1
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Panter S, Ayekoi A, Tesche J, Chen J, Illarionov B, Bacher A, Fischer M, Weber S. Shining a Spotlight on Methyl Groups: Photochemically Induced Dynamic Nuclear Polarization Spectroscopy of 5-Deazariboflavin and Its Nor Analogs. Int J Mol Sci 2024; 25:848. [PMID: 38255921 PMCID: PMC10815406 DOI: 10.3390/ijms25020848] [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: 12/08/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
5-Deazaflavins are analogs of naturally occurring flavin cofactors. They serve as substitutes for natural flavin cofactors to investigate and modify the reaction pathways of flavoproteins. Demethylated 5-deazaflavins are potential candidates for artificial cofactors, allowing us to fine-tune the reaction kinetics and absorption characteristics of flavoproteins. In this contribution, demethylated 5-deazariboflavin radicals are investigated (1) to assess the influence of the methyl groups on the electronic structure of the 5-deazaflavin radical and (2) to explore their photophysical properties with regard to their potential as artificial cofactors. We determined the proton hyperfine structure of demethylated 5-deazariboflavins using photochemically induced dynamic nuclear polarization (photo-CIDNP) spectroscopy, as well as density functional theory (DFT). To provide context, we compare our findings to a study of flavin mononucleotide (FMN) derivatives. We found a significant influence of the methylation pattern on the absorption properties, as well as on the proton hyperfine coupling ratios of the xylene moiety, which appears to be solvent-dependent. This effect is enhanced by the replacement of N5 by C5-H in 5-deazaflavin derivatives compared to their respective flavin counterparts.
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Affiliation(s)
- Sabrina Panter
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (S.P.); (A.A.)
| | - Audrey Ayekoi
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (S.P.); (A.A.)
| | - Jannis Tesche
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (S.P.); (A.A.)
| | - Jing Chen
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (S.P.); (A.A.)
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany; (B.I.); (M.F.)
| | - Adelbert Bacher
- TUM School of Natural Sciences, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany;
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany; (B.I.); (M.F.)
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (S.P.); (A.A.)
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2
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Peña A, Sánchez NS, Padilla-Garfias F, Ramiro-Cortés Y, Araiza-Villanueva M, Calahorra M. The Use of Thioflavin T for the Estimation and Measurement of the Plasma Membrane Electric Potential Difference in Different Yeast Strains. J Fungi (Basel) 2023; 9:948. [PMID: 37755056 PMCID: PMC10532974 DOI: 10.3390/jof9090948] [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: 08/02/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023] Open
Abstract
The use of the cationic, dye thioflavin T (ThT), to estimate the electric plasma membrane potential difference (PMP) via the fluorescence changes and to obtain its actual values from the accumulation of the dye, considering important correction factors by its binding to the internal components of the cell, was described previously for baker's yeast. However, it was considered important to explore whether the method developed could be applied to other yeast strains. Alternative ways to estimate the PMP by using flow cytometry and a multi-well plate reader are also presented here. The methods were tested with other strains of Saccharomyces cerevisiae (W303-1A and FY833), as well as with non-conventional yeasts: Debaryomyces hansenii, Candida albicans, Meyerozyma guilliermondii, and Rhodotorula mucilaginosa. Results of the estimation of the PMP via the fluorescence changes under different conditions were adequate with all strains. Consistent results were also obtained with several mutants of the main monovalent transporters, validating ThT as a monitor for PMP estimation.
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Affiliation(s)
- Antonio Peña
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, México City 04510, Mexico; (F.P.-G.); (M.A.-V.); (M.C.)
| | - Norma Silvia Sánchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, México City 04510, Mexico; (F.P.-G.); (M.A.-V.); (M.C.)
| | - Francisco Padilla-Garfias
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, México City 04510, Mexico; (F.P.-G.); (M.A.-V.); (M.C.)
| | - Yazmín Ramiro-Cortés
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, México City 04510, Mexico;
| | - Minerva Araiza-Villanueva
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, México City 04510, Mexico; (F.P.-G.); (M.A.-V.); (M.C.)
| | - Martha Calahorra
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, México City 04510, Mexico; (F.P.-G.); (M.A.-V.); (M.C.)
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3
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Li B, Tao Y, Mao Z, Gu Q, Han Y, Hu B, Wang H, Lai A, Xing P, Wu QL. Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments. WATER RESEARCH 2023; 234:119833. [PMID: 36889095 DOI: 10.1016/j.watres.2023.119833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.
