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Park S, Pascua E, Lindquist KC, Kimberlin C, Deng X, Mak YSL, Melton Z, Johnson TO, Lin R, Boldajipour B, Abraham RT, Pons J, Sasu BJ, Van Blarcom TJ, Chaparro-Riggers J. Direct control of CAR T cells through small molecule-regulated antibodies. Nat Commun 2021; 12:710. [PMID: 33514714 PMCID: PMC7846603 DOI: 10.1038/s41467-020-20671-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/02/2020] [Indexed: 01/30/2023] Open
Abstract
Antibody-based therapeutics have experienced a rapid growth in recent years and are now utilized in various modalities spanning from conventional antibodies, antibody-drug conjugates, bispecific antibodies to chimeric antigen receptor (CAR) T cells. Many next generation antibody therapeutics achieve enhanced potency but often increase the risk of adverse events. Antibody scaffolds capable of exhibiting inducible affinities could reduce the risk of adverse events by enabling a transient suspension of antibody activity. To demonstrate this, we develop conditionally activated, single-module CARs, in which tumor antigen recognition is directly modulated by an FDA-approved small molecule drug. The resulting CAR T cells demonstrate specific cytotoxicity of tumor cells comparable to that of traditional CARs, but the cytotoxicity is reversibly attenuated by the addition of the small molecule. The exogenous control of conditional CAR T cell activity allows continual modulation of therapeutic activity to improve the safety profile of CAR T cells across all disease indications.
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Affiliation(s)
- Spencer Park
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Lyell Immunopharma, South San Francisco, CA USA
| | - Edward Pascua
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA
| | | | - Christopher Kimberlin
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Asher Bio, South San Francisco, CA USA
| | - Xiaodi Deng
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Dren Bio, San Carlos, CA USA
| | - Yvonne S. L. Mak
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | - Zea Melton
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | | | - Regina Lin
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | - Bijan Boldajipour
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Lyell Immunopharma, South San Francisco, CA USA
| | - Robert T. Abraham
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: Vividion Therapeutics, San Diego, CA USA
| | - Jaume Pons
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,Present Address: ALX Oncology, Burlingame, CA USA
| | - Barbra Johnson Sasu
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
| | - Thomas J. Van Blarcom
- grid.410513.20000 0000 8800 7493Pfizer, La Jolla, CA USA ,grid.507497.8Present Address: Allogene Therapeutics, South San Francisco, CA USA
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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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Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, DeGrado WF. Allosteric cooperation in a de novo-designed two-domain protein. Proc Natl Acad Sci U S A 2020; 117:33246-33253. [PMID: 33318174 PMCID: PMC7776816 DOI: 10.1073/pnas.2017062117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis-Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter Km and a 7-fold decrease in kcat These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Nathan Schmidt
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - James Lincoff
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Zachary X Widel
- Department of Chemistry, Duke University, Durham, NC 27708-0346
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Lijun Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055 Shenzhen, China
- DLX Scientific, Lawrence, KS 66049
| | | | - Michael Grabe
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy;
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001;
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54
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Gräwe A, Stein V. Linker Engineering in the Context of Synthetic Protein Switches and Sensors. Trends Biotechnol 2020; 39:731-744. [PMID: 33293101 DOI: 10.1016/j.tibtech.2020.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022]
Abstract
Linkers play critical roles in the construction of synthetic protein switches and sensors as they functionally couple a receptor with an actuator. With an increasing number of molecular toolboxes and experimental strategies becoming available that can be applied to engineer protein switches and sensors with tailored response functions, optimising the connecting linkers remains an idiosyncratic and empiric process. This review aims to provide an in-depth analysis of linker motifs, the biophysical properties they confer, and how they impact the performance of synthetic protein switches and sensors while identifying trends, mechanisms, and strategies that underlie the most potent switches and sensors.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.
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55
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Abstract
Biological signaling pathways are underpinned by protein switches that sense and respond to molecular inputs. Inspired by nature, engineered protein switches have been designed to directly transduce analyte binding into a quantitative signal in a simple, wash-free, homogeneous assay format. As such, they offer great potential to underpin point-of-need diagnostics that are needed across broad sectors to improve access, costs, and speed compared to laboratory assays. Despite this, protein switch assays are not yet in routine diagnostic use, and a number of barriers to uptake must be overcome to realize this potential. Here, we review the opportunities and challenges in engineering protein switches for rapid diagnostic tests. We evaluate how their design, comprising a recognition element, reporter, and switching mechanism, relates to performance and identify areas for improvement to guide further optimization. Recent modular switches that enable new analytes to be targeted without redesign are crucial to ensure robust and efficient development processes. The importance of translational steps toward practical implementation, including integration into a user-friendly device and thorough assay validation, is also discussed.
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Affiliation(s)
- Hope Adamson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lars J. C. Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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56
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Han L, Shan Q. Pair of Residue Substitutions at the Outer Mouth of the Channel Pore Act as Inputs for a Boolean Logic "OR" Gate Based on the Glycine Receptor. ACS Chem Neurosci 2020; 11:3409-3417. [PMID: 32970400 DOI: 10.1021/acschemneuro.0c00522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The glycine receptor (GlyR) is a ligand-activated chloride channel, whose mutations are the major cause of hereditary hyperekplexia. The hyperekplexia-causing R271Q mutation, which is located at the extracellular outer mouth of the channel pore, dramatically impairs the GlyR function manifesting a reduced sensitivity toward glycine. This study reports that a second mutation, S273D, rescues the function of the R271Q GlyR to that of the wild-type (WT) GlyR. Surprisingly, the S273D mutation, when introduced to the WT GlyR, does not further increase the receptor function. In other words, the compromised function of the 271Q 273S GlyR (i.e., the R271Q GlyR) can be rescued to WT levels by the introduction of either, or both, of the Q271R and S273D substitutions. From the perspective of Boolean logic gates, the Q271R and S273D substitutions act as inputs for an OR gate based on the GlyR. Further experiments revealed that the negative-charge carried by the 273 residue is essential for the expression of the OR gate and that the expression of the OR gate is residue-position-specific. In addition, mechanistic investigation implied that the 273 residue influences the 271 residue, which might underpin the unique nonadditive OR gate relationship between these two residues. Such an ion-channel-based OR gate, expressing output in the form of electrical current, could potentially be developed to digitally manipulate neuronal activity.
