1
|
Jednačak T, Mikulandra I, Smokrović K, Hloušek-Kasun A, Kapustić M, Delaš K, Piantanida I, Jurković M, Bertoša B, Zangger K, Novak P. Antimicrobial macrozones interact with biological macromolecules via two-site binding mode of action: Fluorimetric, NMR and docking studies. Bioorg Chem 2024; 147:107338. [PMID: 38583253 DOI: 10.1016/j.bioorg.2024.107338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Macrozones are novel conjugates of azithromycin and thiosemicarbazones, which exhibit very good in vitro antibacterial activities against susceptible and some resistant bacterial strains thus showing a potential for further development. A combination of spectrometric (fluorimetry, STD and WaterLOGSY NMR) and molecular docking studies provided insights into atomic details of interactions between selected macrozones and biological receptors such as E. coli ribosome and bovine serum albumin. Fluorimetric measurements revealed binding constants in the micro-molar range while NMR experiments provided data on binding epitopes. It has been demonstrated that both STD and WaterLOGSY gave comparable and consistent results unveiling atoms in intimate contacts with biological receptors. Docking studies pointed towards main interactions between macrozones and E. coli ribosome which included specific π - π stacking and hydrogen bonding interactions with thiosemicarbazone part extending down the ribosome exit tunnel. The results of the docking experiments were in fine correlation with those obtained by NMR and fluorimetry. Our investigation pointed towards a two-site binding mechanism of interactions between macrozones and E. coli ribosome which is the most probable reason for their activity against azithromycin-resistant strains. Much better activity of macrozone-nickel coordinated compound against E. coli ribosome compared to other macrozones has been attributed to the higher polarity which enabled better bacterial membrane penetration and binding of the two thiosemicarbazone units thus additionally contributing to the overall binding energy. The knowledge gained in this study should play an important role in anti-infective macrolide design in the future.
Collapse
Affiliation(s)
- Tomislav Jednačak
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Ivana Mikulandra
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Kristina Smokrović
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Andrea Hloušek-Kasun
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Monika Kapustić
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Kristina Delaš
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Ivo Piantanida
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička 54 HR-10000 Zagreb, Croatia.
| | - Marta Jurković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička 54 HR-10000 Zagreb, Croatia
| | - Branimir Bertoša
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Klaus Zangger
- University of Graz, Institute of Chemistry, Organic and Bioorganic Chemistry, Heinrichstraße 28 A-8010 Graz, Austria
| | - Predrag Novak
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia.
| |
Collapse
|
2
|
Bhuin S, Halder S, Saha SK, Chakravarty M. Binding interactions and FRET between bovine serum albumin and various phenothiazine-/anthracene-based dyes: a structure-property relationship. RSC Adv 2021; 11:1679-1693. [PMID: 35424090 PMCID: PMC8693680 DOI: 10.1039/d0ra09580j] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
The present study demonstrates binding interactions and Förster resonance energy transfer (FRET) between bovine serum albumin (BSA) and a series of structurally and electronically diverse phenothiazine (PTZ) and anthracene (ANT) dyes. Upon selective excitation of tryptophan (Trp) residues of BSA, radiationless energy transfer to a dye takes place, resulting in fluorescence quenching of the former. Fluorescence quenching mechanisms, FRET parameters, possible locations, and binding constants of dyes with the BSA have been examined to deduce a structure–property relationship. The mechanism of quenching is apparently static in nature. PTZ dyes with heteroatoms and a pentyl tail (C5-PTZ) attached to them were found to have a stronger binding affinity with BSA as compared to ANT dyes. Stronger binding affinities of C5-PTZ dyes with BSA result in greater energy transfer efficiencies (ET). A dye with a strong electron-withdrawing group present in it has shown better energy accepting capability. A FRET study with dicyanoaniline (DCA) analogs of PTZ and ANT dyes (C5-PTZDCA and ANTDCA, respectively) revealed that ET depends on electronic and structural factors of molecules. An almost orthogonal geometry between ANT and DCA moieties (∼79°) in ANTDCA induces the greater extent of electron transfer from ANT to DCA, showing a higher ET for this dye as compared to C5-PTZDCA in which the torsion angle is only ∼38°. Further, the observed facts have been validated by experimentally determined bandgaps (using cyclic voltammetry experiments) for all the dyes. Thus, the hydrophobic character and the presence of interactive substituents along with the electron-accepting abilities majorly control the FRET for such dyes with BSA. The present study demonstrates binding interactions and Förster resonance energy transfer (FRET) between bovine serum albumin (BSA) and a series of structurally and electronically diverse phenothiazine (PTZ) and anthracene (ANT) dyes.![]()
Collapse
Affiliation(s)
- Shouvik Bhuin
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| | - Sayantan Halder
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| | - Subit Kumar Saha
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| | - Manab Chakravarty
- Department of Chemistry, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campuses Hyderabad-500078 Telangana India
| |
Collapse
|
3
|
Ricart-Ortega M, Berizzi AE, Catena J, Malhaire F, Muñoz L, Serra C, Lebon G, Goudet C, Llebaria A. Development and validation of a mass spectrometry binding assay for mGlu5 receptor. Anal Bioanal Chem 2020; 412:5525-5535. [PMID: 32564119 DOI: 10.1007/s00216-020-02772-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
Abstract
Mass spectrometry (MS) binding assays are a label-free alternative to radioligand or fluorescence binding assays, so the readout is based on direct mass spectrometric detection of the test ligand. The study presented here describes the development and validation of a highly sensitive, rapid, and robust MS binding assay for the quantification of the binding of the metabotropic glutamate 5 (mGlu5) negative allosteric modulator (NAM), MPEP (2-methyl-6-phenylethynylpyridine) at the mGlu5 allosteric binding site. The LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometric) analytical method was established and validated with a deuterated analogue of MPEP as an internal standard. The developed MS binding assay described here allowed for the determination of MS binding affinity estimates that were in agreement with affinity estimates obtained from a tritiated MPEP radioligand saturation binding assay, indicating the suitability of this methodology for determining affinity estimates for compounds that target mGlu5 allosteric binding sites. Graphical abstract.
Collapse
Affiliation(s)
- Maria Ricart-Ortega
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain.,IGF, CNRS, INSERM, University of Montpellier, 34094, Montpellier, France
| | - Alice E Berizzi
- IGF, CNRS, INSERM, University of Montpellier, 34094, Montpellier, France
| | - Juanlo Catena
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain
| | - Fanny Malhaire
- IGF, CNRS, INSERM, University of Montpellier, 34094, Montpellier, France
| | - Lourdes Muñoz
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain.,SIMchem, Service of Synthesis of High Added Value Molecules, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain
| | - Carmen Serra
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain.,SIMchem, Service of Synthesis of High Added Value Molecules, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain
| | - Guillaume Lebon
- IGF, CNRS, INSERM, University of Montpellier, 34094, Montpellier, France
| | - Cyril Goudet
- IGF, CNRS, INSERM, University of Montpellier, 34094, Montpellier, France.
| | - Amadeu Llebaria
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain. .,SIMchem, Service of Synthesis of High Added Value Molecules, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18, 08034, Barcelona, Spain.
| |
Collapse
|
4
|
Kamba PF, Dickson DA, White NA, Ekstrom JL, Koslowsky DJ, Hoogstraten CG. The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein. Sci Rep 2018; 8:16989. [PMID: 30451852 PMCID: PMC6242908 DOI: 10.1038/s41598-018-34377-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/15/2018] [Indexed: 01/30/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins, a helical repeat family of organellar RNA binding proteins, play essential roles in post-transcriptional RNA processing. In Trypanosoma brucei, an expanded family of PPR proteins localize to the parasite’s single mitochondrion, where they are believed to perform important roles in both RNA processing and translation. We studied the RNA binding specificity of the simplest T. brucei PPR protein (KRIPP11) using electrophoretic mobility shift assays, fluorescence anisotropy, circular dichroism spectroscopy, and in vitro selection. We found KRIPP11 to be an RNA binding protein with specificity for sequences of four or more consecutive guanosine residues (G-tracts). Such G-tracts are dramatically enriched in T. brucei mitochondrial transcripts that are destined for extensive uridine insertion/deletion editing but are not present in mRNAs following editing. We further found that the quadruplex oligoguanosine RNA conformation is preferentially recognized by KRIPP11 over other conformational forms, and is bound without disruption of the quadruplex structure. In combination with prior data demonstrating association of KRIPP11 with the small ribosomal subunit, these results suggest possible roles for KRIPP11 in bridging mRNA maturation and translation or in facilitating translation of unusual dual-coded open reading frames.
