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Martínez-Parra JM, Gómez-Ojea R, Daudey GA, Calvelo M, Fernández-Caro H, Montenegro J, Bergueiro J. Exo-chirality of the α-helix. Nat Commun 2024; 15:6987. [PMID: 39143054 PMCID: PMC11325010 DOI: 10.1038/s41467-024-51072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024] Open
Abstract
The structure of helical polymers is dictated by the molecular chirality of their monomer units. Particularly, macromolecular helices with monomer sequence control have the potential to generate chiral topologies. In α-helical folded peptides, the sequential repetition of amino acids generates a chiral layer defined by the amino acid side chains projected outside the amide backbone. Despite being closely related to peptides' structural and functional properties, to the best of our knowledge, a general exo-helical symmetry model has not been yet described for the α-helix. Here, we perform the theoretical, computational, and spectroscopic elucidation of the α-helix principal exo-helical topologies. Non-canonical labeled amino acids are employed to spectroscopically characterize the different exo-helical topologies in solution, which precisely match the theorical prediction. Backbone-to-chromophore distance also shows the expected impact in the exo-helices' geometry and spectroscopic fingerprint. Theoretical prediction and spectroscopic validation of this exo-helical topological model provides robust experimental evidence of the chiral potential on the surface of helical peptides and outlines an entirely new structural scenario for the α-helix.
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Affiliation(s)
- Jose M Martínez-Parra
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Rebeca Gómez-Ojea
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Geert A Daudey
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Martin Calvelo
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Hector Fernández-Caro
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Javier Montenegro
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
| | - Julian Bergueiro
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
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2
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Maity D, Bhaumik SK, Banerjee S. Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies. Phys Chem Chem Phys 2023; 25:12810-12819. [PMID: 37129214 DOI: 10.1039/d3cp00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.
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Affiliation(s)
- Dhananjoy Maity
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Shubhra Kanti Bhaumik
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
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3
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Wu M, Wang Y, Liu Y, Peng C, Shen Y. Luminescence Properties of Cr3+ Doped LiGa5O8 Prepared by Solid-State Synthesis. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Hennig A, Nau WM. Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays. Front Chem 2020; 8:806. [PMID: 33134264 PMCID: PMC7511663 DOI: 10.3389/fchem.2020.00806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.
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Affiliation(s)
- Andreas Hennig
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany.,Institute of Chemistry of New Materials, School of Biology/Chemistry, Universität Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
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5
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Grachev MK, Terekhova IV, Shipilov DA, Kutyasheva NV, Emelianova EY. Dimeric (Oligomeric) Derivatives of Cyclodextrins as a New Class of Supramolecular Systems: Their Synthesis and Inclusion Complexes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020010021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Kopra K, Tong-Ochoa N, Laine M, Eskonen V, Koskinen PJ, Härmä H. Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides. Anal Chim Acta 2019; 1055:126-132. [PMID: 30782363 DOI: 10.1016/j.aca.2018.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022]
Abstract
We have developed a rapid and sensitive universal peptide-based time-resolved luminescence assay for detection of enzymatic post-translational modifications (PTMs). PTMs play essential roles in intracellular signaling and cell regulation, thus providing functional protein diversity in cell. Due this, impaired PTM patterns have been linked to multiple disease states. Clear link between PTMs and pathological conditions have also driven assay development further, but still today most of the methodologies are based on single-specificity or group-specific PTM-recognition. We have previously introduced leuzine-zipper based peptide-break technology as a viable option for universal PTM detection. Here, we introduce peptide-break technology utilizing single-label homogeneous quenching resonance energy transfer (QRET) and charge-based peptide-peptide interaction. We demonstrate the functionality of the new assay concept in phosphorylation, deacetylation, and citrullination. In a comparable study between previously introduced leucine-zipper and the novel charge-based approach, we found equal PTM detection performance and sensitivity, but the peptide design for new targets is simplified with the charged peptides. The new concept allows the use of short <20 amino acid peptides without limitations rising from the leucine-zipper coiled-coil structure. Introduced methodology enables wash-free PTM detection in a 384-well plate format, using low nanomolar enzyme concentrations. Potentially, the peptide-break technique using charged peptides may be applicable for natural peptide sequences directly obtained from the target protein.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Mari Laine
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Päivi J Koskinen
- Section of Physiology and Genetics, Department of Biology, University of Turku, Vesilinnantie 5, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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7
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Espinoza EM, Clark JA, Derr JB, Bao D, Georgieva B, Quina FH, Vullev VI. How Do Amides Affect the Electronic Properties of Pyrene? ACS OMEGA 2018; 3:12857-12867. [PMID: 31458010 PMCID: PMC6644773 DOI: 10.1021/acsomega.8b01581] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/24/2018] [Indexed: 05/12/2023]
Abstract
The electronic properties of amide linkers, which are intricate components of biomolecules, offer a wealth of unexplored possibilities. Herein, we demonstrate how the different modes of attaching an amide to a pyrene chromophore affect the electrochemical and optical properties of the chromophore. Thus, although they cause minimal spectral shifts, amide substituents can improve either the electron-accepting or electron-donating capabilities of pyrene. Specifically, inversion of the amide orientation shifts the reduction potentials by 200 mV. These trends indicate that, although amides affect to a similar extent the energies of the ground and singlet excited states of pyrene, the effects on the doublet states of its radical ions are distinctly different. This behavior reflects the unusually strong orientation dependence of the resonance effects of amide substituents, which should extend to amide substituents on other types of chromophores in general. These results represent an example where the Hammett sigma constants fail to predict substituent effects on electrochemical properties. On the other hand, Swain-Lupton parameters are found to be in good agreement with the observed trends. Examination of the frontier orbitals of the pyrene derivatives and their components reveals the underlying reason for the observed amide effects on the electronic properties of this polycyclic aromatic hydrocarbon and points to key molecular-design strategies for electronic and energy-conversion systems.