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Affiliation(s)
- Lu Han
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Qiang Shan
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong 515041, China
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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57
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Abstract
Linker engineering constitutes a critical, yet frequently underestimated aspect in the construction of synthetic protein switches and sensors. Notably, systematic strategies to engineer linkers by predictive means remain largely elusive to date. This is primarily due to our insufficient understanding how the biophysical properties that underlie linker functions mediate the conformational transitions in artificially engineered protein switches and sensors. The construction of synthetic protein switches and sensors therefore heavily relies on experimental trial-and-error. Yet, methods for effectively generating linker diversity at the genetic level are scarce. Addressing this technical shortcoming, iterative functional linker cloning (iFLinkC) enables the combinatorial assembly of linker elements with functional domains from sequence verified repositories that are developed and stored in-house. The assembly process is highly scalable and given its recursive nature generates linker diversity in a combinatorial and exponential fashion based on a limited number of linker elements.
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58
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Winter DL, Iranmanesh H, Clark DS, Glover DJ. Design of Tunable Protein Interfaces Controlled by Post-Translational Modifications. ACS Synth Biol 2020; 9:2132-2143. [PMID: 32702241 DOI: 10.1021/acssynbio.0c00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design of protein interaction interfaces is a cornerstone of synthetic biology, where they can be used to promote the association of protein subunits into active molecular complexes or into protein nanostructures. In nature, protein interactions can be modulated by post-translational modifications (PTMs) that modify the protein interfaces with the addition and removal of various chemical groups. PTMs thus represent a means to gain control over protein interactions, yet they have seldom been considered in the design of synthetic proteins. Here, we explore the potential of a reversible PTM, serine phosphorylation, to modulate the interactions between peptides. We designed a series of interacting peptide pairs, including heterodimeric coiled coils, that contained one or more protein kinase A (PKA) recognition motifs. Our set of peptide pairs comprised interactions ranging from nanomolar to micromolar affinities. Mass spectrometry analyses showed that all peptides were excellent phosphorylation substrates of PKA, and subsequent phosphate removal could be catalyzed by lambda protein phosphatase. Binding kinetics measurements performed before and after treatment of the peptides with PKA revealed that phosphorylation of the target serines affected both the association and dissociation rates of the interacting peptides. We observed both the strengthening of interactions (up to an 11-fold decrease in Kd) and the weakening of interactions (up to a 180-fold increase in Kd). De novo-designed PTM-modulated interfaces will be useful to control the association of proteins in biological systems using protein-modifying enzymes, expanding the paradigm of self-assembly to encompass controlled assembly of engineerable protein complexes.
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Affiliation(s)
- Daniel L. Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Hasti Iranmanesh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Dominic J. Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. De novo design of modular and tunable allosteric biosensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32743576 DOI: 10.1101/2020.07.18.206946] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Naturally occurring allosteric protein switches have been repurposed for developing novel biosensors and reporters for cellular and clinical applications 1 , but the number of such switches is limited, and engineering them is often challenging as each is different. Here, we show that a very general class of allosteric protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which binding of a peptide key triggers biological outputs of interest 2 . Using broadly applicable design principles, we allosterically couple binding of protein analytes of interest to the reconstitution of luciferase activity and a bioluminescent readout through the association of designed lock and key proteins. Because the sensor is based purely on thermodynamic coupling of analyte binding to switch activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We demonstrate the modularity of this platform by creating biosensors that, with little optimization, sensitively detect the anti-apoptosis protein Bcl-2, the hIgG1 Fc domain, the Her2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac Troponin I and an anti-Hepatitis B virus (HBV) antibody that achieve the sub-nanomolar sensitivity necessary to detect clinically relevant concentrations of these molecules. Given the current need for diagnostic tools for tracking COVID-19 3 , we use the approach to design sensors of antibodies against SARS-CoV-2 protein epitopes and of the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. The latter, which incorporates a de novo designed RBD binder, has a limit of detection of 15pM with an up to seventeen fold increase in luminescence upon addition of RBD. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.
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60
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Bollella P, Edwardraja S, Guo Z, Katz E. Control of Allosteric Protein Electrochemical Switches with Biomolecular and Electronic Signals. J Phys Chem Lett 2020; 11:5549-5554. [PMID: 32602718 DOI: 10.1021/acs.jpclett.0c01223] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The construction of allosteric protein switches is a key goal of synthetic biology. Such switches can be compiled into signaling systems mimicking information and energy processing systems of living organisms. Here we demonstrate construction of a biocatalytic electrode functionalized with a recombinant chimeric protein between pyrroloquinoline quinone-dependent glucose dehydrogenase and calmodulin. This electrode could be activated by calmodulin-binding peptide and showed a high bioelectrocatalytic current (ca. 300 μA) due to efficient direct electron transfer. In order to expand the types of inputs that can be used to activate the developed electrode, we constructed a caged version of calmodulin-binding peptide that could be proteolytically uncaged using a protease of choice. Finally, the complexity of the switchable bioelectrochemical system was further increased by the use of almost any kind of molecule/biomolecule or electronic signal, unequivocally proving the orthogonality of the aforementioned system.
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Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
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Phosphoregulated orthogonal signal transduction in mammalian cells. Nat Commun 2020; 11:3085. [PMID: 32555187 PMCID: PMC7303213 DOI: 10.1038/s41467-020-16895-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Orthogonal tools for controlling protein function by post-translational modifications open up new possibilities for protein circuit engineering in synthetic biology. Phosphoregulation is a key mechanism of signal processing in all kingdoms of life, but tools to control the involved processes are very limited. Here, we repurpose components of bacterial two-component systems (TCSs) for chemically induced phosphotransfer in mammalian cells. TCSs are the most abundant multi-component signal-processing units in bacteria, but are not found in the animal kingdom. The presented phosphoregulated orthogonal signal transduction (POST) system uses induced nanobody dimerization to regulate the trans-autophosphorylation activity of engineered histidine kinases. Engineered response regulators use the phosphohistidine residue as a substrate to autophosphorylate an aspartate residue, inducing their own homodimerization. We verify this approach by demonstrating control of gene expression with engineered, dimerization-dependent transcription factors and propose a phosphoregulated relay system of protein dimerization as a basic building block for next-generation protein circuits. Phosphoregulation is a key mechanism of signal processing. Here the authors build a phosphoregulated relay system in mammalian cells for orthogonal signal transduction.