Collapse
Affiliation(s)
- Pakoyo F Kamba
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Makerere University, Kampala, Uganda
| | - David A Dickson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, Massachusetts, USA
| | - Neil A White
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jennifer L Ekstrom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Donna J Koslowsky
- Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, 48824-1319, USA
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824-1319, USA.
| |
Collapse
|
5
|
Heller GT, Aprile FA, Vendruscolo M. Methods of probing the interactions between small molecules and disordered proteins. Cell Mol Life Sci 2017; 74:3225-3243. [PMID: 28631009 PMCID: PMC5533867 DOI: 10.1007/s00018-017-2563-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.
Collapse
Affiliation(s)
- Gabriella T Heller
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | |
Collapse
|
6
|
Ding F, Xie Y, Peng W, Peng YK. Measuring the bioactivity and molecular conformation of typically globular proteins with phenothiazine-derived methylene blue in solid and in solution: A comparative study using photochemistry and computational chemistry. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:69-80. [PMID: 26950891 DOI: 10.1016/j.jphotobiol.2016.02.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Methylene blue is a phenothiazine agent, that possesses a diversity of biomedical and biological therapeutic purpose, and it has also become the lead compound for the exploitation of other pharmaceuticals such as chlorpromazine and the tricyclic antidepressants. However, the U.S. Food and Drug Administration has acquired cases of detrimental effects of methylene blue toxicities such as hemolytic anemia, methemoglobinemia and phototoxicity. In this work, the molecular recognition of methylene blue by two globular proteins, hemoglobin and lysozyme was characterized by employing fluorescence, circular dichroism (CD) along with molecular modeling at the molecular scale. The recognition of methylene blue with proteins appears fluorescence quenching via static type, this phenomenon does cohere with time-resolved fluorescence lifetime decay that nonfluorescent protein-drug conjugate formation has a strength of 10(4)M(-1), and the primary noncovalent bonds, that is hydrogen bonds, π-conjugated effects and hydrophobic interactions were operated and remained adduct stable. Meantime, the results of far-UV CD and synchronous fluorescence suggest that the α-helix of hemoglobin/lysozyme decreases from 78.2%/34.7% (free) to 58.7%/23.8% (complex), this elucidation agrees well with the elaborate description of three-dimensional fluorescence showing the polypeptide chain of proteins partially destabilized upon conjugation with methylene blue. Furthermore, both extrinsic fluorescent indicator and molecular modeling clearly exhibit methylene blue is situated within the cavity constituted by α1, β2 and α2 subunits of hemoglobin, while it was located at the deep fissure on the lysozyme surface and Trp-62 and Trp-63 residues are nearby. With the aid of computational analyses and combining the wet experiments, it can evidently be found that the recognition ability of proteins for methylene blue is patterned upon the following sequence: lysozyme<hemoglobin<albumin. Basically, the distinction originates from different spatial structures of proteins and noncovalent interactions between proteins and methylene blue. In addition, biological relevance of the biorecognition of methylene blue with proteins was briefly discussed. We hope that this study could provide further standpoint so that one explore the biological activity of methylene blue and also phenothiazines.
Collapse
Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China; Department of Chemistry, China Agricultural University, Beijing 100193, China; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Yong Xie
- State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Research Institute of Chemical Industry Co. Ltd., Shenyang 110021, China
| | - Wei Peng
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China; College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Yu-Kui Peng
- Center for Food Quality Supervision & Testing, Ministry of Agriculture, College of Food Science & Engineering, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
7
|
Peng W, Ding F, Xie Y. Biointeractions of C.I. Acid Red 2 and its structural analogues with transporter albumin: Fluorescence, circular dichroism, and ligand docking approaches. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 154:40-50. [DOI: 10.1016/j.jphotobiol.2015.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 11/08/2015] [Accepted: 11/24/2015] [Indexed: 02/02/2023]
|
8
|
Ding F, Peng W. Biological activity of natural flavonoids as impacted by protein flexibility: an example of flavanones. MOLECULAR BIOSYSTEMS 2015; 11:1119-33. [PMID: 25673513 DOI: 10.1039/c4mb00662c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Naturally multifunctional Rutaceae hesperidin and its aglycone hesperetin have a great variety of biopharmaceutical activities, e.g. anti-cancer, anti-inflammatory, antioxidant and antitumor; however, the influence of the molecular structures of hesperidin and hesperetin, and in particular, the structural properties such as flexibility and dynamic features of protein on the biological activities of these bioactive compounds remains ambiguous. In the present study, the biomolecular recognition of crucial biopolymer - albumin from human serum (HSA) with Rutaceae, the recognition differences between HSA-hesperidin and HSA-hesperetin, the key elements that lead to the discrepancies as well as the structural characters of protein to the recognition processes were comparatively examined by employing biophysical approaches at the molecular scale. The results illustrated distinctly that (1) aglycone hesperetin can form stronger noncovalent bonds with HSA and possess higher recognition stability as compared with hesperidin. This phenomenon suggest that the introduction of glycoside structure into flavanone may possibly not be able to increase the noncovalent recognition of flavanone by a biopolymer, and conversely, this event will probably decrease the recognition capacity. (2) Although hesperidin and hesperetin can be located within subdomains IIA and IIIA, respectively, the conformational stability of flavanones in subdomain IIA is greater than subdomain IIIA; as a result, the recognition ability of subdomain IIIA with flavanones is patently lesser than subdomain IIA. These discrepancies likely originate from the unique characteristics of the respective cavity, or more specifically, subdomain IIA is basically a closed space, whereas subdomain IIIA is a semi-open region. Meanwhile, the detailed analyses of root-mean-square fluctuation interpreted the recognition of flavanones by subdomain IIA on HSA, which would evoke larger conformational alterations in several amino acid residues, and the similar phenomenon also resides in subdomain IIIA, which signifies that the flexible characteristics of different binding patches in protein may possess fairly notable effects on the HSA-flavanones recognition. Moreover, the integral structural changes of HSA exhibit some disparities on account of the dissimilarities of recognition capability to the protein-flavanone biointeractions, and all these conclusions received further forceful supports from fluorescence and circular dichroism experiments in solution. Perhaps the work emerged herein could not only help us to better evaluate the bioavailability of natural flavanones with or without glycoside, but to understand the sketches of the three-dimensional structure trait of certain biomacromolecules for the medicinal properties of flavonoids in the human body.
Collapse
Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China.
| | | |
Collapse
|
9
|
Robin J, Brauer J, Sulmann S, Marino V, Dell’Orco D, Lienau C, Koch KW. Differential Nanosecond Protein Dynamics in Homologous Calcium Sensors. ACS Chem Biol 2015. [PMID: 26204433 DOI: 10.1021/acschembio.5b00278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shaping the temporal response of photoreceptors is facilitated by a well-balanced second messenger cascade, in which two neuronal Ca(2+)-sensor proteins operate in a sequential relay mechanism. Although they share structurally similar sensing units, they differentially activate the same target protein. Here, as a prototypical case in Ca(2+)-mediated signal processing, we investigate differential cellular responsiveness in protein conformational dynamics on a nanosecond time scale. For this, we have site-specifically labeled cysteine residues in guanylate cyclase-activating protein GCAP1 by the fluorescent dye Alexa647 and probed its local environment via time-resolved fluorescence spectroscopy. Fluorescence lifetime and rotational anisotropy measurements reveal a distinct structural movement of the polypeptide chain around position 106 upon release of Ca(2+). This is supported by analyzing the diffusional dye motion in a wobbling-in-a-cone model and by molecular dynamics simulations. We conclude that GCAP1 and its cellular cognate GCAP2 operate by distinctly different switching mechanisms despite their high structural homology.
