1
|
Idili A, Montón H, Medina-Sánchez M, Ibarlucea B, Cuniberti G, Schmidt OG, Plaxco KW, Parolo C. Continuous monitoring of molecular biomarkers in microfluidic devices. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 187:295-333. [PMID: 35094779 DOI: 10.1016/bs.pmbts.2021.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The ability to monitor molecular targets is crucial in fields ranging from healthcare to industrial processing to environmental protection. Devices employing biomolecules to achieve this goal are called biosensors. Over the last half century researchers have developed dozens of different biosensor approaches. In this chapter we analyze recent advances in the biosensing field aiming at adapting these to the problem of continuous molecular monitoring in complex sample streams, and how the merging of these sensors with lab-on-a-chip technologies would be beneficial to both. To do so we discuss (1) the components that comprise a biosensor, (2) the challenges associated with continuous molecular monitoring in complex sample streams, (3) how different sensing strategies deal with (or fail to deal with) these challenges, and (4) the implementation of these technologies into lab-on-a-chip architectures.
Collapse
Affiliation(s)
- Andrea Idili
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States; Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Rome, Italy
| | - Helena Montón
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | | | - Bergoi Ibarlucea
- Institute for Materials Science and Max Bergmann Center for Biomaterials, Technische Universität Dresden, Dresden, Germany; Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center for Biomaterials, Technische Universität Dresden, Dresden, Germany; Center for Advancing Electronics Dresden (CFAED), Technische Universität Dresden, Dresden, Germany
| | - Oliver G Schmidt
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Dresden, Germany; Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz, Germany; School of Science, TU Dresden, Dresden, Germany
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States; Interdepartmental Program in Biomolecular Science and Engineering University of California, Santa Barbara, CA, United States
| | - Claudio Parolo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States; Barcelona Institute for Global Health (ISGlobal) Hospital Clínic, Barcelona, Spain.
| |
Collapse
|
2
|
Chanda K, MM B. Light emitting probes – approaches for interdisciplinary applications. Chem Soc Rev 2021; 50:3706-3719. [DOI: 10.1039/d0cs01444c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Luminescent probes are key components of sensors to detect numerous bio- and chemical-analytes with high sensitivity and specificity. Sensing is the response of events like self-immolation, FRET, electron/charge transfer, etc. upon interaction.
Collapse
Affiliation(s)
- Kaushik Chanda
- Department of Chemistry
- School of Advanced Sciences
- Vellore Institute of Technology
- Vellore 632014
- India
| | - Balamurali MM
- Chemistry Division
- School of Advanced Sciences
- Vellore Institute of Technology
- Chennai 600127
- India
| |
Collapse
|
3
|
Maity D. Selected peptide-based fluorescent probes for biological applications. Beilstein J Org Chem 2020; 16:2971-2982. [PMID: 33335605 PMCID: PMC7722625 DOI: 10.3762/bjoc.16.247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/18/2020] [Indexed: 01/07/2023] Open
Abstract
To understand the molecular interactions, present in living organisms and their environments, chemists are trying to create novel chemical tools. In this regard, peptide-based fluorescence techniques have attracted immense interest. Synthetic peptide-based fluorescent probes are advantageous over protein-based sensors, since they are synthetically accessible, more stable, and can be easily modified in a site-specific manner for selective biological applications. Peptide receptors labeled with environmentally sensitive/FRET fluorophores have allowed direct detection/monitoring of biomolecules in aqueous media and in live cells. In this review, key peptide-based approaches for different biological applications are presented.
