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Cazacu N, Stan DL, Târcă R, Chilom CG. Binding of flavonoids to yeast aldehyde dehydrogenase: a molecular mechanism and computational approach. J Biomol Struct Dyn 2023; 41:11247-11254. [PMID: 36571489 DOI: 10.1080/07391102.2022.2160820] [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: 10/21/2022] [Accepted: 12/15/2022] [Indexed: 12/27/2022]
Abstract
The interaction of three flavonoids, apigenin, fisetin and quercetin with yeast aldehyde dehydrogenase, ALDH was studied by spectroscopic and molecular docking methods. A combination of both static and dynamic processes interaction mechanism for the binding of flavonoids with ALDH was found. The interaction takes place with moderate binding and the interaction was driven by hydrophobic contacts. The microenvironments of the fluorescent amino acids changed upon flavonoids binding. The distances between ALDH and flavonoids determined by Förster Resonant Energy Transfer (FRET) confirmed the results obtained by fluorescence. The structure of ALDH against thermal denaturation was stabilized by apigenin and destabilized by fisetin and quercetin. Molecular docking simulation showed that all flavonoids bind to the same site of ALDH and confirmed the moderate binding straight found in fluorescence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nicoleta Cazacu
- Faculty of Physics, University of Bucharest, Măgurele, Ilfov, Romania
| | - Diana L Stan
- Faculty of Physics, University of Bucharest, Măgurele, Ilfov, Romania
| | - Raluca Târcă
- Faculty of Physics, University of Bucharest, Măgurele, Ilfov, Romania
| | - Claudia G Chilom
- Faculty of Physics, University of Bucharest, Măgurele, Ilfov, Romania
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2
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Gasda PJ, Wiens RC, Reyes-Newell A, Ganguly K, Newell RT, Peterson C, Sandoval B, Ott L, Adikari S, Voit S, Clegg SM, Misra AK, Acosta-Maeda TE, Quinn H, Sharma SK, Dale M, Love SP, Maurice S. OrganiCam: a lightweight time-resolved laser-induced luminescence imager and Raman spectrometer for planetary organic material characterization. APPLIED OPTICS 2021; 60:3753-3763. [PMID: 33983308 DOI: 10.1364/ao.421291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
OrganiCam is a laser-induced luminescence imager and spectrometer designed for standoff organic and biosignature detection on planetary bodies. OrganiCam uses a diffused laser beam (12° cone) to cover a large area at several meters distance and records luminescence on half of its intensified detector. The diffuser can be removed to record Raman and fluorescence spectra from a small spot from 2 m standoff distance. OrganiCam's small size and light weight makes it ideal for surveying organics on planetary surfaces. We have designed and built a brassboard version of the OrganiCam instrument and performed initial tests of the system.
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3
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Rahuel-Clermont S, Bchini R, Barbe S, Boutserin S, André I, Talfournier F. Enzyme Active Site Loop Revealed as a Gatekeeper for Cofactor Flip by Targeted Molecular Dynamics Simulations and FRET-Based Kinetics. ACS Catal 2019. [DOI: 10.1021/acscatal.8b03951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Raphaël Bchini
- Université de Lorraine, CNRS, IMoPA, Campus Biologie Santé, F-54000 Nancy, France
| | - Sophie Barbe
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - Séverine Boutserin
- Université de Lorraine, CNRS, IMoPA, Campus Biologie Santé, F-54000 Nancy, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - François Talfournier
- Université de Lorraine, CNRS, IMoPA, Campus Biologie Santé, F-54000 Nancy, France
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4
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Hofmann L, Tsybovsky Y, Alexander NS, Babino D, Leung NY, Montell C, Banerjee S, von Lintig J, Palczewski K. Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family. Biochemistry 2016; 55:6545-6557. [PMID: 27809489 DOI: 10.1021/acs.biochem.6b00907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The 11-cis-retinylidene chromophore of visual pigments isomerizes upon interaction with a photon, initiating a downstream cascade of signaling events that ultimately lead to visual perception. 11-cis-Retinylidene is regenerated through enzymatic transformations collectively called the visual cycle. The first and rate-limiting enzymatic reaction within this cycle, i.e., the reduction of all-trans-retinal to all-trans-retinol, is catalyzed by retinol dehydrogenases. Here, we determined the structure of Drosophila melanogaster photoreceptor retinol dehydrogenase (PDH) isoform C that belongs to the short-chain dehydrogenase/reductase (SDR) family. This is the first reported structure of a SDR that possesses this biologically important activity. Two crystal structures of the same enzyme grown under different conditions revealed a novel conformational change of the NAD+ cofactor, likely representing a change during catalysis. Amide hydrogen-deuterium exchange of PDH demonstrated changes in the structure of the enzyme upon dinucleotide binding. In D. melanogaster, loss of PDH activity leads to photoreceptor degeneration that can be partially rescued by transgenic expression of human RDH12. Based on the structure of PDH, we analyzed mutations causing Leber congenital amaurosis 13 in a homology model of human RDH12 to obtain insights into the molecular basis of RDH12 disease-causing mutations.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Yaroslav Tsybovsky
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nathan S Alexander
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Darwin Babino
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nicole Y Leung
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Craig Montell
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Surajit Banerjee
