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Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ. Engineering Ca 2+-Dependent DNA Polymerase Activity. ACS Synth Biol 2023; 12:3301-3311. [PMID: 37856140 DOI: 10.1021/acssynbio.3c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Advancements in synthetic biology have provided new opportunities in biosensing, with applications ranging from genetic programming to diagnostics. Next generation biosensors aim to expand the number of accessible environments for measurements, increase the number of measurable phenomena, and improve the quality of the measurement. To this end, an emerging area in the field has been the integration of DNA as an information storage medium within biosensor outputs, leveraging nucleic acids to record the biosensor state over time. However, slow signal transduction steps, due to the time scales of transcription and translation, bottleneck many sensing-DNA recording approaches. DNA polymerases (DNAPs) have been proposed as a solution to the signal transduction problem by operating as both the sensor and responder, but there is presently a lack of DNAPs with functional sensitivity to many desirable target ligands. Here, we engineer components of the Pol δ replicative polymerase complex of Saccharomyces cerevisiae to sense and respond to Ca2+, a metal cofactor relevant to numerous biological phenomena. Through domain insertion and binding site grafting to Pol δ subunits, we demonstrate functional allosteric sensitivity to Ca2+. Together, this work provides an important foundation for future efforts in the development of DNAP-based biosensors.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Namita J Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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2
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Wu CC, Huang SJ, Fu TY, Lin FL, Wang XY, Tan KT. Small-Molecule Modulated Affinity-Tunable Semisynthetic Protein Switches. ACS Sens 2022; 7:2691-2700. [PMID: 36084142 DOI: 10.1021/acssensors.2c01211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Engineered protein switches have been widely applied in cell-based protein sensors and point-of-care diagnosis for the rapid and simple analysis of a wide variety of proteins, metabolites, nucleic acids, and enzymatic activities. Currently, these protein switches are based on two main types of switching mechanisms to transduce the target binding event to a quantitative signal, through a change in the optical properties of fluorescent molecules and the activation of enzymatic activities. In this paper, we introduce a new affinity-tunable protein switch strategy in which the binding of a small-molecule target with the protein activates the streptavidin-biotin interaction to generate a readout signal. In the absence of a target, the biotinylated protein switch forms a closed conformation where the biotin is positioned in close proximity to the protein, imposing a large steric hindrance to prevent the effective binding with streptavidin. In the presence of the target molecule, this steric hindrance is removed, thereby exposing the biotin for streptavidin binding to produce strong fluorescent signals. With this modular sensing concept, various sulfonamide, methotrexate, and trimethoprim drugs can be selectively detected on the cell surface of native and genetically engineered cells using different fluorescent dyes and detection techniques.
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Affiliation(s)
- Chien-Chi Wu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Shao-Jie Huang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Tsung-Yu Fu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Fang-Ling Lin
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Xin-You Wang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
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3
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Ergun Ayva C, Fiorito MM, Guo Z, Edwardraja S, Kaczmarski JA, Gagoski D, Walden P, Johnston WA, Jackson CJ, Nebl T, Alexandrov K. Exploring Performance Parameters of Artificial Allosteric Protein Switches. J Mol Biol 2022; 434:167678. [PMID: 35709893 DOI: 10.1016/j.jmb.2022.167678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 10/18/2022]
Abstract
Biological information processing networks rely on allosteric protein switches that dynamically interconvert biological signals. Construction of their artificial analogues is a central goal of synthetic biology and bioengineering. Receptor domain insertion is one of the leading methods for constructing chimeric protein switches. Here we present an in vitro expression-based platform for the analysis of chimeric protein libraries for which traditional cell survival or cytometric high throughput assays are not applicable. We utilise this platform to screen a focused library of chimeras between PQQ-glucose dehydrogenase and calmodulin. Using this approach, we identified 50 chimeras (approximately 23% of the library) that were activated by calmodulin-binding peptides. We analysed performance parameters of the active chimeras and demonstrated that their dynamic range and response times are anticorrelated, pointing to the existence of an inherent thermodynamic trade-off. We show that the structure of the ligand peptide affects both the response and activation kinetics of the biosensors suggesting that the structure of a ligand:receptor complex can influence the chimera's activation pathway. In order to understand the extent of structural changes in the reporter protein induced by the receptor domains, we have analysed one of the chimeric molecules by CD spectroscopy and hydrogen-deuterium exchange mass spectrometry. We concluded that subtle ligand-induced changes in the receptor domain propagated into the GDH domain and affected residues important for substrate and cofactor binding. Finally, we used one of the identified chimeras to construct a two-component rapamycin biosensor and demonstrated that core switch optimisation translated into improved biosensor performance.