Collapse
Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University, New York, NY 10003, USA
| |
Collapse
|
4
|
Chan NJA, Gu D, Tan S, Fu Q, Pattison TG, O'Connor AJ, Qiao GG. Spider-silk inspired polymeric networks by harnessing the mechanical potential of β-sheets through network guided assembly. Nat Commun 2020; 11:1630. [PMID: 32242004 PMCID: PMC7118121 DOI: 10.1038/s41467-020-15312-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
The high toughness of natural spider-silk is attributed to their unique β-sheet secondary structures. However, the preparation of mechanically strong β-sheet rich materials remains a significant challenge due to challenges involved in processing the polymers/proteins, and managing the assembly of the hydrophobic residues. Inspired by spider-silk, our approach effectively utilizes the superior mechanical toughness and stability afforded by localised β-sheet domains within an amorphous network. Using a grafting-from polymerisation approach within an amorphous hydrophilic network allows for spatially controlled growth of poly(valine) and poly(valine-r-glycine) as β-sheet forming polypeptides via N-carboxyanhydride ring opening polymerisation. The resulting continuous β-sheet nanocrystal network exhibits improved compressive strength and stiffness over the initial network lacking β-sheets of up to 30 MPa (300 times greater than the initial network) and 6 MPa (100 times greater than the initial network) respectively. The network demonstrates improved resistance to strong acid, base and protein denaturants over 28 days. It is known the β-sheet structures in silk-inspired materials generate increased mechanical properties. Here, the authors report on a method of creating silk-inspired materials using in situ formation of β-sheets in an amorphous polymer to replicate the structure of silk and increase the mechanical properties.
Collapse
Affiliation(s)
- Nicholas Jun-An Chan
- Polymer Science Group, Department of Chemical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Dunyin Gu
- Polymer Science Group, Department of Chemical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Shereen Tan
- Polymer Science Group, Department of Chemical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Qiang Fu
- Polymer Science Group, Department of Chemical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Thomas Geoffrey Pattison
- Polymer Science Group, Department of Chemical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Andrea J O'Connor
- Department of Biomedical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Greg G Qiao
- Polymer Science Group, Department of Chemical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
| |
Collapse
|
5
|
Augmenting Peptide Flexibility by Inserting Gamma-Aminobutyric Acid (GABA) in Their Sequence. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10054-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
6
|
Kim I, Song H, Kim C, Kim M, Kyhm K, Kim K, Oh JW. Intermolecular distance measurement with TNT suppressor on the M13 bacteriophage-based Förster resonance energy transfer system. Sci Rep 2019; 9:496. [PMID: 30679611 PMCID: PMC6345812 DOI: 10.1038/s41598-018-36990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/21/2018] [Indexed: 11/09/2022] Open
Abstract
An M13 bacteriophage-based Förster resonance energy transfer (FRET) system is developed to estimate intermolecular distance at the nanoscale using a complex of CdSSe/ZnS nanocrystal quantum dots, genetically engineered M13 bacteriophages labeled with fluorescein isothiocyanate and trinitrotoluene (TNT) as an inhibitor. In the absence of trinitrotoluene, it is observed that a significant spectral shift from blue to green occur, which represents efficient energy transfer through dipole-dipole coupling between donor and acceptor, or FRET-on mode. On the other hand, in the presence of trinitrotoluene, the energy transfer is suppressed, since the donor-to-acceptor intermolecular distance is detuned by the specific capturing of TNT by the M13 bacteriophage, denoted as FRET-off mode. These noble features are confirmed by changes in the fluorescence intensity and the fluorescence decay curve. TNT addition to our system results in reducing the total energy transfer efficiency considerably from 16.1% to 7.6% compared to that in the non-TNT condition, while the exciton decay rate is significantly enhanced. In particular, we confirm that the energy transfer efficiency satisfies the original intermolecular distance dependence of FRET. The relative donor-to-acceptor distance is changed from 70.03 Å to 80.61 Å by inclusion of TNT.
Collapse
Affiliation(s)
- Inhong Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Hyerin Song
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Chuntae Kim
- Department of Nano Fusion Technology, Pusan National University, Busan, 46241, Republic of Korea
| | - Minwoo Kim
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Kwangseuk Kyhm
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Kyujung Kim
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea.
| | - Jin-Woo Oh
- Department of Nano Fusion Technology, Pusan National University, Busan, 46241, Republic of Korea. .,Department of Nanoenergy Engineering, Pusan National University, Busan, 46241, Republic of Korea.
| |
Collapse
|
7
|
Novel DNA/RNA-targeting amino acid beacon for the versatile incorporation at any position within the peptide backbone. Amino Acids 2017; 49:1381-1388. [DOI: 10.1007/s00726-017-2438-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/08/2017] [Indexed: 01/28/2023]
|
8
|
Lim EK, Guk K, Kim H, Chung BH, Jung J. Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon. Chem Commun (Camb) 2016; 52:175-8. [PMID: 26509476 DOI: 10.1039/c5cc05684e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies.