Collapse
Affiliation(s)
- Jörg Robin
- Ultrafast
Nano-Optics, Institute of Physics, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Jens Brauer
- Ultrafast
Nano-Optics, Institute of Physics, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Stefan Sulmann
- Biochemistry,
Department of Neurosciences, Faculty VI, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Valerio Marino
- Department
of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Daniele Dell’Orco
- Department
of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Verona, Italy
- Center
for BioMedical Computing (CBMC), University of Verona, Verona, Italy
| | - Christoph Lienau
- Ultrafast
Nano-Optics, Institute of Physics, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Center
of Interface Science, University of Oldenburg, D-26111 Oldenburg, Germany
- Biochemistry,
Department of Neurosciences, Faculty VI, University of Oldenburg, D-26111 Oldenburg, Germany
| |
Collapse
|
10
|
Zimmerman JR, Johntony O, Steigerwald D, Criss C, Myers BJ, Kinder DH. The Synthesis of a New Class of Highly Fluorescent Chromones via an Inverse-Demand Hetero-Diels-Alder Reaction. Org Lett 2015; 17:3256-9. [PMID: 26102589 DOI: 10.1021/acs.orglett.5b01417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A new class of fluorophores has been developed utilizing an inverse-demand hetero-Diels-Alder reaction with silyl enol ethers and substituted 3-formylchromones. These compounds yield blue to green fluorescence with quantum yields up to 73%. They also exhibit good potential for use as fluorescent probes in biological systems, as they are cell membrane permeable with low cytotoxicity.
Collapse
Affiliation(s)
- Jake R Zimmerman
- †Department of Chemistry and Biochemistry, Ohio Northern University, Ada, Ohio 45810, United States
| | - Olivia Johntony
- †Department of Chemistry and Biochemistry, Ohio Northern University, Ada, Ohio 45810, United States
| | - Daniel Steigerwald
- †Department of Chemistry and Biochemistry, Ohio Northern University, Ada, Ohio 45810, United States
| | - Cody Criss
- †Department of Chemistry and Biochemistry, Ohio Northern University, Ada, Ohio 45810, United States
| | - Brian J Myers
- †Department of Chemistry and Biochemistry, Ohio Northern University, Ada, Ohio 45810, United States
| | - David H Kinder
- ‡Department of Pharmaceutical and Biomedical Sciences, Ohio Northern University, Ada, Ohio 45810, United States
| |
Collapse
|
11
|
Binding of angiogenesis inhibitor kringle 5 to its specific ligands by frontal affinity chromatography. J Chromatogr A 2015; 1401:42-51. [DOI: 10.1016/j.chroma.2015.04.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 04/25/2015] [Accepted: 04/28/2015] [Indexed: 11/21/2022]
|
12
|
Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
Collapse
|
13
|
Heikal AA. Time-resolved fluorescence anisotropy and fluctuation correlation analysis of major histocompatibility complex class I proteins in fibroblast cells. Methods 2013; 66:283-91. [PMID: 23811298 DOI: 10.1016/j.ymeth.2013.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/12/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022] Open
Abstract
Major histocompatibility complex class I proteins, MHC(I), are expressed in almost all nucleated cells and synthesized in the endoplasmic reticulum (ER). The orientation and mobility of these complexes are crucial in their biological function in the immune system, i.e., the cytosolic pathogen peptides loading and their presentation to T-cell receptors at the plasma membrane, where cell destruction is triggered. Here, we investigate the structural flexibility and associations of GFP-encoded MHC(I) alleles (H2L(d)), namely H2L(d)GFPin and H2L(d)GFPout, in cultured mouse fibroblast cells. Time-resolved fluorescence anisotropy of H2L(d)GFPin in the ER indicates a dominant overall tumbling motion of 56±7 ns (ER), with a fast conformational flexibility, as compared with a restricted rotation of H2L(d)GFPout. At the single-molecule level, the diffusion coefficient of H2L(d)GFPin and H2L(d)GFPout in the ER is (1.8±0.5)×10(-9) and (2.1±0.6)×10(-9) cm(2)/s, respectively, as revealed by fluorescence correlation spectroscopy. A complementary immunoblotting of H2L(d)GFP constructs, isolated from mouse fibroblast cells, reveals band at 75 kDa as compared with 29 kDa of the free EGFP. These real-time dynamics provide new insights into the structural flexibility and intracellular associations of GFP-labeled MHC(I) alleles (H2L(d)) in living cells.
Collapse
Affiliation(s)
- Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota-Duluth, Duluth, MN 55812, USA; Department of Pharmacy Practice and Pharmaceutical Sciences, College of Pharmacy, University of Minnesota-Duluth, Duluth, MN 55812, USA.
| |
Collapse
|
14
|
McLoughlin D, Bertelli F, Williams C. The A, B, Cs of G-protein-coupled receptor pharmacology in assay development for HTS. Expert Opin Drug Discov 2013; 2:603-19. [PMID: 23488953 DOI: 10.1517/17460441.2.5.603] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
G-protein-coupled receptors represent one of the most important areas of research in the pharmaceutical industry, being one of the largest druggable gene families. Recognising this fact, manufacturers have developed a huge variety of homogeneous assay technologies that facilitate the quantification of receptor ligand binding events and their downstream signalling cascades. However, while early emphasis was placed on the most sensitive, high-throughput and cost-effective screening technologies to enable identification of the most lead matter for further development, in recent years emphasis has shifted to a focus on maximising the identification of compounds that are new and developing assays that are more biologically/pharmacologically relevant. Therefore, this review provides an overview of the binding and functional techniques available for high-throughput screening, with particular attention on how assay application and configuration can be maximised to ensure their successful identification of relevant chemical matter and thereby optimising project success.
Collapse
Affiliation(s)
- Dj McLoughlin
- HTS CoE, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK +44(0)1304644616 ; +44(0)1304655592 ;
| | | | | |
Collapse
|
15
|
Loison S, Cottet M, Orcel H, Adihou H, Rahmeh R, Lamarque L, Trinquet E, Kellenberger E, Hibert M, Durroux T, Mouillac B, Bonnet D. Selective Fluorescent Nonpeptidic Antagonists For Vasopressin V2 GPCR: Application To Ligand Screening and Oligomerization Assays. J Med Chem 2012; 55:8588-602. [DOI: 10.1021/jm3006146] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphanie Loison
- Laboratoire
d’Innovation
Thérapeutique, UMR7200 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67412 Illkirch, France
| | - Martin Cottet
- CNRS UMR 5203, INSERM U661,
and Université Montpellier I et II, Institut de Génomique
Fonctionnelle, Département de Pharmacologie Moléculaire,
141 rue de la Cardonille, 34094 Montpellier Cedex 5, France
| | - Hélène Orcel
- CNRS UMR 5203, INSERM U661,
and Université Montpellier I et II, Institut de Génomique
Fonctionnelle, Département de Pharmacologie Moléculaire,
141 rue de la Cardonille, 34094 Montpellier Cedex 5, France
| | - Hélène Adihou
- Laboratoire
d’Innovation
Thérapeutique, UMR7200 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67412 Illkirch, France
| | - Rita Rahmeh
- CNRS UMR 5203, INSERM U661,
and Université Montpellier I et II, Institut de Génomique
Fonctionnelle, Département de Pharmacologie Moléculaire,
141 rue de la Cardonille, 34094 Montpellier Cedex 5, France
| | - Laurent Lamarque
- Cisbio Bioassays, Parc Marcel
Boiteux, BP84175, 30200 Codolet, France
| | - Eric Trinquet
- Cisbio Bioassays, Parc Marcel
Boiteux, BP84175, 30200 Codolet, France
| | - Esther Kellenberger
- Laboratoire
d’Innovation
Thérapeutique, UMR7200 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67412 Illkirch, France
| | - Marcel Hibert
- Laboratoire
d’Innovation
Thérapeutique, UMR7200 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67412 Illkirch, France
| | - Thierry Durroux
- CNRS UMR 5203, INSERM U661,
and Université Montpellier I et II, Institut de Génomique
Fonctionnelle, Département de Pharmacologie Moléculaire,
141 rue de la Cardonille, 34094 Montpellier Cedex 5, France
| | - Bernard Mouillac
- CNRS UMR 5203, INSERM U661,
and Université Montpellier I et II, Institut de Génomique
Fonctionnelle, Département de Pharmacologie Moléculaire,
141 rue de la Cardonille, 34094 Montpellier Cedex 5, France
| | - Dominique Bonnet
- Laboratoire
d’Innovation
Thérapeutique, UMR7200 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67412 Illkirch, France
| |
Collapse
|
16
|
Kollmann H, Becker SF, Shirdel J, Scholten A, Ostendorp A, Lienau C, Koch KW. Probing the Ca(2+) switch of the neuronal Ca(2+) sensor GCAP2 by time-resolved fluorescence spectroscopy. ACS Chem Biol 2012; 7:1006-14. [PMID: 22409623 DOI: 10.1021/cb3000748] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report fluorescence lifetime and rotational anisotropy measurements of the fluorescent dye Alexa647 attached to the guanylate cyclase-activating protein 2 (GCAP2), an intracellular myristoylated calcium sensor protein operating in photoreceptor cells. By linking the dye to different protein regions critical for monitoring calcium-induced conformational changes, we could measure fluorescence lifetimes and rotational correlation times as a function of myristoylation, calcium, and position of the attached dye, while GCAP2 was still able to regulate guanylate cyclase in a Ca(2+)-sensitive manner. We observe distinct site-specific variations in the fluorescence dynamics when externally changing the protein conformation. A clear reduction in fluorescence lifetime suggests that in the calcium-free state a dye marker in amino acid position 131 senses a more hydrophobic protein environment than in position 111. Saturating GCAP2 with calcium increases the fluorescence lifetime and hence leads to larger exposure of position 111 to the solvent and at the same time to a movement of position 131 into a hydrophobic protein cleft. In addition, we find distinct, biexponential anisotropy decays reflecting the reorientational motion of the fluorophore dipole and the dye/protein complex, respectively. Our experimental data are well described by a "wobbling-in-a-cone" model and reveal that for dye markers in position 111 of the GCAP2 protein both addition of calcium and myristoylation results in a pronounced increase in orientational flexibility of the fluorophore. Our results provide evidence that the up-and-down movement of an α-helix that is situated between position 111 and 131 is a key feature of the dynamics of the protein-dye complex. Operation of this piston-like movement is triggered by the intracellular messenger calcium.
