1
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Robinson SA, Co JA, Banik SM. Molecular glues and induced proximity: An evolution of tools and discovery. Cell Chem Biol 2024; 31:1089-1100. [PMID: 38688281 DOI: 10.1016/j.chembiol.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.
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Affiliation(s)
| | | | - Steven Mark Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
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2
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Yang Z, Fok HKF, Luo J, Yang Y, Wang R, Huang X, Sun F. B 12-induced reassembly of split photoreceptor protein enables photoresponsive hydrogels with tunable mechanics. SCIENCE ADVANCES 2022; 8:eabm5482. [PMID: 35363531 PMCID: PMC10938628 DOI: 10.1126/sciadv.abm5482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Although the tools based on split proteins have found broad applications, ranging from controlled biological signaling to advanced molecular architectures, many of them suffer from drawbacks such as background reassembly, low thermodynamic stability, and static structural features. Here, we present a chemically inducible protein assembly method enabled by the dissection of the carboxyl-terminal domain of a B12-dependent photoreceptor, CarHC. The resulting segments reassemble efficiently upon addition of cobalamin (AdoB12, MeB12, or CNB12). Photolysis of the cofactors such as AdoB12 and MeB12 further leads to stable protein adducts harboring a bis-His-ligated B12. Split CarHC enables the creation of a series of protein hydrogels, of which the mechanics can be either photostrengthened or photoweakened, depending on the type of B12. These materials are also well suited for three dimensional cell culturing. Together, this new protein chemistry, featuring negligible background autoassembly, stable conjugation, and phototunability, has opened up opportunities for designing smart materials.
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Affiliation(s)
- Zhongguang Yang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Hong Kiu Francis Fok
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiren Luo
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yang Yang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xinyu Huang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
- Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
- HKUST Shenzhen Research Institute, Shenzhen 518057, China
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3
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Dolberg TB, Meger AT, Boucher JD, Corcoran WK, Schauer EE, Prybutok AN, Raman S, Leonard JN. Computation-guided optimization of split protein systems. Nat Chem Biol 2021; 17:531-539. [PMID: 33526893 PMCID: PMC8084939 DOI: 10.1038/s41589-020-00729-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/22/2020] [Indexed: 12/20/2022]
Abstract
Splitting bioactive proteins into conditionally reconstituting fragments is a powerful strategy for building tools to study and control biological systems. However, split proteins often exhibit a high propensity to reconstitute even without the conditional trigger, limiting their utility. Current approaches for tuning reconstitution propensity are laborious, context-specific, or often ineffective. Here, we report a computational design strategy grounded in fundamental protein biophysics to guide experimental evaluation of a sparse set of mutants to identify an optimal functional window. We hypothesized that testing a limited set of mutants would direct subsequent mutagenesis efforts by predicting desirable mutant combinations from a vast mutational landscape. This strategy varies the degree of interfacial destabilization while preserving stability and catalytic activity. We validate our method by solving two distinct split protein design challenges, generating both design and mechanistic insights. This new technology will streamline the generation and use of split protein systems for diverse applications.
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Affiliation(s)
- Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Anthony T Meger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Jonathan D Boucher
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - William K Corcoran
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Elizabeth E Schauer
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Alexis N Prybutok
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA. .,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, USA.