Collapse
Affiliation(s)
- Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Kyeonghye Guk
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and Nanobiotechnology Major, School of Engineering, University of Science and Technology (UST), 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea
| | - Hyeran Kim
- BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Bong-Hyun Chung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Juyeon Jung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| |
Collapse
|
9
|
Song S, Ha K, Guk K, Hwang SG, Choi JM, Kang T, Bae P, Jung J, Lim EK. Colorimetric detection of influenza A (H1N1) virus by a peptide-functionalized polydiacetylene (PEP-PDA) nanosensor. RSC Adv 2016. [DOI: 10.1039/c6ra06689e] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We developed a peptide-functionalized polydiacetylene nanosensor for pH1N1 virus detection with the naked eye.
Collapse
Affiliation(s)
- Sinae Song
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
| | - Kab Ha
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
| | - Kyeonghye Guk
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Seul-Gee Hwang
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Jong Min Choi
- BioNano Health Guard Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon
- Republic of Korea
| | - Taejoon Kang
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Pankee Bae
- BioNano Health Guard Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon
- Republic of Korea
| | - Juyeon Jung
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Eun-Kyung Lim
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
| |
Collapse
|
10
|
Petty JT, Sergev OO, Kantor AG, Rankine IJ, Ganguly M, David FD, Wheeler SK, Wheeler JF. Ten-atom silver cluster signaling and tempering DNA hybridization. Anal Chem 2015; 87:5302-9. [PMID: 25923963 DOI: 10.1021/acs.analchem.5b01265] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Silver clusters with ∼10 atoms are molecules, and specific species develop within DNA strands. These molecular metals have sparsely organized electronic states with distinctive visible and near-infrared spectra that vary with cluster size, oxidation, and shape. These small molecules also act as DNA adducts and coordinate with their DNA hosts. We investigated these characteristics using a specific cluster-DNA conjugate with the goal of developing a sensitive and selective biosensor. The silver cluster has a single violet absorption band (λ(max) = 400 nm), and its single-stranded DNA host has two domains that stabilize this cluster and hybridize with target oligonucleotides. These target analytes transform the weakly emissive violet cluster to a new chromophore with blue-green absorption (λ(max) = 490 nm) and strong green emission (λ(max) = 550 nm). Our studies consider the synthesis, cluster size, and DNA structure of the precursor violet cluster-DNA complex. This species preferentially forms with relatively low amounts of Ag(+), high concentrations of the oxidizing agent O2, and DNA strands with ≳20 nucleotides. The resulting aqueous and gaseous forms of this chromophore have 10 silvers that coalesce into a single cluster. This molecule is not only a chromophore but also an adduct that coordinates multiple nucleobases. Large-scale DNA conformational changes are manifested in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking. Multidentate coordination also stabilizes the single-stranded DNA and thereby inhibits hybridization with target complements. These observations suggest that the silver cluster-DNA conjugate acts like a molecular beacon but is distinguished because the cluster chromophore not only sensitively signals target analytes but also stringently discriminates against analogous competing analytes.
Collapse
Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Orlin O Sergev
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Andrew G Kantor
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Ian J Rankine
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Mainak Ganguly
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Frederic D David
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sandra K Wheeler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - John F Wheeler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| |
Collapse
|
11
|
Li N, Su X, Lu Y. Nanomaterial-based biosensors using dual transducing elements for solution phase detection. Analyst 2015; 140:2916-43. [PMID: 25763412 DOI: 10.1039/c4an02376e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Biosensors incorporating nanomaterials have demonstrated superior performance compared to their conventional counterparts. Most reported sensors use nanomaterials as a single transducer of signals, while biosensor designs using dual transducing elements have emerged as new approaches to further improve overall sensing performance. This review focuses on recent developments in nanomaterial-based biosensors using dual transducing elements for solution phase detection. The review begins with a brief introduction of the commonly used nanomaterial transducers suitable for designing dual element sensors, including quantum dots, metal nanoparticles, upconversion nanoparticles, graphene, graphene oxide, carbon nanotubes, and carbon nanodots. This is followed by the presentation of the four basic design principles, namely Förster Resonance Energy Transfer (FRET), Amplified Fluorescence Polarization (AFP), Bio-barcode Assay (BCA) and Chemiluminescence (CL), involving either two kinds of nanomaterials, or one nanomaterial and an organic luminescent agent (e.g. organic dyes, luminescent polymers) as dual transducers. Biomolecular and chemical analytes or biological interactions are detected by their control of the assembly and disassembly of the two transducing elements that change the distance between them, the size of the fluorophore-containing composite, or the catalytic properties of the nanomaterial transducers, among other property changes. Comparative discussions on their respective design rules and overall performances are presented afterwards. Compared with the single transducer biosensor design, such a dual-transducer configuration exhibits much enhanced flexibility and design versatility, allowing biosensors to be more specifically devised for various purposes. The review ends by highlighting some of the further development opportunities in this field.