Collapse
Affiliation(s)
- Heiko Kollmann
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Simon F. Becker
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Javid Shirdel
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Alexander Scholten
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Anna Ostendorp
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Christoph Lienau
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Ultrafast
Nano-Optics, Institute of Physics and §Biochemistry, Institute of Biology and Environmental
Sciences, Faculty V, University of Oldenburg, D-26111 Oldenburg, Germany
- Center
of Interface Science and
- Research Center Neurosensory Science, University of Oldenburg, D-26111 Oldenburg, Germany
| |
Collapse
|
17
|
Lórenz-Fonfría VA, León X, Padrós E. Studying substrate binding to reconstituted secondary transporters by attenuated total reflection infrared difference spectroscopy. Methods Mol Biol 2012; 914:107-126. [PMID: 22976025 DOI: 10.1007/978-1-62703-023-6_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The determination of protein conformational changes induced by the interaction of substrates with secondary transporters is an important step toward the elucidation of their transport mechanism. Since conformational changes in a protein alter its vibrational patterns, they can be detected with high sensitivity by infrared difference (IR(diff)) spectroscopy without the need for external probes. We describe a general procedure to obtain substrate-induced IR(diff) spectra by alternating perfusion of buffers over an attenuated total reflection (ATR) crystal containing an adhered film of a membrane protein reconstituted in lipids. As an example, we provide specific protocols to obtain melibiose and Na(+)-induced ATR-IR(diff) spectra of reconstituted melibiose permease, a sodium/melibiose co-transporter from E. coli. The presented methodology is applicable in principle to any membrane protein, provided that it can be purified and reconstituted in functional form, and appropriate substrates are available.
Collapse
Affiliation(s)
- Víctor A Lórenz-Fonfría
- Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | | | | |
Collapse
|
18
|
Ostuni A, Miglionico R, Monné M, Castiglione Morelli MA, Bisaccia F. The nucleotide-binding domain 2 of the human transporter protein MRP6. J Bioenerg Biomembr 2011; 43:465-71. [PMID: 21748403 DOI: 10.1007/s10863-011-9372-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/13/2011] [Indexed: 02/03/2023]
Abstract
Multidrug-resistance-associated protein 6 (MRP6/ABCC6) belongs to the ABC transporter family, whose members share many characteristic features including membrane domains and two nucleotide-binding domains (NBD1 and NBD2). These function cooperatively to bind and hydrolyze ATP for the transport of substrates across biological membranes. In this study, MRP6-NBD2 (residues 1252-1503) was expressed in Escherichia coli, purified and structurally and functionally characterized. CD spectra suggested that the protein is folded. Furthermore, NBD2 is shown to be biologically active as it binds ATP and presents ATPase activity although significantly lower compared with isolated NBD1. The mixture of NBD2 and NBD1 exhibited an activity similar to the NBD2 alone, indicating that NBD1 and NBD2 form a heterodimer with the latter limiting ATP hydrolysis. These findings suggest that NBD1 has a higher tendency to form an active homodimer, which is also supported by in silico analysis of energy-minimized dimers of the homology models of the two domains.
Collapse
Affiliation(s)
- Angela Ostuni
- Department of Chemistry "Antonio Mario Tamburro", University of Basilicata, viale Ateneo Lucano 10, 85100 Potenza, Italy.
| | | | | | | | | |
Collapse
|
19
|
Abstract
High-throughput screening (HTS) has been postulated in several quarters to be a contributory factor to the decline in productivity in the pharmaceutical industry. Moreover, it has been blamed for stifling the creativity that drug discovery demands. In this article, we aim to dispel these myths and present the case for the use of HTS as part of a proven scientific tool kit, the wider use of which is essential for the discovery of new chemotypes.
Collapse
|
20
|
Serendipitous stereoselective synthesis of brand-new fluorescent dyes: (1Z)-3-(alkylimino)-1-[(chromone-3-yl)methylene]-1,3-dihydro-9H-furo[3,4-b]chromen-9-one-type fluorophores with blue fluorescence emission properties. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.01.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Dumbrepatil AB, Lee SG, Chung SJ, Lee MG, Park BC, Kim TJ, Woo EJ. Development of a nanoparticle-based FRET sensor for ultrasensitive detection of phytoestrogen compounds. Analyst 2010; 135:2879-86. [PMID: 20877819 DOI: 10.1039/c0an00385a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Phytoestrogens are plant compounds that mimic the actions of endogenous estrogens. The abundance of these chemicals in nature and their potential effects on health require the development of a convenient method to detect phytoestrogens. We have developed a nanoparticle (NP)-conjugated FRET probe based on the human estrogen receptor α (ER) ligand-binding domain (LBD) to detect phytoestrogens. The NP-conjugated FRET probe showed fluorescence signals for genistein, resveratrol and daidzein compounds with Δ ratios of 1.65, 2.60 and 1.37 respectively, which are approximately six times greater compared to individual FRET probes. A significantly higher signal for resveratrol versus genistein and daidzein indicates that the probe can differentiate between antagonistic phytoalexin substances and agonistic isoflavone compounds. NP-conjugated probes demonstrated a wide dynamic range, ranging from 10(-18) to 10(-1) M with EC(50) values of 9.6 × 10(-10), 9.0 × 10(-10) and 9.2 × 10(-10) M for genistein, daidzein and resveratrol respectively, whereas individual probes detected concentrations of 10(-13) to 10(-4) M for phytoestrogens compounds. The time profile revealed that the NP-conjugated probe is stable over 30 h and there is not a significant deviation in the FRET signal at room temperature. These data demonstrate that conjugation of a FRET probe to nanoparticles is able to serve as an effective FRET sensor for monitoring bioactive compounds with significantly increased sensitivity, dynamic range and stability.
