Noncanonical Amino Acids: Methods and Protocols

Description

This volume covers some of the most widely used protocols on nanocanonical amino acids, providing details and advice for users to get each method up and running for their chosen application. Chapters have been divided into three parts describing methods for protein production in the test tube, in prokaryotes, and in eukaryotes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Noncanonical Amino Acids: Methods and Protocols aims to provide readers with techniques that enable them to design new experiments and create new areas of research. Front Matter ....Pages i-xi Front Matter ....Pages 1-1 Leveraging Formylglycine-Generating Enzyme for Production of Site-Specifically Modified Bioconjugates (Robyn M. Barfield, David Rabuka)....Pages 3-16 Artificial Division of Codon Boxes for Expansion of the Amino Acid Repertoire of Ribosomal Polypeptide Synthesis (Yoshihiko Iwane, Takayuki Katoh, Yuki Goto, Hiroaki Suga)....Pages 17-47 Cell-Free Protein Synthesis for Multiple Site-Specific Incorporation of Noncanonical Amino Acids Using Cell Extracts from RF-1 Deletion E. coli Strains (Eiko Seki, Tatsuo Yanagisawa, Shigeyuki Yokoyama)....Pages 49-65 Tub-Tag Labeling; Chemoenzymatic Incorporation of Unnatural Amino Acids (Jonas Helma, Heinrich Leonhardt, Christian P. R. Hackenberger, Dominik Schumacher)....Pages 67-93 Front Matter ....Pages 95-95 Directed Evolution of Orthogonal Pyrrolysyl-tRNA Synthetases in Escherichia coli for the Genetic Encoding of Noncanonical Amino Acids (Moritz J. Schmidt, Daniel Summerer)....Pages 97-111 Genetic Code Expansion in Enteric Bacterial Pathogens (Huangtao Zheng, Shixian Lin, Peng R. Chen)....Pages 113-126 Self-Directed in Cell Production of Methionine Analogue Azidohomoalanine by Synthetic Metabolism and Its Incorporation into Model Proteins (Ying Ma, Martino L. Di Salvo, Nediljko Budisa)....Pages 127-135 Residue-Specific Incorporation of Noncanonical Amino Acids for Protein Engineering (Mark B. van Eldijk, Jan C. M. van Hest)....Pages 137-145 Using Amber and Ochre Nonsense Codons to Code Two Different Noncanonical Amino Acids in One Protein Gene (Jeffery M. Tharp, Wenshe R. Liu)....Pages 147-154 Genetic Incorporation of Unnatural Amino Acids into Proteins of Interest in Streptomyces venezuelae ATCC 15439 (Jingxuan He, Charles E. Melançon III)....Pages 155-168 Expression and Purification of Site-Specifically Lysine-Acetylated and Natively-Folded Proteins for Biophysical Investigations (Michael Lammers)....Pages 169-190 Site-Specific Incorporation of Sulfotyrosine Using an Expanded Genetic Code (Xiang Li, Chang C. Liu)....Pages 191-200 Site-Specific Protein Labeling with Tetrazine Amino Acids (Robert J. Blizzard, True E. Gibson, Ryan A. Mehl)....Pages 201-217 Front Matter ....Pages 219-219 Mapping of Protein Interfaces in Live Cells Using Genetically Encoded Crosslinkers (Lisa Seidel, Irene Coin)....Pages 221-235 Generation of Stable Amber Suppression Cell Lines (Simon J. Elsässer)....Pages 237-245 Trapping Chromatin Interacting Proteins with Genetically Encoded, UV-Activatable Crosslinkers In Vivo (Christian Hoffmann, Heinz Neumann, Petra Neumann-Staubitz)....Pages 247-262 Genetically Encoding Unnatural Amino Acids in Neurons In Vitro and in the Embryonic Mouse Brain for Optical Control of Neuronal Proteins (Ji-Yong Kang, Daichi Kawaguchi, Lei Wang)....Pages 263-277 Genetic Code Expansion- and Click Chemistry-Based Site-Specific Protein Labeling for Intracellular DNA-PAINT Imaging (Ivana Nikić-Spiegel)....Pages 279-295 MultiBacTAG-Genetic Code Expansion Using the Baculovirus Expression System in Sf21 Cells (Christine Koehler, Edward A. Lemke)....Pages 297-311 Production and Chemoselective Modification of Adeno-Associated Virus Site-Specifically Incorporating an Unnatural Amino Acid Residue into Its Capsid (Rachel E. Kelemen, Sarah B. Erickson, Abhishek Chatterjee)....Pages 313-326 Generation of Intramolecular FRET Probes via Noncanonical Amino Acid Mutagenesis (Simone Brand, Yao-Wen Wu)....Pages 327-335 Fluorogenic Tetrazine-Siliconrhodamine Probe for the Labeling of Noncanonical Amino Acid Tagged Proteins (Eszter Kozma, Giulia Paci, Gemma Estrada Girona, Edward A. Lemke, Péter Kele)....Pages 337-363 Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA) and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction (Mathis Baalmann, Marcel Best, Richard Wombacher)....Pages 365-387 Genetic Encoding of Unnatural Amino Acids in C. elegans (Lloyd Davis, Sebastian Greiss)....Pages 389-408 Back Matter ....Pages 409-411