Collapse
Affiliation(s)
- Ning Li
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, 117602 Singapore.
| | | | | |
Collapse
|
12
|
Liu Q, Wang J, Boyd BJ. Peptide-based biosensors. Talanta 2015; 136:114-27. [PMID: 25702993 DOI: 10.1016/j.talanta.2014.12.020] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/26/2014] [Accepted: 12/18/2014] [Indexed: 12/24/2022]
Abstract
Peptides have been used as components in biological analysis and fabrication of novel biosensors for a number of reasons, including mature synthesis protocols, diverse structures and as highly selective substrates for enzymes. Bio-conjugation strategies can provide an efficient way to convert interaction information between peptides and analytes into a measurable signal, which can be used for fabrication of novel peptide-based biosensors. Many sensitive fluorophores can respond rapidly to environmental changes and stimuli manifest as a change in spectral characteristics, hence environmentally-sensitive fluorophores have been widely used as signal markers to conjugate to peptides to construct peptide-based molecular sensors. Additionally, nanoparticles, fluorescent polymers, graphene and near infrared dyes are also used as peptide-conjugated signal markers. On the other hand, peptides may play a generalist role in peptide-based biosensors. Peptides have been utilized as bio-recognition elements to bind various analytes including proteins, nucleic acid, bacteria, metal ions, enzymes and antibodies in biosensors. The selectivity of peptides as an enzymatic substrate has thus been utilized to construct enzyme sensors or enzyme-activity sensors. In addition, progress on immobilization and microarray techniques of peptides has facilitated the progress and commercial application of chip-based peptide biosensors in clinical diagnosis.
Collapse
Affiliation(s)
- Qingtao Liu
- Drug Delivery Disposition and Dynamics-Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia
| | - Jinfeng Wang
- Australian Future Fibres Research and Innovation Centre, Institute for Frontier Materials, Deakin University, Geelong 3217, VIC, Australia
| | - Ben J Boyd
- Drug Delivery Disposition and Dynamics-Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia.
| |
Collapse
|
13
|
Abstract
A molecular peptide beacon was designed for fluorescence detection of IgG in a homogeneous assay.
Collapse
Affiliation(s)
- M. Okochi
- Department of Biotechnology
- Graduate School of Engineering
- Nagoya University
- Nagoya
- Japan
| | - T. Sugita
- Department of Biotechnology
- Graduate School of Engineering
- Nagoya University
- Nagoya
- Japan
| | - M. Tanaka
- Department of Chemical Engineering
- Graduate School of Science and Engineering
- Tokyo Institute of Technology
- Tokyo 152-8552
- Japan
| | - H. Honda
- Department of Biotechnology
- Graduate School of Engineering
- Nagoya University
- Nagoya
- Japan
| |
Collapse
|
14
|
Tsortos A, Grammoustianou A, Lymbouridou R, Papadakis G, Gizeli E. The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor. Chem Commun (Camb) 2015; 51:11504-7. [DOI: 10.1039/c5cc03436a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acoustic sensing of DNA targets using a single probe that produces hybridization products of different conformations.
