1
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Frederiksen A, Gerhards L, Reinholdt P, Kongsted J, Solov'yov IA. Importance of Polarizable Embedding for Absorption Spectrum Calculations of Arabidopsis thaliana Cryptochrome 1. J Phys Chem B 2024. [PMID: 38913544 DOI: 10.1021/acs.jpcb.4c02168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD), a chromophore within cryptochromes, absorbs blue light, initiating electron transfer processes that lead to a biological signaling cascade. A key step in this cascade is the formation of the FAD semiquinone radical (FADH•), characterized through a specific red-light absorption. The absorption spectra of FADH• in cryptochromes are, however, significantly different from those recorded for the cofactor in solution, primarily due to protein-induced shifts in the absorption peaks. This study employs a multiscale approach, combining molecular dynamics (MD) simulations with quantum mechanical/molecular mechanical (QM/MM) methodologies, to investigate the influence of protein dynamics on embedded FADH• absorption. We emphasize the role of the protein's polarizable environment in the shaping of the absorption spectrum, crucial for accurate spectral predictions in cryptochromes. Our findings provide valuable insights into the absorption process, advancing our understanding of cryptochrome functioning.
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Affiliation(s)
- Anders Frederiksen
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Peter Reinholdt
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
- Research Centre for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26111 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
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2
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Kurle-Tucholski P, Wiebeler C, Köhler L, Qin R, Zhao Z, Šimėnas M, Pöppl A, Matysik J. Red Shift in the Absorption Spectrum of Phototropin LOV1 upon the Formation of a Semiquinone Radical: Reconstructing the Orbital Architecture. J Phys Chem B 2024; 128:4344-4353. [PMID: 38688080 PMCID: PMC11089501 DOI: 10.1021/acs.jpcb.4c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/22/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Flavin mononucleotide (FMN) is a ubiquitous blue-light pigment due to its ability to drive one- and two-electron transfer reactions. In both light-oxygen-voltage (LOV) domains of phototropin from the green algae Chlamydomonas reinhardtii, FMN is noncovalently bound. In the LOV1 cysteine-to-serine mutant (C57S), light-induced electron transfer from a nearby tryptophan occurs, and a transient spin-correlated radical pair (SCRP) is formed. Within this photocycle, nuclear hyperpolarization is created by the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect. In a side reaction, a stable protonated semiquinone radical (FMNH·) forms undergoing a significant bathochromic shift of the first electronic transition from 445 to 591 nm. The incorporation of phototropin LOV1-C57S into an amorphous trehalose matrix, stabilizing the radical, allows for application of various magnetic resonance experiments at ambient temperatures, which are combined with quantum-chemical calculations. As a result, the bathochromic shift of the first absorption band is explained by lifting the degeneracy of the molecular orbital energy levels for electrons with alpha and beta spins in FMNH· due to the additional electron.
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Affiliation(s)
- Patrick Kurle-Tucholski
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Christian Wiebeler
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
- Institut
für Physik, Universität Augsburg, Universitätsstraße 1, D-86159 Augsburg, Germany
| | - Lisa Köhler
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Ruonan Qin
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Ziyue Zhao
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Mantas Šimėnas
- Faculty
of Physics, Vilnius University, Sauletekio 3, LT-10257 Vilnius, Lithuania
| | - Andreas Pöppl
- Felix
Bloch Institute for Solid State Physics, Universität Leipzig, Linnéstraße 5, D-04103, Leipzig, Germany
| | - Jörg Matysik
- Institut
für Analytische Chemie, Universität
Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
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3
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Schuhmacher L, Heck S, Pitz M, Mathey E, Lamparter T, Blumhofer A, Leister K, Fischer R. The LOV-domain blue-light receptor LreA of the fungus Alternaria alternata binds predominantly FAD as chromophore and acts as a light and temperature sensor. J Biol Chem 2024; 300:107238. [PMID: 38552736 PMCID: PMC11061223 DOI: 10.1016/j.jbc.2024.107238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 05/04/2024] Open
Abstract
Light and temperature sensing are important features of many organisms. Light may provide energy but may also be used by non-photosynthetic organisms for orientation in the environment. Recent evidence suggests that plant and fungal phytochrome and plant phototropin serve dual functions as light and temperature sensors. Here we characterized the fungal LOV-domain blue-light receptor LreA of Alternaria alternata and show that it predominantly contains FAD as chromophore. Blue-light illumination induced ROS production followed by protein agglomeration in vitro. In vivo ROS may control LreA activity. LreA acts as a blue-light photoreceptor but also triggers temperature-shift-induced gene expression. Both responses required the conserved amino acid cysteine 421. We therefore propose that temperature mimics the photoresponse, which could be the ancient function of the chromoprotein. Temperature-dependent gene expression control with LreA was distinct from the response with phytochrome suggesting fine-tuned, photoreceptor-specific gene regulation.