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Affiliation(s)
- Cagla Ergun Ayva
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Maria M Fiorito
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zhong Guo
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joe A Kaczmarski
- ARC Centre of Excellence in Synthetic Biology, Australia; Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Dejan Gagoski
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Patricia Walden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Wayne A Johnston
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Colin J Jackson
- ARC Centre of Excellence in Synthetic Biology, Australia; Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia. https://twitter.com/Jackson_Lab
| | - Tom Nebl
- Biology Group, Biomedical Manufacturing Program, CSIRO, Bayview Ave/Research Way, Clayton, VIC 3168, Australia
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia; CSIRO-QUT Synthetic Biology Alliance, Brisbane, QLD 4001, Australia; Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4001, Australia.
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4
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Guo Z, Smutok O, Johnston WA, Ayva CE, Walden P, McWhinney B, Ungerer JPJ, Melman A, Katz E, Alexandrov K. Circular Permutated PQQ‐Glucose Dehydrogenase as an Ultrasensitive Electrochemical Biosensor. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy Centre for Genomics and Personalised Health School of Biology and Environmental Science Queensland University of Technology Brisbane QLD 4001 Australia
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science Clarkson University 8 Clarkson Ave. Potsdam NY 13699 USA
| | - Wayne A. Johnston
- CSIRO-QUT Synthetic Biology Alliance ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy Centre for Genomics and Personalised Health School of Biology and Environmental Science Queensland University of Technology Brisbane QLD 4001 Australia
| | - Cagla Ergun Ayva
- CSIRO-QUT Synthetic Biology Alliance ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy Centre for Genomics and Personalised Health School of Biology and Environmental Science Queensland University of Technology Brisbane QLD 4001 Australia
| | - Patricia Walden
- CSIRO-QUT Synthetic Biology Alliance ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy Centre for Genomics and Personalised Health School of Biology and Environmental Science Queensland University of Technology Brisbane QLD 4001 Australia
| | - Brett McWhinney
- Department of Chemical Pathology Pathology Queensland Brisbane QLD 4001 Australia
| | - Jacobus P. J. Ungerer
- Department of Chemical Pathology Pathology Queensland Brisbane QLD 4001 Australia
- Faculty of Health and Behavioural Sciences University of Queensland Brisbane QLD 4072 Australia
| | - Artem Melman
- Department of Chemistry and Biomolecular Science Clarkson University 8 Clarkson Ave. Potsdam NY 13699 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University 8 Clarkson Ave. Potsdam NY 13699 USA
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy Centre for Genomics and Personalised Health School of Biology and Environmental Science Queensland University of Technology Brisbane QLD 4001 Australia
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5
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Alexandrov K, Guo Z, Smutok O, Wayne A Johnston WAJ, Ergun Ayva C, Walden PM, McWhinney B, Ungerer J, Melman A, Katz E. Circular permutated PQQ-glucose dehydrogenase as an ultrasensitive electrochemical biosensor. Angew Chem Int Ed Engl 2021; 61:e202109005. [PMID: 34633119 DOI: 10.1002/anie.202109005] [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] [Received: 07/06/2021] [Indexed: 11/08/2022]
Abstract
Protein biosensors play an increasingly important role as reporters for research and clinical applications. Here we present an approach for the construction of fully integrated but modular electrochemical biosensors based on the principal component of glucose monitors PQQ-glucose dehydrogenase (PQQ-GDH). We designed allosterically regulated circular permutated variants of PQQ-GDH that show large (>10 fold) changes in enzymatic activity following intramolecular scaffolding of the newly generated N- and C termini by ligand binding domain:ligand complexes. The developed biosensors demonstrated sub-nanomolar affinities for small molecules and proteins in colorimetric and electrochemical assays. For instance, the concentration of Cyclosporine A could be measured in 1 ml of undiluted blood with the same accuracy as the leading diagnostic technique that uses 50 times more sample. We further used this biosensor to construct highly porous gold bioelectrodes capable of robustly detecting concentrations of Cyclosporine A as low as 20 pM and retained functionality in samples containing at least 60% human serum. These experiments suggest that the developed biosensor platform is generalizable and may be suitable for Point-of-Care diagnostics.