Collapse
|
15
|
Pattanasiri B, Li YW, Landau DP, Wüst T, Triampo W. Thermodynamics and structural properties of a confined HP protein determined by Wang-Landau simulation. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/454/1/012071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
16
|
Frascione N, Gooch J, Daniel B. Enabling fluorescent biosensors for the forensic identification of body fluids. Analyst 2013; 138:7279-88. [DOI: 10.1039/c3an01372c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
17
|
Peng Q, Kong N, Wang HCE, Li H. Designing redox potential-controlled protein switches based on mutually exclusive proteins. Protein Sci 2012; 21:1222-30. [PMID: 22733630 DOI: 10.1002/pro.2109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Synthetic/artificial protein switches provide an efficient means of controlling protein functions using chemical signals and stimuli. Mutually exclusive proteins, in which only the host or guest domain can remain folded at a given time owing to conformational strain, have been used to engineer novel protein switches that can switch enzymatic functions on and off in response to ligand binding. To further explore the potential of mutually exclusive proteins as protein switches and sensors, we report here a new redox-based approach to engineer a mutually exclusive folding-based protein switch. By introducing a disulfide bond into the host domain of a mutually exclusive protein, we demonstrate that it is feasible to use redox potential to switch the host domain between its folded and unfolded conformations via the mutually exclusive folding mechanism, and thus switching the functionality of the host domain on and off. Our study opens a new and potentially general avenue that uses mutually exclusive proteins to design novel switches able to control the function of a variety of proteins.
Collapse
Affiliation(s)
- Qing Peng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | | |
Collapse
|
18
|
Cerminara M, Desai TM, Sadqi M, Muñoz V. Downhill Protein Folding Modules as Scaffolds for Broad-Range Ultrafast Biosensors. J Am Chem Soc 2012; 134:8010-3. [DOI: 10.1021/ja301092z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele Cerminara
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Tanay M. Desai
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Mourad Sadqi
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Victor Muñoz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
19
|
Wu J, Zou Y, Li C, Sicking W, Piantanida I, Yi T, Schmuck C. A molecular peptide beacon for the ratiometric sensing of nucleic acids. J Am Chem Soc 2012; 134:1958-61. [PMID: 22242714 DOI: 10.1021/ja2103845] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A pyrene-functionalized cationic oligopeptide 1 efficiently binds to double-stranded DNA, as shown by different spectrophotochemical studies. Upon binding, the conformation of 1 changes from a folded to an extended form, which leads to a distinct change in the fluorescence properties. Thus, 1 functions as a molecular peptide beacon, and as it is easily taken up by cells, 1 can also be used for imaging of nucleic acids within cells.
Collapse
Affiliation(s)
- Junchen Wu
- Institute for Organic Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | | | | | | | | | | | | |
Collapse
|
20
|
Lu CH, Li J, Zhang XL, Zheng AX, Yang HH, Chen X, Chen GN. General Approach for Monitoring Peptide–Protein Interactions Based on Graphene–Peptide Complex. Anal Chem 2011; 83:7276-82. [DOI: 10.1021/ac200617k] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chun-Hua Lu
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Juan Li
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Xiao-Long Zhang
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Ai-Xian Zheng
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Xi Chen
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Guo-Nan Chen
- The Key Lab of Analysis and Detection Technology for Food Safety of the Ministry of Education, Fujian Provincial Key Laboratory of Analysis, Detection Technology for Food Safety, College of Chemistry, Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| |
Collapse
|
21
|
Maksay G. Allostery in pharmacology: Thermodynamics, evolution and design. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:463-73. [DOI: 10.1016/j.pbiomolbio.2011.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 01/03/2011] [Indexed: 12/13/2022]
|
22
|
Label-free colorimetric and quantitative detection of cancer marker protein using noncrosslinking aggregation of Au/Ag nanoparticles induced by target-specific peptide probe. Biosens Bioelectron 2011; 26:4804-9. [DOI: 10.1016/j.bios.2011.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 12/12/2022]
|
23
|
Zhuang Z, Jewett AI, Kuttimalai S, Bellesia G, Gnanakaran S, Shea JE. Assisted peptide folding by surface pattern recognition. Biophys J 2011; 100:1306-15. [PMID: 21354404 DOI: 10.1016/j.bpj.2010.12.3735] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/09/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022] Open
Abstract
Natively disordered proteins belong to a unique class of biomolecules whose function is related to their flexibility and their ability to adopt desired conformations upon binding to substrates. In some cases these proteins can bind multiple partners, which can lead to distinct structures and promiscuity in functions. In other words, the capacity to recognize molecular patterns on the substrate is often essential for the folding and function of intrinsically disordered proteins. Biomolecular pattern recognition is extremely relevant both in vivo (e.g., for oligomerization, immune response, induced folding, substrate binding, and molecular switches) and in vitro (e.g., for biosensing, catalysis, chromatography, and implantation). Here, we use a minimalist computational model system to investigate how polar/nonpolar patterns on a surface can induce the folding of an otherwise unstructured peptide. We show that a model peptide that exists in the bulk as a molten globular state consisting of many interconverting structures can fold into either a helix-coil-helix or an extended helix structure in the presence of a complementary designed patterned surface at low hydrophobicity (3.7%) or a uniform surface at high hydrophobicity (50%). However, we find that a carefully chosen surface pattern can bind to and catalyze the folding of a natively unfolded protein much more readily or effectively than a surface with a noncomplementary or uniform distribution of hydrophobic residues.
