Chemical Ligation E-Book
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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Presenting a wide array of information on chemical ligation – one of the more powerful tools for protein and peptide synthesis – this book helps readers understand key methodologies and applications that protein therapeutic synthesis, drug discovery, and molecular imaging.
• Moves from fundamental to applied aspects, so that novice readers can follow the entire book and apply these reactions in the lab
• Presents a wide array of information on chemical ligation reactions, otherwise scattered across the literature, into one source
• Features comprehensive and multidisciplinary coverage that goes from basics to advanced topics
• Helps researchers choose the right chemical ligation technique for their needs
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Veröffentlichungsjahr: 2017
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Table of Contents
Cover
Title Page
Copyright
List of Figures
List of Plates
List of Contributors
Preface
Chapter 1: Introduction to Chemical Ligation Reactions
1.1 Introduction
1.2 Chemical Ligation Chemistries
1.3 Imine Ligations
1.4 Serine/Threonine Ligation (STL)
1.5 Thioether Ligation
1.6 Thioester Ligation
1.7 α-Ketoacid-Hydroxylamine (KAHA) Ligation
1.8 Staudinger Ligation
1.9 Azide–Alkyne Cycloaddition
1.10 Diels–Alder Ligation
References
Chapter 2: Protein Chemical Synthesis by SEA Ligation
2.1 Introduction
2.2 Essential Chemical Properties of SEA Group
2.3 Protein Total Synthesis Using SEA Chemistry – SEA
on/off
Concept
2.4 Chemical Synthesis of HGF/SF Subdomains for Deciphering the Functioning of HGF/SF-MET System
2.5 Conclusion
References
Chapter 3: Development of Serine/Threonine Ligation and Its Applications
3.1 Introduction
3.2 Serine/Threonine Ligation (STL)
3.3 Application of STL in Protein Synthesis
3.4 Conclusion and Outlook
References
Chapter 4: Synthesis of Proteins by Native Chemical Ligation–Desulfurization Strategies
4.1 Introduction
4.2 Ligation–Desulfurization and Early Applications
4.3 Beyond Native Chemical Ligation at Cysteine – The Development of Thiolated Amino Acids and Their Application in Protein Synthesis
4.4 Ligation–Deselenization in the Chemical Synthesis of Proteins
4.5 Conclusions and Future Directions
References
Chapter 5: Synthesis of Chemokines by Chemical Ligation
5.1 Introduction – The Chemokine–Chemokine Receptor Multifunctional System
5.2 Synthesis of Chemokines by Native Chemical Ligation
5.3 Synthesis of Chemokines by Alternative Chemical Ligation
5.4 Semisynthesis of Chemokines by Expressed Protein Ligation
5.5 Prospects
References
Chapter 6: Chemical Synthesis of Glycoproteins by the Thioester Method
6.1 Introduction
6.2 Ligation Methods and Strategy of Glycoprotein Synthesis
6.3 The Synthesis of the Extracellular Ig Domain of Emmprin
6.4 Synthesis of Basal Structure of MUC2
6.5
N
-Alkylcysteine-Assisted Thioesterification Method and Dendrimer Synthesis
6.6 Synthesis of TIM-3
6.7 Resynthesis of Emmprin Ig Domain
6.8 Conclusion
References
Chapter 7: Membrane Proteins: Chemical Synthesis and Ligation
7.1 Introduction
7.2 Methods for the Synthesis and Purification of Membrane Proteins
7.3 Ligation and Refolding
7.4 Illustrative Examples
References
Chapter 8: Chemoselective Modification of Proteins
8.1 Chemical Protein Synthesis
8.2 Chemoselective and Bioorthogonal Reactions
8.3 Site-Selective Protein Modification Approaches
References
Chapter 9: Stable, Versatile Conjugation Chemistries for Modifying Aldehyde-Containing Biomolecules
9.1 Introduction
9.2 Aldehyde as a Bioorthogonal Chemical Handle for Conjugation
9.3 Aldehyde Conjugation Chemistries
9.4 The Pictet–Spengler Ligation
9.5 The Hydrazinyl-Iso-Pictet–Spengler (HIPS) Ligation
9.6 The Trapped-Knoevenagel (thioPz) Ligation
9.7 Applications – Antibody–Drug Conjugates
9.8 Next-Generation HIPS Chemistry – AzaHIPS
9.9 Applications – Protein Engineering
9.10 Applications – Protein Labeling
9.11 Conclusions
References
Chapter 10: Thioamide Labeling of Proteins through a Combination of Semisynthetic Methods
10.1 Introduction
10.2 Thioamide Synthesis