Collapse
Affiliation(s)
- Arti B Dumbrepatil
- Korea Research Institute of Biosciences and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, 305-806, Korea
| | | | | | | | | | | | | |
Collapse
|
22
|
Veiksina S, Kopanchuk S, Rinken A. Fluorescence anisotropy assay for pharmacological characterization of ligand binding dynamics to melanocortin 4 receptors. Anal Biochem 2010; 402:32-9. [DOI: 10.1016/j.ab.2010.03.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/21/2010] [Accepted: 03/13/2010] [Indexed: 11/16/2022]
|
23
|
Palamalai V, Miyagi M. Mechanism of glyceraldehyde-3-phosphate dehydrogenase inactivation by tyrosine nitration. Protein Sci 2010; 19:255-62. [PMID: 20014444 DOI: 10.1002/pro.311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifaceted protein that is involved in numerous processes including glycolysis, translational silencing, transcriptional regulation of specific genes, and acting as a nitric oxide sensor. The precise mechanism on how GAPDH is targeted to these different roles is unclear but believed to involve specific posttranslational modification to the protein. Numerous studies have demonstrated that GAPDH is a target for tyrosine nitration. However, the site of modification and the molecular consequence have not been defined. Rabbit GAPDH with a reversibly protected catalytic cysteine was nitrated in vitro with tetranitromethane, resulting in complete loss of GAPDH catalytic activity. Nitration was estimated as 0.32 mol of nitrotyrosine residue per mole of GAPDH. Mass spectrometry analysis of nitrated GAPDH indicated that Tyr311 and Tyr317 were the sole sites of nitration. The X-ray crystal structure revealed that the distances between Tyr311 and Tyr317 and the cofactor nicotinamide adenine dinucleotide (NAD(+)) were less than 7.2 and 3.7 A, respectively, implying that nitration of these two residues may affect NAD(+) binding. This possibility was assessed using an NAD(+) binding assay, which showed that nitrated GAPDH was incapable of binding NAD(+). Thus, these results strongly suggest that Tyr311 and Tyr317 nitration prohibits NAD(+) binding, leading to the loss of catalytic activity.
Collapse
Affiliation(s)
- Vikram Palamalai
- Department of Biochemistry and Molecular Biology, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | | |
Collapse
|
24
|
Abstract
Imaging membrane dynamics is an important goal, motivated by the abundance of biochemical and biophysical events that are orchestrated at, or by, cellular membranes. The short length scales, fast timescales, and environmental requirements of membrane phenomena present challenges to imaging experiments. Several technical advances offer means to overcome these challenges, and we describe here three powerful techniques applicable to membrane imaging: total internal reflection fluorescence (TIRF) microscopy, fluorescence interference contrast (FLIC) microscopy, and fluorescence correlation spectroscopy (FCS). For each, we discuss the physics underpinning the approach, its practical implementation, and recent examples highlighting its achievements in exploring the membrane environment.
Collapse
Affiliation(s)
- Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | | | | |
Collapse
|
25
|
Zheng XY, Pang EG, Zhao YQ, Jiao Y, Yang BS. Investigation on the Inclusion Behavior of ApoCopC with Vitamin B6. Supramol Chem 2008. [DOI: 10.1080/10610270701491219] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Xiao-Yan Zheng
- a Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education , Shanxi University , Taiyuan, Shanxi, 030006, People's Republic of China
| | - Er-Guo Pang
- a Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education , Shanxi University , Taiyuan, Shanxi, 030006, People's Republic of China
| | - Ya-Qin Zhao
- a Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education , Shanxi University , Taiyuan, Shanxi, 030006, People's Republic of China
| | - Yong Jiao
- a Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education , Shanxi University , Taiyuan, Shanxi, 030006, People's Republic of China
| | - Bin-Sheng Yang
- a Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education , Shanxi University , Taiyuan, Shanxi, 030006, People's Republic of China
| |
Collapse
|
26
|
Krieger F, Mourot A, Araoz R, Kotzyba-Hibert F, Molgó J, Bamberg E, Goeldner M. Fluorescent agonists for the Torpedo nicotinic acetylcholine receptor. Chembiochem 2008; 9:1146-53. [PMID: 18386276 DOI: 10.1002/cbic.200700757] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have synthesized a series of fluorescent acylcholine derivatives carrying different linkers that vary in length and structure and connect the acylcholine unit to the environment-sensitive fluorophores 7-(diethylamino)coumarin-3-carbonyl (DEAC) or N-(7-nitrobenz-2-oxa-1,3-diazol-yl) (NBD). The pharmacological properties of the fluorescent analogues were investigated on heterologously expressed nicotinic acetylcholine receptor (nAChR) from Torpedo californica and on oocytes transplanted with nAChR-rich Torpedo marmorata membranes. Agonist action strongly depends on the length and the structure of the linker. One particular analogue, DEAC-Gly-C6-choline, showed partial agonist behavior with about half of the maximum response of acetylcholine, which is at least 20 times higher than those observed with previously described fluorescent dansyl- and NBD-acylcholine analogues. Binding of DEAC-Gly-C6-choline to Torpedo nAChR induces a strong enhancement of fluorescence intensity. Association and displacement kinetic experiments revealed dissociation constants of 0.5 nM for the alphadelta-binding site and 15.0 nM for the alphagamma-binding site. Both the pharmacological and the spectroscopic properties of this agonist show great promise for characterizing the allosteric mechanism behind the function of the Torpedo nAChR, as well as for drug-screening studies.
Collapse
Affiliation(s)
- Florian Krieger
- Laboratoire de Chimie Bioorganique UMR 7175 LC1 CNRS, Faculté de Pharmacie, Université Louis Pasteur Strasbourg, 74, Route du Rhin, BP24, 67401 Illkirch Cedex, France.
| | | | | | | | | | | | | |
Collapse
|
27
|
Biochemical and Biophysical Analyses of Ras Modification by Ubiquitin. Methods Enzymol 2008. [DOI: 10.1016/s0076-6879(07)38018-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
28
|
Bouquin N, Malinovskii VL, Häner R. Highly efficient quenching of excimer fluorescence by perylene diimide in DNA. Chem Commun (Camb) 2008:1974-6. [DOI: 10.1039/b802193g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
29
|
|
30
|
De Filippis V, Draghi A, Frasson R, Grandi C, Musi V, Fontana A, Pastore A. o-Nitrotyrosine and p-iodophenylalanine as spectroscopic probes for structural characterization of SH3 complexes. Protein Sci 2007; 16:1257-65. [PMID: 17567746 PMCID: PMC2206685 DOI: 10.1110/ps.062726807] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
High-throughput screening of protein-protein and protein-peptide interactions is of high interest both for biotechnological and pharmacological applications. Here, we propose the use of the noncoded amino acids o-nitrotyrosine and p-iodophenylalanine as spectroscopic probes in combination with circular dichroism and fluorescence quenching techniques (i.e., collisional quenching and resonance energy transfer) as a means to determine the peptide orientation in complexes with SH3 domains. Proline-rich peptides bind SH3 modules in two alternative orientations, according to their sequence motifs, classified as class I and class II. The method was tested on an SH3 domain from a yeast myosin that is known to recognize specifically class I peptides. We exploited the fluorescence quenching effects induced by o-nitrotyrosine and p-iodophenylalanine on the fluorescence signal of a highly conserved Trp residue, which is the signature of SH3 domains and sits directly in the binding pocket. In particular, we studied how the introduction of the two probes at different positions of the peptide sequence (i.e., N-terminally or C-terminally) influences the spectroscopic properties of the complex. This approach provides clear-cut evidence of the orientation of the binding peptide in the SH3 pocket. The chemical strategy outlined here can be easily extended to other protein modules, known to bind linear sequence motifs in a highly directional manner.
Collapse
|
31
|
Höfner G, Zepperitz C, Wanner KT. MS Binding Assays – An Alternative to Radioligand Binding. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9783527610907.ch7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
32
|
Issad T, Blanquart C, Gonzalez-Yanes C. The use of bioluminescence resonance energy transfer for the study of therapeutic targets: application to tyrosine kinase receptors. Expert Opin Ther Targets 2007; 11:541-56. [PMID: 17373883 DOI: 10.1517/14728222.11.4.541] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
During recent years, the bioluminescence resonance energy transfer (BRET) methodology has emerged as a powerful technique for the study of protein-protein interactions. This review focuses on recent work demonstrating the power of BRET for the study of tyrosine kinase receptors, using insulin and IGF-1 receptors as models. The authors show that BRET can be used to monitor ligand-induced conformational changes within homodimeric insulin and IGF-1 receptors, as well as heterodimeric insulin/IGF-1 hybrid receptors. BRET can also be used to study, in real time and in living cells, the interaction of tyrosine kinase receptors with cellular partners negatively or positively involved in the regulation of intracellular signalling (protein tyrosine phosphatases, molecular adaptors). In addition, BRET can be used to develop high-throughput screening assays for the search of molecules with therapeutic interest and could, therefore, constitute a valuable tool for laboratories involved in drug discovery.