Collapse
Affiliation(s)
- Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | | | | | | | | | | |
Collapse
|
24
|
Stratton MM, Loh SN. Converting a protein into a switch for biosensing and functional regulation. Protein Sci 2011; 20:19-29. [PMID: 21064163 DOI: 10.1002/pro.541] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins that switch conformations in response to a signaling event (e.g., ligand binding or chemical modification) present a unique solution to the design of reagent-free biosensors as well as molecules whose biological functions are regulated in useful ways. The principal roadblock in the path to develop such molecules is that the majority of natural proteins do not change conformation upon binding their cognate ligands or becoming chemically modified. Herein, we review recent protein engineering efforts to introduce switching properties into binding proteins. By co-opting natural allosteric coupling, joining proteins in creative ways and formulating altogether new switching mechanisms, researchers are learning how to coax conformational changes from proteins that previously had none. These studies are providing some answers to the challenging question: how can one convert a lock-and-key binding protein into a molecular switch?
Collapse
Affiliation(s)
- Margaret M Stratton
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
| | | |
Collapse
|
25
|
Biosensor diagnosis of urinary tract infections: a path to better treatment? Trends Pharmacol Sci 2011; 32:330-6. [PMID: 21458868 DOI: 10.1016/j.tips.2011.03.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 02/08/2023]
Abstract
Urinary tract infection (UTI) is among the most common bacterial infections and poses a significant healthcare burden. The standard culture-based diagnosis of UTI has a typical delay of two to three days. In the absence of definitive microbiological diagnosis at the point of care, physicians frequently initiate empirical broad-spectrum antibiotic treatment, and this has contributed to the emergence of resistant pathogens. Biosensors are emerging as a powerful diagnostic platform for infectious diseases. Paralleling how blood glucose sensors revolutionized the management of diabetes, and how pregnancy tests are now conducted in the home, biosensors are poised to improve UTI diagnosis significantly. Biosensors are amenable to integration with microfluidic technology for point-of-care (POC) applications. This review focuses on promising biosensor technology for UTI diagnosis, including pathogen identification and antimicrobial susceptibility testing, and hurdles to be surpassed in the translation of biosensor technology from bench to bedside.
Collapse
|
26
|
Cheng RR, Uzawa T, Plaxco KW, Makarov DE. Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides. Biophys J 2011; 99:3959-68. [PMID: 21156138 DOI: 10.1016/j.bpj.2010.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 11/03/2010] [Accepted: 11/15/2010] [Indexed: 11/19/2022] Open
Abstract
Understanding the rate at which various parts of a molecular chain come together to facilitate the folding of a biopolymer (e.g., a protein or RNA) into its functional form remains an elusive goal. Here we use experiments, simulations, and theory to study the kinetics of internal loop closure in disordered biopolymers such as single-stranded oligonucleotides and unfolded proteins. We present theoretical arguments and computer simulation data to show that the relationship between the timescale of internal loop formation and the positions of the monomers enclosing the loop can be recast in a form of a universal master dependence. We also perform experimental measurements of the loop closure times of single-stranded oligonucleotides and show that both these and previously reported internal loop closure kinetics of unfolded proteins are well described by this theoretically predicted dependence. Finally, we propose that experimental deviations from the master dependence can then be used as a sensitive probe of dynamical and structural order in unfolded proteins and other biopolymers.
