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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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2
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Campbell MR, Ruiz-Saenz A, Zhang Y, Peterson E, Steri V, Oeffinger J, Sampang M, Jura N, Moasser MM. Extensive conformational and physical plasticity protects HER2-HER3 tumorigenic signaling. Cell Rep 2022; 38:110285. [PMID: 35108526 PMCID: PMC8865943 DOI: 10.1016/j.celrep.2021.110285] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 08/30/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Surface-targeting biotherapeutic agents have been successful in treating HER2-amplified cancers through immunostimulation or chemodelivery but have failed to produce effective inhibitors of constitutive HER2-HER3 signaling. We report an extensive structure-function analysis of this tumor driver, revealing complete uncoupling of intracellular signaling and tumorigenic function from regulation or constraints from their extracellular domains (ECDs). The canonical HER3 ECD conformational changes and exposure of the dimerization interface are nonessential, and the entire ECDs of HER2 and HER3 are redundant for tumorigenic signaling. Restricting the proximation of partner ECDs with bulk and steric clash through extremely disruptive receptor engineering leaves tumorigenic signaling unperturbed. This is likely due to considerable conformational flexibilities across the span of these receptor molecules and substantial undulations in the plane of the plasma membrane, none of which had been foreseen as impediments to targeting strategies. The massive overexpression of HER2 functionally and physically uncouples intracellular signaling from extracellular constraints.
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Affiliation(s)
- Marcia R Campbell
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ana Ruiz-Saenz
- Departments of Cell Biology & Medical Oncology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yuntian Zhang
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elliott Peterson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julie Oeffinger
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maryjo Sampang
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark M Moasser
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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Lyu Z, Genereux JC. Methodologies for Measuring Protein Trafficking across Cellular Membranes. Chempluschem 2021; 86:1397-1415. [PMID: 34636167 DOI: 10.1002/cplu.202100304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/19/2021] [Indexed: 12/11/2022]
Abstract
Nearly all proteins are synthesized in the cytosol. The majority of this proteome must be trafficked elsewhere, such as to membranes, to subcellular compartments, or outside of the cell. Proper trafficking of nascent protein is necessary for protein folding, maturation, quality control and cellular and organismal health. To better understand cellular biology, molecular and chemical technologies to properly characterize protein trafficking (and mistrafficking) have been developed and applied. Herein, we take a biochemical perspective to review technologies that enable spatial and temporal measurement of protein distribution, focusing on both the most widely adopted methodologies and exciting emerging approaches.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
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Hadar D, Gelkop S, Vaserman L, Amiram M. Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria. Chembiochem 2021; 22:1379-1384. [PMID: 33350556 DOI: 10.1002/cbic.202000663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/22/2020] [Indexed: 11/09/2022]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment - typically at a single site or at a few sites per protein - of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l-phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production - using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain - of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.
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Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Sigal Gelkop
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
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Cleveland JD, Tucker CL. Photo-SNAP-tag, a Light-Regulated Chemical Labeling System. ACS Chem Biol 2020; 15:2212-2220. [PMID: 32623878 DOI: 10.1021/acschembio.0c00412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods that allow labeling and tracking of proteins have been instrumental for understanding their function. Traditional methods for labeling proteins include fusion to fluorescent proteins or self-labeling chemical tagging systems such as SNAP-tag or Halo-tag. These latter approaches allow bright fluorophores or other chemical moieties to be attached to a protein of interest through a small fusion tag. In this work, we sought to improve the versatility of self-labeling chemical-tagging systems by regulating their activity with light. We used light-inducible dimerizers to reconstitute a split SNAP-tag (modified human O6-alkylguanine-DNA-alkyltransferase, hAGT) protein, allowing tight light-dependent control of chemical labeling. In addition, we generated a small split SNAP-tag fragment that can efficiently self-assemble with its complement fragment, allowing high labeling efficacy with a small tag. We envision these tools will extend the versatility and utility of the SNAP-tag chemical system for protein labeling applications.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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Spassov DS, Ruiz-Saenz A, Piple A, Moasser MM. A Dimerization Function in the Intrinsically Disordered N-Terminal Region of Src. Cell Rep 2019; 25:449-463.e4. [PMID: 30304684 PMCID: PMC6226010 DOI: 10.1016/j.celrep.2018.09.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 07/09/2018] [Accepted: 09/12/2018] [Indexed: 01/30/2023] Open
Abstract
The mode of regulation of Src kinases has been elucidated by crystallographic studies identifying conserved structured protein modules involved in an orderly set of intramolecular associations and ligand interactions. Despite these detailed insights, much of the complex behavior and diversity in the Src family remains unexplained. A key missing piece is the function of the unstructured N-terminal region. We report here the function of the N-terminal region in binding within a hydrophobic pocket in the kinase domain of a dimerization partner. Dimerization substantially enhances autophosphorylation and phosphorylation of selected substrates, and interfering with dimerization is disruptive to these functions. Dimerization and Y419 phosphorylation are codependent events creating a bistable switch. Given the versatility inherent in this intrinsically disordered region, its multisite phosphorylations, and its divergence within the family, the unique domain likely functions as a central signaling hub overseeing much of the activities and unique functions of Src family kinases. Spassov et al. report that Src exists in cells and functions as a dimer and that dimerization and autophosphorylation are codependent events. Through a comprehensive structure-function analysis, they show that the dimer is an asymmetric dimer held through the interaction of the myristoylated N-terminal unique domain of one partner with a hydrophobic pocket in the kinase domain of another.