10.3 Thioamide Incorporation into Peptides
10.4 Synthesis of Full-Sized Proteins Containing Thioamides
10.5 Applications
10.6 Conclusions
Acknowledgments
References
Chapter 11: Macrocyclic Organo-Peptide Hybrids by Intein-Mediated Ligation: Synthesis and Applications
11.1 Introduction
11.2 Macrocyclic Organo-Peptide Hybrids as Natural-Product-Inspired Macrocycles
11.3 Application of MOrPHs for Targeting α-Helix-Mediated Protein–Protein Interactions
11.4 Conclusions
References
Chapter 12: Protein Ligation by HINT Domains
12.1 Introduction
12.2 Protein Ligation by Protein Splicing
12.3 Naturally Occurring and Artificially Split Inteins for Protein Ligation
12.4 Conditional Protein Splicing
12.5 Inter- and Intramolecular Protein Splicing
12.6 Protein Ligation by Other HINT Domains
12.7 Bottleneck of Protein Ligation by PTS
12.8 Comparison with Other Enzymatic Ligation Methods
12.9 Perspective of Protein Ligation by HINT Domains
12.10 Conclusions and Future Perspectives
Acknowledgment
References
Chapter 13: Chemical Ligation for Molecular Imaging
13.1 Introduction
13.2 Chemical Ligation
13.3 Conclusion
References
Chapter 14: Native Chemical Ligation in Structural Biology
14.1 Introduction
14.2 Protein (Semi)synthesis for Molecular Structure Determination
14.3 Protein (Semi)Synthesis for Understanding Protein Folding, Stability, and Interactions
14.4 Protein (Semi)Synthesis in Enzyme Chemistry
References
Index
End User License Agreement
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Guide
Cover
Table of Contents
Preface
Begin Reading
List of Tables
Chapter 3: Development of Serine/Threonine Ligation and Its Applications
Table 3.1 Synthesis of natural cyclic peptides via peptide thiol SAL ester-mediated cyclization.
Chapter 5: Synthesis of Chemokines by Chemical Ligation
Table 5.1 Chemokines and chemokine analogs synthesized by native chemical ligation.
Table 5.2 Modifications in chemokines introduced by EPL.
Table 5.3 Chemokines completely synthesized by SPPS.
Chapter 8: Chemoselective Modification of Proteins
Table 8.1 List of representative chemoselective and bioorthogonal reactions.
Table 8.2 Variants of strained alkynes.
Table 8.3 Reactivity of dienophiles.
Table 8.4 Reaction kinetics (with TCO
2
) and stability of a selection of tetrazines.
Table 8.5 Fluorogenic tetrazine fluorophores.
Table 8.6 Reactivity of thiol-reactive functions.
Table 8.7 Representative chemical tags for labeling of proteins inside live cells or on the cell surface.
Chapter 12: Protein Ligation by HINT Domains
Table 12.1 Comparison of the different protein ligation methods.
Chapter 14: Native Chemical Ligation in Structural Biology
Table 14.1 X-ray structure of proteins solved by racemic crystallography.
Table 14.2 Example of segmentally labeled proteins analyzed by NMR spectroscopy.
Chemical Ligation
Tools for Biomolecule Synthesis and Modification
Edited by Luca D. D'Andrea and Alessandra Romanelli
This edition first published 2017
© 2017 John Wiley & Sons, Inc.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions.
The right of Luca D. D'Andrea and Alessandra Romanelli to be identified as the authors of this work has been asserted in accordance with law.
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Library of Congress Cataloguing-in-Publication Data
Names: D'Andrea, Luca D., editor. | Romanelli, Alessandra, editor.
Title: Chemical ligation : tools for biomolecule synthesis and modification / edited by Luca D. D'Andrea, Alessandra Romanelli.
Description: Hoboken, NJ : John Wiley & Sons, Inc., 2017. | Includes bibliographical references and index.
Identifiers: LCCN 2016052028 (print) | LCCN 2016052635 (ebook) | ISBN 9781119044109 (cloth) | ISBN 9781119044093 (pdf) | ISBN 9781119044130 (epub)
Subjects: LCSH: Biosynthesis. | Peptides–Synthesis. | Proteins–Synthesis. | Bioorganic chemistry. | Chemistry, Organic.
Classification: LCC QP551 .C51587 2017 (print) | LCC QP551 (ebook) | DDC 612/.015756–dc23
LC record available at https://lccn.loc.gov/2016052028
Cover image: © Catherine Peer / EyeEm/Gettyimages
Cover design by Wiley
List of Figures
Figure 1.1
Schematic representation of the solid-phase peptide synthesis.