Collapse
Affiliation(s)
- Tarik Issad
- Institut Cochin, Department of Cell Biology, Université Paris Descartes, CNRS (UMR 8104), 22 Rue Méchain, 75014 Paris, France.
| | | | | |
Collapse
|
33
|
Schreiter C, Gjoni M, Hovius R, Martinez KL, Segura JM, Vogel H. Reversible sequential-binding probe receptor-ligand interactions in single cells. Chembiochem 2006; 6:2187-94. [PMID: 16270372 DOI: 10.1002/cbic.200500216] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
With the reversible sequential (ReSeq) binding assay,we present a novel approach for the ultrasensitive profiling of receptor function in single living cells. This assay is based on the repetitive application of fluorescent ligands that have fast association-dissociation kinetics. We chose the nicotinic-acetylcholine receptor (nAChR) as a prototypical example and performed ReSeq equilibrium, kinetic, and competition-binding assays using fluorescent derivatives of the antagonist alpha-conotoxin GI (alpha-CnTx). Thereby, we determined the binding constants of unlabeled alpha-CnTx and d-tubocurarine. The high selectivity of alpha-CnTx for muscle-type nAChR made it possible to observe specific binding even in the presence of other nAChR subtypes. Imaging of individual nAChRs and ligand-binding cycles to single cells in microfluidic devices demonstrated the ultimate miniaturization and accuracy of ReSeq-binding assays even at low receptor-expression levels. We expect our approach to be of generic importance for functional screening of compounds or membrane receptors, and for the detailed characterization of rare primary cells.
Collapse
Affiliation(s)
- Christoph Schreiter
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Chimie Physique des Polymères et Membranes, 1015 Lausanne, Switzerland
| | | | | | | | | | | |
Collapse
|
34
|
Adamczyk M, Grote J. EFFICIENT FLUORESCEIN SPIROLACTAM AND BIS-SPIROLACTAM SYNTHESIS. SYNTHETIC COMMUN 2006. [DOI: 10.1081/scc-100105396] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Maciej Adamczyk
- a Department of Chemistry (D9NM), AP-20, Diagnostics Division , Abbott Laboratories , 100 Abbott Park Road, Abbott Park, IL, 60064-6016, U.S.A
| | - Jonathan Grote
- a Department of Chemistry (D9NM), AP-20, Diagnostics Division , Abbott Laboratories , 100 Abbott Park Road, Abbott Park, IL, 60064-6016, U.S.A
| |
Collapse
|
35
|
De Filippis V, Frasson R, Fontana A. 3-Nitrotyrosine as a spectroscopic probe for investigating protein protein interactions. Protein Sci 2006; 15:976-86. [PMID: 16641485 PMCID: PMC2242503 DOI: 10.1110/ps.051957006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
3-Nitrotyrosine (NT) is approximately 10(3)-fold more acidic than Tyr, and its absorption properties are strongly pH-dependent. NT absorbs radiation in the wavelength range where Tyr and Trp emit fluorescence (300-450 nm), and it is essentially nonfluorescent. Therefore, NT may function as an energy acceptor in resonance energy transfer (FRET) studies for investigating ligand protein interactions. Here, the potentialities of NT were tested on the hirudin thrombin system, a well-characterized protease inhibitor pair of key pharmacological importance. We synthesized two analogs of the N-terminal domain (residues 1-47) of hirudin: Y3NT, in which Tyr3 was replaced by NT, and S2R/Y3NT, containing the substitutions Ser2 --> Arg and Tyr3 --> NT. The binding of these analogs to thrombin was investigated at pH 8 by FRET and UV/Vis-absorption spectroscopy. Upon hirudin binding, the fluorescence of thrombin was reduced by approximately 50%, due to the energy transfer occurring between the Trp residues of the enzyme (i.e., the donors) and the single NT of the inhibitor (i.e., the acceptor). The changes in the absorption spectra of the enzyme inhibitor complex indicate that the phenate moiety of NT in the free state becomes protonated to phenol in the thrombin-bound form. Our results indicate that the incorporation of NT can be effectively used to detect protein protein interactions with sensitivity in the low nanomolar range, to uncover subtle structural features at the ligand protein interface, and to obtain reliable Kd values for structure activity relationship studies. Furthermore, advances in chemical and genetic methods, useful for incorporating noncoded amino acids into proteins, highlight the broad applicability of NT in biotechnology and pharmacological screening.
Collapse
Affiliation(s)
- Vincenzo De Filippis
- Department of Pharmaceutical Sciences and CRIBI Biotechnology Center, University of Padua, I-35131 Padua, Italy.
| | | | | |
Collapse
|
36
|
Meyer BH, Martinez KL, Segura JM, Pascoal P, Hovius R, George N, Johnsson K, Vogel H. Covalent labeling of cell-surface proteins for in-vivo FRET studies. FEBS Lett 2006; 580:1654-8. [PMID: 16497304 DOI: 10.1016/j.febslet.2006.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 01/11/2006] [Accepted: 02/06/2006] [Indexed: 10/25/2022]
Abstract
Fluorescence resonance energy transfer (FRET) is a powerful technique to reveal interactions between membrane proteins in live cells. Fluorescence labeling for FRET is typically performed by fusion with fluorescent proteins (FP) with the drawbacks of a limited choice of fluorophores, an arduous control of donor-acceptor ratio and high background fluorescence arising from intracellular FPs. Here we show that these shortcomings can be overcome by using the acyl carrier protein labeling technique. FRET revealed interactions between cell-surface neurokinin-1 receptors simultaneously labeled with a controlled ratio of donors and acceptors. Moreover, using FRET the specific binding of fluorescent agonists could be monitored.
Collapse
Affiliation(s)
- Bruno H Meyer
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut de Science et Ingénierie Chimiques, CH-1015 Lausanne, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Zepperitz C, Höfner G, Wanner KT. MS-Binding Assays: Kinetic, Saturation, and Competitive Experiments Based on Quantitation of Bound Marker as Exemplified by the GABA Transporter mGAT1. ChemMedChem 2006; 1:208-17. [PMID: 16892353 DOI: 10.1002/cmdc.200500038] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new kind of binding assay is described in which the amount of a nonlabeled marker bound to the target is quantified by LC-ESI-MS-MS. This new approach was successfully implemented with nonlabeled NO 711 as marker and the GABA transporter subtype mGAT1 as target. The native marker bound to the target was liberated from the receptor protein by methanol denaturation after filtration. A reliable and sensitive LC-ESI-MS-MS method for the quantitation of NO 711 was developed, and data from mass spectrometric detection were analyzed by nonlinear regression. Kinetic MS-binding experiments yielded values for k+1 and k-1, while in saturation MS-binding experiments, Kd and Bmax values were determined. In competitive MS-binding experiments, Ki values were obtained for various test compounds covering a broad range of affinities for mGAT1. All experiments were performed in 96-well plate format with a filter plate for the separation step which improved the efficiency and throughput of the procedure. The method was validated by classical radioligand-binding experiments with the labeled marker [3H2]NO 711 in parallel. The results obtained from MS-binding experiments were found to be in good agreement with the results of the radioligand-binding assays. The new kind of MS-binding assay presented herein is further adapted to the conventional radioligand-binding assay in that the amount of bound marker is securely quantified. This promises easy implementation in accordance with conventional binding assays without the major drawbacks that are inherent in radioligand or fluorescence binding assays. Therefore, MS-binding assays are a true alternative to classical radioligand-binding assays.
