1
|
Li J, Howard CB, Dey S, Lowry K, Whiley DM, Puttick S, Rose S, Lobb RJ, Wuethrich A, Edwardraja S, Trau M. A universal reagent for detection of emerging diseases using bioengineered multifunctional yeast nanofragments. Nat Nanotechnol 2023; 18:1222-1229. [PMID: 37291255 DOI: 10.1038/s41565-023-01415-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/04/2023] [Indexed: 06/10/2023]
Abstract
Accurate and early detection of biomarkers provides the molecular evidence for disease management, allowing prompt actions and timely treatments to save lives. Multivalent biomolecular interactions between the probe and biomarker as well as controlled probe orientation on material surfaces are keys for highly sensitive detection. Here we report the bioengineering of programmable and multifunctional nanoprobes, which can provide rapid, specific and highly sensitive detection of emerging diseases in a range of widely used diagnostic systems. These nanoprobes composed of nanosized cell wall fragments, termed as synthetic bionanofragments (SynBioNFs), are generated by the fragmentation of genetically programmed yeast cells. SynBioNFs display multiple copies of biomolecules for high-affinity target binding and molecular handles for the precisely orientated attachment on surfaces used in diagnostic platforms. SynBioNFs are demonstrated for the capture and detection of SARS-CoV-2 virions using multiple diagnostic platforms, including surface-enhanced Raman scattering, fluorescence, electrochemical and colorimetric-based lateral flow systems with sensitivity comparable with the gold-standard reverse-transcription quantitative polymerase chain reaction.
Collapse
Affiliation(s)
- Junrong Li
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Christopher B Howard
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
| | - Shuvashis Dey
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Kym Lowry
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Simon Puttick
- Probing Biosystems Future Science Platform, Commonwealth Scientific and Industrial Research Organization, Brisbane, Queensland, Australia
| | - Stephen Rose
- Probing Biosystems Future Science Platform, Commonwealth Scientific and Industrial Research Organization, Brisbane, Queensland, Australia
| | - Richard J Lobb
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
| | - Selvakumar Edwardraja
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
| |
Collapse
|
2
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
3
|
Farokhinejad F, Lane RE, Lobb RJ, Edwardraja S, Wuethrich A, Howard CB, Trau M. Generation of Nanoyeast Single-Chain Variable Fragments as High-Avidity Biomaterials for Dengue Virus Detection. ACS Biomater Sci Eng 2021; 7:5850-5860. [PMID: 34738789 DOI: 10.1021/acsbiomaterials.1c01001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioengineered yeast bio-nanomaterials termed nanoyeasts displaying antibody single-chain variable fragments (scFvs) against diagnostic targets are a promising alternative to monoclonal antibodies (mAbs). A potential limitation for translating nanoyeasts into diagnostic tools is batch-to-batch variability. Herein, we demonstrate a systematic approach for cost-efficient production of highly specific nanoyeasts that enabled accurate dengue virus (DENV) detection by immunoassay (2.5% CV). Yeasts bioengineered to surface express DENV-specific scFvs (up to 66% of the total cell population) were fragmented into nanoyeast fractions trialing sonication, bead beating, and high-pressure disruption methods. Nanoyeast fractions from sonication had optimal target binding, uniform particle size (±89 nm), were stable, and retained diagnostic activity for 7 days at 37 °C compared to traditional mAbs that lost activity after 1 day at 37 °C. We engineered a panel of nanoyeast scFvs targeting DENV nonstructural protein 1 (NS1): (i) specific for serotyping DENV 1-4 and (ii) cross-reactive anti-DENV scFvs that are suitable for "yes/no" diagnostic applications. We demonstrate highly specific nanoyeast scFvs for serotyping DENV. We show that nanoyeast scFvs specifically detect NS1 in simulated patient plasma with a limit of detection of 250 ng/mL, the concentration found in infected patients.
Collapse
Affiliation(s)
- Fahimeh Farokhinejad
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca E Lane
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard J Lobb
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Selvakumar Edwardraja
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alain Wuethrich
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christopher B Howard
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
4
|
Bollella P, Edwardraja S, Guo Z, Vickers CE, Whitfield J, Walden P, Melman A, Alexandrov K, Katz E. Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides. ACS Sens 2021; 6:3596-3603. [PMID: 34637274 DOI: 10.1021/acssensors.1c00845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzymatic polypeptide proteolysis is a widespread and powerful biological control mechanism. Over the last few years, substantial progress has been made in creating artificial proteolytic systems where an input of choice modulates the protease activity and thereby the activity of its substrates. However, all proteolytic systems developed so far have relied on the direct proteolytic cleavage of their effectors. Here, we propose a new concept where protease biosensors with a tunable input uncage a signaling peptide, which can then transmit a signal to an allosteric protein reporter. We demonstrate that both the cage and the regulatory domain of the reporter can be constructed from the same peptide-binding domain, such as calmodulin. To demonstrate this concept, we constructed a proteolytic rapamycin biosensor and demonstrated its quantitative actuation on fluorescent, luminescent, and electrochemical reporters. Using the latter, we constructed sensitive bioelectrodes that detect the messenger peptide release and quantitatively convert the recognition event into electric current. We discuss the application of such systems for the construction of in vitro sensory arrays and in vivo signaling circuits.