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Affiliation(s)
- Lars Schuhmacher
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Steffen Heck
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Michael Pitz
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Elena Mathey
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Tilman Lamparter
- Joseph Kölreuter Institute for Plant Research, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Alexander Blumhofer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Kai Leister
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany.
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4
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Herold D, Brauser M, Kind J, Thiele CM. Evolution of a Combined UV/Vis and NMR Setup with Fixed Pathlengths for Mass-limited Samples. Chemistry 2024; 30:e202304016. [PMID: 38360972 DOI: 10.1002/chem.202304016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/17/2024]
Abstract
The investigation of reaction mechanisms is a complex task that usually requires the use of several techniques. To obtain as much information as possible on the reaction and any intermediates - possibly invisible to one technique - the combination of techniques is a solution. In this work we present a new setup for combined UV/Vis and NMR spectroscopy and compare it to an established alternative. The presented approach allows a versatile usage of different commercially-available components like mirrors and fiber bundles as well as different fixed pathlengths according to double transmission or single transmission measurements. While a previous approach is based on a dip-probe setup for conventional NMR probes, the new one is based on a micro-Helmholtz coil array (LiquidVoxel™). This makes the use of rectangular cuvettes possible, which ensure well-defined pathlengths allowing for quantification of species. Additionally, very low quantities of compound can be analyzed due to the microfabrication and small cuvette size used. As proof-of-principle this new setup for combined UV/Vis and NMR spectroscopy is used to examine a well-studied photochromic system of the dithienylethene compound class. A thorough comparison of the pros and cons of the two setups for combined UV/Vis and NMR measurements is performed.
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Affiliation(s)
- Dominik Herold
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| | - Matthias Brauser
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| | - Jonas Kind
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| | - Christina M Thiele
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
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5
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Sammons T, Gair K, Silverman RG, Shanks S. Assessing the Impact of High Photon Energy Wavelengths on the Treatment of Chronic Neck and Shoulder Pain. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:6672019. [PMID: 37829623 PMCID: PMC10567292 DOI: 10.1155/2023/6672019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
The effect of low-level laser therapy with high photon energy wavelengths, green and violet, for treating chronic musculoskeletal pain was examined in the first-ever clinical trial of its kind. Participants (n = 43) underwent a single 13-minute laser session. The primary measure of effectiveness was the change in initial visual analog pain (VAS) scores observed three minutes posttreatment. The success of a participant was defined in advance as a reduction of ≥30% in VAS scores, while the success of the study was predetermined as achieving a 65 ± 5% success rate among individual participants. Results demonstrated subjects' VAS pain scores decreased from 71.79 to 34.02 (p < 0.0001), while most participants in the study (81.4%) achieved a ≥30% decrease in pain scores. The findings from this clinical investigation provided substantial support for the first Food and Drug Administration clearance (K221987) for the combined application of green and violet lasers.