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Affiliation(s)
- Kirill Alexandrov
- Queensland University of Technology, Centre for Tropical Crops and Biocommodities, 2 george st, 4100, Brisbane, AUSTRALIA
| | - Zhong Guo
- Queensland University of Technology Institute of Health and Biomedical Innovation Research Methods Group: Queensland University of Technology Institute of Health and Biomedical Innovation, CSIRO-QUT synthetic Biology Alliance, AUSTRALIA
| | - Oleh Smutok
- Clarkson University, electrochemistry, UNITED STATES
| | - Wayne A Johnston Wayne A Johnston
- Queensland University of Technology IHBI: Queensland University of Technology Institute of Health and Biomedical Innovation, CSIRO-QUT synthetic Biology Alliance, AUSTRALIA
| | - Cagla Ergun Ayva
- Queensland University of Technology IHBI: Queensland University of Technology Institute of Health and Biomedical Innovation, CSIRO-QUT Synthetic Biology Alliance, AUSTRALIA
| | - Patricia M Walden
- Queensland University of Technology IHBI: Queensland University of Technology Institute of Health and Biomedical Innovation, CSIRO-QUT synthetic biology alliance, AUSTRALIA
| | - Brett McWhinney
- Central Laboratory: Health Support Queensland Pathology Queensland, chemical pathology, AUSTRALIA
| | - Jacobus Ungerer
- Health Support Queensland Pathology Queensland, Chemical Pathology, AUSTRALIA
| | | | - Evgeny Katz
- Clarkson University, electrochemistry, AUSTRALIA
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6
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Intrinsically disordered protein domain of human ameloblastin in synthetic fusion with calmodulin increases calmodulin stability and modulates its function. Int J Biol Macromol 2020; 168:1-12. [PMID: 33290768 DOI: 10.1016/j.ijbiomac.2020.11.216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 11/21/2022]
Abstract
Constantly increasing attention to bioengineered proteins has led to the rapid development of new functional targets. Here we present the biophysical and functional characteristics of the newly designed CaM/AMBN-Ct fusion protein. The two-domain artificial target consists of calmodulin (CaM) and ameloblastin C-terminus (AMBN-Ct). CaM as a well-characterized calcium ions (Ca2+) binding protein offers plenty of options in terms of Ca2+ detection in biomedicine and biotechnologies. Highly negatively charged AMBN-Ct belongs to intrinsically disordered proteins (IDPs). CaM/AMBN-Ct was designed to open new ways of communication synergies between the domains with potential functional improvement. The character and function of CaM/AMBN-Ct were explored by biophysical and molecular modelling methods. Experimental studies have revealed increased stability and preserved CaM/AMBN-Ct function. The results of molecular dynamic simulations (MDs) outlined different interface patterns between the domains with potential allosteric communication within the fusion.