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Affiliation(s)
- Eli M. Espinoza
- Department
of Chemistry, Department of Bioengineering, Department of Biochemistry, and Materials Science
and Engineering Program, University of California, Riverside, California 92521, United States
- Instituto
de Química, Universidade de São
Paulo, Avenida Lineu
Prestes 748, Cidade Universitária, São
Paulo 05508-000, Brazil
| | - John A. Clark
- Department
of Chemistry, Department of Bioengineering, Department of Biochemistry, and Materials Science
and Engineering Program, University of California, Riverside, California 92521, United States
| | - James B. Derr
- Department
of Chemistry, Department of Bioengineering, Department of Biochemistry, and Materials Science
and Engineering Program, University of California, Riverside, California 92521, United States
| | - Duoduo Bao
- Department
of Chemistry, Department of Bioengineering, Department of Biochemistry, and Materials Science
and Engineering Program, University of California, Riverside, California 92521, United States
| | - Boriana Georgieva
- Department
of Chemistry, Department of Bioengineering, Department of Biochemistry, and Materials Science
and Engineering Program, University of California, Riverside, California 92521, United States
| | - Frank H. Quina
- Instituto
de Química, Universidade de São
Paulo, Avenida Lineu
Prestes 748, Cidade Universitária, São
Paulo 05508-000, Brazil
- E-mail: (F.H.Q.)
| | - Valentine I. Vullev
- Department
of Chemistry, Department of Bioengineering, Department of Biochemistry, and Materials Science
and Engineering Program, University of California, Riverside, California 92521, United States
- E-mail: (V.I.V.)
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8
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Groth MC, Rink WM, Meyer NF, Thomas F. Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils. Chem Sci 2018; 9:4308-4316. [PMID: 29780562 PMCID: PMC5944379 DOI: 10.1039/c7sc05342h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/14/2018] [Indexed: 12/14/2022] Open
Abstract
Among the protein folding motifs, which are accessible by de novo design, the parallel heterodimeric coiled coil is most frequently used in bioinspired applications and chemical biology in general. This is due to the straightforward sequence-to-structure relationships, which it has in common with all coiled-coil motifs, and the heterospecificity, which allows control of association. Whereas much focus was laid on designing orthogonal coiled coils, systematic studies on controlling association, for instance by strand displacement, are rare. As a contribution to the design of dynamic coiled-coil-based systems, we studied the strand-displacement mechanism in obligate heterodimeric coiled coils to investigate the suitability of the dissociation constants (KD) as parameters for the prediction of the outcome of strand-displacement reactions. We use two sets of heterodimeric coiled coils, the previously reported N-A x B y and the newly characterized C-A x B y . Both comprise KD values in the μM to sub-nM regime. Strand displacement is explored by CD titration and a FRET-based kinetic assay and is proved to be an equilibrium reaction with half-lifes from a few seconds up to minutes. We could fit the displacement data by a competitive binding model, giving rate constants and overall affinities of the underlying association and dissociation reactions. The overall affinities correlate well with the ratios of KD values determined by CD-thermal denaturation experiments and, hence, support the dissociative mechanism of strand displacement in heterodimeric coiled coils. From the results of more than 100 different displacement reactions we are able to classify three categories of overall affinities, which allow for easy prediction of the equilibrium of strand displacement in two competing heterodimeric coiled coils.
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Affiliation(s)
- Mike C Groth
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - W Mathis Rink
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - Nils F Meyer
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - Franziska Thomas
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
- Center for Biostructural Imaging of Neurodegeneration , Von-Siebold-Straße 3a , 37075 Göttingen , Germany
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9
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Härmä H, Tong-Ochoa N, van Adrichem AJ, Jelesarov I, Wennerberg K, Kopra K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb) 2018; 54:2910-2913. [PMID: 29498735 DOI: 10.1039/c7cc09575a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Post-translational modification (PTM) of proteins plays essential regulatory roles in a variety of pathological conditions. Reliable and practical assays are required to accelerate the discovery of inhibitors and activators for PTM related diseases. Today, methodologies are based on specific or group-specific PTM recognition of e.g. phosphate for kinase activity without extending to other type of PTMs. Here we have established a universal time-resolved luminescence assay on a peptide-break platform for the direct detection of wide variety of PTMs. The developed assay is based on the leucine zipper concept wherein a europium-chelate labeled detection peptide and a non-labeled peptide substrate form a highly luminescent dimer. As an active PTM enzyme at sub or low nanomolar concentration modifies the substrate peptide, the luminescent signal of the detached detection peptide is quenched in the presence of soluble quenchers. The functionality of this universal assay technique has been demonstrated for the monitoring of phosphorylation, dephosphorylation, deacetylation, and citrullination with high applicability also to other PTMs in a high throughput format.
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Affiliation(s)
- Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Turku, Finland.
