Peptides Chemistry and Biology (Wiley, 2002).pdf

Peptides: Chemistry and Biology. Norbert Sewald, Hans-Dieter Jakubke

ISBNs: 3-527-30405-3 (Hardback); 3-527-60068-X (Electronic)

Norbert Sewald and Hans-Dieter Jakubke

Peptides: Chemistry and Biology

Peptides: Chemistry and Biology. Norbert Sewald, Hans-Dieter Jakubke

ISBNs: 3-527-30405-3 (Hardback); 3-527-60068-X (Electronic)

Norbert Sewald and Hans-Dieter Jakubke

Peptides: Chemistry and Biology

Peptides: Chemistry and Biology. Norbert Sewald, Hans-Dieter Jakubke

ISBNs: 3-527-30405-3 (Hardback); 3-527-60068-X (Electronic)

Prof. Dr. Norbert Sewald

Universität Bielefeld

Fakultät für Chemie

Organ. und Bioorgan. Chemie

PO Box 100131

33501 Bielefeld, Germany

This book was carefully produced. Nevertheless,

authors and publisher do not warrant the infor-

mation contained therein to be free of errors.

Readers are advised to keep in mind that state-

ments, data, illustrations, procedural details or

other items may inadvertently be inaccurate.

Prof. em. Dr. Hans-Dieter Jakubke

Universität Leipzig

Institut für Biochemie

Private address:

Albert-Richter-Straße 12

01465 Dresden-Langebrück, Germany

The use of general descriptive names, registered

names, trademarks, etc. in this book does not im-

ply, even in the absence of a specific statement,

that such names are exempt from the relevant

protective laws and regulations and therefore free

for general use.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication Data

A catalogue record for this book is available from

the British Library.

Die Deutsche Bibliothek – CIP-Cataloguing-in-

Publication Data

A catalogue record for this publication is available

from Die Deutsche Bibliothek.

D-69469 Weinheim, 2002

in other languages). No part of this book may be

reproduced in any form – by photoprinting, mi-

crofilm, or any other means – nor transmitted or

translated into machine language without written

permission from the publishers. Registered

names, trademarks, etc. used in this book, even

when not specifically marked as such, are not to

be considered unprotected by law.

Printed in the Federal Republic of Germany

Printed on acid-free paper

Typesetting K+V Fotosatz GmbH, Beerfelden

Printing betz-druck gmbH, Darmstadt

Bookbinding J. Schäffer GmbH & Co.KG,

Grünstadt

ISBN 3-527-30405-3

Cover

The cover picture shows the TPR1 domain of Hop

in complex with -Gly-Pro-Thr-Ile-Glu-Glu-Val-

Asp-OH (GPTIEEVD). TPR domains participate in

the ordered assembly of Hsp70-Hsp90 multichape-

rone complexes.

The TPR1 domain of the adaptor protein Hop

specifically recognizes the C-terminal heptapep-

tide -Pro-Thr-Ile-Glu-Glu-Val-Asp-OH (PTIEEVD)

of the chaperone Hsp70 while the TPR2A domain

of Hop binds the C-terminal pentapeptide -Met-

Glu-Glu-Val-Asp-OH (MEEVD) of the chaperone

Hsp90. The EEVD motif is conserved in all solu-

ble forms of eukaryotic Hsp70 and Hsp90 pro-

teins.

Peptide binding is mediated with the EEVD motif.

Both carboxy groups of the C-terminal aspartate

anchor the peptide by electrostatic interactions.

The hydrophobic residues located N-terminally

within the peptide are critical for specificity.

[C. Scheufler, A. Brinker, G. Bourenkov, S. Pegora-

ro, L. Moroder, H. Bartunik, F. U. Hartl, I. Moarefi,

Structure of TPR domain-peptide complexes: criti-

cal elements in the assembly of the Hsp70-Hsp90

multichaperone machine, Cell 2000, 101, 199; PDB

entry 1ELW (http://www.rcsb.org/pdb/)]

Peptides: Chemistry and Biology. Norbert Sewald, Hans-Dieter Jakubke

ISBNs: 3-527-30405-3 (Hardback); 3-527-60068-X (Electronic)

Contents

Preface XI

Abbreviations XIII

Introduction and Background 1

2 Fundamental Chemical and Structural Principles 5

2.1 Definitions and Main Conformational Features of the Peptide Bond 5

2.2 Building Blocks, Classification, and Nomenclature 7

2.3 Analysis of the Covalent Structure of Peptides and Proteins 11

2.3.1 Separation and Purification 12

2.3.1.1 Separation Principles 12

2.3.1.2 Purification Techniques 16

2.3.1.3 Stability Problems 18

2.3.1.4 Evaluation of Homogeneity 19

2.3.2 Primary Structure Determination 20

2.3.2.1 End Group Analysis 21

2.3.2.2 Cleavage of Disulfide Bonds 23

2.3.2.3 Analysis of Amino Acid Composition 24

2.3.2.4 Selective Methods of Cleaving Peptide Bonds 25

2.3.2.5 N-Terminal Sequence Analysis (Edman Degradation) 27

2.3.2.6 C-terminal Sequence Analysis 29

2.3.2.7 Mass Spectrometry 30

2.3.2.8 Peptide Ladder Sequencing 32

2.3.2.9 Assignment of Disulfide Bonds and Peptide Fragment Ordering 33

2.3.2.10 Location of Post-Translational Modifications and Bound Cofactors 35

2.4 Three-Dimensional Structure 36

2.4.1 Secondary Structure 36

2.4.1.1 Helix 37

2.4.1.2

-Sheet 38

2.4.1.3 Turns 39

2.4.1.4 Amphiphilic Structures 41

2.4.2 Tertiary Structure 43

2.4.2.1 Structure Prediction 46

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