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7
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Rani A, Kavianinia I, Hume P, De Leon-Rodriguez LM, Kihara S, Williams DE, McGillivray DJ, Plank NOV, Gerrard J, Hodgkiss JM, Brimble MA. Directed self-assembly of peptide-diketopyrrolopyrrole conjugates - a platform for bio-organic thin film preparation. SOFT MATTER 2020; 16:6563-6571. [PMID: 32588868 DOI: 10.1039/d0sm01071e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Increased water solubility and long-range intermolecular ordering have been introduced into the fluorescent organic molecule thiophene-diketopyrrolopyrrole (TDPP) via its conjugation to the octapeptide HEFISTAH, which is derived from the protein-protein β-interface of the homo-tetramer protein diaminopimelate decarboxylase. The octapeptide, and its TDPP mono- and cross-linked conjugates were synthesised using 9-fluorenylmethoxycarbonyl (Fmoc) based solid-phase peptide synthesis (SPPS). Unlike the unmodified peptide, the resulting mono-linked and cross-linked peptides showed a fibrous morphology and formed hydrogels at 4 wt% in water at neutral pH, but failed to assemble at pH 2 and pH 9. Further peptide characterization showed that the TDPP organic core enhances peptide self-assembly and that both peptides assembled into fibers with a parallel β-sheet structure. Furthermore, UV-vis spectroscopic analysis suggests that the TDPP molecules form H-type aggregates where the chromophores are likely to be co-facially packed, but rotationally and/or laterally offset from one another. This intermolecular coupling indicates that π-π stacking interactions are highly likely - a favourable sign for charge transport. The enhanced aqueous solubility and self-assembling properties of the TDPP-peptide conjugates allowed the successful preparation of thin films. Atomic force microscopy, X-ray diffraction and UV-vis spectroscopic analysis of these thin films revealed that the hybrid materials retained a fibrous morphology, β-sheet structures and strong intermolecular coupling between neighbouring TDPP molecules. These results open an exciting avenue for bio-organic materials development, through structural and electronic tuning of the TDPP core.
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Affiliation(s)
- Aakanksha Rani
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Iman Kavianinia
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Paul Hume
- MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand and School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6021, New Zealand
| | - Luis M De Leon-Rodriguez
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand.
| | - Shinji Kihara
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - David E Williams
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Natalie O V Plank
- MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand and School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6021, New Zealand
| | - Juliet Gerrard
- School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Justin M Hodgkiss
- MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand and School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6021, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
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8
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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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Edwardraja S, Guo Z, Whitfield J, Lantadilla IR, Johnston WA, Walden P, Vickers CE, Alexandrov K. Caged Activators of Artificial Allosteric Protein Biosensors. ACS Synth Biol 2020; 9:1306-1314. [PMID: 32339455 DOI: 10.1021/acssynbio.9b00500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ability of proteins to interconvert unrelated biochemical inputs and outputs underlays most energy and information processing in biology. A common conversion mechanism involves a conformational change of a protein receptor in response to a ligand binding or a covalent modification, leading to allosteric activity modulation of the effector domain. Designing such systems rationally is a central goal of synthetic biology and protein engineering. A two-component sensory system based on the scaffolding of modules in the presence of an analyte is one of the most generalizable biosensor architectures. An inherent problem of such systems is dependence of the response on the absolute and relative concentrations of the components. Here we use the example of two-component sensory systems based on calmodulin-operated synthetic switches to analyze and address this issue. We constructed "caged" versions of the activating domain thereby creating a thermodynamic barrier for spontaneous activation of the system. We demonstrate that the caged biosensor architectures could operate at concentrations spanning 3 orders of magnitude and are applicable to electrochemical, luminescent, and fluorescent two-component biosensors. We analyzed the activation kinetics of the caged biosensors and determined that the core allosteric switch is likely to be the rate limiting component of the system. These findings provide guidance for predictable engineering of robust sensory systems with inputs and outputs of choice.