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10
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Liu H, Ren F, Zhang H, Han Y, Qin H, Zeng J, Wang Y, Sun Q, Li Z, Gao M. Oral administration of highly bright Cr 3+ doped ZnGa 2O 4 nanocrystals for in vivo targeted imaging of orthotopic breast cancer. J Mater Chem B 2018; 6:1508-1518. [PMID: 32254215 DOI: 10.1039/c7tb03148c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Near-infrared (NIR) long lasting persistent luminescence nanoparticles (PLNPs) have attracted considerable attention in the area of in vivo bioimaging, due to their background-free luminescence characteristics and deep tissue penetration. However, the low fluorescence quantum yield and short afterglow of the currently available PLNPs limit their applications. Here, water-soluble Cr3+-doped ZnGa2O4 PLNPs with the highest quantum yield (η = 20%) ever reported, bright NIR emission, and excellent colloidal stability were successfully prepared by a one-step hydrothermal method. The afterglow of the resultant nanocrystals lasted for more than 5 days and could be repeatedly reactivated by the light (λ = 657 nm) of a portable light emitting diode lamp after decay. These nanocrystals were functionalized with α,ω-dicarboxyl-terminated poly(ethylene glycol) and poly(acrylic acid) to improve their stability and biocompatibility, so that they could be conjugated with a c(RGDyK) peptide and labeled with 99mTc for targeted imaging of orthotopic breast cancer by afterglow luminescence imaging and single-photon emission computed tomography imaging. Our NIR-PLNP probes can effectively avoid tissue auto-fluorescence and the light scattering caused by continuous excitation during the diagnosis of cancer.
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Affiliation(s)
- Hanghang Liu
- Center for Molecular Imaging and Nuclear Medicine, State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China.
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11
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Rapp PB, Omar AK, Shen JJ, Buck ME, Wang ZG, Tirrell DA. Analysis and Control of Chain Mobility in Protein Hydrogels. J Am Chem Soc 2017; 139:3796-3804. [DOI: 10.1021/jacs.6b13146] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter B. Rapp
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Ahmad K. Omar
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Jeff J. Shen
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Maren E. Buck
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Zhen-Gang Wang
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - David A. Tirrell
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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12
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Kikuchi K. Design, synthesis, and biological application of fluorescent sensor molecules for cellular imaging. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 119:63-78. [PMID: 19649586 DOI: 10.1007/10_2008_42] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Cellular imaging has achieved many new biological findings, among them GFP and other fluorescent proteins and small molecule based fluorescent sensors have been widely used, especially in the last decade. The design concept and application of chemical sensors are described, these being FRET based sensors and Zn(2+) sensors.Fluorescence resonance energy transfer (FRET) has been used extensively as the designing principle for fluorescent sensor molecules. One of the most significant advantages of designing sensor molecules with FRET modulation is that it can enable ratiometric measurement in living cells, which reduces the artifact from microscopic imaging systems. The design strategy for the development of small molecular FRET sensors is described in terms of avoiding close contact of donor fluorophore and acceptor fluorophore in aqueous solution. Furthermore, a strategy to design FRET sensors with modulating overlap integrals of donor and acceptor is introduced.Numerous tools for Zn(2+) sensing in living cells have become available in the last 8 years. Among them, fluorescence imaging using fluorescent sensor molecules has been the most popular approach. Some of these sensor molecules can be used to visualize Zn(2+) in living cells. Some of the biological functions of Zn(2+) were clarified using these sensor molecules, especially in neuronal cells, which contain a high concentration of free Zn(2) (+).
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Affiliation(s)
- Kazuya Kikuchi
- Department of Materials and Life Sciences, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita City, 565-0871, Osaka, Japan,
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13
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Alouini MA, Moustoifa EF, Rubio-Albenque S, Berthelot T, Fery-Forgues S, Déléris G. Interaction of Fluorescently Labeled Triethyleneglycol and Peptide Derivatives with β-Cyclodextrin. Chemphyschem 2014; 15:444-57. [DOI: 10.1002/cphc.201301032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Indexed: 11/08/2022]
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14
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Speight LC, Samanta M, Petersson EJ. Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck. Aust J Chem 2014. [DOI: 10.1071/ch13554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.
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15
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Singh SK. Red and near infrared persistent luminescence nano-probes for bioimaging and targeting applications. RSC Adv 2014. [DOI: 10.1039/c4ra08847f] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Schematic representation of the different processes in persistent luminescence: charging (1), stimulation (2), discharging (3) (PET-persistent energy transfer, QT-quantum tunneling).
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Affiliation(s)
- S. K. Singh
- Department of Physics
- Indian Institute of Technology (Banaras Hindu University)
- Varansi-221005, India
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16
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Huang SH, Wu WS, Huang LY, Huang WF, Fu WC, Chen PT, Fang JM, Cheng WC, Cheng TJR, Wong CH. New continuous fluorometric assay for bacterial transglycosylase using Förster resonance energy transfer. J Am Chem Soc 2013; 135:17078-89. [PMID: 24131464 DOI: 10.1021/ja407985m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emergence of antibiotic resistance has prompted scientists to search for new antibiotics. Transglycosylase (TGase) is an attractive target for new antibiotic discovery due to its location on the outer membrane of bacteria and its essential role in peptidoglycan synthesis. Though there have been a few molecules identified as TGase inhibitors in the past thirty years, none of them have been developed into antibiotics for humans. The slow pace of development is perhaps due to the lack of continuous, quantitative, and high-throughput assay available for the enzyme. Herein, we report a new continuous fluorescent assay based on Förster resonance energy transfer, using lipid II analogues with a dimethylamino-azobenzenesulfonyl quencher in the lipid chain and a coumarin fluorophore in the peptide chain. During the process of transglycosylation, the quencher-appended polyprenol is released and the fluorescence of coumarin can be detected. Using this system, the substrate specificity and affinity of lipid II analogues bearing various numbers and configurations of isoprene units were investigated. Moreover, the inhibition constants of moenomycin and two previously identified small molecules were also determined. In addition, a high-throughput screening using the new assay was conducted to identify potent TGase inhibitors from a 120,000 compound library. This new continuous fluorescent assay not only provides an efficient and convenient way to study TGase activities, but also enables the high-throughput screening of potential TGase inhibitors for antibiotic discovery.