Collapse
Affiliation(s)
- Christine Zepperitz
- Department Pharmazie, Zentrum für Pharmaforschung, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | | | | |
Collapse
|
38
|
Tahtaoui C, Guillier F, Klotz P, Galzi JL, Hibert M, Ilien B. On the Use of Nonfluorescent Dye Labeled Ligands in FRET-Based Receptor Binding Studies. J Med Chem 2005; 48:7847-59. [PMID: 16302823 DOI: 10.1021/jm050459+] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficiency of fluorescence resonance energy transfer (FRET) is dependent upon donor-acceptor proximity and spectral overlap, whether the acceptor partner is fluorescent or not. We report here on the design, synthesis, and characterization of two novel pirenzepine derivatives that were coupled to patent blue VF and pinacyanol dyes. These nonfluorescent compounds, when added to cells stably expressing enhanced green fluorescent protein (EGFP)-fused muscarinic M1 receptors, promote EGFP fluorescence extinction in a time-, concentration-, and atropine-dependent manner. They display nanomolar affinity for the muscarinic receptor, determined using either FRET or classical radioligand binding conditions. We provide evidence that these compounds behave as potent acceptors of energy from excited EGFP with quenching efficiencies comparable to those of analogous fluorescent bodipy or rhodamine red pirenzepine derivatives. The advantages they offer over fluorescent ligands are illustrated and discussed in terms of reliability, sensitivity, and wider applicability of FRET-based receptor binding assays.
Collapse
Affiliation(s)
- Chouaib Tahtaoui
- Laboratoire de Pharmacochimie de la Communication Cellulaire, Faculté de Pharmacie, UMR CNRS/ULP 7081, 74 route du Rhin, BP 24, 67401 Illkirch, France
| | | | | | | | | | | |
Collapse
|
39
|
Ilegems E, Pick H, Deluz C, Kellenberger S, Vogel H. Ligand Binding Transmits Conformational Changes across the Membrane-Spanning Region to the Intracellular Side of the 5-HT3 Serotonin Receptor. Chembiochem 2005; 6:2180-5. [PMID: 16254942 DOI: 10.1002/cbic.200500191] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Erwin Ilegems
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | | | | | | | | |
Collapse
|
40
|
Kozlov M, Bergendahl V, Burgess R, Goldfarb A, Mustaev A. Homogeneous fluorescent assay for RNA polymerase. Anal Biochem 2005; 342:206-13. [PMID: 15950166 DOI: 10.1016/j.ab.2005.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Revised: 03/26/2005] [Accepted: 04/14/2005] [Indexed: 11/27/2022]
Abstract
A new method for determination of RNA polymerase (RNAP) activity is presented. The method uses nucleoside tri- and tetraphosphate derivatives carrying 4-methylumbelliferone residue at the terminal phosphate. Incorporation of such compounds in RNA by RNA polymerase is accompanied by release of di- and triphosphate derivatives of 4-methylumbelliferone. Subsequent treatment by alkaline phosphatase produces free 4-methylumbelliferone that is highly fluorescent and can be easily detected. The sensitivity of the method is higher than that reported in previous studies. The validity of the assay has been demonstrated by retrieving the RNAP inhibitors from a collection of 16,000 compounds.
Collapse
Affiliation(s)
- Maxim Kozlov
- Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | | | | | | | | |
Collapse
|
41
|
Piloto AM, Costa SP, Gonçalves MST. A naphtho[2,1-b]furan as a new fluorescent label: synthesis and spectral characterisation. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.05.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
42
|
Shumyantseva VV, Bulko TV, Petushkova NA, Samenkova NF, Kuznetsova GP, Archakov AI. Fluorescent assay for riboflavin binding to cytochrome P450 2B4. J Inorg Biochem 2004; 98:365-70. [PMID: 14729317 DOI: 10.1016/j.jinorgbio.2003.10.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The interactions between the hemoprotein cytochrome P450 2B4 (CYP 2B4) and riboflavin - a low molecular weight component of the flavoprotein NADPH-dependent cytochrome P450 reductase - were investigated by fluorescence spectroscopy. Riboflavin fluorescence quenching by cytochrome P450 2B4 was used to probe the ligand-enzyme binding (lambda(ex)=385 nm, lambda(em)=520 nm). Fluorescence titration experiments showed formation of a complex between cytochrome P450 2B4 and riboflavin with an apparent dissociation constant value, K(d)=8.8+/-1 microM. The fluorescence intensity of riboflavin was decreased with increasing the cytochrome P450 2B4 concentration, indicating the transfer of resonance excitation energy from riboflavin (energy donor) to the cytochrome P450 2B4 heme (energy acceptor). The data obtained are suggestive of the existence of riboflavin binding site(s) on the hemeprotein molecule.
Collapse
Affiliation(s)
- Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya st. 10, Moscow 119992, Russia.
| | | | | | | | | | | |
Collapse
|
43
|
Adie EJ, Francis MJ, Davies J, Smith L, Marenghi A, Hather C, Hadingham K, Michael NP, Milligan G, Game S. CypHer 5: a generic approach for measuring the activation and trafficking of G protein-coupled receptors in live cells. Assay Drug Dev Technol 2004; 1:251-9. [PMID: 15090190 DOI: 10.1089/15406580360545062] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
GPCRs are one of the most popular classes of therapeutic drug targets. It is therefore important to design specific assay formats to readily identify ligands at these receptors. CypHer 5 technology utilizes the general ability of GPCRs to be internalized into the endosomal pathway of a cell in response to agonist ligands. The CypHer 5 dye is fluorescent in acidic environments, but nonfluorescent at neutral pH. When CypHer 5 is bound to a receptor on the extracellular surface of the cell, it is essentially nonfluorescent. On internalization into a cell, it displays a significant increase in fluorescence. Here we demonstrate the detection of agonist activation of two GPCRs in stably transfected live cells using CypHer 5 technology. The G(q)-coupled TRHR-1 and the G(s)-coupled beta(2)-adrenoceptor were both N-terminally tagged with VSV-G. Following addition of CypHer 5-labeled anti-VSV-G antibodies to HEK 293 cells stably expressing the beta(2)-adrenoceptor or CHO-K1 cells stably expressing the TRHR-1, the cells were treated with agonists and then imaged on Amersham Biosciences' IN Cell Analyzer 3000. Data were quantified using a granularity analysis module. Concentration-response curves were obtained with signal-to-background ratios of 7:1 for both receptors. An EC(50) of 0.52 nM was observed on TRH stimulation of the TRHR-1, and an EC(50) of 30 nM was obtained on isoprenaline stimulation of the beta(2)-adrenoceptor. These results demonstrated that the CypHer technology was capable of measuring high-potency agonist responses. The beta(2)-adrenoceptor antagonist, alprenolol, competed for isoprenaline with an IC(50) of 30 nM, indicating that a high-potency antagonist inhibition curve could also be observed using CypHer. CypHer 5 provides a generic tool to measure GPCR activation in a live cell, homogeneous assay format, and may be equally suitable for detecting activation of other classes of cell surface receptors.
Collapse
Affiliation(s)
- Elaine J Adie
- Bioassays, Development, Amersham Biosciences, Whitchurch, Cardiff, United Kingdom.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Tahtaoui C, Parrot I, Klotz P, Guillier F, Galzi JL, Hibert M, Ilien B. Fluorescent pirenzepine derivatives as potential bitopic ligands of the human M1 muscarinic receptor. J Med Chem 2004; 47:4300-15. [PMID: 15294002 DOI: 10.1021/jm040800a] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following a recent description of fluorescence resonance energy transfer between enhanced green fluorescent protein (EGFP)-fused human muscarinic M1 receptors and Bodipy-labeled pirenzepine, we synthesized seven fluorescent derivatives of this antagonist in order to further characterize ligand-receptor interactions. These compounds carry Bodipy [558/568], Rhodamine Red-X [560/580], or Fluorolink Cy3 [550/570] fluorophores connected to pirenzepine through various linkers. All molecules reversibly bind with high affinity to M1 receptors (radioligand and energy transfer binding experiments) provided that the linker contains more than six atoms. The energy transfer efficiency exhibits modest variations among ligands, indicating that the distance separating EGFP from the fluorophores remains almost constant. This also supports the notion that the fluorophores may bind to the receptor protein. Kinetic analyses reveal that the dissociation of two Bodipy derivatives (10 or 12 atom long linkers) is sensitive to the presence of the allosteric modulator brucine, while that of all other molecules (15-24 atom long linkers) is not. The data favor the idea that these analogues might interact with both the acetylcholine and the brucine binding domains.