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Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qiujin Gu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yixuan Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Anxing Lai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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4
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Mosley-Kellum K, Bagde A, Spencer S, Dev S, Singh M. Development of 3D DLP Printed Sustained Release Ibuprofen Tablets and Their Pharmacokinetic Evaluation in Rats. AAPS PharmSciTech 2023; 24:88. [PMID: 36977867 PMCID: PMC11017792 DOI: 10.1208/s12249-023-02544-5] [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: 12/19/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023] Open
Abstract
The objective of the present study was to develop digital light processing (DLP) 3D printed sustained release ibuprofen (IBU) tablets using 3D DLP printers for evaluation in in vitro release and in vivo pharmacokinetic studies with their in vitro-in vivo correlation. The resin formulation and printing parameters were optimized using quality by design (QbD) approach, and IBU tablets were printed using DLP printers which works at 385 and 405 nm wavelengths. Our results demonstrated that formulation consisting of polyethylene glycol diacrylate (PEGDA) 700, water, IBU, and riboflavin printed at 40-s bottom layer exposure time and 30-s exposure time produced tablets using both 385 and 405 nm wavelengths. In vitro dissolution studies showed > 70% drug release at the end of 24 h when printed at 405 nm wavelength with no significant difference between tablets printed at 385 nm. In vivo pharmacokinetic evaluation of the optimized 3D printed tablets printed at 405 nm at oral dose of 30 mg/kg in rats showed sustained release of IBU with significantly (p < 0.05) higher Cmax of 30.12 ± 2.45 µg/mL and AUC(0-24 h) of 318.97 ± 16.98 (µg/mL × h) compared to marketed IBU tablet (control). In vivo-in vitro correlation studies showed 80% of drug was absorbed in vivo within 3 h from the pulverized 3D printed tablet, whereas intact 3D tablet showed sustained release of IBU with > 75% IBU release in 24 h in vitro. Overall, IBU tablets fabricated using DLP printing demonstrated sustained release and enhanced systemic absorption with no significant difference in their release profile at different wavelengths.
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Affiliation(s)
- Keb Mosley-Kellum
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, 32307, USA
| | - Arvind Bagde
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, 32307, USA
| | - Shawn Spencer
- Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Satyanarayan Dev
- Biological Systems Engineering, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, Florida, 32307, USA.
| | - Mandip Singh
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, 32307, USA.
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5
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Chen C, Nardi AN, Amadei A, D’Abramo M. PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method. J Chem Theory Comput 2022; 19:33-41. [PMID: 36378163 PMCID: PMC9835827 DOI: 10.1021/acs.jctc.2c00767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called PyMM, which has been developed to apply a QM/MM approach, the perturbed matrix method, in a simple and efficient way. PyMM requires a classical atomic trajectory of the whole system and a set of unperturbed electronic properties of the ground and electronic excited states. The software output includes a set of the most common perturbed properties, such as the electronic excitation energies and the transitions dipole moments, as well as the eigenvectors describing the perturbed electronic states, which can be then used to estimate whatever electronic property. The software is composed of a simple and complete command-line interface, a set of internal input validation, and three main analyses focusing on (i) the perturbed eigenvector behavior, (ii) the calculation of the electronic absorption spectrum, and (iii) the estimation of the free energy differences along a reaction coordinate.
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Affiliation(s)
| | | | - Andrea Amadei
- Department
of Technological and Chemical Sciences, University of Rome Tor Vergata, Rome00133, Italy
| | - Marco D’Abramo
- Department
of Chemistry, Sapienza University of Rome, Rome00185, Italy,
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6
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Del Galdo S, Chiarini M, Casieri C, Daidone I. High density water clusters observed at high concentrations of the macromolecular crowder PEG400. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Sánchez-Resa D, Daidone I, Djemili R, Adrouche S, Durot S, Heitz V, Zanetti-Polzi L, Ventura B. Photophysical and Computational Insights into Ag(I) Complexation of Porphyrinic Covalent Cages Equipped with Triazoles-Incorporating Linkers. J Phys Chem B 2022; 126:3450-3459. [PMID: 35483006 PMCID: PMC9109141 DOI: 10.1021/acs.jpcb.2c01111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
![]()
The photophysical
characterization of four supramolecular complexes
based on covalent cages 2H-S-2H, 2H-L-2H, Zn-S-2H, and Zn-L-2H, consisting in either
two free-base porphyrins or one Zn(II) porphyrin and one free-base
porphyrin connected by four flexible linkers of different lengths
incorporating triazole binding sites, and their Ag(I) complexation
are reported. The complexation processes have been followed by means
of absorption and emission spectroscopies, and a comprehensive computational
study explains the behavior of the free-base porphyrin-containing
cages. Absorption and emission features have been interpreted on the
bases of conformational changes, metalation processes, and modification
of energy transfer efficiencies occurring in the different cases.