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Affiliation(s)
- Shih-Hsien Huang
- Genomics Research Center, Academia Sinica , 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan
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Godfroy JI, Roostan M, Moroz YS, Korendovych IV, Yin H. Isolated Toll-like receptor transmembrane domains are capable of oligomerization. PLoS One 2012; 7:e48875. [PMID: 23155421 PMCID: PMC3498381 DOI: 10.1371/journal.pone.0048875] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/01/2012] [Indexed: 12/13/2022] Open
Abstract
Toll-like receptors (TLRs) act as the first line of defense against bacterial and viral pathogens by initiating critical defense signals upon dimer activation. The contribution of the transmembrane domain in the dimerization and signaling process has heretofore been overlooked in favor of the extracellular and intracellular domains. As mounting evidence suggests that the transmembrane domain is a critical region in several protein families, we hypothesized that this was also the case for Toll-like receptors. Using a combined biochemical and biophysical approach, we investigated the ability of isolated Toll-like receptor transmembrane domains to interact independently of extracellular domain dimerization. Our results showed that the transmembrane domains had a preference for the native dimer partners in bacterial membranes for the entire receptor family. All TLR transmembrane domains showed strong homotypic interaction potential. The TLR2 transmembrane domain demonstrated strong heterotypic interactions in bacterial membranes with its known interaction partners, TLR1 and TLR6, as well as with a proposed interaction partner, TLR10, but not with TLR4, TLR5, or unrelated transmembrane receptors providing evidence for the specificity of TLR2 transmembrane domain interactions. Peptides for the transmembrane domains of TLR1, TLR2, and TLR6 were synthesized to further study this subfamily of receptors. These peptides validated the heterotypic interactions seen in bacterial membranes and demonstrated that the TLR2 transmembrane domain had moderately strong interactions with both TLR1 and TLR6. Combined, these results suggest a role for the transmembrane domain in Toll-like receptor oligomerization and as such, may be a novel target for further investigation of new therapeutic treatments of Toll-like receptor mediated diseases.
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Affiliation(s)
- James I. Godfroy
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Mohammad Roostan
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Yurii S. Moroz
- Department of Chemistry, Syracuse University, Syracuse, New York, United States of America
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, Syracuse, New York, United States of America
| | - Hang Yin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado, United States of America
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18
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Krizkova S, Zitka O, Adam V, Kizek R, Masarik M, Stiborova M, Eckschlager T, Chavis GJ. Assays for determination of matrix metalloproteinases and their activity. Trends Analyt Chem 2011. [DOI: 10.1016/j.trac.2011.06.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Rullo A, Qian J, Nitz M. Peptide-glycosaminoglycan cluster formation involving cell penetrating peptides. Biopolymers 2011; 95:722-31. [DOI: 10.1002/bip.21641] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 04/01/2011] [Accepted: 04/02/2011] [Indexed: 11/08/2022]
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20
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Kikuchi K. Design, synthesis and biological application of chemical probes for bio-imaging. Chem Soc Rev 2010; 39:2048-53. [DOI: 10.1039/b819316a] [Citation(s) in RCA: 226] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Bordag N, Keller S. α-Helical transmembrane peptides: A “Divide and Conquer” approach to membrane proteins. Chem Phys Lipids 2010; 163:1-26. [PMID: 19682979 DOI: 10.1016/j.chemphyslip.2009.07.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 11/26/2022]
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22
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Müller MM, Windsor MA, Pomerantz WC, Gellman SH, Hilvert D. A rationally designed aldolase foldamer. Angew Chem Int Ed Engl 2009; 48:922-5. [PMID: 19090515 DOI: 10.1002/anie.200804996] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manuel M Müller
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg HCI F339, 8093 Zürich, Switzerland
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23
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Müller M, Windsor M, Pomerantz W, Gellman S, Hilvert D. A Rationally Designed Aldolase Foldamer. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804996] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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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]
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25
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Affiliation(s)
- Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street Toronto, ON, Canada.
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26
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Sahoo H, Hennig A, Florea M, Roth D, Enderle T, Nau WM. Single-label kinase and phosphatase assays for tyrosine phosphorylation using nanosecond time-resolved fluorescence detection. J Am Chem Soc 2007; 129:15927-34. [PMID: 18044894 DOI: 10.1021/ja074975w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The collision-induced fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by hydrogen atom abstraction from the tyrosine residue in peptide substrates was introduced as a single-labeling strategy to assay the activity of tyrosine kinases and phosphatases. The assays were tested for 12 different combinations of Dbo-labeled substrates and with the enzymes p60c-Src Src kinase, EGFR kinase, YOP protein tyrosine phosphatase, as well as acid and alkaline phosphatases, thereby demonstrating a broad application potential. The steady-state fluorescence changed by a factor of up to 7 in the course of the enzymatic reaction, which allowed for a sufficient sensitivity of continuous monitoring in steady-state experiments. The fluorescence lifetimes (and intensities) were found to be rather constant for the phosphotyrosine peptides (ca. 300 ns in aerated water), while those of the unphosphorylated peptides were as short as 40 ns (at pH 7) and 7 ns (at pH 13) as a result of intramolecular quenching. Owing to the exceptionally long fluorescence lifetime of Dbo, the assays were alternatively performed by using nanosecond time-resolved fluorescence (Nano-TRF) detection, which leads to an improved discrimination of background fluorescence and an increased sensitivity. The potential for inhibitor screening was demonstrated through the inhibition of acid and alkaline phosphatases by molybdate.
