Peptide Analysis Protocols

Size: px

Start display at page:

Download "Peptide Analysis Protocols"

Henry Walton
5 years ago
Views:

1 Peptide Analysis Protocols

Methods in Molecular Biology John M. Walker, SERIES EDITOR 36. Peptide Analysis Protocols, edited by Ben M. Dunn and Michael W. Pennington, 1994 35. Peptide Synthesis Protocols, edited by Michael W.

2 Methods in Molecular Biology John M. Walker, SERIES EDITOR 36. Peptide Analysis Protocols, edited by Ben M. Dunn and Michael W. Pennington, Peptide Synthesis Protocols, edited by Michael W. Pennington and Ben M. Dunn, Immunocytochemical Methods and Protocols, edited by Lorette C. Javois, In Situ Hybridization Protocols, edited by K. H. Andy Choo, Basic Protein and Peptide Protocols, edited by John M. Walker, Protocols for Gene Analysis, edited by Adrian J. Harwood, DNA-Protein Interactions, edited by G. GeoffKneale, Chromosome Analysis Protocols, edited by John R. Gosden, Protocols for Nucleic Acid Analysis by Nonradioactive Probes, edited by Peter G. Isaac, Biomembrane Protocols: II. Architecture and Function, edited by John M. Graham and Joan A. Higgins, Protocols for OHgonucleotide Conjugates, edited by Sudhir Agrawal, 199~ 25. Computer Analysis of Sequence Data: Part II, edited by Annette M. Griffin and Hugh G. Griffin, Computer Analysis of Sequence Data: Part I, edited by Annette M. Griffin and Hugh G. Griffin, DNA Sequencing Protocols, edited by Hugh G. Griffin and Annette M. Griffin, Optical Spectroscopy, Microscopy, and Macroscopic Techniques, edited by Christopher Jones, Barbara Mulloy, and Adrian H. Thomas, Protocols in Molecular Parasitology, edited by John E. Hyde, Protocols for Oligonucleotides and Analogs, edited by Sudhir Agrawal, Biomembrane Protocols: I. Isolation and Analysis, edited by John M. Graham and Joan A. Higgins, Transgenesis Techniques, edited by David Murphy and David A. Carter, Spectroscopic Methods and Analyses, edited by Christopher Jones, Barbara Mulloy, and Adrian H. Thomas, Enzymes of Molecular Biology, edited by Michael M. Burrell, PCR Protocols, edited by Bruce A. White, Glycoprotein Analysis in Biomedicine, edited by Elizabeth F. Hounsell, Protocols in Molecular Neurobiology, edited by Alan Longstaff and Patricia Revest, Pulsed-Field Gel Electrophoresis, edited by Margit Burmeister and Levy Ulanovsky, Practical Protein Chromatography, edited by Andrew Kenney and Susan Fowell, Immunochemical Protocols, edited by Margaret M. Manson, Protocols in Human Molecular Genetics, edited by Christopher G. Mathew, 1991 Earlier volumes are still available, Contact Humana for details,

3 Peptide Analysis Protocols Edited by Ben M. Dunn University of Florida, Gainesville, FL and Michael W. Pennington Bachem Bioscience, King of Prussia, PA Humana Press ~ Totowa, New Jersey

4 1994 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. This publication is printed on acid-free paper. ANSI Z (American National Standards Institute) Permanence of Paper for Printed Library Materials Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Humana Press Inc., provided that the base fee of US $4.00 per copy, plus US $00.20 per page, is paid directly to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [ /94 $ $00.20]. Printed in the United States of America Library of Congress Cataloging in Publication Data Peptide analysis protocols/edited by Ben M. Dunn and Michael W. Pennington p. cm.--(methods in molecular biology; 36) Companion v. to: Peptide synthesis protocols. Includes index. ISBN (acid-free paper) 1. Peptides--Analysis--Laboratory manuals. I. Dunn, Ben M. II. Pennington, Michael W. III. Peptide synthesis protiocols. IV. Series: Methods in molecular biology (Totowa, N.J.); 36 QP552.P4P ' dc CIP

Preface As the technology base for the preparation of increasingly complex peptides has improved, the methods for their purification and analysis have also been improved and supplemented.