Collapse
Affiliation(s)
- Ryan R Cheng
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, USA
| | | | | | | |
Collapse
|
27
|
Golynskiy MV, Koay MS, Vinkenborg JL, Merkx M. Engineering Protein Switches: Sensors, Regulators, and Spare Parts for Biology and Biotechnology. Chembiochem 2011; 12:353-61. [DOI: 10.1002/cbic.201000642] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Indexed: 12/31/2022]
|
28
|
Plaxco KW, Soh HT. Switch-based biosensors: a new approach towards real-time, in vivo molecular detection. Trends Biotechnol 2011; 29:1-5. [PMID: 21106266 PMCID: PMC3010506 DOI: 10.1016/j.tibtech.2010.10.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/18/2010] [Accepted: 10/25/2010] [Indexed: 01/21/2023]
Abstract
Although the ability to monitor specific molecules in vivo in real-time could revolutionize many aspects of healthcare, the technological challenges that stand in the way of reaching this goal are considerable and are poorly met by most existing analytical approaches. Nature, however, has already solved the problem of real-time molecular detection in complex media by employing biomolecular "switches". That is, protein and nucleic acids that sense chemical cues and, by undergoing specific, binding-induced conformational changes, transduce this recognition into high-gain signal outputs. Here, we argue that devices that employ such switches represent a promising route towards versatile, real-time molecular monitoring in vivo.
Collapse
Affiliation(s)
- Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
29
|
Abstract
Protein disorder is abundant in proteomes throughout all kingdoms of life and serves many biologically important roles. Disordered states of proteins are challenging to study experimentally due to their structural heterogeneity and tendency to aggregate. Computer simulations, which are not impeded by these properties, have recently emerged as a useful tool to characterize the conformational ensembles of intrinsically disordered proteins. In this review, we provide a survey of computational studies of protein disorder with an emphasis on the interdisciplinary nature of these studies. The application of simulation techniques to the study of disordered states is described in the context of experimental and bioinformatics approaches. Experimental data can be incorporated into simulations, and simulations can provide predictions for experiment. In this way, simulations have been integrated into the existing methodologies for the study of disordered state ensembles. We provide recent examples of simulations of disordered states from the literature and our own work. Throughout the review, we emphasize important predictions and biophysical understanding made possible through the use of simulations. This review is intended as both an overview and a guide for structural biologists and theoretical biophysicists seeking accurate, atomic-level descriptions of disordered state ensembles.
Collapse
Affiliation(s)
- Sarah Rauscher
- Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | | |
Collapse
|
30
|
Vallée-Bélisle A, Plaxco KW. Structure-switching biosensors: inspired by Nature. Curr Opin Struct Biol 2010; 20:518-26. [PMID: 20627702 DOI: 10.1016/j.sbi.2010.05.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/03/2010] [Accepted: 05/04/2010] [Indexed: 01/30/2023]
Abstract
Chemosensing in nature relies on biomolecular switches, biomolecules that undergo binding-induced changes in conformation or oligomerization to transduce chemical information into specific biochemical outputs. Motivated by the impressive performance of these natural 'biosensors,' which support continuous, real-time detection in highly complex environments, significant efforts have gone into the adaptation of such switches into artificial chemical sensors. Ongoing advances in the fields of protein and nucleic acid engineering (e.g. computational protein design, directed evolution, selection strategies and labeling chemistries) have greatly enhanced our ability to design new structure-switching sensors. Coupled with the development of advanced optical readout mechanisms, including genetically encoded fluorophores, and electrochemical readouts supporting detection directly in highly complex sample matrices, switch-based sensors have already seen deployment in applications ranging from real time, in vivo imaging to the continuous monitoring of drugs in blood serum.
