Noncanonical Amino Acids: Methods and Protocols

403 Pages·2018·9.61 MB·English

by  Edward A. Lemke (eds.)

Methods in
Molecular Biology 1728
Edward A. Lemke Editor
Noncanonical
Amino Acids
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
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Noncanonical Amino Acids
Methods and Protocols
Edited by
Edward A. Lemke
Structural and Computational Biology Unit & Cell Biology and Biophysics Unit,
EMBL, Heidelberg, Germany; Departments of Biology and Chemistry,
Pharmacy and Geosciences, Johannes Gutenberg-University, Mainz, Germany;
Institute of Molecular Biology (IMB), Mainz, Germany
Editor
Edward A. Lemke
Structural and Computational Biology Unit &
Cell Biology and Biophysics Unit
EMBL
Heidelberg, Germany
Departments of Biology and Chemistry, Pharmacy and Geosciences
Johannes Gutenberg-University
Mainz, Germany
Institute of Molecular Biology (IMB)
Mainz, Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-7573-0 ISBN 978-1-4939-7574-7 (eBook)
https://doi.org/10.1007/978-1-4939-7574-7
Library of Congress Control Number: 2017964669
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Preface
Over billions of years of evolution, nature has developed multiple types of organisms from just
“20 + 2” naturally occurring amino acids. Over roughly the last three decades, mankind
equipped itself with the tools for expanding the genetic code in ways that theoretically could
enable us to extend this number to infinity. Only a few years ago, papers reporting on genetic
code expansion typically started with an introduction reporting a list of things that the encod-
ing of novel noncanonical amino acids (also known as “non-natural amino acids” or “unnatu-
ral amino acids”) might enable scientists to achieve, such as the photochemical control of
protein function, or the installation of epigenetic marks or chemical handles for further reac-
tions. Today, it is probably fair to say that almost anything might be possible, taking into
account that at least 200 different noncanonical amino acids with different functionalities
have been encoded into a variety of organisms in a site-specific or proteome-wide manner.
In the 24 chapters constituting this book, we cover some of the most widely used pro-
tocols, providing detail and advice for users to get each method up and running for their
chosen application. The protocols have been grouped into three parts, describing methods
for protein production in the test tube, in prokaryotes, and in eukaryotes. However, these
should not be seen as strict categories. Modern genetic code expansion systems are fre-
quently orthogonal in many hosts, which means that they can be developed in one and then
simply transferred to another. The choice of appropriate host enables different applications,
ranging from cell-free to multicellular organism production of proteins having novel func-
tionality. From this collection of protocols, readers will learn techniques that enable them
to design new experiments and new areas of research to be created. Ideas that could simply
not be thought of before.
I would like to thank all the authors for their extensive efforts in contributing to this
book, and for taking the time to develop detailed protocols that also alert the reader to the
many pitfalls that over the years they encountered and overcame as these methods matured.
I am particularly grateful to my research team who were involved extensively in helping
me to compile this book.