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Affiliation(s)
| | - Kirk Gair
- Clinical Study Site, Laser Chiropractic, West Covina, CA, USA
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6
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Jara Fornerod M, Alvarez-Fernandez A, Michalska M, Papakonstantinou I, Guldin S. Glucose Oxidase Loading in Ordered Porous Aluminosilicates: Exploring the Potential of Surface Modification for Electrochemical Glucose Sensing. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:7577-7587. [PMID: 37780408 PMCID: PMC10536975 DOI: 10.1021/acs.chemmater.3c01202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/22/2023] [Indexed: 10/03/2023]
Abstract
Enzymatic electrochemical sensors have become the leading glucose detection technology due to their rapid response, affordability, portability, selectivity, and sensitivity. However, the performance of these sensors is highly dependent on the surface properties of the electrode material used to store glucose oxidase and its ability to retain enzymatic activity under variable environmental conditions. Mesoporous thin films have recently attracted considerable attention as promising candidates for enzyme storage and activity preservation due to their well-defined nanoarchitecture and tunable surface properties. Herein, we systematically compare pathways for the immobilization of glucose oxidase (GOx) and their effectiveness in electrochemical glucose sensing, following modification protocols that lead to the electrostatic attraction (amino functionalization), covalent bonding (aldehyde functionalization), and electrostatic repulsion (oxygen plasma treatment) of the ordered porous aluminosilicate-coated electrodes. By direct comparison using a quartz crystal microbalance, we demonstrate that glucose oxidase can be loaded in a nanoarchitecture with a pore size of ∼50 nm and pore interconnections of ∼35 nm using the native aluminosilicate surface, as well as after amino or aldehyde surface modification, while oxygen plasma exposure of the native surface inhibits glucose oxidase loading. Despite a variety of routes for enzyme loading, quantitative electrochemical glucose sensing between 0 and 20 mM was only possible when the porous surface was functionalized with amino groups, which we relate to the role of surface chemistry in accessing the underlying substrate. Our results highlight the impact of rational surface modification on electrochemical biosensing performance and demonstrate the potential of tailoring porous nanoarchitecture surfaces for biosensing applications.
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Affiliation(s)
| | - Alberto Alvarez-Fernandez
- Department
of Chemical Engineering, University College
London, Torrington Place, London WC1E 7JE, U.K.
| | - Martyna Michalska
- Department
of Electronic & Electrical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K.
| | - Ioannis Papakonstantinou
- Department
of Electronic & Electrical Engineering, University College London, Torrington Place, London WC1E 7JE, U.K.
| | - Stefan Guldin
- Department
of Chemical Engineering, University College
London, Torrington Place, London WC1E 7JE, U.K.
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7
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Herzog JM, Sick V. Quantitative Spectroscopic Characterization of Near-UV/visible E. coli (pYAC4), B. subtilis (PY79), and Green Bread Mold Fungus Fluorescence for Diagnostic Applications. J Fluoresc 2023; 33:1813-1825. [PMID: 36847932 DOI: 10.1007/s10895-023-03183-6] [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: 01/18/2023] [Accepted: 02/13/2023] [Indexed: 03/01/2023]
Abstract
Ultraviolet (UV)-excited visible fluorescence is an attractive option for low-cost, low-complexity, rapid imaging of bacterial and fungal samples for imaging diagnostics in the biomedical community. While several studies have shown there is potential for identification of microbial samples, very little quantitative information is available in the literature for the purposes of diagnostic design. In this work, two non-pathogenic bacteria samples (E. coli pYAC4, and B. subtilis PY79) and a wild-cultivated green bread mold fungus sample are characterized spectroscopically for the purpose of diagnostic design. For each sample, fluorescence spectra excited with low-power near-UV continuous wave (CW) sources, and extinction and elastic scattering spectra are captured and compared. Absolute fluorescence intensity per cell excited at 340 nm is estimated from imaging measurements of aqueous samples. The results are used to estimate detection limits for a prototypical imaging experiment. It was found that fluorescence imaging is feasible for as few as 35 bacteria cells (or [Formula: see text]30 µm3 of bacteria) per pixel, and that the fluorescence intensity per unit volume is similar for the three samples tested here. A discussion and model of the mechanism of bacterial fluorescence in E. coli is provided.
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Affiliation(s)
- Joshua M Herzog
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward St., Ann Arbor, MI 48109, USA.