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Affiliation(s)
- Harekrushna Sahoo
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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27
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Toutchkine A, Han WG, Ullmann M, Liu T, Bashford D, Noodleman L, Hahn KM. Experimental and DFT studies: novel structural modifications greatly enhance the solvent sensitivity of live cell imaging dyes. J Phys Chem A 2007; 111:10849-60. [PMID: 17918807 DOI: 10.1021/jp073197r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural modifications of previously reported merocyanine dyes (Toutchkine, A.; Kraynov, V.; Hahn, K. J. Am. Chem. Soc. 2003, 125, 4132-4145) were found to greatly enhance the solvent dependence of their absorbance and fluorescence emission maxima. Density functional theory (DFT) calculations have been performed to understand the differences in optical properties between the new and previously synthesized dyes. Absorption and emission energies were calculated for several new dyes using DFT vertical self-consistent reaction field (VSCRF) methods. Geometries of ground and excited states were optimized with a conductor-like screening model (COSMO) and self-consistent field (SCF) methods. The new dyes have enhanced zwitterionic character in the ground state and much lower polarity in the excited state, as shown by the DFT-VSCRF calculations. Consistently, the position of the absorption bands are strongly blue-shifted in more polar solvent (methanol compared to benzene), as predicted by the DFT spectral calculations. Inclusion of explicit H-bonding solvent molecules within the quantum model further enhances the predicted shifts and is consistent with the observed spectral broadening. Smaller but significant spectral shifts in polar versus nonpolar solvent are predicted and observed for emission bands. The new dyes show large fluorescence quantum yields in polar hydrogen-bonding solvents; qualitatively, the longest bonds along the conjugated chain at the excited S1 state minimum are shorter in the more polar solvent, inhibiting photoisomerization. The loss of photostability of the dyes is a consequence of the reaction with and electron transfer to singlet oxygen, starting oxidative dye cleavage. The calculated vertical ionization potentials of three dyes I-SO, AI-SO(4), and AI-BA(4) in benzene and methanol are consistent with their relative photobleaching rates; the charge distributions along the conjugated chains for the three dyes are similarly predictive of higher reaction rates for AI-SO(4) and AI-BA(4) than for I-SO. Time-dependent DFT calculations were also performed on AI-BA(4); these were less accurate than the VSCRF method in predicting the absorption energy shift from benzene to methanol.
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Affiliation(s)
- Alexei Toutchkine
- Department of Pharmacology and Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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28
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Shen W, Kornfield JA, Tirrell DA. Dynamic Properties of Artificial Protein Hydrogels Assembled through Aggregation of Leucine Zipper Peptide Domains. Macromolecules 2007. [DOI: 10.1021/ma0615194] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Julia A. Kornfield
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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29
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Algar WR, Massey M, Krull UJ. Fluorescence resonance energy transfer and complex formation between thiazole orange and various dye-DNA conjugates: implications in signaling nucleic acid hybridization. J Fluoresc 2006; 16:555-67. [PMID: 16794869 DOI: 10.1007/s10895-006-0091-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 03/22/2006] [Indexed: 11/25/2022]
Abstract
Fluorescence resonance energy transfer (FRET) was investigated between the intercalating dye thiazole orange (TO), and the dyes Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethyl Rhodamine (TAMRA), Iowa Black FQ (IabFQ), and Iowa Black RQ (IabRQ), which were covalently immobilized at the end of dsDNA oligonucleotides. In addition to determining that TO was an effective energy donor, FRET efficiency data obtained from fluorescence lifetime measurements indicated that TO intercalated near the middle of the 19mer oligonucleotide sequence that was used in this study. Discrepancies in FRET efficiencies obtained from intensity and lifetime measurements led to the investigation of non-fluorescent complex formation between TAMRA and modified TO. The hydrophobicity of TO was modified by the addition of either an alkyl or polyethylene glycol (PEG) side-chain to study effects of dimer and aggregate formation. It was found that at stoichiometric excesses of modified TO, fluorescence quenching of TAMRA was observed, and that this could be correlated to the hydrophobicity of a TO-chain species. The TAMRA:TO-chain association constant for the TO-alkyl system was 0.043+/-0.002 M(-1), while that obtained for the TO-PEG was 0.037+/-0.002 M(-1). From the perspective of method development for the transduction of hybridization events, we present and evaluate a variety of schemes based on energy transfer between TO and an acceptor dye, and discuss the implications of complex formation in such schemes.
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Affiliation(s)
- W Russ Algar
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, South Building, Room 2035, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
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30
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Affiliation(s)
- Andreas Hennig
- School of Engineering and Science, International University Bremen, Campus Ring 1, 28759 Bremen, Germany
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31
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Hossain MA, Mihara H, Ueno A. Novel peptides bearing pyrene and coumarin units with or without beta-cyclodextrin in their side chains exhibit intramolecular fluorescence resonance energy transfer. J Am Chem Soc 2005; 125:11178-9. [PMID: 16220922 DOI: 10.1021/ja036427y] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Novel peptides bearing the pyrene/coumarin FRET pair in their side chains have been designed and synthesized. Peptide 1 having endogenous beta-cyclodextrin (beta-CD) in the side chain exhibits FRET in aqueous solution, indicating that coumarin, being accommodated into the CD cavity, is separated from pyrene. Guest-induced quenching of the fluorophores in 1 indicates that coumarin, being excluded from the CD cavity, comes into close contact with pyrene. Peptide 2 shows FRET only after addition of external beta-CD that again reflects the idea that beta-CD surely caps the coumarin unit in its hydrophobic cavity, and, therefore, quenching of the fluorophores can be prevented in FRET peptide probes. With this strategy, various peptide-based FRET probes can be developed that would be useful for studying biological phenomena in living cells.