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Affiliation(s)
- Selvakumar Edwardraja
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 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, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Jason Whitfield
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
| | | | - Wayne A. Johnston
- 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, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- 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, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - 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, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
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10
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Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites. Sci Rep 2019; 9:16957. [PMID: 31740686 PMCID: PMC6861286 DOI: 10.1038/s41598-019-53464-z] [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: 07/12/2019] [Accepted: 10/24/2019] [Indexed: 11/27/2022] Open
Abstract
For protein mutagenesis, a common expectation is that important positions will behave like on/off “toggle” switches (i.e., a few substitutions act like wildtype, most abolish function). However, there exists another class of important positions that manifests a wide range of functional outcomes upon substitution: “rheostat” positions. Previously, we evaluated rheostat positions located near the allosteric binding sites for inhibitor alanine (Ala) and activator fructose-1,6-bisphosphate (Fru-1,6-BP) in human liver pyruvate kinase. When substituted with multiple amino acids, many positions demonstrated moderate rheostatic effects on allosteric coupling between effector binding and phosphoenolpyruvate (PEP) binding in the active site. Nonetheless, the combined outcomes of all positions sampled the full range of possible allosteric coupling (full tunability). However, that study only evaluated allosteric tunability of “local” positions, i.e., positions were located near the binding sites of the allosteric ligand being assessed. Here, we evaluated tunability of allosteric coupling when mutated sites were distant from the allosterically-coupled binding sites. Positions near the Ala binding site had rheostatic outcomes on allosteric coupling between Fru-1,6-BP and PEP binding. In contrast, positions in the Fru-1,6-BP site exhibited modest effects on coupling between Ala and PEP binding. Analyzed in aggregate, both PEP/Ala and PEP/Fru-1,6-BP coupling were again fully tunable by amino acid substitutions at this limited set of distant positions. Furthermore, some positions exhibited rheostatic control over multiple parameters and others exhibited rheostatic effects on one parameter and toggle control over a second. These findings highlight challenges in efforts to both predict/interpret mutational outcomes and engineer functions into proteins.
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11
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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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12
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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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13
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Gorman SD, D'Amico RN, Winston DS, Boehr DD. Engineering Allostery into Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:359-384. [PMID: 31707711 PMCID: PMC7508002 DOI: 10.1007/978-981-13-8719-7_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Our ability to engineer protein structure and function has grown dramatically over recent years. Perhaps the next level in protein design is to develop proteins whose function can be regulated in response to various stimuli, including ligand binding, pH changes, and light. Endeavors toward these goals have tested and expanded on our understanding of protein function and allosteric regulation. In this chapter, we provide examples from different methods for developing new allosterically regulated proteins. These methods range from whole insertion of regulatory domains into new host proteins, to covalent attachment of photoswitches to generate light-responsive proteins, and to targeted changes to specific amino acid residues, especially to residues identified to be important for relaying allosteric information across the protein framework. Many of the examples we discuss have already found practical use in medical and biotechnology applications.
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Affiliation(s)
- Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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14
