Editorial Cite This: Biochemistry 2018, 57, 4605−4606
pubs.acs.org/biochemistry
Special Issue on Discovering New Tools
Biochemistry 2018.57:4605-4606. Downloaded from pubs.acs.org by 193.93.194.141 on 08/09/18. For personal use only.
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(Columbia University, New York, NY) presents a mathematical approach for interpreting NMR Carr−Purcell−Meiboom− Gill (CPMG) relaxation dispersion data for biological macromolecules.
here is little doubt that new tools catalyze new experiments. Even in the past decade, novel biochemical methods have paved the way for transformative innovations in cellular imaging,1 molecular cloning,2 genome engineering,3 gene regulation, and more. Manuscripts that accurately and completely describe protocols for these tools are an essential component of scientific literature, as they ensure that the tools are not only broadly disseminated but also robust and reproducible. In 2017, Biochemistry launched From the Bench, its first manuscript type dedicated to the publication of novel protocols in all areas of biological chemistry. This special issue, dedicated exclusively to new methods, includes a collection of terrific and wide-ranging From the Bench contributions that each provide step-by-step experimental guidelines. We are delighted to highlight the discovery of new tools as part of the new Biochemistry.
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METHODS IN SYNTHETIC BIOLOGY In many ways, synthetic biology lies at the very core of (and demands much of) modern biological chemistry. In that spirit, this issue includes a description of a new metabolic engineering method from Virginia Cornish (Columbia University), a yeast three-hybrid assay for detecting the biosynthesis of tetracyclines, a major class of antibiotics. Chang Liu (University of California, Irvine, CA) employs an expanded genetic code system to selectively incorporate sulfotyrosine into the antiHIV antibody E51, thereby enabling characterization of the sulfation patterns responsible for HIV-neutralizing activity. Karmella Haynes (Arizona State University, Tempe, AZ) reports an experimental pipeline for generating synthetic reader proteins to bind to modified chromatin in vitro and in living cells. John Milligan and Andrew Ellington (The University of Texas at Austin, Austin, TX) describe a cellbased selection strategy to isolate mutant DNA polymerases that can tolerate high temperature and efficiently displace strands for nucleic acid amplification reactions. John Chodera (Memorial Sloan Kettering Cancer Center, New York, NY) creates an open access set of human kinase domain constructs that can be employed by researchers to quickly generate proteins for downstream applications such as screening new inhibitors.
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MONITORING PROTEIN DYNAMICS AND INTERACTIONS This issue contains a number of papers that report new methods to interrogate protein structure, function, reactivity, and interactions. Nobuhiko Tokuriki (University of British Columbia, Vancouver, BC) leverages sequence-similarity networks to study enzyme families and discover new enzyme-catalyzed reactions. Jesse Rinehart and Benjamin Turk (Yale University, New Haven, CT) develop a technique termed SERIOHL-KILR (serine-oriented human library− kinase library reactions) to profile the substrate specificity of serine kinases. Carsten Schultz (Oregon Health & Science University, Portland, OR) details a methodology for detecting protein−protein interactions based on a novel diazirene-based amino acid cross-linker bearing a click handle for further functionalization. Gideon Schreiber (Weizmann Institute of Science, Rehovot, Israel) reports a method for selecting fastbinding mutant proteins, originating from a random yeast library, to assess protein−protein interaction kinetics in vitro. Roger Goody (Max Planck Institute of Molecular Physiology, Dortmund, Germany) describes a number of assays to determine binding and equilibria constants for competitive inhibitors of Ras family GTPases, facilitating rapid preliminary assessment of oncotherapeutic inhibitors.
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NEW TOOLS IN SPECTROSCOPY This issue also describes a number of new creative new strategies to push the boundaries of various spectroscopic techniques. A collaborative effort from Uwe Bergmanna (Stanford University, Stanford, CA) and Jan Kernb, Vittal Yachandrab, and Junko Yanob (Lawrence Berkeley National Laboratory, Berkeley, CA) describes the use of X-ray emission spectroscopy as a tool for validating the state of metalloenzymes in real time. Alexander Barnes (Washington University in St. Louis, St. Louis, MO) combines dynamic nuclear polarization and magic angle spinning for highresolution nuclear magnetic resonance (NMR) spectroscopic characterization of intact human cells. Arthur Palmer © 2018 American Chemical Society
FRONTIERS IN FLUORESCENCE
And let’s not forget the spectacularly important role of fluorescence microscopy in modern biological chemistry. Xin Zhang (The Pennsylvania State University, University Park, PA) provides a new tool to visualize protein homeostasis in live cells; a HaloTag-based fluorogenic sensor detects proteome stress via an aggregation-induced fluorescence turn-on mechanism. Douglas Auld (Novartis, Cambridge, MA) and Brian Webb (Thermo Fisher Scientific, Rockford, IL) introduce TurboLuc, a novel luciferase construct for biochemical assays and high-throughput screening. Surfaceinduced fluorescence attenuation (SIFA) is a protocol developed by Shuxin Hu and Ming Li (Chinese Academy of Sciences, Beijing, China) to probe the movement of proteins in lipid bilayers. Leveraging energy transfer from a fluorophore to a graphene oxide surface, SIFA is able to monitor threedimensional movement of fluorophore-labeled proteins in biological membranes. John Milligan and Andrew Ellington (The University of Texas at Austin) describe a cell-based selection strategy to isolate mutant DNA polymerases that can Special Issue: Discovering New Tools Received: July 23, 2018 Published: August 7, 2018 4605
DOI: 10.1021/acs.biochem.8b00778 Biochemistry 2018, 57, 4605−4606
Biochemistry
Editorial
tolerate high temperature and efficiently displace strands for nucleic acid amplification reactions. A new method from Joseph Wedekind (University of Rochester, Rochester, NY), combines icSHAPE (in cell selective 2′-hydroxyl acylation analyzed by primer extension) with GFP reporter gene expression, allowing in-cell chemical probing of RNA structure and riboswitch dynamics.
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FUTURE As Biochemistry continues to grow and change, our special issues underscore the journal’s expansion across all areas of modern biological chemistry. In addition to this special collection of new methods, we’ve highlighted exciting advances in cellular organization, molecular neurobiology, and, of course, mechanistic enzymology. Stay tuned for more in 2019 and beyond. Alanna Schepartz,* Editor-in-Chief Department of Chemistry, Yale University
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AUTHOR INFORMATION
ORCID
Alanna Schepartz: 0000-0003-2127-3932 Notes
Views expressed in this editorial are those of the author and not necessarily the views of the ACS.
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REFERENCES
(1) Schepartz, A. (2017) Introducing the “Seeing into Cells” Special Issue. Biochemistry 56, 5161. (2) Avery, O. T., MacLeod, C. M., and McCarty, M. (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III. J. Exp. Med. 93, 345. (3) Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. (2012) A Programmable Dial-RNAGuided DNA Endonuclease in Adaptive Bacterial Immunity. Science 337, 816.
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DOI: 10.1021/acs.biochem.8b00778 Biochemistry 2018, 57, 4605−4606