Figure 1.2
Chemical preparation of a polypeptide by convergent synthesis in solution phase.
Figure 1.3
The chemical ligation general concept. A single polypeptide chain is obtained by covalently joining two peptide segments through the reaction of two mutually reactive functional groups. The type of covalent bond generated at the junction site depends on the reactive groups employed for the ligation reaction.
Figure 1.4
Derivatization of the C-terminus of a recombinant protein with an oxyamine functional group using intein chemistry.
Figure 1.5
The native chemical ligation reaction mechanism.
Figure 1.6
Amino acid analogs used in native chemical ligation–desulfurization synthetic strategies.
Figure 1.7
The mechanism of intein splicing.
Figure 1.8
Preparation of recombinant α-thioester proteins (a) or N-terminal cysteinyl-proteins (b) using engineered inteins.
Figure 1.9
Schematic mechanism of protein trans-splicing. Int
N
and Int
C
are the halves, N- and C-terminal, respectively, of a split intein.
Figure 2.1
Structure of the bis(2-sulfanylethyl)amido (SEA) group.
Figure 2.2
Protein synthesis by N-to-C solid-phase sequential ligation of unprotected peptide segments using the SEA
off
group as a latent thioester surrogate. The peptide segment elongation cycle consists in activating the SEA
off
group by a SEA–thiol exchange reaction and then performing an NCL reaction in the presence of MPAA (see also Scheme 2.11). (a) Synthesis of a model 135 amino acid polypeptide. A sample was treated with NaOH after each elongation cycle and analyzed by LC–MS to verify the completeness of the coupling step (right). (b) Characterization of the purified 135-amino-acid model polypeptide.
Figure 2.3
Design of the multivalent semisynthetic NB and K1B-streptavidin scaffolds.
Figure 2.5
Binding of NB/S or K1B/S complexes to purified recombinant or endogenous MET receptor. (a) NB, K1B and MET-Fc binding assay: increasing concentrations of NB or K1B were mixed with extracellular MET domain fused with human IgG1-Fc (MET-Fc) and incubated with streptavidin AlphaScreen
®
donor beads and Protein A acceptor beads. Error bars correspond to standard error (±SD) of triplicates. (b) Endogenous MET capture. Streptavidin-coated beads loaded with NB or K1B were incubated with HeLa or CaPan1 total cell lysates. Input, flow-through, and elution fractions from NB or K1 loaded beads were analyzed by specific total MET Western blot.
Figure 2.6
HeLa cells were treated with increasing concentrations of mature HGF/SF, K1B/S, NK1, and K1B/Ab for 7 min. Activation levels of Akt (a) and ERK (b) were measured using HTRF technology and plotted as the 665/620 nm HTRF signal ratio. (c) Cell scattering assay. MDCK isolated cell islets were incubated for 18 h in culture media with HGF/SF (HGF), K1B, K1B/S, and NK1. Cells were then stained and observed under microscope (40×). (d) Angiogenesis. Mice were injected with a mixture of Matrigel and HGF/SF (HGF), VEGF, NK1, K1B/S, K1B, or S. Hemoglobin absorbance was measured and concentration was determined using a rate hemoglobin standard curve and plug weight.
Figure 5.1
Native chemical ligation reaction mechanism demonstrated for the synthesis of glycosylated XCL1. The first step is an intermolecular trans-thioesterification, where the thioester is cleaved from the N-terminal fragment. Next a spontaneous intramolecular S→N acyl transfer leads to the native peptide bond between both protein segments.
Figure 5.2
Generation of lipidated chemokines demonstrated for CXCL12. The first CXCL12 (1–33) fragment is synthesized by SPPS coupling the β-carboxy group of an Asp-Oallyl-amino acid at position 33 on Rink amide resin. Next, the allyl protection group is removed and thioesterification of the segment is performed with ethyl-2-mercaptopropionate. The CXCL12 fragment is cleaved from the resin as amide leading to the native Asn amino acid at position 33. The fragment CXCL12 (34–68) that is lipidated is synthesized by SPPS with a Dde protection at Lys68, the lipidation position. After Dde cleavage, Fmoc-Glu is attached at that position via its γ-carboxy group. Fmoc is removed by piperidine, and the fatty acid is coupled at the amino function of the carboxyl group of Glu. Finally, the peptide is cleaved from the resin and NCL is performed.
Figure 5.3
The approach of N
