotein components of biological samples (see Note 1).

The Bradford assay relies on the binding of the dye Coomassie Blue G250 to tein Detailed studies indicate that the free dye can exist in four different ionic formsfor which the pKa values are 1.15, 1.82, and 12.4 (2) Of the three charged forms of the

pro-dye that predominate in the acidic assay reagent solution, the more cationic red andgreen forms have absorbance maxima at 470 nm and 650 nm, respectively In contrast,the more anionic blue form of the dye, which binds to protein, has an absorbance maxi-mum at 590 nm Thus, the quantity of protein can be estimated by determining theamount of dye in the blue ionic form This is usually achieved by measuring the absor-

bance of the solution at 595 nm (see Note 2).

The dye appears to bind most readily to arginyl and lysyl residues of proteins (3,4).

This specificity can lead to variation in the response of the assay to different proteins,

which is the main drawback of the method (see Note 3) The original Bradford assay shows large variation in response between different proteins (5–7) Several modifications to the method have been developed to overcome this problem (see Note 4) How-

ever, these changes generally result in a less robust assay that is often more susceptible

to interference by other chemicals Consequently, the original method devised byBradford remains the most convenient and widely used formulation Two types of assayare described here: the standard assay, which is suitable for measuring between 10 and

100µg of protein, and the microassay, which detects between 1 and 10 µg of protein.The latter, although more sensitive, is also more prone to interference from other com-pounds because of the greater amount of sample relative to dye reagent in this form ofthe assay

Trang 36

16 Kruger

2 Materials

1 Reagent: The assay reagent is made by dissolving 100 mg of Coomassie Blue G250 in

50 mL of 95% ethanol The solution is then mixed with 100 mL of 85% phosphoric acid

and made up to 1 L with distilled water (see Note 5).

The reagent should be filtered through Whatman no 1 filter paper and then stored in anamber bottle at room temperature It is stable for several weeks However, during this timedye may precipitate from solution and so the stored reagent should be filtered before use

2 Protein standard (see Note 6) Bovine γ-globulin at a concentration of 1 mg/mL(100µg/mL for the microassay) in distilled water is used as a stock solution This should

be stored frozen at –20oC Since the moisture content of solid protein may vary duringstorage, the precise concentration of protein in the standard solution should be determinedfrom its absorbance at 280 nm The absorbance of a 1 mg/mL solution of γ-globulin, in a1-cm light path, is 1.35 The corresponding values for two alternative protein standards,bovine serum albumin and ovalbumin, are 0.66 and 0.75, respectively

3 Plastic and glassware used in the assay should be absolutely clean and detergent free.Quartz (silica) spectrophotometer cuvettes should not be used, as the dye binds to thismaterial Traces of dye bound to glassware or plastic can be removed by rinsing withmethanol or detergent solution

3 Methods

3.1 Standard Assay Method

1 Pipet between 10 and 100 µg of protein in 100 µL total volume into a test tube If theapproximate sample concentration is unknown, assay a range of dilutions (1, 1:10, 1:100,1:1000) Prepare duplicates of each sample

2 For the calibration curve, pipet duplicate volumes of 10, 20, 40, 60, 80, and 100 µL of

1 mg/mL γ-globulin standard solution into test tubes, and make each up to 100 µL withdistilled water Pipet 100 µL of distilled water into a further tube to provide the reagentblank

3 Add 5 mL of protein reagent to each tube and mix well by inversion or gentle mixing Avoid foaming, which will lead to poor reproducibility

vortex-4 Measure the A595 of the samples and standards against the reagent blank between 2 min

and 1 h after mixing (see Note 7) The 100 µg standard should give an A595 value of about0.4 The standard curve is not linear, and the precise absorbance varies depending on theage of the assay reagent Consequently, it is essential to construct a calibration curve for

each set of assays (see Note 8).

3.2 Microassay Method

This form of the assay is more sensitive to protein Consequently, it is useful when

the amount of the unknown protein is limited (see also Note 9).

1 Pipet duplicate samples containing between 1 and 10 µg in a total volume of 100 µL into1.5-mL polyethylene microfuge tubes If the approximate sample concentration isunknown, assay a range of dilutions (1, 1:10, 1:100, 1:1000)

2 For the calibration curve, pipet duplicate volumes of 10, 20, 40, 60, 80, and 100 µL of

100µg/mL γ-globulin standard solution into microfuge tubes, and adjust the volume to

100µL with water Pipet 100 µL of distilled water into a tube for the reagent blank

3 Add 1 mL of protein reagent to each tube and mix gently, but thoroughly

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4 Measure the absorbance of each sample between 2 and 60 min after addition of the protein

reagent The A595 value of a sample containing 10 µgγ-globulin is 0.45 Figure 1 shows

the response of three common protein standards using the microassay method

4 Notes

1 The Bradford assay is relatively free from interference by most commonly used cal reagents However, a few chemicals may significantly alter the absorbance of the rea-

biochemi-gent blank or modify the response of proteins to the dye (Table 1) The materials that are

most likely to cause problems in biological extracts are detergents and ampholytes (3,8).