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62
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Gräwe A, Ranglack J, Weber W, Stein V. Engineering artificial signalling functions with proteases. Curr Opin Biotechnol 2020; 63:1-7. [DOI: 10.1016/j.copbio.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 01/01/2023]
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63
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Mazmanian K, Sargsyan K, Lim C. How the Local Environment of Functional Sites Regulates Protein Function. J Am Chem Soc 2020; 142:9861-9871. [PMID: 32407086 DOI: 10.1021/jacs.0c02430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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64
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Gräwe A, Ranglack J, Weyrich A, Stein V. iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains. Nucleic Acids Res 2020; 48:e24. [PMID: 31925441 PMCID: PMC7039005 DOI: 10.1093/nar/gkz1210] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 02/02/2023] Open
Abstract
Recent years have witnessed increasing efforts to engineer artificial biological functions through recombination of modular-organized toolboxes of protein scaffolds and parts. A critical, yet frequently neglected aspect concerns the identity of peptide linkers or spacers connecting individual domains which remain poorly understood and challenging to assemble. Addressing these limitations, iFlinkC comprises a highly scalable DNA assembly process that facilitates the combinatorial recombination of functional domains with linkers of varying length and flexibility, thereby overcoming challenges with high GC-content and the repeat nature of linker elements. The capacity of iFLinkC is demonstrated in the construction of synthetic protease switches featuring PDZ-FN3-based affinity clamps and single-chain FKBP12-FRB receptors as allosteric inputs. Library screening experiments demonstrate that linker space is highly plastic as the induction of allosterically regulated protease switches can vary from >150-fold switch-ON to >13-fold switch-OFF solely depending on the identity of the connecting linkers and relative orientation of functional domains. In addition, Pro-rich linkers yield the most potent switches contradicting the conventional use of flexible Gly-Ser linkers. Given the ease and efficiency how functional domains can be readily recombined with any type of linker, iFLinkC is anticipated to be widely applicable to the assembly of any type of fusion protein.
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Affiliation(s)
- Alexander Gräwe
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Jan Ranglack
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Anastasia Weyrich
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
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65
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Farrants H, Tarnawski M, Müller TG, Otsuka S, Hiblot J, Koch B, Kueblbeck M, Kräusslich HG, Ellenberg J, Johnsson K. Chemogenetic Control of Nanobodies. Nat Methods 2020; 17:279-282. [PMID: 32066961 DOI: 10.1038/s41592-020-0746-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/01/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows interrogation of their roles in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.
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Affiliation(s)
- Helen Farrants
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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66
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Stines-Chaumeil C, Mavré F, Kauffmann B, Mano N, Limoges B. Mechanism of Reconstitution/Activation of the Soluble PQQ-Dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus: A Comprehensive Study. ACS OMEGA 2020; 5:2015-2026. [PMID: 32039339 PMCID: PMC7003513 DOI: 10.1021/acsomega.9b04034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
The ability to switch on the activity of an enzyme through its spontaneous reconstitution has proven to be a valuable tool in fundamental studies of enzyme structure/reactivity relationships or in the design of artificial signal transduction systems in bioelectronics, synthetic biology, or bioanalytical applications. In particular, those based on the spontaneous reconstitution/activation of the apo-PQQ-dependent soluble glucose dehydrogenase (sGDH) from Acinetobacter calcoaceticus were widely developed. However, the reconstitution mechanism of sGDH with its two cofactors, i.e., pyrroloquinoline quinone (PQQ) and Ca2+, remains unknown. The objective here is to elucidate this mechanism by stopped-flow kinetics under single-turnover conditions. The reconstitution of sGDH exhibited biphasic kinetics, characteristic of a square reaction scheme associated with two activation pathways. From a complete kinetic analysis, we were able to fully predict the reconstitution dynamics and also to demonstrate that when PQQ first binds to apo-sGDH, it strongly impedes the access of Ca2+ to its enclosed position at the bottom of the enzyme binding site, thereby greatly slowing down the reconstitution rate of sGDH. This slow calcium insertion may purposely be accelerated by providing more flexibility to the Ca2+ binding loop through the specific mutation of the calcium-coordinating P248 proline residue, reducing thus the kinetic barrier to calcium ion insertion. The dynamic nature of the reconstitution process is also supported by the observation of a clear loop shift and a reorganization of the hydrogen-bonding network and van der Waals interactions observed in both active sites of the apo and holo forms, a structural change modulation that was revealed from the refined X-ray structure of apo-sGDH (PDB: 5MIN).
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Affiliation(s)
- Claire Stines-Chaumeil
- CNRS,
Université de Bordeaux, CRPP, UMR 5031, 115 Avenue Schweitzer, F-33600 Pessac, France
| | - François Mavré
- Université
de Paris, Laboratoire d’Electrochimie Moléculaire, UMR
7591, CNRS, F-75013 Paris, France
| | - Brice Kauffmann
- CNRS
UMS 3033, INSERM US001, Université de Bordeaux, IECB, 2, Rue Robert Escarpit, F-33607 Pessac, France
| | - Nicolas Mano
- CNRS,
Université de Bordeaux, CRPP, UMR 5031, 115 Avenue Schweitzer, F-33600 Pessac, France
| | - Benoît Limoges
- Université
de Paris, Laboratoire d’Electrochimie Moléculaire, UMR
7591, CNRS, F-75013 Paris, France
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67
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Magneto-controlled enzyme reactions. Methods Enzymol 2020. [PMID: 31931981 DOI: 10.1016/bs.mie.2019.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Various approaches to magneto-controlled biocatalytic enzyme reactions are discussed with specific example systems. Magnetic nano- and micro-size particles functionalized with enzymes or cofactors/electron transfer mediators have been used to translocate the components of the biocatalytic processes and to activate/inhibit their reactions. Magneto-induced deposition of the functionalized particles on an electrode surface resulted in activation of bioelectrocatalytic reactions. On the other hand, magneto-induced removal of the particles from the electrode surface resulted in the inhibition of the electrochemical reactions. Aggregation/disaggregation of enzyme-modified magnetic nanoparticles resulted in different mechanisms of biocatalytic cascades, changing them reversibly between substrate diffusion and substrate channeling processes. Magnetohydrodynamic activation of bioelectrocatalytic processes allowed enhancement of a biofuel cell operation. Overall, a large variety of possible magneto-controlled enzyme reactions is briefly discussed, particularly emphasizing their applications in different bioelectronic systems.