5 Preface As the technology base for the preparation of increasingly complex peptides has improved, the methods for their purification and analysis have also been improved and supplemented. Peptide science routinely utilizes tools and techniques that are common to organic chemistry, protein chemistry, biophysical chemistry, enzymology, pharmacology, and molecular biology. A fundamental understanding of each of these areas is essential for interpreting all of the data that a peptide scientist may see. The purpose of Peptide Analysis Protocols is to provide the novice with sufficient practical information necessary to begin developing useful analysis and separation skills. Understanding and developing these skills will ultimately yield a scientist with broadened knowledge and good problem-solving abilities. Although numerous books that address different specialties, such as HPLC, FAB-MS, CE, and NMR, have been written, until now no single volume has reviewed all of these techniques with a focus on "getting started" in separation and analysis of peptides. This volume will also provide those who already possess practical knowledge of the more advanced aspects of peptide science with detailed applications for each of these protocols. Because the chapters have been written by researchers active in each of the fields that they discuss, a great deal of information on and insight into solution of real problems that they have encountered is presented. Examplary results are clearly demonstrated and discussed. For more advanced investigations, supplementary experiments are often suggested. Additionally, Peptide Analysis Protocols contains several applications and extensions of peptide science. Thus, we include chapters on such topics as the construction of peptide libraries, recombinant peptide synthesis, immunochemical methods used for peptides, the kinetic analysis of proteases using peptide substrates, and de novo protein design and synthesis. These represent state-of-the-art technologies and

6 vi Preface applications that make this volume complete when used in combination with its companion work in this series, Peptide Synthesis Protocols. It is hoped that after reading Peptide Analysis Protocols and applying the techniques described, the reader can develop successful separations, analyses, and applications of each of his or her peptides. We wish to thank the authors for their excellent contributions and cooperation. Ben M. Dunn Michael W. Pennington

7 Contents Preface... v Companion Volume Contents... ix Contributors... xi CH. 1. CH. 2. CH. 3. CH. 4. CH. 5. CH. 6. CH. 7. CH. 8. CH. 9. CH. 10. CH. 11. Gel-Filtration Chromotography, Daniel M. Bollag... 1 Ion-Exchange Chromatography, Daniel M. Bollag Reversed-Phase HPLC: Analytical Procedure, Udo Nirenberg Reversed-Phase High-Performance Liquid Chromatography: A Semipreparative Methodology, Michael E. Byrnes Applications of Strong Cation-Exchange (SCX)-HPLC in Synthetic Peptide Analysis, Dan L. Crimmins Principles and Practice of Peptide Analysis with Capillary Zone Electrophoresis, Thomas E. Wheat Fast Atom Bombardment Mass Spectrometric Characterization of Peptides, P. R. Das and B. N. Pramanik Sequence Analysis of Peptide Resins from Boc/Benzyl Solid-Phase Synthesis, Jan Pohl NMR Spectroscopy of Peptides and Proteins, Mark G. Hinds and Raymond S. Norton Techniques for Conjugation of Synthetic Peptides to Carrier Molecules, J. Mark Carter Epitope Prediction Methods, J. Mark Carter...!93 vii

8 viii Contents Crt. 12. CH. 13. Cia. 14. CH. 15. CH. 16. CH. 17. Epitope Mapping of a Protein Using the Geysen (PEPSCAN) Procedure, J. Mark Carter Analysis of Proteinase Specificity by Studies of Peptide Substrates: The Use of UV and Fluorescence Spectroscopy to Quantitate Rates of Enzymatic Cleavage, Ben M. Dunn, Paula E. Scarborough, Ruth Davenport, and Wieslaw Swietnicki Synthesis of Recombinant Peptides, Gino Van Heeke, Jay S. Stout, and Fred W. Wagner De Novo Design of Proteins: Template-Assembled Synthetic Proteins (TASP), Gabriele Tuchscherer, Verena Steiner, Karl-Heinz Altmann, and Man fred Mutter Chemical Synthesis of the Aspartic Proteinase from Human Immunodeficiency Virus (HIV), Paul D. Hoeprich, Jr Multiple and Combinatorial Peptide Synthesis: Chemical Development and Biological Applications, Philip C. Andrews, Daniele M. Leonard, Wayne L. Cody, and Tomi K. Sawyer Index