Collapse
Affiliation(s)
- Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
31
|
Lubin AA, Plaxco KW. Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. Acc Chem Res 2010; 43:496-505. [PMID: 20201486 DOI: 10.1021/ar900165x] [Citation(s) in RCA: 374] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biomolecular recognition is versatile, specific, and high affinity, qualities that have motivated decades of research aimed at adapting biomolecules into a general platform for molecular sensing. Despite significant effort, however, so-called "biosensors" have almost entirely failed to achieve their potential as reagentless, real-time analytical devices; the only quantitative, reagentless biosensor to achieve commercial success so far is the home glucose monitor, employed by millions of diabetics. The fundamental stumbling block that has precluded more widespread success of biosensors is the failure of most biomolecules to produce an easily measured signal upon target binding. Antibodies, for example, do not change their shape or dynamics when they bind their recognition partners, nor do they emit light or electrons upon binding. It has thus proven difficult to transduce biomolecular binding events into a measurable output signal, particularly one that is not readily spoofed by the binding of any of the many potentially interfering species in typical biological samples. Analytical approaches based on biomolecular recognition are therefore mostly cumbersome, multistep processes relying on analyte separation and isolation (such as Western blots, ELISA, and other immunochemical methods); these techniques have proven enormously useful, but are limited almost exclusively to laboratory settings. In this Account, we describe how we have refined a potentially general solution to the problem of signal detection in biosensors, one that is based on the binding-induced "folding" of electrode-bound DNA probes. That is, we have developed a broad new class of biosensors that employ electrochemistry to monitor binding-induced changes in the rigidity of a redox-tagged probe DNA that has been site-specifically attached to an interrogating electrode. These folding-based sensors, which have been generalized to a wide range of specific protein, nucleic acid, and small-molecule targets, are rapid (responding in seconds to minutes), sensitive (detecting sub-picomolar to micromolar concentrations), and reagentless. They are also greater than 99% reusable, are supported on micrometer-scale electrodes, and are readily fabricated into densely packed sensor arrays. Finally, and critically, their signaling is linked to a binding-specific change in the physics of the probe DNA, and not simply to adsorption of the target onto the sensor head. Accordingly, they are selective enough to be employed directly in blood, crude soil extracts, cell lysates, and other grossly contaminated clinical and environmental samples. Indeed, we have recently demonstrated the ability to quantitatively monitor a specific small molecule in real-time directly in microliters of flowing, unmodified blood serum. Because of their sensitivity, substantial background suppression, and operational convenience, these folding-based biosensors appear potentially well suited for electronic, on-chip applications in pathogen detection, proteomics, metabolomics, and drug discovery.
Collapse
Affiliation(s)
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry
- Biomolecular Science and Engineering Program
| |
Collapse
|
32
|
Abstract
The study of protein folding requires a method to drive unfolding, which is typically accomplished by altering solution conditions to favor the denatured state. This has the undesirable consequence that the molecular forces responsible for configuring the polypeptide chain are also changed. It would therefore be useful to develop methods that can drive unfolding without the need for destabilizing solvent conditions. Here we introduce a new method to accomplish this goal, which we call steric trapping. In the steric trap method, the target protein is labeled with two biotin tags placed close in space so that both biotin tags can only be bound by streptavidin when the protein unfolds. Thus, binding of the second streptavidin is energetically coupled to unfolding of the target protein. Testing the method on a model protein, dihydrofolate reductase (DHFR), we find that streptavidin binding can drive unfolding and that the apparent binding affinity reports on changes in DHFR stability. Finally, by employing the slow off-rate of wild-type streptavidin, we find that DHFR can be locked in the unfolded state. The steric trap method provides a simple method for studying aspects of protein folding and stability in native solvent conditions, could be used to specifically unfold selected domains, and could be applicable to membrane proteins.
Collapse
Affiliation(s)
- Tracy M Blois
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| | | | | | | |
Collapse
|
33
|
Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors. Proc Natl Acad Sci U S A 2009; 106:13802-7. [PMID: 19666496 DOI: 10.1073/pnas.0904005106] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding-induced biomolecular switches are used throughout nature and, increasingly, throughout biotechnology for the detection of chemical moieties and the subsequent transduction of this detection into useful outputs. Here we show that the thermodynamics of these switches are quantitatively described by a simple 3-state population-shift model, in which the equilibrium between a nonbinding, nonsignaling state and the binding-competent, signaling state is shifted toward the latter upon target binding. Because of this, their performance is determined by the tradeoff inherent to their switching thermodynamics; while a switching equilibrium constant favoring the nonbinding, nonsignaling, conformation ensures a larger signal change (more molecules are poised to respond), it also reduces affinity (binding must overcome a more unfavorable conformational free energy). We then derive and employ the relationship between switching thermodynamics and switch signaling to rationally tune the dynamic range and detection limit of a representative structure-switching biosensor, a molecular beacon, over 4 orders of magnitude. These findings demonstrate that the performance of biomolecular switches can be rationally tuned via mutations that alter their switching thermodynamics and suggest a mechanism by which the performance of naturally occurring switches may have evolved.
Collapse
|
34
|
Pazos E, Vázquez O, Mascareñas JL, Eugenio Vázquez M. Peptide-based fluorescent biosensors. Chem Soc Rev 2009; 38:3348-59. [DOI: 10.1039/b908546g] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|