| | - Volker Sick
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward St., Ann Arbor, MI 48109, USA
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8
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Bosso A, Tortora F, Culurciello R, Di Nardo I, Pistorio V, Carraturo F, Colecchia A, Di Girolamo R, Cafaro V, Notomista E, Ingenito R, Pizzo E. Simultaneous Irradiation with UV-A, -B, and -C Lights Promotes Effective Decontamination of Planktonic and Sessile Bacteria: A Pilot Study. Int J Mol Sci 2023; 24:12951. [PMID: 37629131 PMCID: PMC10454392 DOI: 10.3390/ijms241612951] [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: 07/19/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Surfaces in highly anthropized environments are frequently contaminated by both harmless and pathogenic bacteria. Accidental contact between these contaminated surfaces and people could contribute to uncontrolled or even dangerous microbial diffusion. Among all possible solutions useful to achieve effective disinfection, ultraviolet irradiations (UV) emerge as one of the most "Green" technologies since they can inactivate microorganisms via the formation of DNA/RNA dimers, avoiding the environmental pollution associated with the use of chemical sanitizers. To date, mainly UV-C irradiation has been used for decontamination purposes, but in this study, we investigated the cytotoxic potential on contaminated surfaces of combined UV radiations spanning the UV-A, UV-B, and UV-C spectrums, obtained with an innovative UV lamp never conceived so far by analyzing its effect on a large panel of collection and environmental strains, further examining any possible adverse effects on eukaryotic cells. We found that this novel device shows a significant efficacy on different planktonic and sessile bacteria, and, in addition, it is compatible with eukaryotic skin cells for short exposure times. The collected data strongly suggest this new lamp as a useful device for fast and routine decontamination of different environments to ensure appropriate sterilization procedures.
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Affiliation(s)
- Andrea Bosso
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
| | - Francesca Tortora
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
| | - Rosanna Culurciello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
| | - Ilaria Di Nardo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
| | - Valeria Pistorio
- Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Inserm, 75012 Paris, France;
| | - Federica Carraturo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
- Hygiene Laboratory, Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80146 Naples, Italy
| | - Andrea Colecchia
- Physics Department “Ettore Pancini”, University of Naples Federico II, 80126 Naples, Italy;
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
| | - Valeria Cafaro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
| | | | - Elio Pizzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.T.); (R.C.); (I.D.N.); (F.C.); (V.C.); (E.N.)
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80126 Naples, Italy
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9
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Fraikin GY, Belenikina NS, Rubin AB. Molecular Bases of Signaling Processes Regulated by Cryptochrome Sensory Photoreceptors in Plants. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:770-782. [PMID: 37748873 DOI: 10.1134/s0006297923060056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 09/27/2023]
Abstract
The blue-light sensors, cryptochromes, compose the extensive class of flavoprotein photoreceptors, regulating signaling processes in plants underlying their development, growth, and metabolism. In several algae, cryptochromes may act not only as sensory photoreceptors but also as photolyases, catalyzing repair of the UV-induced DNA lesions. Cryptochromes bind FAD as the chromophore at the photolyase homologous region (PHR) domain and contain the cryptochrome C-terminal extension (CCE), which is absent in photolyases. Photosensory process in cryptochrome is initiated by photochemical chromophore conversions, including formation of the FAD redox forms. In the state with the chromophore reduced to neutral radical (FADH×), the photoreceptor protein undergoes phosphorylation, conformational changes, and disengagement from the PHR domain and CCE with subsequent formation of oligomers of cryptochrome molecules. Photooligomerization is a structural basis of the functional activities of cryptochromes, since it ensures formation of their complexes with a variety of signaling proteins, including transcriptional factors and regulators of transcription. Interactions in such complexes change the protein signaling activities, leading to regulation of gene expression and plant photomorphogenesis. In recent years, multiple papers, reporting novel, more detailed information about the molecular mechanisms of above-mentioned processes were published. The present review mainly focuses on analysis of the data contained in these publications, particularly regarding structural aspects of the cryptochrome transitions into photoactivated states and regulatory signaling processes mediated by the cryptochrome photoreceptors in plants.
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Affiliation(s)
| | | | - Andrey B Rubin
- Lomonosov Moscow State University, Moscow, 119991, Russia
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10
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Wang J, Liu Y. Systematic Theoretical Study on the pH-Dependent Absorption and Fluorescence Spectra of Flavins. Molecules 2023; 28:molecules28083315. [PMID: 37110549 PMCID: PMC10146991 DOI: 10.3390/molecules28083315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Flavins are a class of organic compounds with the basic structure of 7,8-dimethy-10-alkyl isoalloxazine. They are ubiquitous in nature and participate in many biochemical reactions. Due to various existing forms, there is a lack of systematic research on the absorption and fluorescence spectra of flavins. In this study, employing the density functional theory (DFT) and time-dependent (TD) DFT, we calculated the pH-dependent absorption and fluorescence spectra of flavin of three redox states (quinone, semiquinone, and hydroquinone) in solvents. The chemical equilibrium of three redox states of flavins and the pH effect on the absorption spectra and fluorescence spectra of flavins were carefully discussed. The conclusion helps with identifying the existing forms of flavins in solvent with different pH values.