These can be removed from the sample solution by gel filtration, dialysis, or precipitation

of protein with calcium phosphate (9,10) Alternatively, they can be included in the

rea-gent blank and calibration standards at the same concentration as that found in the sample.The presence of base in the assay increases absorbance by shifting the equilibrium of thefree dye toward the anionic form This may present problems when measuring protein

content in concentrated basic buffers (3) Guanidine hydrochloride and sodium ascorbate compete with dye for protein, leading to underestimation of the protein content (3).

2 Binding of protein to Coomassie Blue G250 may shift the absorbance maximum of the

blue ionic form of the dye from 590 nm to 620 nm (2) It might, therefore, appear more

sensible to measure the absorbance at the higher wavelength However, at the usual pH ofthe assay, an appreciable proportion of the dye is in the green form (λmax= 650 nm) whichinterferes with absorbance measurement of the dye–protein complex at 620 nm Measure-ment at 595 nm represents the best compromise between maximizing the absorbence due

to the dye–protein complex while minimizing that due to the green form of the free dye (2–4; but see also Note 9).

Fig 1 Variation in the response of proteins in the Bradford assay The extent of protein–dyecomplex formation was determined for bovine serum albumin (䊏),γ-globulin (䊉), and ovalbu-

min (䉱) using the microassay Each value is the mean of four determinations For each set of

measurements the standard error was <5% of the mean value The data allow comparisons to bemade between estimates of protein content obtained using these protein standards

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18 Kruger

3 The dye does not bind to free arginine or lysine, or to peptides smaller than about 3000 Da

(4,11) Many peptide hormones and other important bioactive peptides fall into the latter

cat-egory, and the Bradford assay is not suitable for quantifying the amounts of such compounds

4 The assay technique described here is subject to variation in sensitivity between

indi-vidual proteins (see Table 2) Several modifications have been suggested that reduce this variability (5–7,12) Generally, these rely on increasing either the dye content or the pH of

the solution In one variation, adjusting the pH by adding NaOH to the reagent improvesthe sensitivity of the assay and greatly reduces the variation observed with different pro-

teins (7) (This is presumably caused by an increase the proportion of free dye in the blue

form, the ionic species that reacts with protein.) However, the optimum pH is critically

dependent on the source and concentration of the dye (see Note 5) Moreover, the

modi-fied assay is far more sensitive to interference from detergents in the sample

Particular care should be taken when measuring the protein content of membrane tions The conventional assay consistently underestimates the amount of protein in mem-brane-rich samples Pretreatment of the samples with membrane-disrupting agents such

frac-as NaOH or detergents may reduce this problem, but the results should be treated with

caution (13) A useful alternative is to precipitate protein from the sample using calcium phosphate and remove contaminating lipids (and other interfering substances, see Note 1)

by washing with 80% ethanol (9,10).

5 The amount of soluble dye in Coomassie Blue G250 varies considerably between sources,and suppliers’ figures for dye purity are not a reliable estimate of the Coomassie Blue

G250 content (14) Generally, Serva Blue G is regarded to have the greatest dye content

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and should be used in the modified assays discussed in Note 4 However, the quality of the

dye is not critical for routine protein determination using the method described in this

chapter The data presented in Fig 1 were obtained using Coomassie Brilliant Blue G

(C.I 42655; product code B-0770, Sigma-Aldrich)

6 Whenever possible the protein used to construct the calibration curve should be the same

as that being determined Often this is impractical and the dye response of a sample isquantified relative to that of a “generic” protein Bovine serum albumin (BSA) is com-monly used as the protein standard because it is inexpensive and readily available in apure form The major argument for using this protein is that it allows the results to becompared directly with those of the many previous studies that have used bovine serumalbumin as a standard However, it suffers from the disadvantage of exhibiting an unusu-ally large dye response in the Bradford assay, and thus, may underestimate the proteincontent of a sample Increasingly, bovine γ-globulin is being promoted as a more suitablegeneral standard, as the dye binding capacity of this protein is closer to the mean of those

proteins that have been compared (Table 2) Because of the variation in response between

different proteins, it is essential to specify the protein standard used when reporting surements of protein amounts using the Bradford assay

mea-7 Generally, it is preferable to use a single new disposable polystyrene semimicrocuvettethat is discarded after a series of absorbance measurements Rinse the cuvette with reagentbefore use, zero the spectrophotometer on the reagent blank and then do not remove thecuvette from the machine Replace the sample in the cuvette gently using a disposablepolyethylene pipet