Mainz, Germany Edward A. Lemke
v
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Part I EngInEErIng In thE tEst tubE
1 Leveraging Formylglycine-Generating Enzyme for Production
of Site-Specifically Modified Bioconjugates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Robyn M. Barfield and David Rabuka
2 Artificial Division of Codon Boxes for Expansion of the Amino Acid Repertoire
of Ribosomal Polypeptide Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Yoshihiko Iwane, Takayuki Katoh, Yuki Goto, and Hiroaki Suga
3 Cell-Free Protein Synthesis for Multiple Site-Specific Incorporation
of Noncanonical Amino Acids Using Cell Extracts from RF-1 Deletion
E . coli Strains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Eiko Seki, Tatsuo Yanagisawa, and Shigeyuki Yokoyama
4 Tub-Tag Labeling; Chemoenzymatic Incorporation of Unnatural
Amino Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Jonas Helma, Heinrich Leonhardt, Christian P.R. Hackenberger,
and Dominik Schumacher
Part II EngInEErIng In ProkaryotEs
5 Directed Evolution of Orthogonal Pyrrolysyl-tRNA Synthetases
in Escherichia coli for the Genetic Encoding of Noncanonical Amino Acids . . . . . 97
Moritz J. Schmidt and Daniel Summerer
6 Genetic Code Expansion in Enteric Bacterial Pathogens . . . . . . . . . . . . . . . . . . . 113
Huangtao Zheng, Shixian Lin, and Peng R. Chen
7 Self-Directed in Cell Production of Methionine Analogue Azidohomoalanine
by Synthetic Metabolism and Its Incorporation into Model Proteins . . . . . . . . . 127
Ying Ma, Martino L. Di Salvo, and Nediljko Budisa
8 Residue-Specific Incorporation of Noncanonical Amino Acids for Protein
Engineering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Mark B. van Eldijk and Jan C. M. van Hest
9 Using Amber and Ochre Nonsense Codons to Code Two Different
Noncanonical Amino Acids in One Protein Gene . . . . . . . . . . . . . . . . . . . . . . . . 147
Jeffery M. Tharp and Wenshe R. Liu
10 Genetic Incorporation of Unnatural Amino Acids into Proteins of Interest
in Streptomyces venezuelae ATCC 15439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Jingxuan He and Charles E. Melançon III
vii
viii Contents
11 Expression and Purification of Site-Specifically Lysine- Acetylated
and Natively-Folded Proteins for Biophysical Investigations . . . . . . . . . . . . . . . . 169
Michael Lammers
12 Site-Specific Incorporation of Sulfotyrosine Using an Expanded
Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Xiang Li and Chang C. Liu
13 Site-Specific Protein Labeling with Tetrazine Amino Acids . . . . . . . . . . . . . . . . . 201
Robert J. Blizzard, True E. Gibson, and Ryan A. Mehl
Part III EngInEErIng In EukaryotEs
14 Mapping of Protein Interfaces in Live Cells Using Genetically
Encoded Crosslinkers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Lisa Seidel and Irene Coin
15 Generation of Stable Amber Suppression Cell Lines . . . . . . . . . . . . . . . . . . . . . . 237
Simon J. Elsässer
16 Trapping Chromatin Interacting Proteins with Genetically Encoded,
UV-Activatable Crosslinkers In Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Christian Hoffmann, Heinz Neumann, and Petra Neumann-Staubitz
17 Genetically Encoding Unnatural Amino Acids in Neurons In Vitro
and in the Embryonic Mouse Brain for Optical Control of Neuronal Proteins . . 263
Ji-Yong Kang, Daichi Kawaguchi, and Lei Wang
18 Genetic Code Expansion- and Click Chemistry-Based Site- Specific Protein
Labeling for Intracellular DNA-PAINT Imaging . . . . . . . . . . . . . . . . . . . . . . . . 279
Ivana Nikić-Spiegel
19 MultiBacTAG-Genetic Code Expansion Using the Baculovirus Expression
System in Sf21 Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Christine Koehler and Edward A. Lemke
20 Production and Chemoselective Modification of Adeno- Associated Virus
Site-Specifically Incorporating an Unnatural Amino Acid Residue into Its Capsid . . . . . 313
Rachel E. Kelemen, Sarah B. Erickson, and Abhishek Chatterjee
21 Generation of Intramolecular FRET Probes via Noncanonical
Amino Acid Mutagenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Simone Brand and Yao-Wen Wu