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Affiliation(s)
- Danislav S Spassov
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ana Ruiz-Saenz
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amit Piple
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark M Moasser
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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Andreoni A, Davis CM, Tian L. Measuring brain chemistry using genetically encoded fluorescent sensors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Zheng JT, Zhang N, Yu YH, Gong PT, Li XH, Wu N, Wang C, Wang XC, Li X, Li JH, Zhang XC. Identification of a TRBD zinc finger-interacting protein in Giardia duodenalis and its regulation of telomerase. Parasit Vectors 2019; 12:568. [PMID: 31783771 PMCID: PMC6884763 DOI: 10.1186/s13071-019-3821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/21/2019] [Indexed: 11/10/2022] Open
Abstract
Background Giardia duodenalis causes giardiasis, with diarrhea as the primary symptom. The trophozoite proliferation of this zoonotic parasite is mainly affected by telomerase, although the mechanism of telomerase regulation has not been thoroughly analyzed. Methods This study was performed to identify the telomerase RNA-binding domain (TRBD)-interacting protein in G. duodenalis and its regulation of telomerase. Interaction between TRBD and interacting proteins was verified via pulldown assays and co-immunoprecipitation (co-IP) techniques, and the subcellular localization of the protein interactions was determined in vivo via split SNAP-tag labeling. The hammerhead ribozyme was designed to deplete the mRNA of TRBD-interacting proteins. Results Using TRBD as bait, we identified zinc-finger domain (ZFD)-containing proteins and verified it via pulldown and co-IP experiments. Protein-protein interaction occurred in the nuclei of 293T cells and both nuclei of G. duodenalis. The hammerhead ribozyme depleted ZFD mRNA levels, which reduced the reproduction rate of G. duodenalis, telomerase activity and telomere length. Conclusions Our findings suggest that ZFD may regulate telomere function in G. duodenalis nuclei.
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Affiliation(s)
- Jing-Tong Zheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.,Department of Pathogenobiology, College of Basic Medicine, Jilin University, Changchun, 130021, Jilin, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.,State and Local Joint Engineering Laboratory for Animal Models of Human Diseases, Academy of Translational Medicine, First Hospital, Jilin University, Changchun, 130021, China
| | - Yan-Hui Yu
- Clinical Laboratory of Second Hospital, Jilin University, Changchun, 130021, China
| | - Peng-Tao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xian-He Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Na Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Can Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xiao-Cen Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jian-Hua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
| | - Xi-Chen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
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Schneider AFL, Hackenberger CPR. Fluorescent labelling in living cells. Curr Opin Biotechnol 2017; 48:61-68. [PMID: 28395178 DOI: 10.1016/j.copbio.2017.03.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/10/2017] [Indexed: 11/15/2022]
Abstract
The labelling of proteins with green fluorescent protein enabled the visualization of proteins in living cells for the first time. Since then, much progress has been made in the field. Modern strategies allow the labelling of proteins in live cells through a range of specialized methods with sophisticated chemical probes that show enhanced photophysical properties compared to fluorescent proteins. This review briefly summarizes recent advances in the field of fluorescent chemical protein labelling inside living cells and illustrates key aspects on the requirements and advantages of each given method.
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Affiliation(s)
- Anselm Fabian Lowell Schneider
- Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, D-13125 Berlin, Germany
| | - Christian Peter Richard Hackenberger
- Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, D-13125 Berlin, Germany; Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, D-12489 Berlin, Germany.
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10
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Wu L, Wang X, Zhang J, Luan T, Bouveret E, Yan X. Flow Cytometric Single-Cell Analysis for Quantitative in Vivo Detection of Protein–Protein Interactions via Relative Reporter Protein Expression Measurement. Anal Chem 2017; 89:2782-2789. [DOI: 10.1021/acs.analchem.6b03603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lina Wu
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Xu Wang
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Jianqiang Zhang
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Tian Luan
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Emmanuelle Bouveret
- Laboratory of
Macromolecular System Engineering, Institute of Microbiology
of the Mediterranean, Aix-Marseille Université and Centre National de la Recherche Scientifique, Marseille 13402, France
| | - Xiaomei Yan
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
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