Table 2

Comparison of the Response of Different Proteins in

the Bradford Assay

Relative absorbance

For each protein, the response is expressed relative to that of the same

concentration of BSA The data for assays 1 and 2 are recalculated from

refs 5 and 7, respectively.

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20 Kruger

8 The standard curve is nonlinear because of problems introduced by depletion of the amount

of free dye These problems can be avoided, and the linearity of the assay improved, by

plotting the ratio of absorbances at 595 and 450 nm (15) If this approach is adopted, the

absolute optical density of the free dye and dye–protein complex must be determined bymeasuring the absorbance of the mixture at each wavelength relative to that of a cuvettecontaining only water (and no dye reagent) As well as improving the linearity of thecalibration curve, taking the ratio of the absorbances at the two wavelengths increases the

accuracy and improves the sensitivity of the assay by up to 10-fold (15).

9 For routine measurement of the protein content of many samples the microassay may be

adapted for use with a microplate reader (7,16) The total volume of the modified assay is

limited to 210 µL by reducing the volume of each component Ensure effective mixing of theassay components by pipetting up to 10 µL of the protein sample into each well before adding

200µL of the dye reagent If a wavelength of 595 nm cannot be selected on the microplatereader, absorbance may be measured at any wavelength between 570 nm and 610 nm How-ever, absorbance measurements at wavelengths other than 595 nm will decrease the sensitiv-ity of response and may increase the minimum detection limit of the protocol

10 For studies on the use of the Bradford assay in analyzing glycoproteins, see Note 9 in

Chapter 3

References

1 Bradford, M M (1976) A rapid and sensitive method for the quantitation of microgram

quantities of protein utilizing the principle of protein-dye binding Analyt Biochem 72,

248–254

2 Chial, H J., Thompson, H B., and Splittgerber, A G (1993) A spectral study of the charge

forms of Coomassie Blue G Analyt Biochem 209, 258–266.

3 Compton, S J and Jones, C G (1985) Mechanism of dye response and interference in the

Bradford protein assay Analyt Biochem 151, 369–374.

4 Congdon, R W., Muth, G W., and Splittgerber, A G (1993) The binding interaction of

Coomassie Blue with proteins Analyt Biochem 213, 407–413.

5 Friendenauer, S and Berlet, H H (1989) Sensitivity and variability of the Bradford

pro-tein assay in the presence of detergents Analyt Biochem 178, 263–268.

6 Reade, S M and Northcote, D H (1981) Minimization of variation in the response to

different proteins of the Coomassie Blue G dye-binding assay for protein Analyt Biochem.

116, 53–64.

7 Stoscheck, C M (1990) Increased uniformity in the response of the Coomassie Blue

pro-tein assay to different propro-teins Analyt Biochem 184, 111–116.

8 Spector, T (1978) Refinement of the Coomassie Blue method of protein quantitation Asimple and linear spectrophotometric assay for <0.5 to 50 µg of protein Analyt Biochem.

86, 142–146.

9 Pande, S V and Murthy, M S R (1994) A modified micro-Bradford procedure for

elimi-nation of interference from sodium dodecyl sulfate, other detergents, and lipids Analyt.

Biochem 220, 424–426.

10 Zuo, S.-S and Lundahl, P (2000) A micro-Bradford membrane protein assay Analyt.

Biochem 284, 162–164.

11 Sedmak, J J and Grossberg, S E (1977) A rapid, sensitive and versatile assay for protein

using Coomassie Brilliant Blue G250 Analyt Biochem 79, 544–552.

12 Peterson, G L (1983) Coomassie blue dye binding protein quantitation method, in ods in Enzymology, vol 91 (Hirs, C H W and Timasheff, S N., eds.), Academic Press,

Meth-New York

Tiêu đề	The Protein Protocols Handbook
Tác giả	John M. Walker
Trường học	University of Hertfordshire
Chuyên ngành	Protein Chemistry
Thể loại	Handbook
Năm xuất bản	2002
Thành phố	Hatfield

Định dạng
Số trang	1.103
Dung lượng	12 MB