Table Of ContentTopics in Current Chemistry Collections
Henning Jacob Jessen Editor
Phosphate Labeling
and Sensing in
Chemical Biology
Topics in Current Chemistry Collections
Journal Editors
Massimo Olivucci, Siena, Italy and Bowling Green, USA
Wai-Yeung Wong, Hong Kong
Series Editors
Hagan Bayley, Oxford, UK
Kendall N. Houk, Los Angeles, USA
Greg Hughes, Codexis Inc, USA
Christopher A. Hunter, Cambridge, UK
Seong-Ju Hwang, Seoul, South Korea
Kazuaki Ishihara, Nagoya, Japan
Barbara Kirchner, Bonn, Germany
Michael J. Krische, Austin, Texas
Delmar Larsen, Davis, USA
Jean-Marie Lehn, Strasbourg, France
Rafael Luque, Córdoba, Spain
Jay S. Siegel, Tianjin, China
Joachim Thiem, Hamburg, Germany
Margherita Venturi, Bologna, Italy
Chi-Huey Wong, Taipei, Taiwan
Henry N.C. Wong, Hong Kong
Vivian Wing-Wah Yam, Hong Kong
Chunhua Yan, Beijing, China
Shu-Li You, Shanghai, China
Aims and Scope
The series Topics in Current Chemistry Collections presents critical reviews from
the journal Topics in Current Chemistry organized in topical volumes. The scope
of coverage is all areas of chemical science including the interfaces with related
disciplines such as biology, medicine and materials science.
The goal of each thematic volume is to give the non-specialist reader, whether in
academia or industry, a comprehensive insight into an area where new research is
emerging which is of interest to a larger scientific audience.
Each review within the volume critically surveys one aspect of that topic and
places it within the context of the volume as a whole. The most significant
developments of the last 5 to 10 years are presented using selected examples to
illustrate the principles discussed. The coverage is not intended to be an
exhaustive summary of the field or include large quantities of data, but should
rather be conceptual, concentrating on the methodological thinking that will allow
the non-specialist reader to understand the information presented.
Contributions also offer an outlook on potential future developments in the field.
Moreinformationaboutthisseriesathttp://www.springer.com/series/14181
Henning Jacob Jessen
Editor
Phosphate Labeling
and Sensing in Chemical
Biology
With contributions from
G. Michael Blackburn • Kayla Borland • Ilya Captain • Amit K. Dutta
Susanne Ermert • Dorothea Fiedler • Stephan M. Hacker
Itaru Hamachi • Henning Jacob Jessen • Jacek Jemielity • Yi Jin
Joanna Kowalska • Patrick A. Limbach • Alan M. Marmelstein
Marcin Warminski • Andreas Marx • Robert W. Molt Jr.
Javier Moreno • Akio Ojida • Adolfo Saiardi • Pawel J. Sikorski
Miranda S. C. Wilson • Jirarut Wongkongkatep
Editor
Henning Jacob Jessen
Institute of Organic Chemistry
Albert-Ludwigs-University of Freiburg
Freiburg im Breisgau
Baden-Württemberg, Germany
Originally published in Top Curr Chem (Z) Volume 375 (2016),
© Springer International Publishing Switzerland 2017
ISSN 2367-4067 ISSN 2367-4075 (electronic)
Topics in Current Chemistry Collections
ISBN 978-3-319-60356-8 ISBN 978-3-319-60357-5 (eBook)
DOI 10.1007/978-3-319-60357-5
Library of Congress Control Number: 2017945302
© Springer International Publishing AG 2017
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of
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The use of general descriptive names, registered names, trademarks, service marks, etc. in this
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Contents
Preface ...................................................................................................................... vii
Fluorescence Sensing of Inorganic Phosphate and Pyrophosphate
Using Small Molecular Sensors and Their Applications ...................................... 1
Jirarut Wongkongkatep, Akio Ojida, Itaru Hamachi
Metal Fluorides: Tools for Structural and Computational Analysis
of Phosphoryl Transfer Enzymes .......................................................................... 35
Yi Jin, Robert W. Molt Jr., G. Michael Blackburn
Importance of Radioactive Labelling to Elucidate Inositol
Polyphosphate Signalling ....................................................................................... 67
Miranda S. C. Wilson, Adolfo Saiardi
Applications and Advantages of Stable Isotope Phosphate Labeling
of RNA in Mass Spectrometry ............................................................................... 89
Kayla Borland, Patrick A. Limbach
New Synthetic Methods for Phosphate Labeling ............................................... 105
Amit K. Dutta, Ilya Captain, Henning Jacob Jessen
Phosphate-Modified Nucleotides for Monitoring Enzyme Activity ................. 153
Susanne Ermert, Andreas Marx, Stephan M. Hacker
Chemical Approaches to Studying Labile Amino Acid Phosphorylation ....... 179
Alan M. Marmelstein, Javier Moreno, Dorothea Fiedler
Applications of Phosphate Modification and Labeling
to Study (m)RNA Caps ......................................................................................... 211
Marcin Warminski, Pawel J. Sikorski, Joanna Kowalska, Jacek Jemielity
v
Preface
The essential role of phosphate in biology has inspired researchers throughout the
decades. The 1987 classic article “Why nature chose phosphates” 1 by F. Westheimer
remains one of the most insightful analyses in this area. This important and
fundamental question has led to several seminal sequels: “Why nature really chose
phosphate” 2 by A. Warshel and “Why nature chose phosphate to modify proteins” 3
by T. Hunter.