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Affiliation(s)
- Jinyu Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yajun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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11
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Grigorenko B, Domratcheva T, Nemukhin A. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules 2023; 28:molecules28052405. [PMID: 36903648 PMCID: PMC10005588 DOI: 10.3390/molecules28052405] [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: 01/27/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.
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Affiliation(s)
- Bella Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Correspondence:
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12
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Huix-Rotllant M, Schwinn K, Pomogaev V, Farmani M, Ferré N, Lee S, Choi CH. Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT. J Chem Theory Comput 2023; 19:147-156. [PMID: 36574493 DOI: 10.1021/acs.jctc.2c01010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.
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Affiliation(s)
| | - Karno Schwinn
- Aix-Marseille Univ, CNRS, ICR, Marseille13013, France
| | - Vladimir Pomogaev
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Maryam Farmani
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, Marseille13013, France
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
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13
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Lim SY, Jang JI, Yoon H, Kim HM. Spectroscopic Study of Time-Varying Optical Redox Ratio in NADH/FAD Solution. J Phys Chem B 2022; 126:9840-9849. [PMID: 36399328 DOI: 10.1021/acs.jpcb.2c05292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Autofluorescence imaging has been widely applied as advanced noninvasive diagnostics for in vivo and ex vivo tissues. The optical redox ratio (ORR), which is defined as the fluorescence intensity ratio between reduced nicotine adenine dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD), has been used as a diagnostic parameter strongly, because NADH and FAD play an important role in energetic and respiratory metabolism as coenzymes. The ORR method has provided successful assessment in cancer diagnosis including breast, cervical, and oral cancer; few studies have been reported about optical and chemical interference between two molecules resulting in a change in ORR values. In this study, we investigated the variations in ORR values of NADH/FAD mixtures dissolved in tris(hydroxymethyl)aminomethane, phosphate buffer, and deionized water environments. In vitro solutions were prepared in various concentration ratios and the experimental and theoretical ORR values were obtained from fluorescence and absorption spectra in time series. Based on the spectroscopic analysis, we concluded that the inner filter effect causes an instant decrease in FAD fluorescence just after dissolution and that the oxidation-reduction coupled with oxygenation reaction results in time-varying decreases in NADH fluorescence and FAD emission.
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Affiliation(s)
- Soo Yeong Lim
- Department of Chemistry, Kookmin University, 77, Jeongneung-ro, Seongbuk-gu, Seoul02707, Republic of Korea
| | - Jin Il Jang
- Department of Chemistry, Kookmin University, 77, Jeongneung-ro, Seongbuk-gu, Seoul02707, Republic of Korea
| | - Hongman Yoon
- Division of Convergence Technology, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do10408, Republic of Korea
| | - Hyung Min Kim
- Department of Chemistry, Kookmin University, 77, Jeongneung-ro, Seongbuk-gu, Seoul02707, Republic of Korea
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14
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Islam Z, Aldous N, Choi S, Schmidt F, Mifsud B, Abdelalim EM, Kolatkar PR. Flavin Adenine Dinucleotide (FAD) and Pyridoxal 5'-Phosphate (PLP) Bind to Sox9 and Alter the Expression of Key Pancreatic Progenitor Transcription Factors. Int J Mol Sci 2022; 23:ijms232214051. [PMID: 36430529 PMCID: PMC9694089 DOI: 10.3390/ijms232214051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Cofactor flavin adenine dinucleotide (FAD), a compound with flavin moiety and a derivative of riboflavin (vitamin B2), is shown to bind to Sox9 (a key transcription factor in early pancreatic development) and, subsequently, induce a large increase in markers of pancreatic development, including Ngn3 and PTF1a. Pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, also binds to Sox9 and results in a similar increase in pancreatic development markers. Sox9 is known to be specifically important for pancreatic progenitors. Previously, there was no known link between FAD, PLP, or other co-factors and Sox9 for function. Thus, our findings show the mechanism by which FAD and PLP interact with Sox9 and result in the altered expression of pancreatic progenitor transcription factors involved in the pancreas development.