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68
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Bollella P, Edwardraja S, Guo Z, Alexandrov K, Katz E. Control of allosteric electrochemical protein switch using magnetic signals. Chem Commun (Camb) 2020; 56:9206-9209. [PMID: 32662462 DOI: 10.1039/d0cc04284f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The artificial chimeric enzyme with allosteric features was activated with a magnetic field applied at a distance.
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Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology
- The University of Queensland
- Brisbane
- Australia
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance
- ARC Centre of Excellence in Synthetic Biology
- Centre for Agriculture and the Bioeconomy
- Institute of Health and Biomedical Innovation
- Institute for Future Environments
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance
- ARC Centre of Excellence in Synthetic Biology
- Centre for Agriculture and the Bioeconomy
- Institute of Health and Biomedical Innovation
- Institute for Future Environments
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science
- Clarkson University
- Potsdam
- USA
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69
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Adamson H, Ajayi MO, Campbell E, Brachi E, Tiede C, Tang AA, Adams TL, Ford R, Davidson A, Johnson M, McPherson MJ, Tomlinson DC, Jeuken LJC. Affimer-Enzyme-Inhibitor Switch Sensor for Rapid Wash-free Assays of Multimeric Proteins. ACS Sens 2019; 4:3014-3022. [PMID: 31578863 DOI: 10.1021/acssensors.9b01574] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Robust technology is required to underpin rapid point-of-care and in-field diagnostics to improve timely decision making across broad sectors. An attractive strategy combines target recognition and signal generating elements into an "active" enzyme-switch that directly transduces target-binding into a signal. However, approaches that are broadly applicable to diverse targets remain elusive. Here, an enzyme-inhibitor switch sensor was developed by insertion of non-immunoglobulin Affimer binding proteins, between TEM1-β-lactamase and its inhibitor protein, such that target binding disrupts the enzyme-inhibitor complex. Design principles for a successful switch architecture are illustrated by the rapid (min), simple (wash-free), and sensitive (pM) quantification of multimeric target analytes in biological samples (serum, plasma, leaf extracts), across three application areas. A therapeutic antibody (Herceptin), protein biomarker (human C-reactive protein), and plant virus (cow pea mosaic virus) were targeted, demonstrating assays for therapeutic drug monitoring, health diagnostics, and plant pathogen detection, respectively. Batch-to-batch reproducibility, shelf-life stability, and consistency with validated enzyme-linked immunosorbent assay analysis confirm that the principle of an Affimer-enzyme-inhibitor switch provides a platform for point-of-care and in-field diagnostics.
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Affiliation(s)
| | | | | | | | | | | | | | - Robert Ford
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Alex Davidson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Matt Johnson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
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70
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Jiang Y, Li X, Morrow BR, Pothukuchy A, Gollihar J, Novak R, Reilly CB, Ellington AD, Walt DR. Single-Molecule Mechanistic Study of Enzyme Hysteresis. ACS CENTRAL SCIENCE 2019; 5:1691-1698. [PMID: 31660437 PMCID: PMC6813718 DOI: 10.1021/acscentsci.9b00718] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 05/04/2023]
Abstract
Hysteresis is an important feature of enzyme-catalyzed reactions, as it reflects the influence of enzyme regulation in the presence of ligands such as substrates or allosteric molecules. In typical kinetic studies of enzyme activity, hysteretic behavior is observed as a "lag" or "burst" in the time course of the catalyzed reaction. These lags and bursts are due to the relatively slow transition from one state to another state of the enzyme molecule, with different states having different kinetic properties. However, it is difficult to understand the underlying mechanism of hysteresis by observing bulk reactions because the different enzyme molecules in the population behave stochastically. In this work, we studied the hysteretic behavior of mutant β-glucuronidase (GUS) using a high-throughput single-molecule array platform and investigated the effect of thermal treatment on the hysteresis.
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Affiliation(s)
- Yu Jiang
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Xiang Li
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Barrett R. Morrow
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Arti Pothukuchy
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Jimmy Gollihar
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Richard Novak
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Charles B. Reilly
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Andrew D. Ellington
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
- E-mail:
| | - David R. Walt
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
- E-mail:
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71
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Ghanbarpour A, Pinger C, Esmatpour Salmani R, Assar Z, Santos EM, Nosrati M, Pawlowski K, Spence D, Vasileiou C, Jin X, Borhan B, Geiger JH. Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches. J Am Chem Soc 2019; 141:17125-17132. [PMID: 31557439 DOI: 10.1021/jacs.9b04664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Cody Pinger
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Rahele Esmatpour Salmani
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Zahra Assar
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Elizabeth M Santos
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Meisam Nosrati
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Kathryn Pawlowski
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Dana Spence
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Chrysoula Vasileiou
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Xiangshu Jin
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Babak Borhan
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - James H Geiger
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
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72
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Godwin WC, Hoffmann GF, Gray TJ, Hughes RM. Imaging of morphological and biochemical hallmarks of apoptosis with optimized optogenetic tools. J Biol Chem 2019; 294:16918-16929. [PMID: 31582560 DOI: 10.1074/jbc.ra119.009141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/27/2019] [Indexed: 01/14/2023] Open
Abstract
Creation of optogenetic switches for specific activation of cell death pathways can provide insights into apoptosis and could also form a basis for noninvasive, next-generation therapeutic strategies. Previous work has demonstrated that cryptochrome 2 (Cry2)/cryptochrome-interacting β helix-loop-helix (CIB), a blue light-activated protein-protein dimerization module from the plant Arabidopsis thaliana, together with BCL2-associated X apoptosis regulator (BAX), an outer mitochondrial membrane-targeting pro-apoptotic protein, can be used for light-mediated initiation of mitochondrial outer membrane permeabilization (MOMP) and downstream apoptosis. In this work, we further developed the original light-activated Cry2-BAX system (hereafter referred to as OptoBAX) by improving the photophysical properties and light-independent interactions of this optogenetic switch. The resulting optogenetic constructs significantly reduced the frequency of light exposure required for membrane permeabilization activation and also decreased dark-state cytotoxicity. We used OptoBAX in a series of experiments in Neuro-2a and HEK293T cells to measure the timing of the dramatic morphological and biochemical changes occurring in cells after light-induced MOMP. In these experiments, we used OptoBAX in tandem with fluorescent reporters to image key events in early apoptosis, including membrane inversion, caspase cleavage, and actin redistribution. We then used these data to construct a timeline of biochemical and morphological events in early apoptosis, demonstrating a direct link between MOMP-induced redistribution of actin and apoptosis progression. In summary, we created a next-generation Cry2/CIB-BAX system requiring less frequent light stimulation and established a timeline of critical apoptotic events, providing detailed insights into key steps in early apoptosis.