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4
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Yudenko A, Smolentseva A, Maslov I, Semenov O, Goncharov IM, Nazarenko VV, Maliar NL, Borshchevskiy V, Gordeliy V, Remeeva A, Gushchin I. Rational Design of a Split Flavin-Based Fluorescent Reporter. ACS Synth Biol 2021; 10:72-83. [PMID: 33325704 DOI: 10.1021/acssynbio.0c00454] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments. In recent years, light-oxygen-voltage (LOV) domains of several photoreceptor proteins have been developed into flavin-based fluorescent proteins (FbFPs) that, under some circumstances, can outperform commonly used fluorescent proteins such as GFP. Here, we show that CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein from Chloroflexus aggregans, can serve as a split fluorescent reporter. We use the available genetic and structural information to identify three loops between the conserved secondary structure elements, Aβ-Bβ, Eα-Fα, and Hβ-Iβ, that tolerate insertion of flexible poly-Gly/Ser segments and eventually splitting. We demonstrate that the designed split pairs, when fused to interacting proteins, are fluorescent in vivo in E. coli and human cells and have low background fluorescence. Our results enable probing protein-protein interactions in anaerobic conditions without using exogenous fluorophores and provide a basis for further development of LOV and PAS (Per-Arnt-Sim) domain-based fluorescent reporters and optogenetic tools.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nina L. Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38044 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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5
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Kimchi O, Goodrich CP, Courbet A, Curatolo AI, Woodall NB, Baker D, Brenner MP. Self-assembly-based posttranslational protein oscillators. SCIENCE ADVANCES 2020; 6:6/51/eabc1939. [PMID: 33328225 PMCID: PMC7744077 DOI: 10.1126/sciadv.abc1939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems.
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Affiliation(s)
- Ofer Kimchi
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA.
| | - Carl P Goodrich
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Agnese I Curatolo
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA
| | - Nicholas B Woodall
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Michael P Brenner
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA
- Kavli Institute for Bionano Science and Technology Harvard University, Cambridge, MA 02138, USA
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6
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Verbič A, Praznik A, Jerala R. A guide to the design of synthetic gene networks in mammalian cells. FEBS J 2020; 288:5265-5288. [PMID: 33289352 DOI: 10.1111/febs.15652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Synthetic biology aims to harness natural and synthetic biological parts and engineering them in new combinations and systems, producing novel therapies, diagnostics, bioproduction systems, and providing information on the mechanism of function of biological systems. Engineering cell function requires the rewiring or de novo construction of cell information processing networks. Using natural and synthetic signal processing elements, researchers have demonstrated a wide array of signal sensing, processing and propagation modules, using transcription, translation, or post-translational modification to program new function. The toolbox for synthetic network design is ever-advancing and has still ample room to grow. Here, we review the diversity of synthetic gene networks, types of building modules, techniques of regulation, and their applications.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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7
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Díaz Galicia ME, Aldehaiman A, Hong S, Arold ST, Grünberg R. Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls. Methods Enzymol 2019; 621:131-152. [DOI: 10.1016/bs.mie.2019.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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8
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Kolos JM, Voll AM, Bauder M, Hausch F. FKBP Ligands-Where We Are and Where to Go? Front Pharmacol 2018; 9:1425. [PMID: 30568592 PMCID: PMC6290070 DOI: 10.3389/fphar.2018.01425] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/19/2018] [Indexed: 12/24/2022] Open
Abstract
In recent years, many members of the FK506-binding protein (FKBP) family were increasingly linked to various diseases. The binding domain of FKBPs differs only in a few amino acid residues, but their biological roles are versatile. High-affinity ligands with selectivity between close homologs are scarce. This review will give an overview of the most prominent ligands developed for FKBPs and highlight a perspective for future developments. More precisely, human FKBPs and correlated diseases will be discussed as well as microbial FKBPs in the context of anti-bacterial and anti-fungal therapeutics. The last section gives insights into high-affinity ligands as chemical tools and dimerizers.