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Affiliation(s)
- Zeyaul Islam
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Noura Aldous
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Sunkyu Choi
- Proteomics Core, Weill Cornell Medicine, Doha P.O. Box 24144, Qatar
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine, Doha P.O. Box 24144, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Essam M. Abdelalim
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Prasanna R. Kolatkar
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 34110, Qatar
- Correspondence: ; Tel.: +974-445-45889; Fax: +974-445-41770
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15
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Wang J, Liu Y. Vibrationally resolved absorption and fluorescence spectra of flavins: A theoretical simulation in the gas phase. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jinyu Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry Beijing Normal University Beijing China
| | - Ya‐Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry Beijing Normal University Beijing China
- Center for Advanced Materials Research Beijing Normal University Zhuhai China
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16
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Gusliakova OI, Prikhozhdenko ES, Plastun VO, Mayorova OA, Shushunova NA, Abdurashitov AS, Kulikov OA, Abakumov MA, Gorin DA, Sukhorukov GB, Sindeeva OA. Renal Artery Catheterization for Microcapsules' Targeted Delivery to the Mouse Kidney. Pharmaceutics 2022; 14:1056. [PMID: 35631642 PMCID: PMC9144148 DOI: 10.3390/pharmaceutics14051056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The problem of reducing the side effects associated with drug distribution throughout the body in the treatment of various kidney diseases can be solved by effective targeted drug delivery. The method described herein involves injection of a drug encapsulated in polyelectrolyte capsules to achieve prolonged local release and long-term capillary retention of several hours while these capsules are administered via the renal artery. The proposed method does not imply disruption (puncture) of the renal artery or aorta and is suitable for long-term chronic experiments on mice. In this study, we compared how capsule size and dosage affect the target kidney blood flow. It has been established that an increase in the diameter of microcapsules by 29% (from 3.1 to 4.0 μm) requires a decrease in their concentration by at least 50% with the same suspension volume. The photoacoustic method, along with laser speckle contrast imaging, was shown to be useful for monitoring blood flow and selecting a safe dose. Capsules contribute to a longer retention of a macromolecular substance in the target kidney compared to its free form due to mechanical retention in capillaries and slow impregnation into surrounding tissues during the first 1-3 h, which was shown by fluorescence tomography and microscopy. At the same time, the ability of capillaries to perform almost complete "self-cleaning" from capsular shells during the first 12 h leads to the preservation of organ tissues in a normal state. The proposed strategy, which combines endovascular surgery and the injection of polymer microcapsules containing the active substance, can be successfully used to treat a wide range of nephropathies.
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Affiliation(s)
- Olga I. Gusliakova
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (E.S.P.); (V.O.P.); (O.A.M.); (N.A.S.)
| | - Ekaterina S. Prikhozhdenko
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (E.S.P.); (V.O.P.); (O.A.M.); (N.A.S.)
| | - Valentina O. Plastun
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (E.S.P.); (V.O.P.); (O.A.M.); (N.A.S.)
| | - Oksana A. Mayorova
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (E.S.P.); (V.O.P.); (O.A.M.); (N.A.S.)
| | - Natalia A. Shushunova
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (E.S.P.); (V.O.P.); (O.A.M.); (N.A.S.)
| | - Arkady S. Abdurashitov
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 3 Nobel Str., 143005 Moscow, Russia; (A.S.A.); (G.B.S.)
| | - Oleg A. Kulikov
- Institute of Medicine, National Research Ogarev Mordovia State University, 68 Bolshevistskaya Str., 430005 Saransk, Russia;
| | - Maxim A. Abakumov
- Department of Medical Nanobiotecnology, Pirogov Russian National Research Medical University, 1 Ostrovityanova Str., 117997 Moscow, Russia;
| | - Dmitry A. Gorin
- Center for Photonics and Quantum Materials, Skolkovo Institute of Science and Technology, 3 Nobel Str., 143005 Moscow, Russia;
| | - Gleb B. Sukhorukov
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 3 Nobel Str., 143005 Moscow, Russia; (A.S.A.); (G.B.S.)