22 Fluorogenic Tetrazine-Siliconrhodamine Probe for the Labeling
of Noncanonical Amino Acid Tagged Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Eszter Kozma, Giulia Paci, Gemma Estrada Girona, Edward A. Lemke,
and Péter Kele
23 Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA)
and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction . . . . . . . . . . 365
Mathis Baalmann, Marcel Best, and Richard Wombacher
24 Genetic Encoding of Unnatural Amino Acids in C . elegans . . . . . . . . . . . . . . . . . 389
Lloyd Davis and Sebastian Greiss
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409
Contributors
MathIs baalMann • Institute of Pharmacy and Molecular Biotechnology,
Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
robyn M. barfIEld • Catalent Pharma Solutions, Emeryville, CA, USA
MarcEl bEst • Institute of Pharmacy and Molecular Biotechnology,
Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
robErt J. blIzzard • Department of Biochemistry and Biophysics, Oregon State
University, Corvallis, OR, USA
sIMonE brand • Chemical Genomics Centre of the Max Planck Society, Dortmund,
Germany
nEdIlJko budIsa • Biocatalysis Group, Department of Chemistry, Berlin Institute of
Technology/TU Berlin, Berlin, Germany
abhIshEk chattErJEE • Department of Chemistry, Boston College, Chestnut Hill, MA,
USA
PEng r. chEn • Peking-Tsinghua Center for Life Sciences, Beijing, China;
Beijing National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University,
Beijing, China
IrEnE coIn • Institute of Biochemistry, University of Leipzig, Leipzig, Germany
lloyd davIs • Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK
Mark b. van EldIJk • Division of Chemistry and Chemical Engineering,
California Institute of Technology, Pasadena, CA, USA
sIMon J. ElsässEr • Science for Life Laboratory, Division of Translational Medicine
and Chemical Biology, Department of Medical Biochemistry and Biophysics,
Karolinska Institutet, Stockholm, Sweden
sarah b. ErIckson • Department of Chemistry, Boston College, Chestnut Hill, MA, USA
gEMMa Estrada gIrona • Structural and Computational Biology Unit,
European Molecular Biology Laboratory, Heidelberg, Germany; Cell Biology
and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
truE E. gIbson • Department of Biochemistry and Biophysics, Oregon State University,
Corvallis, OR, USA
yukI goto • Department of Chemistry, Graduate School of Science, The University of
Tokyo, Tokyo, Japan
sEbastIan grEIss • Centre for Integrative Physiology, University of Edinburgh, Edinburgh,
UK
chrIstIan P.r. hackEnbErgEr • Department of Chemical-Biology,
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany;
Department of Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
JIngxuan hE • Department of Chemistry and Chemical Biology, University of New
Mexico, Albuquerque, NM, USA
ix
x Contributors
Jonas hElMa • Department of Biology II, Center for Integrated Protein Science Munich,
Ludwig Maximilians Universität München, Planegg-Martinsried, München, Germany
Jan c.M. van hEst • Institute for Molecules and Materials, Radboud University
Nijmegen, Nijmegen, The Netherlands
chrIstIan hoffMann • Georg August University Göttingen, Göttingen, Germany;
Accurion GmbH, Göttingen, Germany
yoshIhIko IwanE • Department of Chemistry, Graduate School of Science,
The University of Tokyo, Tokyo, Japan
JI-yong kang • Department of Neuroscience, School of Medicine, Tufts University, Boston,
MA, USA
takayukI katoh • Department of Chemistry, Graduate School of Science,
The University of Tokyo, Tokyo, Japan
daIchI kawaguchI • Graduate School of Pharmaceutical Sciences, The University of Tokyo,
Tokyo, Japan
PétEr kElE • Chemical Biology Research Group, Research Centre for Natural Sciences,
Institute of Organic Chemistry, Hungarian Academy of Sciences, Budapest, Hungary
rachEl E. kElEMEn • Department of Chemistry, Boston College, Chestnut Hill, MA, USA
chrIstInE koEhlEr • Structural and Computational Biology Unit, EMBL, Heidelberg,
Germany; Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany;
Department of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany;
Institute of Molecular Biology (IMB), Mainz, Germany