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Affiliation(s)
- Mohammed Akhter Hossain
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama 226-8501, Japan
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32
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33
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Zhou M, Ghosh I. Noncovalent Multivalent Assembly of Jun Peptides on a Leucine Zipper Dendrimer Displaying Fos Peptides. Org Lett 2004; 6:3561-4. [PMID: 15387548 DOI: 10.1021/ol0485262] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] The synthesis and characterization of a new leucine-zipper dendrimer (LZD) is reported that displays four copies of the peptide corresponding to the coiled-coiled dimerization domain of Fos. Circular dichroism spectroscopy, fluorescence titration, and sedimentation equilibrium experiments demonstrate that Fos-LZD can noncovalently assemble four copies of the peptide corresponding to the coiled-coil domain of Jun. This work provides the basis for the future construction of noncovalently assembled multivalent protein assemblies displaying any protein of interest.
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Affiliation(s)
- Min Zhou
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
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34
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Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys J 2004; 87:3421-9. [PMID: 15315956 PMCID: PMC1304808 DOI: 10.1529/biophysj.103.032839] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A peptide containing glycine at a and d positions of a heptad motif was synthesized to investigate the possibility that membrane-soluble peptides with a Gly-based, left-handed helical packing motif would associate. Based on analytical ultracentrifugation in C14-betaine detergent micelles, the peptide did associate in a monomer-dimer equilibrium, although the association constant was significantly less than that reported for the right-handed dimer of the glycophorin A transmembrane peptide in similar detergents. Fluorescence resonance energy transfer (FRET) experiments conducted on peptides labeled at their N-termini with either tetramethylrhodamine (TMR) or 7-nitrobenz-2-oxa-1,3-diazole (NBD) also indicated association. However, analysis of the FRET data using the usual assumption of complete quenching for NBD-TMR pairs in the dimer could not be quantitatively reconciled with the analytical ultracentrifugation-measured dimerization constant. This led us to develop a general treatment for the association of helices to either parallel or antiparallel structures of any aggregation state. Applying this treatment to the FRET data, constraining the dimerization constant to be within experimental uncertainty of that measured by analytical ultracentrifugation, we found the data could be well described by a monomer-dimer equilibrium with only partial quenching of the dimer, suggesting that the helices are most probably antiparallel. These results also suggest that a left-handed Gly heptad repeat motif can drive membrane helix association, but the affinity is likely to be less strong than the previously reported right-handed motif described for glycophorin A.
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Affiliation(s)
- James D Lear
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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35
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Kikuchi K, Takakusa H, Nagano T. Recent advances in the design of small molecule-based FRET sensors for cell biology. Trends Analyt Chem 2004. [DOI: 10.1016/s0165-9936(04)00608-9] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Hossain MA, Mihara H, Ueno A. Fluorescence resonance energy transfer in a novel cyclodextrin–Peptide conjugate for detecting steroid molecules. Bioorg Med Chem Lett 2003; 13:4305-8. [PMID: 14643314 DOI: 10.1016/j.bmcl.2003.09.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A novel cyclodextrin conjugated peptide, 1, having two different fluorophores, coumarin and pyrene, in the side chains has been designed and synthesized. The circular dichroism study reveals that 1 shows typical alpha-helix pattern, and forms intramolecular inclusion complex with coumarin. The fluorescence emission study shows that the peptide exhibits intramolecular fluorescence resonance energy transfer (FRET) without quenching of two fluorophores. We have determined the binding constants of 1 for various biologically important steroid molecules as guests using the guest-responsive variation in the fluorescence emission intensity of coumarin.
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Affiliation(s)
- Mohammed Akhter Hossain
- Department of Bioengineering, Tokyo Institute of Technology, 4259Nagatsuta, Midori, Yokohama 226-8501, Japan
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37
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Heinlein T, Knemeyer JP, Piestert O, Sauer M. Photoinduced Electron Transfer between Fluorescent Dyes and Guanosine Residues in DNA-Hairpins. J Phys Chem B 2003. [DOI: 10.1021/jp0348068] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Heinlein
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Jens-Peter Knemeyer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Oliver Piestert
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Markus Sauer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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38
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Abstract
beta-cyclodextrin-based receptors were synthesized and tested for their ability to induce a helical fold in peptides bearing hydrophobic amino acid residues in the i, i+11- or i, i+14-positions. Circular dichroism experiments revealed that a dimeric beta-cylodextrin receptor synthesized from a [1,1'-biphenyl]-4,4'-dithiol core demonstrated an ability to fold a designed peptide bearing the artificial amino acid L-p-t-butylphenylalanine in the i, i+11-positions, while other dimeric and monomeric receptors failed to do so. Titration studies were performed using both circular dichroism and calorimetry, the analysis of which yielded an apparent K(a) on the order of 10(4)-10(5) M(-1). However, no evidence could be obtained for helical folding with a peptide carrying tryptophan residues in place of the p-t-butylphenylalanine units. Our studies suggest that receptors of this type may be useful in molecular recognition of hydrophobic, already alpha-helical peptides in aqueous solution.
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Affiliation(s)
- David Wilson
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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39
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Neuweiler H, Schulz A, Böhmer M, Enderlein J, Sauer M. Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level. J Am Chem Soc 2003; 125:5324-30. [PMID: 12720444 DOI: 10.1021/ja034040p] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a single-molecule-sensitive method to determine the rate of contact formation and dissociation between tryptophan and an oxazine derivative (MR121) on the basis of measurements of the photon distance distribution. Two short peptides (15 and 20 amino acids) derived from the transactivation domain of the human oncoprotein p53 were investigated. With the fluorophore attached at the N-terminal end of the flexible peptides, fluorescence of the dye is efficiently quenched upon contact formation with a tryptophan residue. The mechanism responsible for the efficient fluorescence quenching observed in the complexes is assumed to be a photoinduced electron-transfer reaction occurring predominantly at van der Waals contact. Fluorescence fluctuations caused by intramolecular contact formation and dissociation were recorded using confocal fluorescence microscopy with two avalanche photodiodes and the time-correlated single-photon-counting technique, enabling a temporal resolution of 1.2 ns. Peptides containing a tryptophan residue at positions 9 and 8, respectively, show contact formation with rate constants of 1/120 and 1/152 ns(-1), respectively. Whereas the rate constants of contact formation most likely directly report on biopolymer chain mobility, the dissociation rate constants of 1/267 and 1/742 ns(-1), respectively, are significantly smaller and reflect strong hydrophobic interactions between the dye and tryptophan. Fluorescence experiments on point-mutated peptides where tryptophan is exchanged by phenylalanine show no fluorescence quenching.