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Olga A. Sindeeva
- Science Medical Center, Saratov State University, 83 Astrakhanskaya Str., 410012 Saratov, Russia; (E.S.P.); (V.O.P.); (O.A.M.); (N.A.S.)
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 3 Nobel Str., 143005 Moscow, Russia; (A.S.A.); (G.B.S.)
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17
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Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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Reinholdt P, Kongsted J, Lipparini F. Fast Approximate but Accurate QM/MM Interactions for Polarizable Embedding. J Chem Theory Comput 2021; 18:344-356. [PMID: 34951300 DOI: 10.1021/acs.jctc.1c01037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The coupling between the quantum (QM) and classical (MM) regions is often one of the computational bottlenecks when applying polarizable QM/MM to computational spectroscopy. In this Article, we explore three strategies to approximate the QM/MM coupling based on multipole expansion techniques. The implementations of these approximations are benchmarked in terms of both accuracy and computational efficiency and are furthermore applied to the calculation of spectroscopic properties including both one- and two-photon absorption strengths. We show that the proposed strategies provide significant computational savings without compromising the accuracy of the calculated spectroscopic properties.
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Affiliation(s)
- Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56127 Pisa, Italy
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19
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Kar RK, Chasen S, Mroginski MA, Miller AF. Tuning the Quantum Chemical Properties of Flavins via Modification at C8. J Phys Chem B 2021; 125:12654-12669. [PMID: 34784473 DOI: 10.1021/acs.jpcb.1c07306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH2, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.
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Affiliation(s)
- Rajiv K Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Sam Chasen
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Maria-Andrea Mroginski
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Anne-Frances Miller
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.,Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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20
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Dozova N, Lacombat F, Lombard M, Hamdane D, Plaza P. Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX. Phys Chem Chem Phys 2021; 23:22692-22702. [PMID: 34605505 DOI: 10.1039/d1cp03379d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH-) as prosthetic group and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH- in ThyX is only mildly more constrained than that of free FADH- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH- photophysics to the constraints exerted by its immediate surroundings.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Pascal Plaza
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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21
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Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM. Molecules 2021; 26:molecules26196021. [PMID: 34641565 PMCID: PMC8513085 DOI: 10.3390/molecules26196021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.
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22
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Sedenho GC, Modenez I, Mendes GR, Crespilho FN. The role of extracellular polymeric substance matrix on Saccharomyces cerevisiae bioelectricity. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.139080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Lee YJ, Dai N, Müller SI, Guan C, Parker MJ, Fraser ME, Walsh SE, Sridar J, Mulholland A, Nayak K, Sun Z, Lin YC, Comb DG, Marks K, Gonzalez R, Dowling DP, Bandarian V, Saleh L, Corrêa IR, Weigele PR. Pathways of thymidine hypermodification. Nucleic Acids Res 2021; 50:3001-3017. [PMID: 34522950 PMCID: PMC8989533 DOI: 10.1093/nar/gkab781] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/12/2021] [Indexed: 11/15/2022] Open
Abstract
The DNAs of bacterial viruses are known to contain diverse, chemically complex modifications to thymidine that protect them from the endonuclease-based defenses of their cellular hosts, but whose biosynthetic origins are enigmatic. Up to half of thymidines in the Pseudomonas phage M6, the Salmonella phage ViI, and others, contain exotic chemical moieties synthesized through the post-replicative modification of 5-hydroxymethyluridine (5-hmdU). We have determined that these thymidine hypermodifications are derived from free amino acids enzymatically installed on 5-hmdU. These appended amino acids are further sculpted by various enzyme classes such as radical SAM isomerases, PLP-dependent decarboxylases, flavin-dependent lyases and acetyltransferases. The combinatorial permutations of thymidine hypermodification genes found in viral metagenomes from geographically widespread sources suggests an untapped reservoir of chemical diversity in DNA hypermodifications.
