1
|
Clayton AHA. Spectral Relaxation Imaging Microscopy II: Complex Dynamics. Int J Mol Sci 2023; 24:12271. [PMID: 37569641 PMCID: PMC10419246 DOI: 10.3390/ijms241512271] [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: 07/05/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The dynamics of condensed matter can be measured by the time-dependent Stokes shift of a suitable fluorescent probe. The time-dependent spectral correlation function is typically described by one or more spectral relaxation correlation times, which, in liquid solvents, characterize the timescales of the dipolar relaxation processes around the excited-state probe. The phasor plot provides a powerful approach to represent and analyze time and frequency-domain data acquired as images, thus providing a spatial map of spectral dynamics in a complex structure such as a living cell. Measurements of the phase and modulation at two emission wavelength channels were shown to be sufficient to extract a single excited-state lifetime and a single spectral relaxation correlation time, supplying estimates of the mean rate of excited-state depopulation and the mean rate of spectral shift. In the present contribution, two more issues were addressed. First, the provision of analytic formulae allowing extraction of the initial generalized polarization and the relaxed generalized polarization, which characterize the fluorescence spectrum of the unrelaxed state and the fully relaxed state. Second, improved methods of model discrimination and model parameter extraction for more complex spectral relaxation phenomena. The analysis workflow was illustrated with examples from the literature.
Collapse
Affiliation(s)
- Andrew H A Clayton
- Cell Biophysics Laboratory, Department of Physics and Astronomy, Optical Sciences Centre, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne 3122, Australia
| |
Collapse
|
2
|
Prakash R, Goodlett DW, Varghese S, Andrys J, Gbadamosi FA, Arriaza RH, Patel M, Tiwari PB, Borowski T, Chruszcz M, Shimizu LS, Upadhyay G. Development of fluorophore labeled or biotinylated anticancer small molecule NSC243928. Bioorg Med Chem 2023; 79:117171. [PMID: 36680947 PMCID: PMC9892358 DOI: 10.1016/j.bmc.2023.117171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/23/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Small molecule NSC243928 binds with LY6K, a potential target for the treatment of triple-negative breast cancer, and induces cancer cell death with an unclear mechanism. We have developed chemical tools to identify the molecular mechanisms of NSC243928-LY6K interaction. Herein, we report on the development and synthesis of biotinylated and fluorophore-tethered derivatives of NSC243928 guided by docking studies and molecular dynamics. Surface plasmon resonance assay indicates that these derivatives retained a direct binding with LY6K protein. Confocal analysis revealed that nitrobenzoxadiazole (NBD) fluorophore tagged NSC243928 is retained in LY6K expressing cancer cells. These novel modified compounds will be employed in future in vitro and in vivo studies to understand the molecular mechanisms of NSC243928 mediated cancer cell death. These studies will pave the path for developing novel targeted therapeutics and understanding any potential side-effects of these treatments for hard-to-treat cancers such as triple-negative breast cancer or other cancers with high expression of LY6K.
Collapse
Affiliation(s)
- Rahul Prakash
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Dustin W Goodlett
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sheelu Varghese
- Henry M. Jackson Foundation, Bethesda, MD, USA; Department of Pathology, Uniformed Services University, Bethesda, MD, USA
| | - Justyna Andrys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Niezapominajek 8, Krakow 30-239, Poland
| | - Fahidat A Gbadamosi
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Ricardo H Arriaza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Megha Patel
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Purushottam B Tiwari
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Niezapominajek 8, Krakow 30-239, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Geeta Upadhyay
- John P. Murtha Cancer Center, Bethesda, MD, USA; Department of Pathology, Uniformed Services University, Bethesda, MD, USA; Department of Oncology, Georgetown University Medical Center, Washington, DC, USA.