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Affiliation(s)
| | | | | | - Felix Hausch
- Department of Chemistry, Institute of Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
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9
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Computational design of chemogenetic and optogenetic split proteins. Nat Commun 2018; 9:4042. [PMID: 30279442 PMCID: PMC6168510 DOI: 10.1038/s41467-018-06531-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 09/10/2018] [Indexed: 12/28/2022] Open
Abstract
Controlling protein activity with chemogenetics and optogenetics has proven to be powerful for testing hypotheses regarding protein function in rapid biological processes. Controlling proteins by splitting them and then rescuing their activity through inducible reassembly offers great potential to control diverse protein activities. Building split proteins has been difficult due to spontaneous assembly, difficulty in identifying appropriate split sites, and inefficient induction of effective reassembly. Here we present an automated approach to design effective split proteins regulated by a ligand or by light (SPELL). We develop a scoring function together with an engineered domain to enable reassembly of protein halves with high efficiency and with reduced spontaneous assembly. We demonstrate SPELL by applying it to proteins of various shapes and sizes in living cells. The SPELL server (spell.dokhlab.org) offers an automated prediction of split sites. Designing split protein approaches is time consuming and often results in high background activity due to spontaneous assembly. Here the authors present an automated approach which uses a split energy scoring function to identify optimal protein split sites and reduces spontaneous assembly.
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10
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Drikic M, De Buck J. Split trehalase as a versatile reporter for a wide range of biological analytes. Biotechnol Bioeng 2018; 115:1128-1136. [DOI: 10.1002/bit.26556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/17/2018] [Accepted: 01/30/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Marija Drikic
- Faculty of Veterinary Medicine, Department of Production Animal Health; University of Calgary; Calgary Alberta Canada
| | - Jeroen De Buck
- Faculty of Veterinary Medicine, Department of Production Animal Health; University of Calgary; Calgary Alberta Canada
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11
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Michnick SW. More than One Way to Skin a Catalyst. Cell Chem Biol 2017; 24:1196-1197. [PMID: 29053950 DOI: 10.1016/j.chembiol.2017.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this issue of Cell Chemical Biology, Diaz et al. (2017) report a strategy to achieve temporal, spatial, and stoichiometric control over the protein kinase cAbl in living cells. They achieve this by splitting cAbl into two inactive fragments that form an active kinase upon small molecule addition, potentially providing a general way to probe the wiring of signal transduction networks.
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Affiliation(s)
- Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada.
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12
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Zhao J, Stains CI. Identification of a Fragmented Small GTPase Capable of Conditional Effector Binding. RSC Adv 2017; 7:12265-12268. [PMID: 28966788 DOI: 10.1039/c6ra25575b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A fragmented small GTPase capable of conditional effector binding is described. The effector binding function of this split-GTPase can be modulated using a small molecule input, thus allowing for the potential design of cellular signaling pathways.
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Affiliation(s)
- Jia Zhao
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, United States
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13
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Diaz JE, Morgan CW, Minogue CE, Hebert AS, Coon JJ, Wells JA. A Split-Abl Kinase for Direct Activation in Cells. Cell Chem Biol 2017; 24:1250-1258.e4. [PMID: 28919041 DOI: 10.1016/j.chembiol.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/15/2017] [Accepted: 08/02/2017] [Indexed: 12/18/2022]
Abstract
To dissect the cellular roles of individual kinases, it is useful to design tools for their selective activation. We describe the engineering of a split-cAbl kinase (sKin-Abl) that is rapidly activated in cells with rapamycin and allows temporal, dose, and compartmentalization control. Our design strategy involves an empirical screen in mammalian cells and identification of split site in the N lobe. This split site leads to complete loss of activity, which can be restored upon small-molecule-induced dimerization in cells. Remarkably, the split site is transportable to the related Src Tyr kinase and the distantly related Ser/Thr kinase, AKT, suggesting broader applications to kinases. To quantify the fold induction of phosphotyrosine (pTyr) modification, we employed quantitative proteomics, NeuCode SILAC. We identified a number of known Abl substrates, including autophosphorylation sites and novel pTyr targets, 432 pTyr sites in total. We believe that this split-kinase technology will be useful for direct activation of protein kinases in cells.
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Affiliation(s)
- Juan E Diaz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Charles W Morgan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA; Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53706, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
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14
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Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.