Collapse
Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
- Department of Chemistry, University of Bari A. Moro, Via E. Orabona 4, Bari 70125, Italy
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, 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, Centre for Genomics and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GP.O. Box 2583, Brisbane, Queensland 4001, Australia
| | - Jason Whitfield
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, 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, Queensland 4001, Australia
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - 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, Queensland 4001, Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| |
Collapse
|
5
|
Li J, Wuethrich A, Edwardraja S, Lobb RJ, Puttick S, Rose S, Howard CB, Trau M. Amplification-Free SARS-CoV-2 Detection Using Nanoyeast-scFv and Ultrasensitive Plasmonic Nanobox-Integrated Nanomixing Microassay. Anal Chem 2021; 93:10251-10260. [PMID: 34264067 PMCID: PMC8290924 DOI: 10.1021/acs.analchem.1c01657] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023]
Abstract
The implementation of accurate and sensitive molecular detection for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is paramount to effectively control the ongoing coronavirus disease 2019 (COVID-19) pandemic. In this regard, we herein propose the specific and highly sensitive SARS-CoV-2 detection based on nanoyeast single-chain-variable fragment (scFv) and ultrasensitive plasmonic nanobox-integrated nanomixing microassay. Importantly, this designed platform showcases the utility of nanoyeast-scFvs as specific capture reagents targeting the receptor-binding domain (RBD) of the virus and as monoclonal antibody alternatives suitable for cost-effective mass production and frequent testing. By capitalizing on single-particle active nanoboxes as plasmonic nanostructures for surface-enhanced Raman scattering (SERS), the microassay utilizes highly sensitive Raman signals to indicate virus infection. The developed microassay further integrated nanomixing for accelerating molecular collisions. Through the synergistic working of nanoyeast-scFv, plasmonic nanoboxes, and nanomixing, the highly specific and sensitive SARS-CoV-2 detection is achieved as low as 17 virus/μL without any molecular amplification. We successfully demonstrate SARS-CoV-2 detection in saliva samples of simulated patients at clinically relevant viral loads, suggesting the possibility of this platform for accurate and noninvasive patient screening.
Collapse
Affiliation(s)
- Junrong Li
- Centre
for Personalized Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Alain Wuethrich
- Centre
for Personalized Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Selvakumar Edwardraja
- Centre
for Personalized Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Richard J. Lobb
- Centre
for Personalized Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Simon Puttick
- Probing
Biosystems Future Science Platform, Commonwealth
Scientific and Industrial Research Organization, Brisbane, QLD 4029, Australia
| | - Stephen Rose
- Probing
Biosystems Future Science Platform, Commonwealth
Scientific and Industrial Research Organization, Brisbane, QLD 4029, Australia
| | - Christopher B. Howard
- Centre
for Personalized Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Centre
for Personalized Nanomedicine, Australian
Institute for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane, QLD 4072, Australia
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
6
|
Bollella P, Guo Z, Edwardraja S, Krishna Kadambar V, Alexandrov K, Melman A, Katz E. Self-powered molecule release systems activated with chemical signals processed through reconfigurable Implication or Inhibition Boolean logic gates. Bioelectrochemistry 2020; 138:107735. [PMID: 33482577 DOI: 10.1016/j.bioelechem.2020.107735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023]
Abstract
The Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates were realized using switchable chimeric pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH-Clamp) containing a fused affinity clamp unit recognizing a signal-peptide. The second component of the logic gate was the wild-type PQQ-glucose dehydrogenase working cooperatively with the PQQ-GDH-Clamp enzyme. The IMPLY and INHIB gates were realized using the same enzyme composition activated with differently defined input signals, thus representing reconfigurable logic systems. The logic gates were first tested while operating in a solution with optical analysis of the output signals. Then, the enzymes were immobilized on a buckypaper electrode for electrochemical transduction of the output signals. The switchable modified electrodes mimicking the IMPLY or INHIB logic gates were integrated with an oxygen-reducing electrode modified with bilirubin oxidase to operate as a biofuel cell activated/inhibited by various input signal combinations processed either by IMPLY or INHIB logic gates. The switchable biofuel cell was used as a self-powered device triggering molecule release function controlled by the logically processed molecule signals.
