Synthetic and Enzymatic Modifications of the Peptide Backbone

1st Edition, Volume 656 - July 27, 2021
Imprint: Academic Press
Editor: E.James Petersson
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 2 1 2 5 3 - 0
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 2 1 2 5 4 - 7

Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of au… Read more

Synthetic and Enzymatic Modifications of the Peptide Backbone

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Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors.

Cover image
Title page
Table of Contents
Copyright
Contributors
Preface
Chapter One: Hydrogen bond surrogate helices as minimal mimics of protein α-helices
Abstract
1: Introduction
2: Hydrogen bond surrogate α-helices
3: HBS helices as mimics of helical protein interfaces
4: Synthesis and purification of HBS helices
5: Biophysical analysis of HBS helices
6: Summary
Acknowledgments
Chapter Two: Opportunities and challenges in the synthesis of thioamidated peptides
Abstract
1: Introduction
2: Development of thio-peptide synthesis
3: Materials
4: Protocol for thio-peptide synthesis
5: Challenges and troubleshooting in thioamidated peptide/protein synthesis
6: Thioamidated peptide synthesis with disulfide bond
7: Concluding remarks
Chapter Three: Urea based foldamers
Abstract
1: Introduction
2: Helical structures of N,N′-linked oligoureas and oligourea/peptide chimeras
3: Applications of urea-based foldamers
4: Main strategies to synthesize oligourea-based foldamers
5: Synthetic protocols
6: Concluding remarks and future directions
Acknowledgments
Chapter Four: Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics
Abstract
1: Introduction
2: Characterization of folded structure in heterogeneous-backbone proteomimetics
3: Analysis of folding energetics in proteomimetics
4: Summary
Acknowledgments
Chapter Five: Synthesis and study of macrocyclic β-hairpin peptides for investigating amyloid oligomers
Abstract
1: Introduction
2: Synthesis of macrocyclic β-hairpin peptides
3: Methods for studying the self-assembly of macrocyclic β-hairpin peptides
4: Concluding remarks
Acknowledgments
Chapter Six: Solid phase submonomer azapeptide synthesis
Abstract
1: Introduction
2: Materials and equipment
3: Synthetic procedural details
4: Quantification and statistical analysis
5: Advantages
6: Limitations
7: Safety considerations and standards
8: Alternative methods
Chapter Seven: Chloroalkene dipeptide isosteres as peptidomimetics
Abstract
1: Introduction
2: Overview of alkene-type dipeptide isosteres
3: Design and concept of chloroalkene dipeptide isosteres
4: Concept of Xaa-Gly type (Z)-chloroalkene dipeptide isosteres: Single electron transfer reduction using organocopper reagents
5: Concept of Xaa-Yaa type (Z)-chloroalkene dipeptide isosteres: Asymmetric construction based on latent intramolecular stereogenic centers
6: Stereoselective synthesis of (Z)-chloroalkene dipeptide isosteres
7: Application of a chloroalkene dipeptide isostere: Synthesis of a cadi-containing cyclic Arg-Gly-Asp peptide
8: Summary
Chapter Eight: Submonomer synthesis of sequence defined peptoids with diverse side-chains
Abstract
1: Introduction
2: Materials
3: Solid-phase peptoid synthesis
4: Submonomer amines
5: Cleavage and side-chain deprotection
6: Characterization and purification
Acknowledgments
Chapter Nine: Synthesis and conformation of backbone N-aminated peptides
Abstract
1: Introduction
2: Backbone N-amino scanning of β-strand and β-sheet peptides
3: Protocols for N-amino peptide synthesis
4: Synthetic considerations and optimization
5: Summary
Acknowledgements
Chapter Ten: Incorporating thioamides into proteins by native chemical ligation
Abstract
1: Introduction
2: Ligation strategy and design
3: Chemical synthesis of thioamide precursor
4: N-terminal ligation: Thioamide-containing N-terminal fragment and expressed C-terminal fragment
5: C-terminal ligation: Expressed N-terminal fragment and thioamide-containing C-terminal fragment
6: Applications of thioamide proteins
7: Conclusion
Acknowledgment
Chapter Eleven: The enzymology of oxazolone and thioamide synthesis in methanobactin
Abstract
1: Introduction
2: Bioinformatics and prediction of MbnB metal binding
3: Cloning, expression, and purification of key biosynthetic enzymes
4: Cofactor identification and characterization
5: Enzyme activity and kinetics
6: Conclusion
Acknowledgments
Chapter Twelve: Mechanistic studies of non-canonical amino acid mutagenesis
Abstract
1: Introduction
2: Preparation of ncAA-tRNAs
3: Assessing the performance of ncAA-tRNAs in translation
4: Conclusions and future outlook
Acknowledgments
Chapter Thirteen: Enzyme-mediated backbone N-methylation in ribosomally encoded peptides
Abstract
1: Introduction
2: Extraction and analysis of backbone N-methylated peptide macrocycles from fungal cultures
3: Production of backbone N-methylated peptide precursor proteins in E. coli
4: Production of backbone N-methylated peptide macrocycles in P. pastoris
5: LC-MS analysis of backbone N-methylated peptides
6: Summary
Acknowledgments
Chapter Fourteen: Enzymatic thioamidation of peptide backbones
Abstract
1: Introduction
2: Cloning, expression and purification of the enzymes and peptides
3: Enzyme activity assays and mass spectrometric analysis
4: Variants preparation and substrate scope analysis
5: Fluorescence polarization binding studies
6: ATP utilization analysis and mechanistic studies
7: Kinetic analysis
8: Summary
Chapter Fifteen: Initiating protein synthesis with noncanonical monomers in vitro and in vivo
Abstract
1: Introduction
2: Initiating translation with substituted benzoic acid and 1,3-dicarbonyl monomers in vitro
3: Initiating translation with noncanonical amino acids in vivo
4: Summary
Acknowledgments
Chapter Sixteen: Incorporation of backbone modifications in mRNA-displayable peptides
Abstract
1: Introduction
2: Incorporation of multiple MeAAs by tuning EF-Tu affinities of MeAA-tRNAs
3: Post-translational modification to install azoles
4: Conclusion and perspectives
Acknowledgments
Chapter Seventeen: Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli
Abstract
1: Introduction
2: Key resources table
3: Materials and equipment
4: Step-by-step method details
5: Expected outcomes
6: Notes and considerations
7: Advantages
8: Limitations
9: Optimization and troubleshooting
10: Safety considerations and standards
11: Alternative methods/procedures
Acknowledgments
Chapter Eighteen: Peptide backbone modifications in lanthipeptides
Abstract
1: Introduction
2: Expression and purification of BsjA peptide substrates
3: Expression, purification, and activity assays of BsjM
4: Expression, purification, and activity assays of BsjP and the protease domain of BsjT for removal of the leader peptide
5: Expression, purification, and activity assays of BsjJB
6: Product and reaction characterization methods
7: Class I, III, and IV dehydratases
8: Summary
Acknowledgments

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