Amino Acids, Peptides and Proteins: Volume 40

258 Pages·2015·7.85 MB·English

by  Maxim Ryadnov

Amino Acids, Peptides and Proteins
Volume 40

A Specialist Periodical Report
Amino Acids, Peptides
and Proteins
Volume 40
Editors
Maxim Ryadnov, National Physical Laboratory and
University of Edinburgh, UK
Ferenc Hudecz, Eo¨tvo¨s Lorand University, Budapest, Hungary
Authors
Szilvia Bo+sze, Eo¨tvo¨s L. University, Budapest, Hungary
Marco Crisma, Institute of Biomolecular Chemistry, Padova Unit, CNR,
Italy
Gabriella Csik, Semmelweis University, Budapest, Hungary
Emiliana De Santis, National Physical Laboratory, Teddington, UK
Fernando Formaggio, Institute of Biomolecular Chemistry, Padova Unit,
CNR, and University of Padova, Italy
Takayuki Fukuda, Okayama University, Japan
Ferenc Hudecz, Eo¨tvo¨s L. University, Budapest, Hungary
Mizuki Kitamatsu, Okayama University, Japan
Alicja Kluczyk, University of Wrocław, Poland
A´da´m Orosz, Semmelweis University, Budapest, Hungary
Maxim G. Ryadnov, National Physical Laboratory, Teddington, UK
Hiromi Sasamoto, Okayama University, Japan
Kohei Shingai, Okayama University, Japan
Masahiko Sisido, Okayama University, Japan
Piotr Stefanowicz, University of Wrocław, Poland
Zbigniew Szewczuk, University of Wrocław, Poland
Claudio Toniolo, Institute of Biomolecular Chemistry, Padova Unit, CNR,
and University of Padova, Italy
ISBN: 978-1-78262-059-4
eISBN: 978-1-78262-268-0
ISSN: 1361-5904
DOI: 10.1039/9781782622680
A catalogue record for this book is available from the British Library
r The Royal Society of Chemistry 2016
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Preface
DOI: 10.1039/9781782622680-FP005
Thisvolumecontinuesthemissionoftheseriesinprovidingasystematic
and state-of-the-art overview of major research and development trends
in peptide and protein science. Unlike many books and periodical re-
views,thisseries,sinceitsinceptionbackin1969,aimstocoverdifferent
areas of the field irrespective of their popularity or immediacy index in-
cluding those that had limited coverage in recent years. Each volume
reviews literature predominantly published over the last two–three years
andoutlinesbackgroundconceptsthatunderpinfundamental,emerging
and evolving disciplines and technologies. This approach is integral to
each chapter in the series which grants each volume with a unique per-
spectiveallowingthe monitoringofspecificadvancesindiscretesubject
areas while keeping touch with foundations.
This 40th volume opens with a chapter reviewing the essence of pep-
tide and protein science – peptide bond formation (Crisma, Formaggio,
Toniolo). The chapter is offered as a critical discussion that is built
around reaction mechanisms in the context of reactivity and regiospe-
cificity of peptide bond formation. Five major classes of C-component
reactive derivatives of amino acids and peptides are cross-compared
including fluorides, anhydrides, esters, azides and amides. The com-
parisonisbasedon3DX-raystructuresofthederivativesandtacklesthe
persistentissuesofchemicalandopticalhomogeneityofthereaction.Of
direct relevance to the efficiency of peptide synthesis appears the prob-
lemofdevelopingderivatizationreagentsforthequantitativeanalysisof
post-translational modifications – capabilities that are increasingly nee-
ded for modern ‘‘omics’’ approaches. This is the focus of a following
chapter (Stefanowicz, Kluczyk, Szewczuk) which reviews the criticality of
determiningamino-acidsequencestounderstandbiologicalprocessesat
the molecular level. The chapter describes how mass spectrometry an-
alysiscombinedwithchemicalmodificationshasbeenandisadvancing
proteome research. A specific emphasis is made on soft ionization
techniquesandtargetsforchemicaltaggingincludingexperimental and
more traditional strategies. Derivatisation reagents are categorised in
termsofprotonaffinity,charge,chemicalandenzymaticmethodsandin
relation to target functional groups (thiols, amines, carboxyls). Pros and
consoflabel-freemethods andisotopiclabellingarediscussedfrom the
perspectiveofanalyticalreproducibilityandprecisionaswellasmethods
applicablefordirectanalysisinbiologicalmedia.Astepforwardtowards
the biotechnological developments of amino-acid labelling is taken in
the next two chapters. In one (Sisido, Fukuda, Shingai, Kitamatsu,
Sasamoto), a particular emphasis is placed on the application of fluor-
escently labelled amino acids for screening cancer-cell binding peptides
in situ and in vivo. The chapter describes different peptide screening
protocols and compares their efficiency in in-solution and on-substrate
formats. Experimental methodologies including higher order screening
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and the solubility optimisation of selected sequences are given for de-
tailed searches of peptide libraries and sub-libraries of short peptide
unitsinavarietyofculturedcellsandinvivo.Anotherchapter(Oroszand
Csik) instead looks into direct therapeutic effects of a new class of mo-
lecular modalities, photosensitizers, which induce oxidative damages of
cellular membranes and therefore hold promise in medicine. Usually
referred to as photodynamic therapy, the strategy fully relies on photo-
sensitiser conjugates with peptides and proteins and, by association, on
the efficiency of the conjugation. The latter forms the bedrock of the