| |
Collapse
|
3
|
Li RS, Wen C, Huang CZ, Li N. Functional molecules and nano-materials for the Golgi apparatus-targeted imaging and therapy. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Pal S, Chattopadhyay A. Hydration Dynamics in Biological Membranes: Emerging Applications of Terahertz Spectroscopy. J Phys Chem Lett 2021; 12:9697-9709. [PMID: 34590862 DOI: 10.1021/acs.jpclett.1c02576] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Water drives the spontaneous self-assembly of lipids and proteins into quasi two-dimensional biological membranes that act as catalytic scaffolds for numerous processes central to life. However, the functional relevance of hydration in membrane biology is only beginning to be addressed, predominantly because of challenges associated with direct measurements of hydration microstructure and dynamics in a biological milieu. Our recent work on the novel interplay of membrane electrostatics and crowding in shaping membrane hydration dynamics utilizing terahertz (THz) spectroscopy represents an important step in this context. In this Perspective, we provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules. We further highlight the immense (and largely untapped) potential of the THz toolbox in addressing contemporary problems in membrane biology, while emphasizing the adaptability of the analytical framework reported recently by us to such studies.
Collapse
Affiliation(s)
- Sreetama Pal
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | | |
Collapse
|
5
|
Environment-Sensitive Fluorescence of 7-Nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-Labeled Ligands for Serotonin Receptors. Molecules 2021; 26:molecules26133848. [PMID: 34202630 PMCID: PMC8270269 DOI: 10.3390/molecules26133848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Serotonin is a neurotransmitter that plays a crucial role in the regulation of several behavioral and cognitive functions by binding to a number of different serotonin receptors present on the cell surface. We report here the synthesis and characterization of several novel fluorescent analogs of serotonin in which the fluorescent NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl) group is covalently attached to serotonin. The fluorescent ligands compete with the serotonin1A receptor specific radiolabeled agonist for binding to the receptor. Interestingly, these fluorescent ligands display a high environmental sensitivity of their fluorescence. Importantly, the human serotonin1A receptor stably expressed in CHO-K1 cells could be specifically labeled with one of the fluorescent ligands with minimal nonspecific labeling. Interestingly, we show by spectral imaging that the NBD-labeled ligand exhibits a red edge excitation shift (REES) of 29 nm when bound to the receptor, implying that it is localized in a restricted microenvironment. Taken together, our results show that NBD-labeled serotonin analogs offer an attractive fluorescent approach for elucidating the molecular environment of the serotonin binding site in serotonin receptors. In view of the multiple roles played by the serotonergic systems in the central and peripheral nervous systems, these fluorescent ligands would be useful in future studies involving serotonin receptors.
Collapse
|
6
|
Malacrida L, Ranjit S, Jameson DM, Gratton E. The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. Annu Rev Biophys 2021; 50:575-593. [PMID: 33957055 DOI: 10.1146/annurev-biophys-062920-063631] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.
Collapse
Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay.,Advanced Bioimaging Unit, Institut Pasteur Montevideo and Universidad de la República-Uruguay, 11400 Montevideo, Uruguay
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
| |
Collapse
|
7
|
Coates C, Kerruth S, Helassa N, Török K. Kinetic Mechanisms of Fast Glutamate Sensing by Fluorescent Protein Probes. Biophys J 2019; 118:117-127. [PMID: 31787209 DOI: 10.1016/j.bpj.2019.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/01/2019] [Accepted: 11/11/2019] [Indexed: 01/18/2023] Open
Abstract
We have developed probes based on the bacterial periplasmic glutamate/aspartate binding protein with either an endogenously fluorescent protein or a synthetic fluorophore as the indicator of glutamate binding for studying the kinetic mechanism of glutamate binding. iGluSnFR variants termed iGluh, iGlum, and iGlul cover a broad range of Kd-s (5.8 μM and 2.1 and 50 mM, respectively), and a novel fluorescently labeled indicator, Fl-GluBP, has a Kd of 9.7 μM. The fluorescence response kinetics of all the probes are consistent with a two-step mechanism involving ligand binding and isomerization either of the apo or the ligand-bound binding protein. Although the previously characterized ultrafast indicators iGluu and iGluf had monophasic fluorescence enhancement that occurred in the rate limiting isomerization step, the sensors described here all have biphasic binding kinetics with fluorescence increases occurring both in the glutamate binding and the isomerization steps. For iGlum and iGlul, the data indicate prebinding conformational change followed by ligand binding. In contrast, for iGluh and Fl-GluBP, glutamate binding is followed by isomerization. Thus, the effects of structural heterogeneity introduced by single amino acid changes around the binding site on the kinetic path of interactions with glutamate are revealed. Remarkably, glutamate binding with a diffusion-limited rate constant to iGluh and Fl-GluBP is detected for the first time, hinting at the underlying mechanism of the supremely rapid activation of the highly homologous α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor by glutamate binding.