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Diaferia C, Balasco N, Sibillano T, Giannini C, Vitagliano L, Morelli G, Accardo A. Structural Characterization of Self-Assembled Tetra-Tryptophan Based Nanostructures: Variations on a Common Theme. Chemphyschem 2018. [PMID: 29542851 DOI: 10.1002/cphc.201800026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over the years, a large number of multidisciplinary investigations has unveiled that the self-assembly of short peptides and even of individual amino acids can generate a variety of different biomaterials. In this framework, we have recently reported that polyethylene glycol (PEG) conjugates of short homopeptides, containing aromatic amino acids such as phenylalanine (Phe, F) and naphthylalanine (Nal), are able to form elongated fibrillary aggregates having interesting chemical and physical properties. We here extend these analyses characterizing the self-assembling propensity of PEG6 -W4, a PEG adduct of the tetra-tryptophan (W4) sequence. A comprehensive structural characterization of PEG6 -W4 was obtained, both in solution and at the solid state, through the combination of spectroscopic, microscopic, X-ray scattering and computational techniques. Collectively, these studies demonstrate that this peptide is able to self-assemble in fibrillary networks characterized by a cross β-structure spine. The present findings clearly demonstrate that aromatic residues display a general propensity to induce self-aggregation phenomenon, despite the significant differences in the physicochemical properties of their side chains.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134-, Naples, Italy
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples (Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples (Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134-, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134-, Naples, Italy
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15
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Teanphonkrang S, Janke S, Chaiyen P, Sucharitakul J, Suginta W, Khunkaewla P, Schuhmann W, Ruff A, Schulte A. Tuned Amperometric Detection of Reduced β-Nicotinamide Adenine Dinucleotide by Allosteric Modulation of the Reductase Component of the p-Hydroxyphenylacetate Hydroxylase Immobilized within a Redox Polymer. Anal Chem 2018; 90:5703-5711. [PMID: 29633834 DOI: 10.1021/acs.analchem.7b05467] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the fabrication of an amperometric NADH biosensor system that employs an allosterically modulated bacterial reductase in an adapted osmium(III)-complex-modified redox polymer film for analyte quantification. Chains of complexed Os(III) centers along matrix polymer strings make electrical connection between the immobilized redox protein and a graphite electrode disc, transducing enzymatic oxidation of NADH into a biosensor current. Sustainable anodic signaling required (1) a redox polymer with a formal potential that matched the redox switch of the embedded reductase and avoided interfering redox interactions and (2) formation of a cross-linked enzyme/polymer film for stable biocatalyst entrapment. The activity of the chosen reductase is enhanced upon binding of an effector, i.e. p-hydroxy-phenylacetic acid ( p-HPA), allowing the acceleration of the substrate conversion rate on the sensor surface by in situ addition or preincubation with p-HPA. Acceleration of NADH oxidation amplified the response of the biosensor, with a 1.5-fold increase in the sensitivity of analyte detection, compared to operation without the allosteric modulator. Repetitive quantitative testing of solutions of known NADH concentration verified the performance in terms of reliability and analyte recovery. We herewith established the use of allosteric enzyme modulation and redox polymer-based enzyme electrode wiring for substrate biosensing, a concept that may be applicable to other allosteric enzymes.
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Affiliation(s)
- Somjai Teanphonkrang
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Salome Janke
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry , Chulalongkorn University , 10330 Bangkok , Thailand
| | - Wipa Suginta
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand.,Center of Excellence (CoE) in Advanced Functional Materials, Institute of Science , Suranaree University of Technology , Nakhon Ratchasima 30000 , Thailand
| | - Panida Khunkaewla
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Wolfgang Schuhmann
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Adrian Ruff
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
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16
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Nussbaumer MG, Nguyen PQ, Tay PKR, Naydich A, Hysi E, Botyanszki Z, Joshi NS. Bootstrapped Biocatalysis: Biofilm-Derived Materials as Reversibly Functionalizable Multienzyme Surfaces. ChemCatChem 2017; 9:4328-4333. [PMID: 30519367 PMCID: PMC6277024 DOI: 10.1002/cctc.201701221] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 01/04/2023]
Abstract
Cell-free biocatalysis systems offer many benefits for chemical manufacturing, but their widespread applicability is hindered by high costs associated with enzyme purification, modification, and immobilization on solid substrates, in addition to the cost of the material substrates themselves. Herein, we report a "bootstrapped" biocatalysis substrate material that is produced directly in bacterial culture and is derived from biofilm matrix proteins, which self-assemble into a nanofibrous mesh. We demonstrate that this material can simultaneously purify and immobilize multiple enzymes site specifically and directly from crude cell lysates by using a panel of genetically programmed, mutually orthogonal conjugation domains. We further demonstrate the utility of the technique in a bienzymatic stereoselective reduction coupled with a cofactor recycling scheme. The domains allow for several cycles of selective removal and replacement of enzymes under mild conditions to regenerate the catalyst system.