discussion and highlights synthesis strategies, types of peptide carriers,
from oligopeptide sensors and proteins to nanoscale conjugates, and
their specific application targets. Photochemotherapy forms another
substantial part of the discussion and focuses on antimicrobial and
anticancer approaches including a contemporary reference to bioactive
peptide sequences. The review of antimicrobial approaches takes an ul-
timate turn in the next chapter which explains the impact peptides and
proteins have on the treatment and diagnosis of M. tuberculosis in-
fections(BoszeandHudecz).Hereadisease-centricfocusismatchedbya
comprehensivecoverageoftheproblemwithaparticularattentiongiven
tomethodologies andtools that enable thediscoveryofnewbiomarkers
and peptide-based therapies. The challenges of epitope mapping, geno-
micandinsilicomethodsaswellasinvitro,exvivoandinvivovalidation
of identified epitopes and proteins are combined in one coherent dis-
cussion. By acknowledging the nature of the bacterium the chapter
guidesthereaderthroughkeydevelopmentsofimmunodiagnosticassays
in accord with new epitope selections. M. tuberculosis peptidomes and
proteomesareclassifiedaccordingtocellepitoperegions(Tcells,Bcells)
while epitopes are presented in structural categories of linear peptides,
conjugates, nanostructures and epitope-containing fusion proteins. The
review culminates with applications including cell targeting, vaccine
development and diagnostics. A specialist role of nanotechnology high-
lightedthroughoutthisvolumecrystalisesinthelastchapter(DeSantis,
Ryadnov) which explores inter-relationships between peptide sequence,
folding and self-assembly for the construction of self-assembling motifs
andtheirproducts–nanoscalematerials.Fourmajormaterialformsare
described with each provided with established examples. As the dis-
cussion develops the importance of commercialisation of peptide self-
assembled materials becomes apparent and its near future prospects
arereviewedincomparisontonon-peptidematerialsderivedfromother
and somewhat more traditional molecular classes. A variety of appli-
cations ranging from antimicrobials to nanoscale vectors for gene ther-
apy and extracellular matrices for regenerative medicine closes up
the volume.
To sum up, each chapter is structured to give as contemporary a cov-
erage as practical while allowing for comparisons of existing concepts
and approaches. Each provides an outlook of likely future develops
and perspectives as a part of discussion or summary. The chapters are
written by leading scientists in their respective domains which ensures
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expert-enabledaccesstoaworldwideinformationsourceofbroadappeal
to research organisations and industry.
We wish to dedicate this volume to the former co-editor of the
seriesProfessorEtelkaFarkas(DebrecenUniversity,Hungary).Wethank
her for all her diligent work to enable the resurrection of this series
and for her outstanding contributions to maintain the high standard of
the SPR.
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CONTENTS
Cover
Nanoscaletopographic(AFM)and
chemical(secondaryionmass
spectrometry)imagesof
antimicrobialporescreatedbyan
antimicrobialpeptide,amhelin,
inmimeticbacterialmembranes.
ImagecourtesyofJean-Nicolas
Audinot(CentredeRecherche
PublicGabrielLippmann,
Luxembourg).
Preface v
Insight into peptide bond formation from 3D-structural 1
chemistry
Marco Crisma, Fernando Formaggio and Claudio Toniolo
1 Introduction 1
2 Carboxylic fluorides 2
3 Carboxylic anhydrides 4
4 Carboxylic esters 8
5 Carboxylic azides 24
6 Carboxylic amides 26
7 Summary and future perspectives 28
References 29
Derivatization of peptides for improved detection by mass 36
spectrometry
Piotr Stefanowicz, Alicja Kluczyk and Zbigniew Szewczuk
1 Introduction 36
2 Targets for chemical tagging 39
3 Fixed charge chemical modifications of peptides and 40
proteins
4 Post-translational modifications 48
5 Tagging of peptides with isotopic labels 51
AminoAcids,Pept.Proteins,2016,40,ix–xi | ix
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6 Studying derivatization: peptide modifications on solid 62
support
7 Conclusions and perspective remarks 68
Abbreviations 69
References 70
Fluorescently labelled amino acids and peptides for efficient 75
screening in situ and in vivo
Masahiko Sisido, Takayuki Fukuda, Kohei Shingai,
Mizuki Kitamatsu and Hiromi Sasamoto
1 Introduction 75
2 Fluorescent amino acids and multi-fluorophore 76
screening
3 In-solution peptide screening against intact proteins 81
4 In situ peptide screening against dish-cultured cells 82
5 In vivo peptide screening using multiple fluorophores 95
6 Conclusion 97
List of abbreviations 98
References 99
Peptide/protein conjugates of photosensitizers 100
A´da´m Orosz and Gabriella Csik
1 Introduction 100
2 Synthesis: strategies and approaches 102
3 Synthetic peptide carriers 107
4 Polypeptide and nano conjugates 119
5 Protein carriers 126
6 Outline, perspective 134
Abbreviations 136
References 137
Proteins and peptides for the immunodiagnosis and therapy of 146
Mycobacterium tuberculosis infections
Szilvia Bo+sze and Ferenc Hudecz
1 Introduction 146
2 Identification of T cell epitope regions 148
3 Identification of B cell epitope regions 157
4 Epitope manipulation 165
5 Applications 180
6 Outline, perspective 185
Abbreviations 186
x | AminoAcids,Pept.Proteins,2016,40,ix–xi