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Affiliation(s)
- Walton C Godwin
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - George F Hoffmann
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Taylor J Gray
- Department of Biology, East Carolina University, Greenville, North Carolina 27858
| | - Robert M Hughes
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
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73
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Langan RA, Boyken SE, Ng AH, Samson JA, Dods G, Westbrook AM, Nguyen TH, Lajoie MJ, Chen Z, Berger S, Mulligan VK, Dueber JE, Novak WRP, El-Samad H, Baker D. De novo design of bioactive protein switches. Nature 2019; 572:205-210. [PMID: 31341284 PMCID: PMC6733528 DOI: 10.1038/s41586-019-1432-8] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular interactions. We design a static, five-helix 'cage' with a single interface that can interact either intramolecularly with a terminal 'latch' helix or intermolecularly with a peptide 'key'. Encoded on the latch are functional motifs for binding, degradation or nuclear export that function only when the key displaces the latch from the cage. We describe orthogonal cage-key systems that function in vitro, in yeast and in mammalian cells with up to 40-fold activation of function by key. The ability to design switchable protein functions that are controlled by induced conformational change is a milestone for de novo protein design, and opens up new avenues for synthetic biology and cell engineering.
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Affiliation(s)
- Robert A Langan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, USA
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew H Ng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, UCSF, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, UC Berkeley, Berkeley, CA, USA
| | - Jennifer A Samson
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Galen Dods
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Alexandra M Westbrook
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Taylor H Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, USA
| | - Stephanie Berger
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Vikram Khipple Mulligan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John E Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Walter R P Novak
- Department of Chemistry, Wabash College, Crawfordsville, IN, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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74
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Bilal M, Cui J, Iqbal HMN. Tailoring enzyme microenvironment: State-of-the-art strategy to fulfill the quest for efficient bio-catalysis. Int J Biol Macromol 2019; 130:186-196. [PMID: 30817963 DOI: 10.1016/j.ijbiomac.2019.02.141] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 02/08/2023]
Abstract
Enzymes as green industrial biocatalysts have become a powerful norm that offers several advantages over traditional catalytic agents with regard to process efficiency, reusability, sustainability, and overall cost-effective ratio. However, enzymes obtained from natural origins are often engineered/tailored since their native forms do not fulfill the acute need for the industrial application. Revolutionary developments in protein engineering provide excellent opportunities for designing and constructing novel industrial biocatalysts with improved functional properties including catalytic activity, stability, substrate specificity, and reaction product inhibition. Momentum in enzyme immobilization has enabled robustness and optimal functions in extreme industrial environments, such as high temperature or organic solvents. The emergence of multi-enzyme catalytic cascade based on a combination of biocatalysts presents multifarious opportunities in biosynthesis, biocatalysis, and biotransformation. This review focuses on the emerging and state-of-the-art enzyme engineering trends and approaches to constructing innovative nano- and microstructured biocatalysts with enhanced catalytic activity and stability features requisite for industrial exploitation. Continuous key developments in this direction together with protein engineering in unique ways might offer ever-increasing opportunities for future biocatalysis-based industrial bioprocesses.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No 29, 13th, Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico.
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75
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Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. NAT MACH INTELL 2019. [DOI: 10.1038/s42256-019-0049-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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76
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Guo Z, Johnston WA, Whitfield J, Walden P, Cui Z, Wijker E, Edwardraja S, Retamal Lantadilla I, Ely F, Vickers C, Ungerer JPJ, Alexandrov K. Generalizable Protein Biosensors Based on Synthetic Switch Modules. J Am Chem Soc 2019; 141:8128-8135. [DOI: 10.1021/jacs.8b12298] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhong Guo
- CSIRO-QUT Synthetic Biology alliance, Centre for Tropical Crops and Biocommodities, School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Wayne A. Johnston
- CSIRO-QUT Synthetic Biology alliance, Centre for Tropical Crops and Biocommodities, School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Jason Whitfield
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Patricia Walden
- CSIRO-QUT Synthetic Biology alliance, Centre for Tropical Crops and Biocommodities, School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zhenling Cui
- CSIRO-QUT Synthetic Biology alliance, Centre for Tropical Crops and Biocommodities, School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Elvira Wijker
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, 5600, The Netherlands
| | - Selvakumar Edwardraja
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Fernanda Ely
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Claudia Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
| | - Jacobus P. J. Ungerer
- Department of Chemical Pathology, Pathology Queensland, Brisbane, QLD 4001, Australia
- Faculty of Health and Behavioral Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology alliance, Centre for Tropical Crops and Biocommodities, School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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77
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Ligand-induced conformational switch in an artificial bidomain protein scaffold. Sci Rep 2019; 9:1178. [PMID: 30718544 PMCID: PMC6362204 DOI: 10.1038/s41598-018-37256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/28/2018] [Indexed: 11/15/2022] Open
Abstract
Artificial proteins binding any predefined “target” protein can now be efficiently generated using combinatorial libraries based on robust protein scaffolds. αRep is such a family of artificial proteins, based on an α-solenoid protein repeat scaffold. The low aggregation propensity of the specific “binders” generated from this library opens new protein engineering opportunities such as the creation of biosensors within multidomain constructions. Here, we have explored the properties of two new types of artificial bidomain proteins based on αRep structures. Their structural and functional properties are characterized in detail using biophysical methods. The results clearly show that both bidomain proteins adopt a closed bivalve shell-like conformation, in the ligand free form. However, the presence of ligands induces a conformational transition, and the proteins adopt an open form in which each domain can bind its cognate protein partner. The open/closed equilibria alter the affinities of each domain and induce new cooperative effects. The binding-induced relative domain motion was monitored by FRET. Crystal structures of the chimeric proteins indicate that the conformation of each constituting domain is conserved but that their mutual interactions explain the emergent properties of these artificial bidomain proteins. The ligand-induced structural transition observed in these bidomain proteins should be transferable to other αRep proteins with different specificity and could provide the basis of a new generic biosensor design.