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Affiliation(s)
- Martin G Nussbaumer
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 (USA)
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 (USA)
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
| | - Pei K R Tay
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 (USA)
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
| | - Alexander Naydich
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
| | - Erisa Hysi
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
| | - Zsofia Botyanszki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 (USA)
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
| | - Neel S Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 (USA)
- Joshi School of Engineering and Applied Sciences Harvard University Cambridge, MA 02138 (USA)
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17
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Kellmann SJ, Dübel S, Thie H. A strategy to identify linker-based modules for the allosteric regulation of antibody-antigen binding affinities of different scFvs. MAbs 2017; 9:404-418. [PMID: 28055297 PMCID: PMC5384732 DOI: 10.1080/19420862.2016.1277302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Antibody single-chain variable fragments (scFvs) are used in a variety of applications, such as for research, diagnosis and therapy. Essential for these applications is the extraordinary specificity, selectivity and affinity of antibody paratopes, which can also be used for efficient protein purification. However, this use is hampered by the high affinity for the protein to be purified because harsh elution conditions, which may impair folding, integrity or viability of the eluted biomaterials, are typically required. In this study, we developed a strategy to obtain structural elements that provide allosteric modulation of the affinities of different antibody scFvs for their antigen. To identify suitable allosteric modules, a complete set of cyclic permutations of calmodulin variants was generated and tested for modulation of the affinity when substituting the linker between VH and VL. Modulation of affinity induced by addition of different calmodulin-binding peptides at physiologic conditions was demonstrated for 5 of 6 tested scFvs of different specificities and antigens ranging from cell surface proteins to haptens. In addition, a variety of different modulator peptides were tested. Different structural solutions were found in respect of the optimal calmodulin permutation, the optimal peptide and the allosteric effect for scFvs binding to different antigen structures. Significantly, effective linker modules were identified for scFvs with both VH-VL and VL-VH architecture. The results suggest that this approach may offer a rapid, paratope-independent strategy to provide allosteric regulation of affinity for many other antibody scFvs.
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Affiliation(s)
- Sarah-Jane Kellmann
- a Miltenyi Biotec GmbH, Friedrich-Ebert-Straße , Bergisch Gladbach , Germany
| | - Stefan Dübel
- b Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics , Braunschweig , Germany
| | - Holger Thie
- a Miltenyi Biotec GmbH, Friedrich-Ebert-Straße , Bergisch Gladbach , Germany
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18
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Biosensors based on β-galactosidase enzyme: Recent advances and perspectives. Anal Biochem 2017; 535:1-11. [DOI: 10.1016/j.ab.2017.07.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/08/2017] [Accepted: 07/18/2017] [Indexed: 11/19/2022]
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19
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Younger AKD, Dalvie NC, Rottinghaus AG, Leonard JN. Engineering Modular Biosensors to Confer Metabolite-Responsive Regulation of Transcription. ACS Synth Biol 2017; 6:311-325. [PMID: 27744683 DOI: 10.1021/acssynbio.6b00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Efforts to engineer microbial factories have benefitted from mining biological diversity and high throughput synthesis of novel enzymatic pathways, yet screening and optimizing metabolic pathways remain rate-limiting steps. Metabolite-responsive biosensors may help to address these persistent challenges by enabling the monitoring of metabolite levels in individual cells and metabolite-responsive feedback control. We are currently limited to naturally evolved biosensors, which are insufficient for monitoring many metabolites of interest. Thus, a method for engineering novel biosensors would be powerful, yet we lack a generalizable approach that enables the construction of a wide range of biosensors. As a step toward this goal, we here explore several strategies for converting a metabolite-binding protein into a metabolite-responsive transcriptional regulator. By pairing a modular protein design approach with a library of synthetic promoters and applying robust statistical analyses, we identified strategies for engineering biosensor-regulated bacterial promoters and for achieving design-driven improvements of biosensor performance. We demonstrated the feasibility of this strategy by fusing a programmable DNA binding motif (zinc finger module) with a model ligand binding protein (maltose binding protein), to generate a novel biosensor conferring maltose-regulated gene expression. This systematic investigation provides insights that may guide the development of additional novel biosensors for diverse synthetic biology applications.
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Affiliation(s)
- Andrew K. D. Younger
- Interdisciplinary
Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil C. Dalvie
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Austin G. Rottinghaus
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Joshua N. Leonard
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert
H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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20
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Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.
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Affiliation(s)
- Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
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21
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Guo Z, Johnston WA, Stein V, Kalimuthu P, Perez-Alcala S, Bernhardt PV, Alexandrov K. Engineering PQQ-glucose dehydrogenase into an allosteric electrochemical Ca2+ sensor. Chem Commun (Camb) 2016; 52:485-8. [DOI: 10.1039/c5cc07824e] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Electrochemical biosensors convert biological events to an electrical current.