Collapse
Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4001, QLD, Australia
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane 4072, QLD, Australia
| | - Vasantha Krishna Kadambar
- 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, School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4001, QLD, 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.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
9
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
10
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
| |
Collapse
|
11
|
Edwardraja S, Eichinger A, Theobald I, Sommer CA, Reichert AJ, Skerra A. Rational Design of an Anticalin-Type Sugar-Binding Protein Using a Genetically Encoded Boronate Side Chain. ACS Synth Biol 2017; 6:2241-2247. [PMID: 28937743 DOI: 10.1021/acssynbio.7b00199] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The molecular recognition of carbohydrates plays a fundamental role in many biological processes. However, the development of carbohydrate-binding reagents for biomedical research and use poses a challenge due to the generally poor affinity of proteins toward sugars in aqueous solution. Here, we describe the effective molecular recognition of pyranose monosaccharides (in particular, galactose and mannose) by a rationally designed protein receptor based on the human lipocalin scaffold (Anticalin). Complexation relies on reversible covalent cis-diol boronate diester formation with a genetically encoded l-boronophenylalanine (Bpa) residue which was incorporated as a non-natural amino acid at a sterically permissive position in the ligand pocket of the Anticalin, as confirmed by X-ray crystallography. Compared with the metal-ion and/or avidity-dependent oligovalent lectins that prevail in nature, our approach offers a novel and promising route to generate tight sugar-binding reagents both as research reagents and for biomedical applications.
Collapse
Affiliation(s)
- Selvakumar Edwardraja
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Andreas Eichinger
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Ina Theobald
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Carina Andrea Sommer
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Andreas J. Reichert
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Arne Skerra
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| |
Collapse
|
12
|
Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. Biochim Biophys Acta Bioenerg 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
Collapse
Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| |
Collapse
|
13
|
Edwardraja S, Munussami G, Goyal A, Lee SG. Generation of efficient fingerprint for GFP-like fold and computational identification of potential GFP-like homologs. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0362-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Olson TL, Espiritu E, Edwardraja S, Simmons CR, Williams JC, Ghirlanda G, Allen JP. Design of dinuclear manganese cofactors for bacterial reaction centers. Biochim Biophys Acta 2015; 1857:539-547. [PMID: 26392146 DOI: 10.1016/j.bbabio.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
Abstract
A compelling target for the design of electron transfer proteins with novel cofactors is to create a model for the oxygen-evolving complex, a Mn4Ca cluster, of photosystem II. A mononuclear Mn cofactor can be added to the bacterial reaction center, but the addition of multiple metal centers is constrained by the native protein architecture. Alternatively, metal centers can be incorporated into artificial proteins. Designs for the addition of dinuclear metal centers to four-helix bundles resulted in three artificial proteins with ligands for one, two, or three dinuclear metal centers able to bind Mn. The three-dimensional structure determined by X-ray crystallography of one of the Mn-proteins confirmed the design features and revealed details concerning coordination of the Mn center. Electron transfer between these artificial Mn-proteins and bacterial reaction centers was investigated using optical spectroscopy. After formation of a light-induced, charge-separated state, the experiments showed that the Mn-proteins can donate an electron to the oxidized bacteriochlorophyll dimer of modified reaction centers, with the Mn-proteins having additional metal centers being more effective at this electron transfer reaction. Modeling of the structure of the Mn-protein docked to the reaction center showed that the artificial protein likely binds on the periplasmic surface similarly to cytochrome c2, the natural secondary donor. Combining reaction centers with exogenous artificial proteins provides the opportunity to create ligands and investigate the influence of inhomogeneous protein environments on multinuclear redox-active metal centers. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
Collapse
Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| |
Collapse
|
15
|
Flores M, Olson TL, Wang D, Edwardraja S, Shinde S, Williams JC, Ghirlanda G, Allen JP. Copper Environment in Artificial Metalloproteins Probed by Electron Paramagnetic Resonance Spectroscopy. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marco Flores
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Tien L. Olson
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Dong Wang
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Selvakumar Edwardraja
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sandip Shinde