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78
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TerAvest M. Fast bioelectrical switches. Nat Chem Biol 2019; 15:99-100. [DOI: 10.1038/s41589-018-0212-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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79
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Gamella M, Guo Z, Alexandrov K, Katz E. Bioelectrocatalytic Electrodes Modified with PQQ‐Glucose Dehydrogenase‐Calmodulin Chimera Switchable by Peptide Signals: Pathway to Generic Bioelectronic Systems Controlled by Biomolecular Inputs. ChemElectroChem 2019. [DOI: 10.1002/celc.201801095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maria Gamella
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699–5810 USA
| | - Zhong Guo
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699–5810 USA
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80
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Converting a Periplasmic Binding Protein into a Synthetic Biosensing Switch through Domain Insertion. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4798793. [PMID: 30719443 PMCID: PMC6335823 DOI: 10.1155/2019/4798793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022]
Abstract
All biosensing platforms rest on two pillars: specific biochemical recognition of a particular analyte and transduction of that recognition into a readily detectable signal. Most existing biosensing technologies utilize proteins that passively bind to their analytes and therefore require wasteful washing steps, specialized reagents, and expensive instruments for detection. To overcome these limitations, protein engineering strategies have been applied to develop new classes of protein-based sensor/actuators, known as protein switches, responding to small molecules. Protein switches change their active state (output) in response to a binding event or physical signal (input) and therefore show a tremendous potential to work as a biosensor. Synthetic protein switches can be created by the fusion between two genes, one coding for a sensor protein (input domain) and the other coding for an actuator protein (output domain) by domain insertion. The binding of a signal molecule to the engineered protein will switch the protein function from an “off” to an “on” state (or vice versa) as desired. The molecular switch could, for example, sense the presence of a metabolite, pollutant, or a biomarker and trigger a cellular response. The potential sensing and response capabilities are enormous; however, the recognition repertoire of natural switches is limited. Thereby, bioengineers have been struggling to expand the toolkit of molecular switches recognition repertoire utilizing periplasmic binding proteins (PBPs) as protein-sensing components. PBPs are a superfamily of bacterial proteins that provide interesting features to engineer biosensors, for instance, immense ligand-binding diversity and high affinity, and undergo large conformational changes in response to ligand binding. The development of these protein switches has yielded insights into the design of protein-based biosensors, particularly in the area of allosteric domain fusions. Here, recent protein engineering approaches for expanding the versatility of protein switches are reviewed, with an emphasis on studies that used PBPs to generate novel switches through protein domain insertion.
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81
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Atkinson JT, Campbell IJ, Thomas EE, Bonitatibus SC, Elliott SJ, Bennett GN, Silberg JJ. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat Chem Biol 2018; 15:189-195. [PMID: 30559426 DOI: 10.1038/s41589-018-0192-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Biological electron transfer is challenging to directly regulate using environmental conditions. To enable dynamic, protein-level control over energy flow in metabolic systems for synthetic biology and bioelectronics, we created ferredoxin logic gates that utilize transcriptional and post-translational inputs to control energy flow through a synthetic electron transfer pathway that is required for bacterial growth. These logic gates were created by subjecting a thermostable, plant-type ferredoxin to backbone fission and fusing the resulting fragments to a pair of proteins that self-associate, a pair of proteins whose association is stabilized by a small molecule, and to the termini of a ligand-binding domain. We show that the latter domain insertion design strategy yields an allosteric ferredoxin switch that acquires an oxygen-tolerant [2Fe-2S] cluster and can use different chemicals, including a therapeutic drug and an environmental pollutant, to control the production of a reduced metabolite in Escherichia coli and cell lysates.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Ian J Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, USA
| | - Emily E Thomas
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, USA
| | | | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA, USA
| | - George N Bennett
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA.
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82
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Aupič J, Lapenta F, Jerala R. SwitCCh: Metal-Site Design for Controlling the Assembly of a Coiled-Coil Homodimer. Chembiochem 2018; 19:2453-2457. [PMID: 30260542 DOI: 10.1002/cbic.201800578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Indexed: 11/09/2022]
Abstract
Conformational change of proteins in response to chemical or physical signals is the underlying principle of many regulatory and transport mechanisms in biological systems. The ability to design proteins the conformational state of which can be precisely and reversibly controlled would facilitate the development of molecular machines tailored for specific applications. Here we explore metal-binding site design to engineer a peptide-based conformational switch called SwitCCh that assembles into a homodimeric coiled-coil in response to the addition of ZnII ions or low pH. Addition of ZnII promoted formation of a parallel homodimer with an increase in thermal stability by more than 30 °C. The peptide could be reversibly cycled between the coiled-coil and random conformation. Furthermore, the SwitCCh peptide was orthogonal to the previously developed coiled-coil dimer set, indicating it could be used for regulated self-assembly of coiled-coil based nanostructures and materials.