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Affiliation(s)
- Zhong Guo
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
| | - Wayne A. Johnston
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
| | - Viktor Stein
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
| | - Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | | | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
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22
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Stein V, Alexandrov K. Synthetic protein switches: design principles and applications. Trends Biotechnol 2015; 33:101-10. [DOI: 10.1016/j.tibtech.2014.11.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 12/22/2022]
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23
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Yu K, Liu C, Kim BG, Lee DY. Synthetic fusion protein design and applications. Biotechnol Adv 2014; 33:155-164. [PMID: 25450191 DOI: 10.1016/j.biotechadv.2014.11.005] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/10/2014] [Accepted: 11/11/2014] [Indexed: 11/16/2022]
Abstract
Synthetic fusion proteins can be designed to achieve improved properties or new functionality by synergistically incorporating multiple proteins into one complex. The fusion of two or more protein domains enhances bioactivities or generates novel functional combinations with a wide range of biotechnological and (bio)pharmaceutical applications. In this review, initially, we summarize the commonly used approaches for constructing fusion proteins. For each approach, the design strategy and desired properties are elaborated with examples of recent studies in the areas of biocatalysts, protein switches and bio-therapeutics. Subsequently, the progress in structural prediction of fusion proteins is presented, which can potentially facilitate the structure-based systematic design of fusion proteins toward identifying the best combinations of fusion partners. Finally, the current challenges and future directions in this field are discussed.
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Affiliation(s)
- Kai Yu
- Department of Chemical and Biomolecular Engineering, Synthetic Biology Research Consortium, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Chengcheng Liu
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151742, South Korea
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, Synthetic Biology Research Consortium, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore 138668, Singapore.
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24
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Way JC, Collins JJ, Keasling JD, Silver PA. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 2014; 157:151-61. [PMID: 24679533 DOI: 10.1016/j.cell.2014.02.039] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/26/2013] [Accepted: 02/19/2014] [Indexed: 01/17/2023]
Abstract
Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering.
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Affiliation(s)
- Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02115, USA
| | - Jay D Keasling
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint Bioenergy Institute, Emeryville, CA 94608, USA; Synthetic Biology Engineering Research Center (SynBERC), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Synthetic Biology Engineering Research Center (SynBERC), University of California, Berkeley, Berkeley, CA 94720, USA.
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25
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Xia Y, DiPrimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weis DD, Anderson JC, Karanicolas J. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation. J Am Chem Soc 2013; 135:18840-9. [PMID: 24313858 DOI: 10.1021/ja407644b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. However, rationally identifying analogous de novo binding sites in other enzymes represents a key challenge for extending this approach to introduce allosteric control into other enzymes. Here we show that mutation sites leading to protein inactivation via tryptophan-to-glycine substitution and allowing (partial) reactivation by the subsequent addition of indole are remarkably frequent. Through a suite of methods including a cell-based reporter assay, computational structure prediction and energetic analysis, fluorescence studies, enzymology, pulse proteolysis, X-ray crystallography, and hydrogen-deuterium mass spectrometry, we find that these switchable proteins are most commonly modulated indirectly, through control of protein stability. Addition of indole in these cases rescues activity not by reverting a discrete conformational change, as we had observed in the sole previously reported example, but rather rescues activity by restoring protein stability. This important finding will dramatically impact the design of future switches and sensors built by this approach, since evaluating stability differences associated with cavity-forming mutations is a far more tractable task than predicting allosteric conformational changes. By analogy to natural signaling systems, the insights from this study further raise the exciting prospect of modulating stability to design optimal recognition properties into future de novo switches and sensors built through chemical rescue of structure.
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Affiliation(s)
- Yan Xia
- Department of Molecular Biosciences, ‡Department of Chemistry, §Protein Structure Laboratory, and ∥Center for Bioinformatics, University of Kansas , Lawrence, Kansas 66045, United States
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