EsztEr kozMa • Chemical Biology Research Group, Research Centre for Natural Sciences,
Institute of Organic Chemistry, Hungarian Academy of Sciences, Budapest, Hungary
MIchaEl laMMErs • Institute for Genetics and Cologne Excellence Cluster on Cellular
Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne,
Germany
Edward a. lEMkE • Structural and Computational Biology Unit & Cell Biology and
Biophysics Unit, EMBL, Heidelberg, Germany; Departments of Biology and Chemistry,
Pharmacy and Geosciences, Johannes Gutenberg-University, Mainz, Germany; Institute of
Molecular Biology (IMB), Mainz, Germany
hEInrIch lEonhardt • Department of Biology II, Center for Integrated Protein Science
Munich, Ludwig Maximilians Universität München, Planegg-Martinsried, München,
Germany
xIang lI • Department of Biomedical Engineering, University of California, Irvine, CA,
USA
shIxIan lIn • Beijing National Laboratory for Molecular Sciences, Synthetic and
Functional Biomolecules Center, College of Chemistry and Molecular Engineering,
Peking University, Beijing, China
chang c. lIu • Department of Biomedical Engineering, University of California, Irvine,
CA, USA; Department of Chemistry, University of California, Irvine, CA, USA;
Department of Molecular Biology and Biochemistry, University of California, Irvine,
CA, USA
wEnshE r. lIu • Department of Chemistry, Texas A&M University, College Station, TX,
USA
yIng Ma • Biocatalysis Group, Department of Chemistry, Berlin Institute of Technology/
TU Berlin, Berlin, Germany
Contributors xi
ryan a. MEhl • Department of Biochemistry and Biophysics, Oregon State University,
Corvallis, OR, USA
charlEs E. MElançon III • Department of Chemistry and Chemical Biology,
University of New Mexico, Albuquerque, NM, USA; Department of Biology, Center for
Biomedical Engineering, University of New Mexico, Albuquerque, NM, USA
hEInz nEuMann • Georg August University Göttingen, Göttingen, Germany;
Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
PEtra nEuMann-staubItz • Georg August University Göttingen, Göttingen, Germany;
Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
Ivana nIkIć-Spiegel • Werner Reichardt Centre for Integrative Neuroscience (CIN),
The Eberhard Karls University of Tübingen, Tübingen, Germany
gIulIa PacI • Structural and Computational Biology Unit, European Molecular Biology
Laboratory, Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular
Biology Laboratory, Heidelberg, Germany
davId rabuka • Catalent Pharma Solutions, Emeryville, CA, USA
MartIno l. dI salvo • Dipartimento di Scienze Biochimiche “A . Rossi Fanelli”,
Sapienza Università di Roma, Rome, Italy
MorItz J. schMIdt • University of Konstanz, Constance, Germany
doMInIk schuMachEr • Department of Chemical-Biology, Leibniz-Forschungsinstitut für
Molekulare Pharmakologie (FMP), Berlin, Germany; Department of Chemistry,
Humboldt Universität zu Berlin, Berlin, Germany
lIsa sEIdEl • Institute of Biochemistry, University of Leipzig, Leipzig, Germany
EIko sEkI • RIKEN Structural Biology Laboratory, Yokohama, Japan
hIroakI suga • Department of Chemistry, Graduate School of Science, The University of
Tokyo, Tokyo, Japan; JST-CREST, Tokyo, Japan
danIEl suMMErEr • University of Konstanz, Constance, Germany; Department of
Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
JEffEry M. tharP • Department of Chemistry, Texas A&M University,
College Station, TX, USA
lEI wang • Department of Pharmaceutical Chemistry, University of California,
San Francisco, CA, USA; Cardiovascular Research Institute, University of California,
San Francisco, CA, USA
rIchard woMbachEr • Institute of Pharmacy and Molecular Biotechnology,
Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
yao-wEn wu • Chemical Genomics Centre of the Max Planck Society, Dortmund,
Germany; Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
tatsuo yanagIsawa • RIKEN Structural Biology Laboratory, Yokohama, Japan
shIgEyukI yokoyaMa • RIKEN Structural Biology Laboratory, Yokohama, Japan
huangtao zhEng • Peking-Tsinghua Center for Life Sciences, Beijing, China;
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China