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Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Doctoral Study Programme in Chemical Sciences, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia
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83
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Filipov Y, Zakharchenko A, Minko S, Katz E. Magneto‐Controlled Biocatalytic Cascades with Logically Processed Input Signals – Substrate Channeling versus Free Diffusion. Chemphyschem 2018; 19:3035-3043. [DOI: 10.1002/cphc.201800851] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
| | | | - Sergiy Minko
- Nanostructured Materials Lab University of Georgia Athens GA 30602 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
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84
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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85
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Aper SJA, den Hamer A, Wouters SFA, Lemmens LJM, Ottmann C, Brunsveld L, Merkx M. Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks. ACS Synth Biol 2018; 7:2216-2225. [PMID: 30125482 PMCID: PMC6154215 DOI: 10.1021/acssynbio.8b00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protease signaling and scaffold-induced control of protein-protein interactions represent two important mechanisms for intracellular signaling. Here we report a generic and modular approach to control the activity of scaffolding proteins by protease activity, creating versatile molecular platforms to construct synthetic signaling networks. Using 14-3-3 proteins as a structurally well-characterized and important class of scaffold proteins, three different architectures were explored to achieve optimal protease-mediated control of scaffold activity, fusing either one or two monovalent inhibitory ExoS peptides or a single bivalent ExoS peptide to T14-3-3 using protease-cleavable linkers. Analysis of scaffolding activity before and after protease-induced cleavage revealed optimal control of 14-3-3 activity for the system that contained monovalent ExoS peptides fused to both the N-and C-terminus, each blocking a single T14-3-3 binding site. The protease-activatable 14-3-3 scaffolds were successfully applied to construct a three-step signaling cascade in which dimerization and activation of FGG-caspase-9 on an orthogonal supramolecular platform resulted in activation of a 14-3-3 scaffold, which in turn allowed 14-3-3-templated complementation of a split-luciferase. In addition, by combining 14-3-3-templated activation of caspase-9 with a caspase-9-activatable 14-3-3 scaffold, the first example of a synthetic self-activating protease signaling network was created. Protease-activatable 14-3-3 proteins thus represent a modular platform whose properties can be rationally engineered to fit different applications, both to create artificial in vitro synthetic molecular networks and as a novel signaling hub to re-engineer intracellular signaling pathways.
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Affiliation(s)
- Stijn J. A. Aper
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F. A. Wouters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lenne J. M. Lemmens
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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86
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Apta-Smith MJ, Hernandez-Fernaud JR, Bowman AJ. Evidence for the nuclear import of histones H3.1 and H4 as monomers. EMBO J 2018; 37:embj.201798714. [PMID: 30177573 PMCID: PMC6166134 DOI: 10.15252/embj.201798714] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022] Open
Abstract
Newly synthesised histones are thought to dimerise in the cytosol and undergo nuclear import in complex with histone chaperones. Here, we provide evidence that human H3.1 and H4 are imported into the nucleus as monomers. Using a tether-and-release system to study the import dynamics of newly synthesised histones, we find that cytosolic H3.1 and H4 can be maintained as stable monomeric units. Cytosolically tethered histones are bound to importin-alpha proteins (predominantly IPO4), but not to histone-specific chaperones NASP, ASF1a, RbAp46 (RBBP7) or HAT1, which reside in the nucleus in interphase cells. Release of monomeric histones from their cytosolic tether results in rapid nuclear translocation, IPO4 dissociation and incorporation into chromatin at sites of replication. Quantitative analysis of histones bound to individual chaperones reveals an excess of H3 specifically associated with sNASP, suggesting that NASP maintains a soluble, monomeric pool of H3 within the nucleus and may act as a nuclear receptor for newly imported histone. In summary, we propose that histones H3 and H4 are rapidly imported as monomeric units, forming heterodimers in the nucleus rather than the cytosol.
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Affiliation(s)
| | | | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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87
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Lancaster L, Abdallah W, Banta S, Wheeldon I. Engineering enzyme microenvironments for enhanced biocatalysis. Chem Soc Rev 2018; 47:5177-5186. [PMID: 29796541 DOI: 10.1039/c8cs00085a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.
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Affiliation(s)
- Louis Lancaster
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA.
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88
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Protein Engineering Strategies to Expand CRISPR-Cas9 Applications. Int J Genomics 2018; 2018:1652567. [PMID: 30155473 PMCID: PMC6098869 DOI: 10.1155/2018/1652567] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
The development of precise and modulated methods for customized manipulation of DNA is an important objective for the study and engineering of biological processes and is essential for the optimization of gene therapy, metabolic flux, and synthetic gene networks. The clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 is an RNA-guided site-specific DNA-binding complex that can be reprogrammed to specifically interact with a desired DNA sequence target. CRISPR-Cas9 has been used in a wide variety of applications ranging from basic science to the clinic, such as gene therapy, gene regulation, modifying epigenomes, and imaging chromosomes. Although Cas9 has been successfully used as a precise tool in all these applications, some limitations have also been reported, for instance (i) a strict dependence on a protospacer-adjacent motif (PAM) sequence, (ii) aberrant off-target activity, (iii) the large size of Cas9 is problematic for CRISPR delivery, and (iv) lack of modulation of protein binding and endonuclease activity, which is crucial for precise spatiotemporal control of gene expression or genome editing. These obstacles hinder the use of CRISPR for disease treatment and in wider biotechnological applications. Protein-engineering approaches offer solutions to overcome the limitations of Cas9 and generate robust and efficient tools for customized DNA manipulation. Here, recent protein-engineering approaches for expanding the versatility of the Streptococcus pyogenes Cas9 (SpCas9) is reviewed, with an emphasis on studies that improve or develop novel protein functions through domain fusion or splitting, rational design, and directed evolution.
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89
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Carpenter AC, Paulsen IT, Williams TC. Blueprints for Biosensors: Design, Limitations, and Applications. Genes (Basel) 2018; 9:E375. [PMID: 30050028 PMCID: PMC6115959 DOI: 10.3390/genes9080375] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/23/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Biosensors are enabling major advances in the field of analytics that are both facilitating and being facilitated by advances in synthetic biology. The ability of biosensors to rapidly and specifically detect a wide range of molecules makes them highly relevant to a range of industrial, medical, ecological, and scientific applications. Approaches to biosensor design are as diverse as their applications, with major biosensor classes including nucleic acids, proteins, and transcription factors. Each of these biosensor types has advantages and limitations based on the intended application, and the parameters that are required for optimal performance. Specifically, the choice of biosensor design must consider factors such as the ligand specificity, sensitivity, dynamic range, functional range, mode of output, time of activation, ease of use, and ease of engineering. This review discusses the rationale for designing the major classes of biosensor in the context of their limitations and assesses their suitability to different areas of biotechnological application.
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Affiliation(s)
- Alexander C Carpenter
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia.
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia.