9 Contents of the companion volume: Peptide Synthesis Protocols (Note: Cross references to these chapters will include the notation PSP) Preface Companion Volume Contents Contributors CH. 1. CH. 2. CH. 3. CH. 4. CH. 5. CH. 6. CH. 7. CH. 8. CH. 9. CH. 10. CH. 11. Procedures to Improve Difficult Couplings, Michael W. Pennington and Michael E. Byrnes Methods for Removing the Fmoc Group, Gregg B. Fields Solvents for Solid-Phase Peptide Synthesis, Cynthia G. Fields and Gregg B. Fields HF Cleavage and Deprotection Procedures for Peptides Synthesized Using a Boc/Bzl Strategy, Michael W. Pennington Acid Cleavage/Deprotection in Fmoc/tBu Solid-Phase Peptide Synthesis, Fritz Dick Bromoacetylated Synthetic Peptides: Starting Materials for Cyclic Peptides, Peptomers, and Peptide Conjugates, Frank A. Robey Formation of Disulfide Bonds in Synthetic Peptides and Proteins, David Andreau, Fernando Albericio, Ndria A. Sol~, Mark C. Munson, Marc Ferrer, and George Barany Site-Specific Chemical Modification Procedures, Michael W. Pennington Synthesis of Phosphopeptides Containing O-Phosphoserine and O-Phosphothreonine, Anatol Arendt and Paul A. Hargrave Solid-Phase Synthesis of Phosphorylated Tyr-Peptides by "Phosphite Triester" Phosphorylation, Michael W. Pennington Design of Novel Synthetic Peptides Including Cyclic Conformationally and Topographically Constrained Analogs, Victor J. Hruby and G. Gregg Bonner ix

10 x Cn. 12. Cml3. CH. 14. Cn. 15. Companion Volume Contents Solid-Phase Synthesis of Peptides Containing the CH2NH Reduced Bond Surrogate, Michael W. Pennington Approaches to the Asymmetric Synthesis of Unusual Amino Acids, Victor J. Hruby and Xinhua Qian Synthesis of Fully Protected Peptide Fragments, Monika Mergler Peptide Synthesis via Fragment Condensation, Rolf Nyfeler Index

11 Contributors KARL-HEINZ ALTMANN Section de Chimie, Universite de Lausanne, Lausanne, Switzerland. Present Address: Ciba-Geigy AG, Basel, Switzerland PHILIP C. ANDREWS Department of Biological Chemistry, University of Michigan, Ann Arbor, MI DANIEL M. BOLLAG Merck, Sharpe, and Dohme, West Point, PA MICHAEL E. BYRNES Bachem Bioscience, King of Prussia, PA J. MARK CARTER Cytogen, Princeton, NJ WAYNE L. CODY Department of Chemistry, Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Co., Ann Arbor, MI DAN L. CRIMMINS Core Protein/Peptide Facility, Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, MO P. R. DAS Schering-Plough Research Institute, Kenilworth, NJ RUTH DAVENPORT Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL BEN M. DONN Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL MARK G. HINDS NMR Laboratory, Biomolecular Research Institute, Parkville, Australia PAUL D. HOEPRICH, JR. Applied Biosystems Inc., Foster City, CA DANIELE M. LEONARD Department of Chemistry, Parke-Davis Pharmaceutical Research, Warner-Lambert Co., Ann Arbor, MI MANFRED MUTTER Section de Chimie, Universite de Lausanne, Lausanne, Switzerland UDO NIRENBERG Bachem Feinchemikalien AG, Bubendo~ Switzerland xi

12 xii Contributors RAYMOND S. NORTON NMR Laboratory, Biomolecular Research Institute, Parkville, Australia JAN POnE "Microchemical Facility, Winship Cancer Center, Emory University School of Medicine, Atlanta, GA B. N. PRAMANIK Schering-Plough Research Institute, Kenilworth, NJ TOMI K. SAWYER Department of Chemistry, Parke-Davis Pharmaceutical Reserach, Warner-Lambert Co., Ann Arbor, MI PAULA E. SCARBOROUGH Department of Pathology, Duke University, Durham, NC VERENA STEINER Section de Chimie, Universite de Lausanne, Lausanne, Switzerland. Present Address: Ciba-Geigy AG, Basel, Switzerland JAY S. STOUT BioNebraska Inc., Lincoln, NE WIESLAW SwIEr~Cra Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL GABRmLE TtJCHSCHERER Section de Chimie, Universite de Lausanne, Lausanne, Switzerland GINO VAN HEEKE Protein Expression Laboratory, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL; BioNebraska, Inc. Lincoln, NE FRED W. WAGNER BioNebraska Inc., Lincoln, NE; Department of Biochemistry, University of Nebraska, Lincoln, NE THOMAS E. WHEAT Analytical Technology Inc., Boston, MA

Microscopy, Optical Spectroscopy, and Macroscopic Techniques

Microscopy, Optical Spectroscopy, and Macroscopic Techniques Methods in Molecular Biology John M, Walker, SERIES EDITOR 22. Microscopy, Optical Spectroscopy, and Macroscopic Techniques, edited by Christopher