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - JoAnn C. Williams
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - James P. Allen
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| |
Collapse
|
16
|
Muppidi A, Doi K, Edwardraja S, Pulavarti SVSRK, Szyperski T, Wang HG, Lin Q. Targeted delivery of ubiquitin-conjugated BH3 peptide-based Mcl-1 inhibitors into cancer cells. Bioconjug Chem 2014; 25:424-32. [PMID: 24410055 PMCID: PMC3974624 DOI: 10.1021/bc4005574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BH3 peptides are key mediators of apoptosis and have served as the lead structures for the development of anticancer therapeutics. Previously, we reported the application of a simple cysteine-based side chain cross-linking chemistry to NoxaBH3 peptides that led to the generation of the cross-linked NoxaBH3 peptides with increased cell permeability and higher inhibitory activity against Mcl-1 ( Muppidi, A., Doi, K., Edwardraja, S., Drake, E. J., Gulick, A. M., Wang, H.-G., Lin, Q. ( 2012 ) J. Am. Chem. Soc. 134 , 14734 ). To deliver cross-linked NoxaBH3 peptides selectively into cancer cells for enhanced efficacy and reduced systemic toxicity, here we report the conjugation of the NoxaBH3 peptides with the extracellular ubiquitin, a recently identified endogenous ligand for CXCR4, a chemokine receptor overexpressed in cancer cells. The resulting ubiquitin-NoxaBH3 peptide conjugates showed increased inhibitory activity against Mcl-1 and selective killing of the CXCR4-expressing cancer cells. The successful delivery of the NoxaBH3 peptides by ubiquitin into cancer cells suggests that the ubiquitin/CXCR4 axis may serve as a general route for the targeted delivery of anticancer agents.
Collapse
Affiliation(s)
- Avinash Muppidi
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | | | | | | | | | | | | |
Collapse
|
17
|
Zhou S, Mohan Raj S, Ashok S, Edwardraja S, Lee SG, Park S. Cloning, expression and characterization of 3-hydroxyisobutyrate dehydrogenase from Pseudomonas denitrificans ATCC 13867. PLoS One 2013; 8:e62666. [PMID: 23658760 PMCID: PMC3642240 DOI: 10.1371/journal.pone.0062666] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/23/2013] [Indexed: 11/24/2022] Open
Abstract
The gene encoding an NAD+-dependent, 3-hydroxyisobutyrate dehydrogenase (3HIBDH-IV) from Pseudomonas denitrificans ATCC 13867 was cloned and expressed in Escherichia coli BL 21 (DE3) and characterized to understand its physiological relevance in the degradation of 3-hydroxypropionic acid (3-HP). The deduced amino acid sequence showed high similarity to other 3-hydroxyisobutyrate dehydrogenase isozymes (3HIBDHs) of P. denitrificans ATCC 13867. A comparison of 3HIBDH-IV with its relevant enzymes along with molecular docking studies suggested that Lys171, Asn175 and Gly123 are important for its catalytic function on 3-hydroxyacids. The recombinant 3HIBDH-IV was purified to homogeneity utilizing a Ni-NTA-HP resin column in high yield. 3HIBDH-IV was very specific to (S)-3-hydroxyisobutyrate, but also catalyzed the oxidation of 3-HP to malonate semialdehyde. The specific activity and half-saturation constant (Km) for 3-HP at 30°C and pH 9.0 were determined to be 17 U/mg protein and 1.0 mM, respectively. Heavy metals, such as Ag+ and Hg2+, completely inhibited the 3HIBDH-IV activity, whereas dithiothreitol, 2-mercaptoethanol and ethylenediaminetetraacetic acid increased its activity 1.5–1.8-fold. This paper reports the characteristics of 3HIBDH-IV as well as its probable role in 3-HP degradation.
Collapse
Affiliation(s)
- Shengfang Zhou
- Department of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan, Korea
| | - Subramanian Mohan Raj
- Department of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan, Korea
- Centre for Research and Development, PRIST University, Thanjavur, India
| | - Somasundar Ashok
- Department of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan, Korea
| | - Selvakumar Edwardraja
- Department of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan, Korea
- Technical University of Munich, Lehrstuhl für Biologische Chemie, Freising-Weihenstephan, Germany
| | - Sun-gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan, Korea
| | - Sunghoon Park
- Department of Chemical and Biomolecular Engineering, Pusan National University, Geumjeong-gu, Busan, Korea
- * E-mail:
| |
Collapse
|
18
|
Muppidi A, Doi K, Edwardraja S, Drake EJ, Gulick AM, Wang HG, Lin Q. Rational design of proteolytically stable, cell-permeable peptide-based selective Mcl-1 inhibitors. J Am Chem Soc 2012; 134:14734-7. [PMID: 22920569 DOI: 10.1021/ja306864v] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct chemical modifications provide a simple and effective means to "translate" bioactive helical peptides into potential therapeutics targeting intracellular protein-protein interactions. We previously showed that distance-matching bisaryl cross-linkers can reinforce peptide helices containing two cysteines at the i and i+7 positions and confer cell permeability to the cross-linked peptides. Here we report the first crystal structure of a biphenyl-cross-linked Noxa peptide in complex with its target Mcl-1 at 2.0 Å resolution. Guided by this structure, we remodeled the surface of this cross-linked peptide through side-chain substitution and N-methylation and obtained a pair of cross-linked peptides with substantially increased helicity, cell permeability, proteolytic stability, and cell-killing activity in Mcl-1-overexpressing U937 cells.