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Affiliation(s)
- Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
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15
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Abstract
An optimal tool to unravel the role of a specific player within a cellular network or process requires its spatiotemporally resolved perturbation. Chemically induced dimerization (CID) by the rapamycin system has proven useful to induce protein dimerization or translocation with high spatiotemporal precision. Recently, we and others have added reversibility of the dimerization event as a novel feature to CID approaches. Among those, our reversible chemical dimerizer (rCD1) shows the fastest release kinetics observed, comparable to optogenetic methods. Induction and termination of enzyme activities, including phosphatidylinositol 3-kinase (PI3K) and 5-phosphatase (5Ptase), therefore allowed us to monitor the relaxation of the downstream effectors within living cells by imaging and traditional biochemical methods. Because switching off the rCD1-induced enzyme activity is sufficiently fast, it is possible to estimate kinetic parameters for enzyme activity and metabolism. Fast reversible CIDs are therefore unique tools for performing semiquantitative biochemistry in intact cells. In this chapter, we discuss advantages and constraints for the design of reversible CID applications. We provide detailed protocols for rCD1 synthesis, CID component expression in and delivery to mammalian cells and the determination of enzyme kinetics inside intact cells by a specially designed image acquisition and data analysis method.
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Affiliation(s)
- M Schifferer
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - S Feng
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - F Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - C Schultz
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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16
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Bosmans RPG, Briels JM, Milroy LG, de Greef TFA, Merkx M, Brunsveld L. Supramolecular Control over Split-Luciferase Complementation. Angew Chem Int Ed Engl 2016; 55:8899-903. [PMID: 27356091 PMCID: PMC5113697 DOI: 10.1002/anie.201602807] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/17/2016] [Indexed: 01/18/2023]
Abstract
Supramolecular split-enzyme complementation restores enzymatic activity and allows for on-off switching. Split-luciferase fragment pairs were provided with an N-terminal FGG sequence and screened for complementation through host-guest binding to cucurbit[8]uril (Q8). Split-luciferase heterocomplex formation was induced in a Q8 concentration dependent manner, resulting in a 20-fold upregulation of luciferase activity. Supramolecular split-luciferase complementation was fully reversible, as revealed by using two types of Q8 inhibitors. Competition studies with the weak-binding FGG peptide revealed a 300-fold enhanced stability for the formation of the ternary heterocomplex compared to binding of two of the same fragments to Q8. Stochiometric binding by the potent inhibitor memantine could be used for repeated cycling of luciferase activation and deactivation in conjunction with Q8, providing a versatile module for in vitro supramolecular signaling networks.
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Affiliation(s)
- Ralph P G Bosmans
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Jeroen M Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.
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17
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Bosmans RPG, Briels JM, Milroy LG, de Greef TFA, Merkx M, Brunsveld L. Supramolecular Control over Split-Luciferase Complementation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602807] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ralph P. G. Bosmans
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Jeroen M. Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
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18
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Zhang G, Li J, Xie R, Fan X, Liu Y, Zheng S, Ge Y, Chen PR. Bioorthogonal Chemical Activation of Kinases in Living Systems. ACS CENTRAL SCIENCE 2016; 2:325-31. [PMID: 27280167 PMCID: PMC4882735 DOI: 10.1021/acscentsci.6b00024] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 05/06/2023]
Abstract
Selective manipulation of protein kinases under living conditions is highly desirable yet extremely challenging, particularly in a gain-of-function fashion. Here we employ our recently developed bioorthogonal cleavage reaction as a general strategy for intracellular activation of individual kinases. Site-specific incorporation of trans-cyclooctene-caged lysine in place of the conserved catalytic lysine, in conjunction with the cleavage partner dimethyl-tetrazine, allowed efficient lysine decaging with the kinase activity chemically rescued in living systems.