Collapse
Affiliation(s)
- Catherine Coates
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom
| | - Silke Kerruth
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom
| | - Nordine Helassa
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom
| | - Katalin Török
- Molecular and Clinical Sciences Research Institute, St. George's University of London, London, United Kingdom.
| |
Collapse
|
8
|
García C, Losada A, Sacristán MA, Martínez-Leal JF, Galmarini CM, Lillo MP. Dynamic cellular maps of molecular species: Application to drug-target interactions. Sci Rep 2018; 8:1140. [PMID: 29348621 PMCID: PMC5773516 DOI: 10.1038/s41598-018-19694-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/03/2018] [Indexed: 11/20/2022] Open
Abstract
The design of living cell studies aimed at deciphering the mechanism of action of drugs targeting proteins with multiple functions, expressed in a wide range of concentrations and cellular locations, is a real challenge. We recently showed that the antitumor drug plitidepsin (APL) localizes sufficiently close to the elongation factor eEF1A2 so as to suggest the formation of drug-protein complexes in living cells. Here we present an extension of our previous micro-spectroscopy study, that combines Generalized Polarization (GP) images, with the phasor approach and fluorescence lifetime imaging microscopy (FLIM), using a 7-aminocoumarin drug analog (APL*) as fluorescence tracer. Using the proposed methodology, we were able to follow in real time the formation and relative distribution of two sets of APL-target complexes in live cells, revealing two distinct patterns of behavior for HeLa-wt and APL resistant HeLa-APL-R cells. The information obtained may complement and facilitate the design of new experiments and the global interpretation of the results obtained with other biochemical and cell biology methods, as well as possibly opening new avenues of study to decipher the mechanism of action of new drugs.
Collapse
Affiliation(s)
- Carolina García
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Madrid, Spain
| | - Alejandro Losada
- Departamento de Biología Celular y Farmacogenómica, Pharma Mar S.A., Colmenar Viejo, Madrid, Spain
| | - Miguel A Sacristán
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Madrid, Spain
| | | | - Carlos M Galmarini
- Departamento de Biología Celular y Farmacogenómica, Pharma Mar S.A., Colmenar Viejo, Madrid, Spain
| | - M Pilar Lillo
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Madrid, Spain.
| |
Collapse
|
9
|
Huang TF, Tseng SH, Wang HY, Chan MC. Widely wavelength tunable fast intensity-modulated light source for biophotonic applications. OPTICS LETTERS 2017; 42:2790-2793. [PMID: 28708170 DOI: 10.1364/ol.42.002790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
High modulation depth, fast (megahertz to gigahertz), intensity-modulated light sources of various wavelengths within the 0.7-1.35 μm bio-penetration window are highly desirable for many biophotonic diagnosis systems. In this Letter, we present a novel scheme of a wavelength tunable, ultra-broadband light source which simply consists of a pump laser, a nonlinear fiber, and demodulation circuits. The working wavelength range of the light source is from 0.7 to 1.35 μm which covers a vast part of the bio-penetration window, and its modulation frequencies extends from tens of megahertz to gigahertz. The performances of the proposed light source in either working wavelength range or modulation frequency bandwidth are much superior to any typical laser diodes or solid state lasers currently employed in the frequency-domain or other biophotonic utilization. The wide applicability of this novel light source in diverse biophotonic applications can be observed from our carefully designed diffused optical spectroscopy phantom measurement.
Collapse
|