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14850, United States.,Northeastern Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Johannes von Lintig
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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5
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Misra AK, Acosta-Maeda TE, Sharma SK, McKay CP, Gasda PJ, Taylor GJ, Lucey PG, Flynn L, Abedin MN, Clegg SM, Wiens R. "Standoff Biofinder" for Fast, Noncontact, Nondestructive, Large-Area Detection of Biological Materials for Planetary Exploration. ASTROBIOLOGY 2016; 16:715-729. [PMID: 27623200 DOI: 10.1089/ast.2015.1400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
UNLABELLED We developed a prototype instrument called the Standoff Biofinder, which can quickly locate biological material in a 500 cm(2) area from a 2 m standoff distance with a detection time of 0.1 s. All biogenic materials give strong fluorescence signals when excited with UV and visible lasers. In addition, the luminescence decay time of biogenic compounds is much shorter (<100 ns) than the micro- to millisecond decay time of transition metal ions and rare-earth ions in minerals and rocks. The Standoff Biofinder takes advantage of the short lifetime of biofluorescent materials to obtain real-time fluorescence images that show the locations of biological materials among luminescent minerals in a geological context. The Standoff Biofinder instrument will be useful for locating biological material during future NASA rover, lander, and crewed missions. Additionally, the instrument can be used for nondestructive detection of biological materials in unique samples, such as those obtained by sample return missions from the outer planets and asteroids. The Standoff Biofinder also has the capacity to detect microbes and bacteria on space instruments for planetary protection purposes. KEY WORDS Standoff Biofinder-Luminescence-Time-resolved fluorescence-Biofluorescence-Planetary exploration-Planetary protection-Noncontact nondestructive biodetection. Astrobiology 16, 715-729.
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Affiliation(s)
- Anupam K Misra
- 1 Hawaii Institute of Geophysics and Planetology, University of Hawaii at Mānoa , Honolulu, Hawaii
| | - Tayro E Acosta-Maeda
- 1 Hawaii Institute of Geophysics and Planetology, University of Hawaii at Mānoa , Honolulu, Hawaii
| | - Shiv K Sharma
- 1 Hawaii Institute of Geophysics and Planetology, University of Hawaii at Mānoa , Honolulu, Hawaii
| | | | | | - G Jeffrey Taylor
- 1 Hawaii Institute of Geophysics and Planetology, University of Hawaii at Mānoa , Honolulu, Hawaii
| | - Paul G Lucey
- 1 Hawaii Institute of Geophysics and Planetology, University of Hawaii at Mānoa , Honolulu, Hawaii
| | - Luke Flynn
- 1 Hawaii Institute of Geophysics and Planetology, University of Hawaii at Mānoa , Honolulu, Hawaii
| | | | - Samuel M Clegg
- 3 Los Alamos National Laboratory , Los Alamos, New Mexico
| | - Roger Wiens
- 3 Los Alamos National Laboratory , Los Alamos, New Mexico
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6
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A computational integrating kinetic study on the flexible active site of human acetaldehyde dehydrogenase 1. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Integration of inhibition kinetics and molecular dynamics simulations to determine the effects of Zn2+ on acetaldehyde dehydrogenase 1. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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8
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Gasda PJ, Acosta-Maeda TE, Lucey PG, Misra AK, Sharma SK, Taylor GJ. Next generation laser-based standoff spectroscopy techniques for Mars exploration. APPLIED SPECTROSCOPY 2015; 69:173-92. [PMID: 25587811 DOI: 10.1366/14-07483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In the recent Mars 2020 Rover Science Definition Team Report, the National Aeronautics and Space Administration (NASA) has sought the capability to detect and identify elements, minerals, and most importantly, biosignatures, at fine scales for the preparation of a retrievable cache of samples. The current Mars rover, the Mars Science Laboratory Curiosity, has a remote laser-induced breakdown spectroscopy (LIBS) instrument, a type of quantitative elemental analysis, called the Chemistry Camera (ChemCam) that has shown that laser-induced spectroscopy instruments are not only feasible for space exploration, but are reliable and complementary to traditional elemental analysis instruments such as the Alpha Particle X-Ray Spectrometer. The superb track record of ChemCam has paved the way for other laser-induced spectroscopy instruments, such as Raman and fluorescence spectroscopy. We have developed a prototype remote LIBS-Raman-fluorescence instrument, Q-switched laser-induced time-resolved spectroscopy (QuaLITy), which is approximately 70 000 times more efficient at recording signals than a commercially available LIBS instrument. The increase in detection limits and sensitivity is due to our development of a directly coupled system, the use of an intensified charge-coupled device image detector, and a pulsed laser that allows for time-resolved measurements. We compare the LIBS capabilities of our system with an Ocean Optics spectrometer instrument at 7 m and 5 m distance. An increase in signal-to-noise ratio of at least an order of magnitude allows for greater quantitative analysis of the elements in a LIBS spectrum with 200-300 μm spatial resolution at 7 m, a Raman instrument capable of 1 mm spatial resolution at 3 m, and bioorganic fluorescence detection at longer distances. Thus, the new QuaLITy instrument fulfills all of the NASA expectations for proposed instruments.
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Affiliation(s)
- Patrick J Gasda
- Hawai'i Institute for Geophysics and Planetology, University of Hawai'i, Mānoa, 1680 East West Road, Honolulu, Hawai'i 96822 USA
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