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90
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Steel H, Papachristodoulou A. Probing Intercell Variability Using Bulk Measurements. ACS Synth Biol 2018; 7:1528-1537. [PMID: 29799736 DOI: 10.1021/acssynbio.8b00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of noise is critical when assessing the design and function of synthetic biological systems. Cell-to-cell variability can be quantified experimentally using single-cell measurement techniques such as flow cytometry and fluorescent microscopy. However, these approaches are costly and impractical for high-throughput parallelized experiments, which are frequently conducted using plate-reader devices. In this paper we describe reporter systems that allow estimation of the cell-to-cell variability in a biological system's output using only measurements of a cell culture's bulk properties. We analyze one potential implementation of such a system that is based upon a fluorescent protein FRET reporter pair, finding that with typical parameters from the literature it is able to reliably estimate variability. We also briefly describe an alternate implementation based upon an activating sRNA circuit. The feasible region of parameter values for which the reporter system can function is assessed, and the dependence of its performance on both extrinsic and intrinsic noise is investigated. Experimental realization of these constructs can yield novel reporter systems that allow measurement of a synthetic gene circuit's output, as well as the intrapopulation variability of this output, at little added cost.
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Affiliation(s)
- Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
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91
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Abstract
Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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92
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Kaiser CE, Rincon Pabon JP, Khowsathit J, Castaldi MP, Kazmirski SL, Weis DD, Zhang AX, Karanicolas J. Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue. ACS Synth Biol 2018; 7:1152-1162. [PMID: 29609459 DOI: 10.1021/acssynbio.8b00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.
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Affiliation(s)
- Christine E. Kaiser
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Juan Pablo Rincon Pabon
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - M. Paola Castaldi
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Structure and Biophysics, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - David D. Weis
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew X. Zhang
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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93
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A novel 76-mer peptide mimic with the synergism of superoxide dismutase and glutathione peroxidase. In Vitro Cell Dev Biol Anim 2018; 54:335-345. [DOI: 10.1007/s11626-018-0240-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/24/2018] [Indexed: 01/02/2023]
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94
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Yang F, Zuo X, Fan C, Zhang XE. Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwx134] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.
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Affiliation(s)
- Fan Yang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, CAS Excellence Center for Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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95
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Koushanpour A, Gamella M, Guo Z, Honarvarfard E, Poghossian A, Schöning MJ, Alexandrov K, Katz E. Ca2+-Switchable Glucose Dehydrogenase Associated with Electrochemical/Electronic Interfaces: Applications to Signal-Controlled Power Production and Biomolecular Release. J Phys Chem B 2017; 121:11465-11471. [DOI: 10.1021/acs.jpcb.7b11151] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ashkan Koushanpour
- Department
of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Maria Gamella
- Department
of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Zhong Guo
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
| | - Elham Honarvarfard
- Department
of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
| | - Arshak Poghossian
- Institute
of Nano- and Biotechnologies, FH Aachen, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Mußmann-Str.
1, D-52428 Jülich, Germany
- Institute
of Complex Systems (ICS-8), Research Centre Jülich GmbH, D-52425 Jülich, Germany
| | - Michael J. Schöning
- Institute
of Nano- and Biotechnologies, FH Aachen, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Mußmann-Str.
1, D-52428 Jülich, Germany
- Institute
of Complex Systems (ICS-8), Research Centre Jülich GmbH, D-52425 Jülich, Germany
| | - Kirill Alexandrov
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
| | - Evgeny Katz
- Department
of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699-5810, United States
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96
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Lamba V, Yabukarski F, Herschlag D. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. J Am Chem Soc 2017; 139:11089-11095. [PMID: 28719738 DOI: 10.1021/jacs.7b03547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control of enzyme activity is fundamental to biology and represents a long-term goal in bioengineering and precision therapeutics. While several powerful molecular strategies have been developed, limitations remain in their generalizability and dynamic range. We demonstrate a control mechanism via separate small molecules that turn on the enzyme (activator) and turn off the activation (blocker). We show that a pocket created near the active site base of the enzyme ketosteriod isomerase (KSI) allows efficient and saturable base rescue when the enzyme's natural general base is removed. Binding a small molecule with similar properties but lacking general-base capability in this pocket shuts off rescue. The ability of small molecules to directly participate in and directly block catalysis may afford a broad controllable dynamic range. This approach may be amenable to numerous enzymes and to engineering and screening approaches to identify activators and blockers with strong, specific binding for engineering and therapeutic applications.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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97
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Stein V, Nabi M, Alexandrov K. Ultrasensitive Scaffold-Dependent Protease Sensors with Large Dynamic Range. ACS Synth Biol 2017; 6:1337-1342. [PMID: 28291337 DOI: 10.1021/acssynbio.6b00370] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rational construction of synthetic protein switches with predefined input-output parameters constitutes a key goal of synthetic biology with many potential applications ranging from metabolic engineering to diagnostics. Yet, generally applicable strategies to construct tailor-engineered protein switches have so far remained elusive. Here, we use SpyTag/SpyCatcher-mediated protein ligation to engineer modularly organized, scaffold-dependent protease sensors that exploit a combination of affinity targeting and protease-inducible protein-protein interactions. We use this architecture to create a suite of integrated signal sensing and amplification circuits that can detect the activity of α-thrombin and prostate specific antigen with a dynamic range covering 5 orders of magnitude. We determine the key design features critical for signal transmission between protease-based sensors, transducers, and actuators.
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Affiliation(s)
- Viktor Stein
- Institute
for Molecular Biosciences, The University of Queensland, QBP Building 80, St Lucia, Queensland 4072, Australia
| | - Masuda Nabi
- Institute
for Molecular Biosciences, The University of Queensland, QBP Building 80, St Lucia, Queensland 4072, Australia
| | - Kirill Alexandrov
- Institute
for Molecular Biosciences, The University of Queensland, QBP Building 80, St Lucia, Queensland 4072, Australia
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98
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Dressler OJ, Casadevall I Solvas X, deMello AJ. Chemical and Biological Dynamics Using Droplet-Based Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:1-24. [PMID: 28375703 DOI: 10.1146/annurev-anchem-061516-045219] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas. We then discuss a wide range of analytical methods that have been successfully adapted for analyte detection in droplets. Finally, we highlight a diversity of studies where droplet-based microfluidic strategies have enabled the characterization of dynamic systems that would otherwise have remained unexplorable.
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Affiliation(s)
- Oliver J Dressler
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland;
| | | | - Andrew J deMello
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland;
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99
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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100
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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