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Affiliation(s)
- Hannes Neuweiler
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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40
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Toutchkine A, Kraynov V, Hahn K. Solvent-sensitive dyes to report protein conformational changes in living cells. J Am Chem Soc 2003; 125:4132-45. [PMID: 12670235 DOI: 10.1021/ja0290882] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Covalent attachment of solvent-sensitive fluorescent dyes to proteins is a powerful tool for studying protein conformational changes, ligand binding, or posttranslational modifications. We report here new merocyanine dyes that make possible the quantitation of such protein activities in individual living cells. The quantum yield of the new dyes is sharply dependent on solvent polarity or viscosity, enabling them to report changes in their protein environment. This is combined with other stringent requirements needed in a live cell imaging dye, including appropriate photophysical properties (excitation >590 nm, high fluorescence quantum yield, high extinction coefficient), good photostability, minimal aggregation in water, and excellent water solubility. The dyes were derivatized with iodoacetamide and succinimidyl ester side chains for site-selective covalent attachment to proteins. A novel biosensor of Cdc42 activation made with one of the new dyes showed a 3-fold increase in fluorescence intensity in response to GTP-binding by Cdc42. The dyes reported here should be useful in the preparation of live cell biosensors for a diverse range of protein activities.
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Affiliation(s)
- Alexei Toutchkine
- Department of Cell Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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41
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Roy BC, Chandra B, Hromas D, Mallik S. Synthesis of new, pyrene-containing, metal-chelating lipids and sensing of cupric ions. Org Lett 2003; 5:11-4. [PMID: 12509878 DOI: 10.1021/ol026891s] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The syntheses of several saturated, pyrene-containing, metal-chelating lipids are described. These lipids are capable of strongly binding to transition metal ions employing the metal-chelating headgroup. The excimer-to-monomer ratio of the pyrene groups changes with addition of cupric ions to the liposomes. Three other transition metal ions (Zn(2+), Ni(2+), and Hg(2+)) did not cause any appreciable changes in the excimer-to-monomer ratio. [reaction--see text]
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Affiliation(s)
- Bidhan C Roy
- Department of Chemistry, North Dakota State University, Fargo, ND 58105, USA
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42
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Jones G, Vullev VI. Photoinduced electron transfer between non-native donor-acceptor moieties incorporated in synthetic polypeptide aggregates. Org Lett 2002; 4:4001-4. [PMID: 12423071 DOI: 10.1021/ol026656+] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of analogous photoactive polypeptides that form helical homo and hetero aggregates in aqueous media were prepared. A pyrenyl ketone (the principal chromophore and an electron acceptor) was attached to the N-termini. An electron donor, amidoethylcarbazole, was introduced as a side chain of a non-native amino acid, NCb, 14 residues away. Photoinduced electron-transfer rate constants of the order of 10(8) s(-1) between remote pyrene and carbazole were measured. [structure: see text]
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Affiliation(s)
- Guilford Jones
- Department of Chemistry and Photonics Center, Boston University, Boston, MA 02215, USA.
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43
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Strauss J, Daub J. Optically active cyclic hexapeptides with covalently attached pyrene probes: selective alkaline earth metal ion recognition using excimer emission. Org Lett 2002; 4:683-6. [PMID: 11869101 DOI: 10.1021/ol0170354] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] The synthesis of two optically active pyrene-modified cyclic hexapetides and their selectivity toward the complexation of alkaline earth metal ions are reported. Complexation was studied by optical and chiroptical methods. The cyclic peptides are forming 2:1 sandwich complexes with the metal ions.
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Affiliation(s)
- Jörg Strauss
- Institut für Organische Chemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg
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Hudgins RR, Huang F, Gramlich G, Nau WM. A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides. J Am Chem Soc 2002; 124:556-64. [PMID: 11804484 DOI: 10.1021/ja010493n] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fluorescent amino acid derivative (Fmoc-DBO) has been synthesized, which contains 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a small, hydrophilic fluorophore with an extremely long fluorescence lifetime (325 ns in H2O and 505 ns in D2O under air). Polypeptides containing both the DBO residue and an efficient fluorescence quencher allow the measurement of rate constants for intramolecular end-to-end contact formation. Bimolecular quenching experiments indicated that Trp, Cys, Met, and Tyr are efficient quenchers of DBO (k(q) = 20, 5.1, 4.5, and 3.6 x 10(8) M(-1) x s(-1) in D2O), while the other amino acids are inefficient. The quenching by Trp, which was selected as an intrinsic quencher, is presumed to involve exciplex-induced deactivation. Flexible, structureless polypeptides, Trp-(Gly-Ser)n-DBO-NH2, were prepared by standard solid-phase synthesis, and the rates of contact formation were measured through the intramolecular fluorescence quenching of DBO by Trp with time-correlated single-photon counting, laser flash photolysis, and steady-state fluorometry. Rate constants of 4.1, 6.8, 4.9, 3.1, 2.0, and 1.1 x 10(7) s(-1) for n = 0, 1, 2, 4, 6, and 10 were obtained. Noteworthy was the relatively slow quenching for the shortest peptide (n = 0). The kinetic data are in agreement with recent transient absorption studies of triplet probes for related peptides, but the rate constants are significantly larger. In contrast to the flexible structureless Gly-Ser polypeptides, the polyproline Trp-Pro4-DBO-NH2 showed insignificant fluorescence quenching, suggesting that a high polypeptide flexibility and the possibility of probe-quencher contact is essential to induce quenching. Advantages of the new fluorescence-based method for measuring contact formation rates in biopolymers include high accuracy, fast time range (100 ps-1 micros), and the possibility to perform measurements in water under air.