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Affiliation(s)
- Yan-Jiun Lee
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Nan Dai
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Stephanie I Müller
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Chudi Guan
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Mackenzie J Parker
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Morgan E Fraser
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Shannon E Walsh
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Janani Sridar
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Andrew Mulholland
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Krutika Nayak
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Zhiyi Sun
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Yu-Cheng Lin
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Donald G Comb
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Katherine Marks
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Reyaz Gonzalez
- Chemistry Department, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA02125, USA
| | - Daniel P Dowling
- Chemistry Department, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA02125, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East Salt Lake City, UT 84112, USA
| | - Lana Saleh
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Ivan R Corrêa
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
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24
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Oleate Hydratase from Lactobacillus rhamnosus ATCC 53103: A FADH2-Dependent Enzyme with Remarkable Industrial Potential. Catalysts 2021. [DOI: 10.3390/catal11091051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Recently, we described the preparation of the recombinant oleate hydratase from Lactobacillus rhamnosus ATCC 53103. We observed that the purified C-terminal His-tagged enzyme was completely inactive and the catalytic activity was partially restored only in presence of a large amount of flavin adenine dinucleotide (FAD). In the present work, we assess that this hydratase in the presence of the reduced form of flavin adenine dinucleotide (FADH2) is at least one hundred times as active as in the presence of the same concentration of FAD. By means of two different biochemical processes, we demonstrated unambiguously that oleate hydratase from Lactobacillus rhamnosus ATCC 53103 is a FADH2-dependent enzyme. As a first relevant application of this discovery, we devised a preparative procedure for the stereoselective synthesis of (R)-10-hydroxystearic acid. Accordingly, the hydration of oleic acid (up to 50 g/L) is performed on a multigram scale using the recombinant hydratase and FADH2 generated in situ as cofactor. The produced (R)-10-hydroxystearic acid (ee > 97%) precipitates from the reaction solvent (water/glycerol/ethanol) and is conveniently recovered by simple filtration (>90% yield).
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Cellini A, Yuan Wahlgren W, Henry L, Pandey S, Ghosh S, Castillon L, Claesson E, Takala H, Kübel J, Nimmrich A, Kuznetsova V, Nango E, Iwata S, Owada S, Stojković EA, Schmidt M, Ihalainen JA, Westenhoff S. The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallogr D Struct Biol 2021; 77:1001-1009. [PMID: 34342273 PMCID: PMC8329860 DOI: 10.1107/s2059798321005830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Leticia Castillon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Valentyna Kuznetsova
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Eriko Nango
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St Louis Avenue, Chicago, IL 60625, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Janne A. Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
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Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCRJ 2021; 8:342-350. [PMID: 33953921 PMCID: PMC8086157 DOI: 10.1107/s2052252521001949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/18/2021] [Indexed: 05/21/2023]
Abstract
Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium Thermotoga maritima is reported at 2.0 Å resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.
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Affiliation(s)
- Timothy Wiryaman
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Hong P, Ning LC, Wu AA, Tan K, Lu X. Insights into the mechanism of fatty acid photodecarboxylase: A theoretical investigation. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Huix-Rotllant M, Schwinn K, Ferré N. Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome. Phys Chem Chem Phys 2021; 23:1666-1674. [PMID: 33415326 DOI: 10.1039/d0cp06070d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Infrared (IR) spectroscopy is an undoubtedly valuable tool for analyzing vibrations, conformational changes, and chemical reactions of biological macromolecules. Currently, there is a lack of theoretical methods to create a model successfully and efficiently simulate and interpret the origin of the spectral signatures, which are often complex to analyze. Here, we develop a new method for IR vibrational spectroscopy based on analytic second derivatives of electrostatic embedding QM/MM energy, the computation of electric dipole moments with respect to nuclear perturbations and the localization of normal modes. In addition to the IR spectrum, the method can provide the origin of each peak from clearly identified molecular motions of constituent fragments. As a proof of concept, we analyze the IR spectra of flavin adenine dinucleotides in water and in Arabidopsis thaliana cryptochrome proteins for four redox forms, in addition to the difference IR spectra before and after illumination with blue light. We show that the main peaks in the difference spectrum are due to N-H hydrogen out-of-plane motions and hydrogen bendings.
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Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021; 154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Andrew C Simmonett
- National Institutes of Health-National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
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Huix-Rotllant M, Ferré N. Analytic Energy, Gradient, and Hessian of Electrostatic Embedding QM/MM Based on Electrostatic Potential-Fitted Atomic Charges Scaling Linearly with the MM Subsystem Size. J Chem Theory Comput 2020; 17:538-548. [DOI: 10.1021/acs.jctc.0c01075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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