Collapse
Affiliation(s)
- Chouaib Tahtaoui
- Laboratoire de Pharmacochimie de la Communication Cellulaire, Faculté de Pharmacie, UMR CNRS/ULP 7081, IFR 85, 74 route du Rhin, BP 10413, 67412 Illkirch, France
| | | | | | | | | | | | | |
Collapse
|
45
|
Lieto AM, Thompson NL. Total internal reflection with fluorescence correlation spectroscopy: nonfluorescent competitors. Biophys J 2004; 87:1268-78. [PMID: 15298929 PMCID: PMC1304465 DOI: 10.1529/biophysj.103.035030] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2003] [Accepted: 04/21/2004] [Indexed: 01/18/2023] Open
Abstract
Total internal reflection with fluorescence correlation spectroscopy is a method for measuring the surface association/dissociation rate constants and absolute densities of fluorescent molecules at the interface of a planar substrate and solution. This method can also report the apparent diffusion coefficient and absolute concentration of fluorescent molecules very close to the surface. Theoretical expressions for the fluorescence fluctuation autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave, in solution, contribute to the fluorescence fluctuations have been published previously. In the work described here, the nature of the autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave contribute to the fluorescence fluctuations, and when fluorescent and nonfluorescent molecules compete for surface binding sites, is described. The autocorrelation function depends in general on the kinetic association and dissociation rate constants of the fluorescent and nonfluorescent molecules, the surface site density, the concentrations of fluorescent and nonfluorescent molecules in solution, the solution diffusion coefficients of the two chemical species, the depth of the evanescent field, and the size of the observed area on the surface. Both general and approximate expressions are presented.
Collapse
Affiliation(s)
- Alena M Lieto
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | |
Collapse
|
46
|
Hegener O, Jordan R, Häberlein H. Dye-Labeled Benzodiazepines: Development of Small Ligands for Receptor Binding Studies Using Fluorescence Correlation Spectroscopy. J Med Chem 2004; 47:3600-5. [PMID: 15214787 DOI: 10.1021/jm021009+] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate benzodiazepine receptor binding studies by fluorescence correlation spectroscopy (FCS), the four fluorophores fluorescein, tetramethylrhodamine, Oregon Green 488, and Alexa 532 were coupled to the benzodiazepine Ro 07-1986/602 (Ro). Binding assays to polyclonal antibodies to benzodiazepines and at the native benzodiazepine receptor on the membrane of rat hippocampal neurons were established to examine the dye-labeled ligands for their benzodiazepine character and their binding behavior. Both the fluorescein and the Oregon Green488 moiety led to a loss of the benzodiazepine receptor binding of the corresponding Ro derivatives. Antibody recognition and interactions to the receptor were observed for the tetramethylrhodamine derivative (K(D) = 96.0 +/- 9.5 nM) but with a high amount of nonspecific binding at the cell membrane of about 50%. In saturation experiments a K(D) value of 97.2 +/- 8.5 nM was found for the Alexa Fluor 532 derivative-antibody interaction. Investigation of the binding of this ligand to the benzodiazepine receptor in FCS cell measurements led to confirmation of high specific binding behavior with a K(D) value of 9.9 +/- 1.9 nM. A nonspecific binding of <10% was observed after coincubation with 1 microM of midazolam. The different properties of the labeled benzodiazepine derivatives and the requirements of the fluorophore in small dye-labeled ligands in FCS binding studies, at the membrane of living cells, are discussed.
Collapse
Affiliation(s)
- Oliver Hegener
- Department of Pharmaceutical Biology, Philipps-University of Marburg, Deutschhausstrasse 17A, D-35032 Marburg, Germany
| | | | | |
Collapse
|
47
|
Naylor S, Kumar R. Emerging role of mass spectrometry in structural and functional proteomics. ADVANCES IN PROTEIN CHEMISTRY 2004; 65:217-48. [PMID: 12964371 DOI: 10.1016/s0065-3233(03)01021-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Stephen Naylor
- Beyond Genomics, Inc., Waltham, Massachusetts 02451, USA
| | | |
Collapse
|
48
|
Goedhart J, Bono JJ, Bisseling T, Gadella TWJ. Identical accumulation and immobilization of sulfated and nonsulfated Nod factors in host and nonhost root hair cell walls. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:884-92. [PMID: 14558690 DOI: 10.1094/mpmi.2003.16.10.884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nod factors are signaling molecules secreted by Rhizobium bacteria. These lipo-chitooligosaccharides (LCOs) are required for symbiosis with legumes and can elicit specific responses at subnanomolar concentrations on a compatible host. How plants perceive LCOs is unclear. In this study, using fluorescent Nod factor analogs, we investigated whether sulfated and nonsulfated Nod factors were bound and perceived differently by Medicago truncatula and Vicia sativa root hairs. The bioactivity of three novel sulfated fluorescent LCOs was tested in a root hair deformation assay on M. truncatula, showing bioactivity down to 0.1 to 1 nM. Fluorescence microscopy of plasmolyzed M. truncatula root hairs shows that sulfated fluorescent Nod factors accumulate in the cell wall of root hairs, whereas they are absent from the plasma membrane when applied at 10 nM. When the fluorescent Nod factor distribution in medium surrounding a root was studied, a sharp decrease in fluorescence close to the root hairs was observed, visualizing the remarkable capacity of root hairs to absorb Nod factors from the medium. Fluorescence correlation microscopy was used to study in detail the mobilities of sulfated and nonsulfated fluorescent Nod factors which are biologically active on M. truncatula and V. sativa, respectively. Remarkably, no difference between sulfated and nonsulfated Nod factors was observed: both hardly diffuse and strongly accumulate in root hair cell walls of both M. truncatula and V. sativa. The implications for the mode of Nod factor perception are discussed.
Collapse
Affiliation(s)
- Joachim Goedhart
- Laboratory for Molecular Biology, MicroSpectroscopy Center Wageningen, Department of Plant Sciences, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
| | | | | | | |
Collapse
|
49
|
Eggeling C, Brand L, Ullmann D, Jäger S. Highly sensitive fluorescence detection technology currently available for HTS. Drug Discov Today 2003; 8:632-41. [PMID: 12867149 DOI: 10.1016/s1359-6446(03)02752-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homogeneous fluorescence methods are providing an important tool for HTS technologies. A wide range of different techniques have been established on the market, with read-outs ranging from total fluorescence intensity to statistical analysis of fluorescence fluctuations for biochemical assays or fluorescence imaging techniques for cellular systems. Each method has its own advantages and limitations, which have to be accounted for when designing a specific assay. Here, recently developed fluorescence techniques and some of their applications, with a particular focus on sensitivity, are summarized and their principles are presented.
Collapse
Affiliation(s)
- Christian Eggeling
- Evotec OAI / Evotec Technologies, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | | | | | | |
Collapse
|
50
|
Scheibner KA, Zhang Z, Cole PA. Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions. Anal Biochem 2003; 317:226-32. [PMID: 12758261 DOI: 10.1016/s0003-2697(03)00087-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Determination of protein oligomerization state can be technically challenging. We have combined the methods of expressed protein ligation (EPL) and fluorescence resonance energy transfer (FRET) for the analysis of protein homo-oligomerization states. We have attached fluorescein (donor) and rhodamine (acceptor) chromophores via dipeptide linkages to the C-termini of three recombinant proteins and examined the potential for FRET between mixtures of these semisynthetic proteins. The known protein dimer (glutathione S-transferase) showed evidence of FRET and the known protein monomer (SH2 domain phosphatase-1) did not display FRET. Using this method, the previously uncharacterized circadian rhythm enzyme, serotonin N-acetyltransferase, displayed significant FRET, indicating its likely propensity for dimerization or more complex oligomerization. These results establish the potential of the union of EPL and FRET in the analysis of protein-protein interactions and provide insight into the unusual enzymatic behavior of a key circadian rhythm enzyme.
Collapse
Affiliation(s)
- Kara A Scheibner
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Rm. 316, Hunterian Bldg., Baltimore, MD 21205, USA
| | | | | |
Collapse
|