Collapse
Affiliation(s)
- Avinash Muppidi
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA
| | | | | | | | | | | | | |
Collapse
|
19
|
Li N, Lim RKV, Edwardraja S, Lin Q. Copper-free Sonogashira cross-coupling for functionalization of alkyne-encoded proteins in aqueous medium and in bacterial cells. J Am Chem Soc 2011; 133:15316-9. [PMID: 21899368 DOI: 10.1021/ja2066913] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioorthogonal reactions suitable for functionalization of genetically or metabolically encoded alkynes, for example, copper-catalyzed azide-alkyne cycloaddition reaction ("click chemistry"), have provided chemical tools to study biomolecular dynamics and function in living systems. Despite its prominence in organic synthesis, copper-free Sonogashira cross-coupling reaction suitable for biological applications has not been reported. In this work, we report the discovery of a robust aminopyrimidine-palladium(II) complex for copper-free Sonogashira cross-coupling that enables selective functionalization of a homopropargylglycine (HPG)-encoded ubiquitin protein in aqueous medium. A wide range of aromatic groups including fluorophores and fluorinated aromatic compounds can be readily introduced into the HPG-containing ubiquitin under mild conditions with good to excellent yields. The suitability of this reaction for functionalization of HPG-encoded ubiquitin in Escherichia coli was also demonstrated. The high efficiency of this new catalytic system should greatly enhance the utility of Sonogashira cross-coupling in bioorthogonal chemistry.
Collapse
Affiliation(s)
- Nan Li
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | | | | | | |
Collapse
|
20
|
Edwardraja S, Sriram S, Govindan R, Budisa N, Lee SG. Enhancing the thermal stability of a single-chain Fv fragment by in vivo global fluorination of the proline residues. ACTA ACUST UNITED AC 2011; 7:258-65. [DOI: 10.1039/c0mb00154f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
21
|
Edwardraja S, Neelamegam R, Ramadoss V, Venkatesan S, Lee SG. Redesigning of anti-c-Met single chain Fv antibody for the cytoplasmic folding and its structural analysis. Biotechnol Bioeng 2010; 106:367-75. [DOI: 10.1002/bit.22702] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
22
|
Ayyadurai N, Neelamegam R, Nagasundarapandian S, Edwardraja S, Park HS, Lee SJ, Yoo TH, Yoon H, Lee SG. Importance of expression system in the production of unnatural recombinant proteins in Escherichia coli. BIOTECHNOL BIOPROC E 2009. [DOI: 10.1007/s12257-009-0009-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
23
|
Kim YJ, Neelamegam R, Heo MA, Edwardraja S, Paik HJ, Lee SG. Improving the productivity of single-chain Fv antibody against c-Met by rearranging the order of its variable domains. J Microbiol Biotechnol 2008; 18:1186-1190. [PMID: 18600066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Single-chain Fv (scFv) antibody against c-Met is expected to be employed in clinical treatment or imaging of cancer cells owing to the important biological roles of c-Met in the proliferation of malignancies. Here, we show that the productivity of scFv against c-Met in Escherichia coli is significantly influenced by the orientation of its variable domains. We generated anti-c-Met scFv antibodies with two different domain orders (i.e., VL-linker-VH and VH-linker-VL), expressed them in the cytoplasm of E. coli trx/ gor deleted mutant, and compared their specific activities as well as their productivities. Productivity of total and functional anti-c-Met scFv with VH/VL orientation was more than five times higher than that with VL/VH format. Coexpression of DsbC enhanced the yield of soluble amounts of anti-c-Met scFv protein for both constructs. The purified scFv antibodies of the two different formats exhibited almost the same antigen-binding activities. We also compared the productivities and specific activities of anti-c-Met diabodies with VH/VL or VL/VH formats and obtained similar results to the case of scFv antibodies.
Collapse
Affiliation(s)
- Yu-Jin Kim
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, Korea
| | | | | | | | | | | |
Collapse
|