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Affiliation(s)
- Robert R Hudgins
- Departement Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Vullev VI, Jones G. Photoinduced charge transfer in helical polypeptides. RESEARCH ON CHEMICAL INTERMEDIATES 2002. [DOI: 10.1163/15685670260469429] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sun XL, Liu H, Orban JM, Sun L, Chaikof EL. Synthesis and terminal functionalization of a polymerizable phosphatidylethanolamine. Bioconjug Chem 2001; 12:673-7. [PMID: 11562184 DOI: 10.1021/bc015502w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the design and synthesis of bifunctional phospholipid conjugates, which contain a polymerizable acrylate group and a terminal linker, such as biotin or N-(epsilon-maleimidocaproyl (EMC), to facilitate bioconjugation reactions. The lipid conjugate can be used to generate a multifunctional substrate-supported phospholipid film that is further stabilized via in-situ photocopolymerization.
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Affiliation(s)
- X L Sun
- Laboratory for Biomolecular Materials Research, Department of Surgery and Bioengineering, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Jones G, Vullev VI. Contribution of a pyrene fluorescence probe to the aggregation propensity of polypeptides. Org Lett 2001; 3:2457-60. [PMID: 11483034 DOI: 10.1021/ol016123l] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] Two synthetic polypeptides, TT1p and TT1b, have been used in comparative aggregation equilibrium studies. The findings reveal that a single alkylpyrene moiety in TT1p contributes about 30% of the polypeptide dimerization energy in aqueous media. This result not only is informative with regard to the aggregation properties of these particular photoactive polypeptides but also provides a quantitative understanding of the limitations on the use of pyrene chromophores as emission probes.
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Affiliation(s)
- G Jones
- Department of Chemistry and Photonics Center, Boston University, Boston, MA 02215, USA.
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Jones G, Vullev VI. Ground- and Excited-State Aggregation Properties of a Pyrene Derivative in Aqueous Media. J Phys Chem A 2001. [DOI: 10.1021/jp010087q] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guilford Jones
- Department of Chemistry and Photonics Center, Boston University, Boston, Massachusetts 02215
| | - Valentine I. Vullev
- Department of Chemistry and Photonics Center, Boston University, Boston, Massachusetts 02215
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49
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Grosset AM, Gibney BR, Rabanal F, Moser CC, Dutton PL. Proof of principle in a de novo designed protein maquette: an allosterically regulated, charge-activated conformational switch in a tetra-alpha-helix bundle. Biochemistry 2001; 40:5474-87. [PMID: 11331012 DOI: 10.1021/bi002504f] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New understanding of the engineering and allosteric regulation of natural protein conformational switches (such as those that couple chemical and ionic signals, mechanical force, and electro/chemical free energy for biochemical activation, catalysis, and motion) can be derived from simple de novo designed synthetic protein models (maquettes). We demonstrate proof of principle of both reversible switch action and allosteric regulation in a tetra-alpha-helical bundle protein composed of two identical di-helical subunits containing heme coordinated at a specific position close to the disulfide loop region. Individual bundles assume one of two switch states related by large-scale mechanical changes: a syn-topology (helices of the different subunits parallel) or anti-topology (helices antiparallel). Both the spectral properties of a coproporphyrin probe appended to the loop region and the distance-dependent redox interaction between the hemes identify the topologies. Beginning from a syn-topology, introduction of ferric heme in each subunit (either binding or redox change) shifts the topological balance by 25-50-fold (1.9-2.3 kcal/mol) to an anti-dominance. Charge repulsion between the two internal cationic ferric hemes drives the syn- to anti-switch, as demonstrated in two ways. When fixed in the syn-topology, the second ferric heme binding is 25-80-fold (1.9-2.6 kcal/mol) weaker than the first, and adjacent heme redox potentials are split by 80 mV (1.85 kcal/mol), values that energetically match the shift in topological balance. Allosteric and cooperative regulation of the switch by ionic strength exploits the shielded charge interactions between the two hemes and the exposed, cooperative interactions between the coproporphyrin carboxylates.
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Affiliation(s)
- A M Grosset
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104, USA
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50
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Takakusa H, Kikuchi K, Urano Y, Higuchi T, Nagano T. Intramolecular fluorescence resonance energy transfer system with coumarin donor included in beta-cyclodextrin. Anal Chem 2001; 73:939-42. [PMID: 11289439 DOI: 10.1021/ac001016a] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In aqueous solutions, the fluorescence of the intramolecular fluorescence resonance energy-transfer (FRET) system 1 was strongly quenched, because of close contact between the donor and acceptor moieties. FRET occurred, and the acceptor fluorescence was increased, by adding beta-cyclodextrin (beta-CD) to aqueous solutions of 1. Spectral analysis supported the idea that the FRET enhancement was due to the formation of an inclusion complex of the coumarin moiety in beta-CD, resulting in separation of the fluorophores. On the basis of this result, we propose that covalent binding of coumarin to beta-CD will provide a FRET cassette molecule. So, compound 2 bearing beta-CD covalently was designed and synthesized. Fluorescence intensity of 2 was enhanced markedly compared to the intensity of 3. Applying this FRET system, various FRET probes that will be useful for ratio imaging and also the high-throughput screening will be provided.
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Affiliation(s)
- H Takakusa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan
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