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Affiliation(s)
- Gong Zhang
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua
Center for Life Sciences, Beijing, China
| | - Jie Li
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Ran Xie
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Xinyuan Fan
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Yanjun Liu
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Siqi Zheng
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Yun Ge
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
| | - Peng R. Chen
- Beijing
National Laboratory for Molecular Sciences, Synthetic and Functional
Biomolecules Center, Department of Chemical Biology, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua
Center for Life Sciences, Beijing, China
- E-mail:
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19
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Chemically induced dimerization: reversible and spatiotemporal control of protein function in cells. Curr Opin Chem Biol 2015; 28:194-201. [DOI: 10.1016/j.cbpa.2015.09.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/21/2015] [Accepted: 09/07/2015] [Indexed: 12/21/2022]
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20
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Chemical biology strategies for posttranslational control of protein function. ACTA ACUST UNITED AC 2015; 21:1238-52. [PMID: 25237866 DOI: 10.1016/j.chembiol.2014.08.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023]
Abstract
A common strategy to understand a biological system is to selectively perturb it and observe its response. Although technologies now exist to manipulate cellular systems at the genetic and transcript level, the direct manipulation of functions at the protein level can offer significant advantages in precision, speed, and reversibility. Combining the specificity of genetic manipulation and the spatiotemporal resolution of light- and small molecule-based approaches now allows exquisite control over biological systems to subtly perturb a system of interest in vitro and in vivo. Conditional perturbation mechanisms may be broadly characterized by change in intracellular localization, intramolecular activation, or degradation of a protein-of-interest. Here we review recent advances in technologies for conditional regulation of protein function and suggest further areas of potential development.
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21
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Camacho-Soto K, Castillo-Montoya J, Tye B, Ogunleye LO, Ghosh I. Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 2014; 136:17078-86. [PMID: 25409264 DOI: 10.1021/ja5080745] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.
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Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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22
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Hughes RM, Lawrence DS. Optogenetic engineering: light-directed cell motility. Angew Chem Int Ed Engl 2014; 53:10904-7. [PMID: 25156888 PMCID: PMC4196877 DOI: 10.1002/anie.201404198] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/25/2014] [Indexed: 11/10/2022]
Abstract
Genetically encoded, light-activatable proteins provide the means to probe biochemical pathways at specific subcellular locations with exquisite temporal control. However, engineering these systems in order to provide a dramatic jump in localized activity, while retaining a low dark-state background remains a significant challenge. When placed within the framework of a genetically encodable, light-activatable heterodimerizer system, the actin-remodelling protein cofilin induces dramatic changes in the F-actin network and consequent cell motility upon illumination. We demonstrate that the use of a partially impaired mutant of cofilin is critical for maintaining low background activity in the dark. We also show that light-directed recruitment of the reduced activity cofilin mutants to the cytoskeleton is sufficient to induce F-actin remodeling, formation of filopodia, and directed cell motility.
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Affiliation(s)
- Robert M. Hughes
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, and Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
| | - David S. Lawrence
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, and Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599 (USA)
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23
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Hughes RM, Lawrence DS. Optogenetic Engineering: Light-Directed Cell Motility. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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24
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Segall-Shapiro TH, Meyer AJ, Ellington AD, Sontag ED, Voigt CA. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Mol Syst Biol 2014; 10:742. [PMID: 25080493 PMCID: PMC4299498 DOI: 10.15252/msb.20145299] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic genetic systems share resources with the host, including machinery for transcription
and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate
high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors
and activators) that enable switching between different promoters and modulation of activity. Here,
we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be
co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa ‘σ
fragment’, and fragments with different specificity can direct the remaining 601-aa
‘core fragment’ to different promoters. Using these parts, we have built a resource
allocator that sets the core fragment concentration, which is then shared by multiple σ
fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional
capacity available to a synthetic system. Further, positive and negative regulation is implemented
using a 67-aa N-terminal ‘α fragment’ and a null (inactivated) σ
fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters
responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via
different schemes, which we demonstrate by building a system which adjusts promoter activity to
compensate for the difference in copy number of two plasmids.
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Affiliation(s)
- Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Eduardo D Sontag
- Department of Mathematics, Rutgers University, Piscataway, NJ, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
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