This topical collection addresses the focused and practical questions: How can
phosphate be labeled and which key labeling techniques have emerged preeminent
over the years? Although there are countless applications of phosphate labeling in
chemical biology, there are select techniques upon which the most significant
studies are based. The practical recurrence of these techniques is a hallmark of this
collection; these examples of phosphate labeling serve as a passe-partout pertinent
to understanding chemical biology approaches to the many phosphorylated natural
products that could not be covered in this collection. In this sense, I hope that the
choice of examples will be useful for researchers from other fields of research as
well.
Two recent and insightful collections in Topics in Current Chemistry, edited by
J.-L. Montchamp (Phosphorous Chemistry I & II, 2015) motivated the choice towards
complementary topics with a more biological perspective. The term “labeling” in
the title is interpreted in a broad sense as can be seen in the different contributions.
I. Hamachi covers phosphate and pyrophosphate sensors, in which the “labeling”
occurs through hydrogen bonding, coordination chemistry, aggregation induced
phenomena, and chemical reactions. M. Blackburn then discusses the concept of
“nuclear mutation” in which the phosphate group is replaced with metal fluorides
for studies into the function of different enzymes and how QM calculations aid this
field of research. A. Saiardi discusses the use of radioactive phosphorous as a
powerful analytical beacon and its application to understand inositol polyphosphate
1 Westheimer F. H. (1987), Science, 235, 1173-1178.
2 Kamerlin S. C., Sharma P. K., Prasad R. B., Warshel A. (2013), Q. Rev. Biophys., 46, 1-132.
3 Hunter, T. (2012), Phil. Trans. R. Soc. B, 367, 2513–2516 .
vii
Preface
metabolism. P. Limbach reviews another highly useful, stable isotopic replacement:
18O vs 16O-phosphates and their value in studying RNA biology by mass spectrometry.
My postdocs, Amit Dutta and Ilya Captain, (and I) provide an overview of recent
synthetic approaches towards organophosphates and analogues thereof. This
contribution is also meant as an entry to the following contributions, which make
extensive use of such modified probes. S. Hacker and A. Marx discuss the
development of phosphate-modified nucleotides and how such tools can be used to
monitor enzymatic activity. The contribution by D. Fiedler covers synthetic
approaches to phosphorylated unstable amino-acids and peptides and how such
unstable modifications can be replaced by stable analogues that enable further
biological studies. J. Jemielity finally shows how many of the previously described
labels and approaches were successfully applied to understand the rich biology of
the RNA cap structure.
Clearly, investigations into the chemistry and biology of phosphate(s) offers
many research opportunities. Such studies are at the intersection of disciplines
where many exciting questions are waiting to be solved. How do cells control
phosphate acquisition and distribution? How do cells sense phosphate availability?
How has the phosphate group become one of the basic motifs in life? How can one
design and make probes to study these processes? This topical collection offers a
good starting point for those who wish to improve their understanding into the
mysteries of this important modification.
Thanks are due to the many prominent researchers that have contributed to this
work, some of them with articles, others with highly judicious comments. I personally
would like to thank the editorial staff of Topics in Current Chemistry and the
editorial board for choosing me to help assemble this collection.
viii
TopCurrChem(Z)(2017)375:30
DOI10.1007/s41061-017-0120-0
REVIEW
Fluorescence Sensing of Inorganic Phosphate
and Pyrophosphate Using Small Molecular Sensors
and Their Applications
Jirarut Wongkongkatep1 • Akio Ojida2 • Itaru Hamachi3
Received:28October2016/Accepted:1February2017/Publishedonline:1March2017
(cid:2)SpringerInternationalPublishingSwitzerland2017
Abstract The aim of this contribution is to provide an introduction and a brief
summary of the principle of fluorescence molecular sensors specific to inorganic
phosphate (Pi) and inorganic pyrophosphate (PPi) as well as their applications. In
our introduction we describe the impact of both Pi and PPi in the living organism
and in the environment, followed by a description of the principle of fluorescence
molecular sensors and the sensing mechanism in solution. We then focus on
exciting research which has emerged in recent years on the development of fluo-
rescentsensorsspecifictoPiandPPi,categorizedbychemicalinteractionsbetween
the sensor and the target molecule, such as hydrogen bonding, coordination
chemistry, displacement assay, aggregation induced emission or quenching, and
chemical reactions.
ThisarticleispartoftheTopicalCollection‘‘PhosphateLabelingandSensinginChemicalBiology’’;
editedbyHenningJessen.
& ItaruHamachi
[email protected]
JirarutWongkongkatep
[email protected]
AkioOjida
[email protected]
1 DepartmentofBiotechnology,FacultyofScience,MahidolUniversity,272Rama6Road,
Bangkok10400,Thailand
2 GraduateSchoolofPharmaceuticalSciences,KyushuUniversity,3-1-1Maidashi,Higashi-ku,
Fukuoka812-8582,Japan
3 DepartmentofSyntheticChemistryandBiologicalChemistry,GraduateSchoolofEngineering,
KyotoUniversity,Katsura,Nishikyo-ku,Kyoto615-8510,Japan
123
Reprinted from the journal 1
TopCurrChem(Z)(2017)375:30
Keywords Fluorescencedetection(cid:2)Molecularsensor(cid:2)Phosphate(cid:2)Pyrophosphate(cid:2)
Imaging
1 Introduction
Phosphatesplayacentralroleinthebuildingofthemostfundamentalmoleculesin
living organisms, such as DNA and RNA. Along with proteins and carbohydrates,
DNA and RNA constitute the three major macromolecules essential for all known
forms of life. Phosphates are also major constituents of membrane lipids (in the
form of phospholipids) and are involved in many biological processes, including
skeletal development and bone integrity, energy metabolism, cell sensing, and
regulation of protein synthesis [1]. Approximately 85% of total body inorganic
phosphate (Pi) is found in bone, primarily in association with calcium in
hydroxyapatite crystals deposited onto the collagen matrix [2]. The remainder is
in soft tissue, with only approximately 1% in extracellular fluids [3]. Prolonged Pi
deficiency results in hypophosphatemia with accompanying serious biological
consequences,suchasimpairedmineralizationofboneresultinginosteomalaciaor
rickets,dysfunctionofthecentralnervoussystem,increasederythrocytemembrane
rigidity,abnormalfunctionofleukocytesandplatelets,weaknessofrhabdomyolysis
and muscle, and cardiac dysfunction andrespiratory failure [4–7].At the otherend
of the spectrum, hyperphosphatemia is now recognized to decrease life expectancy
and lead to seizures, cardiac dysrhythmias, chronic kidney disease, muscle
weakness and tetany, decreased visual acuity, soft tissue calcification, and
eventually death [8–13]. Therefore, controlling the Pi concentration is critical for
the well-being of the organism.
Inorganic pyrophosphate (PPi), the dimeric form of Pi and a by-product of
cellular hydrolysis of ATP, DNA polymerization, and other metabolic processes,
is a biologically important target given its role in many crucial reactions
[14, 15]. The difference in PPi concentrations in a variety of biological
environments may be a diagnostic marker for various clinical conditions. For
example, abnormally high levels of PPi in synovial fluid are observed for
patients with calcium pyrophosphate crystal deposition disease [16–19]. Hence,
the sensing and imaging of PPi has become an important research target.
Phosphates are not only essential factors in living organisms, they are also
important as components of several medicinal drugs and fertilizers. Eutrophi-
cation in the aquatic ecosystem is often related to pollution from phosphates and
phosphorylated compounds [20, 21]. Due to their importance in both biological
and environmental fields, great efforts have been made to develop systems
capable of selectively sensing phosphates and their related compounds. Several
comprehensive reviews describing the recognition of phosphate molecules by
artificial receptors have been published [22–32].
Molecular sensors for phosphate anions usually consist of a Pi/PPi binding
(receptor) site covalently linked to a sensing unit, such as a fluorophore (Fig. 1).
One of the main difficulties in designing appropriate binding sites for Pi arises
from the high hydration energy of this anion (-2765 kJ/mol) that places it near
123
2 Reprinted from the journal