In all cages, except 2H-L-2H, the coordination of four
Ag(I) ions to the lateral triazole groups of the linkers leads to
the enlargement of their cavity. Only for 2H-L-2H is
a different behavior observed, where the process of silver metalation
of the porphyrins’ core prevails.
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Affiliation(s)
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Ryan Djemili
- Laboratoire de Synthèse des Assemblages Moléculaires Multifonctionnels, Institut de Chimie de Strasbourg, CNRS/UMR 7177, Université de Strasbourg, 67000 Strasbourg, France
| | - Sonia Adrouche
- Laboratoire de Synthèse des Assemblages Moléculaires Multifonctionnels, Institut de Chimie de Strasbourg, CNRS/UMR 7177, Université de Strasbourg, 67000 Strasbourg, France
| | - Stéphanie Durot
- Laboratoire de Synthèse des Assemblages Moléculaires Multifonctionnels, Institut de Chimie de Strasbourg, CNRS/UMR 7177, Université de Strasbourg, 67000 Strasbourg, France
| | - Valérie Heitz
- Laboratoire de Synthèse des Assemblages Moléculaires Multifonctionnels, Institut de Chimie de Strasbourg, CNRS/UMR 7177, Université de Strasbourg, 67000 Strasbourg, France
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8
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Absorption and stationary fluorescent spectra of molecular sensors in solution: A computational study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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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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10
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Chiş V, Vinţeler E. Excitation energies for anionic drugs predicted by PBE0, TPSS and τHCTH density functionals. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131120] [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]
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11
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Astanov SK, Kasimova GK, Kurtaliev EN, Nizomov NN, Jumabaev A. Electronic nature and structure of aggregates of riboflavin molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119177. [PMID: 33257239 DOI: 10.1016/j.saa.2020.119177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/25/2020] [Accepted: 10/31/2020] [Indexed: 06/12/2023]
Abstract
Aggregation process of riboflavin molecules in binary mixtures: water - dioxane, water - DMSO, and ethanol - isobutanol, were investigated using spectroscopic methods and quantum-chemical calculation. It was shown that at a constant concentration of riboflavin and different ratios of binary mixtures, a deformation of the electronic absorption spectra with a hypochromic effect is observed. The observed changes are caused by the formation of a hydrogen bond and dipole-dipole interaction between riboflavin molecules, which is accompanied by a shift and resonance splitting of excited electronic levels.
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Affiliation(s)
- Salikh Kh Astanov
- Bukhara Engineering and Technological Institute, Murtazaeva str., 15, 200117 Bukhara, Uzbekistan.
| | - Guzal K Kasimova
- Bukhara Engineering and Technological Institute, Murtazaeva str., 15, 200117 Bukhara, Uzbekistan
| | - Eldar N Kurtaliev
- Samarkand State University, University Blvd., 15, 140104 Samarkand, Uzbekistan.
| | - Negmat N Nizomov
- Samarkand State University, University Blvd., 15, 140104 Samarkand, Uzbekistan
| | - Abduvakhid Jumabaev
- Samarkand State University, University Blvd., 15, 140104 Samarkand, Uzbekistan
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12
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Theoretical modeling of optical spectra of N(1) and N(10) substituted lumichrome derivatives. ACTA CHIMICA SLOVACA 2021. [DOI: 10.2478/acs-2020-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
A systematic study of (7,8-dimethylated) alloxazine, isoalloxazine, and their derivatives with substituted N(1) and N(10) positions was conducted using the density functional theory. The main aim of this work was the direct investigation of substituent effect on the molecular structure. Furthermore, HOMED aromaticity indices were calculated to describe the scope of the geometry changes. Frontier molecular orbitals of reference alloxazine, isoalloxazine and lumichrome derivatives were discussed by means of changes in their shape and energy levels. Photophysical properties were analyzed by determination of optical transition energies using the TD-DFT method. Obtained results were compared with previously published experimental data.
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13
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Wörner S, Leier J, Michenfelder NC, Unterreiner A, Wagenknecht H. Directed Electron Transfer in Flavin Peptides with Oligoproline-Type Helical Conformation as Models for Flavin-Functional Proteins. ChemistryOpen 2020; 9:1264-1269. [PMID: 33318882 PMCID: PMC7729625 DOI: 10.1002/open.202000199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
To mimic the charge separation in functional proteins we studied flavin-modified peptides as models. They were synthesized as oligoprolines that typically form a polyproline type-II helix, because this secondary structure supports the electron transfer properties. We placed the flavin as photoexcitable chromophore and electron acceptor at the N-terminus. Tryptophans were placed as electron donors to direct the electron transfer over 0-3 intervening prolines. Spectroscopic studies revealed competitive photophysical pathways. The reference peptide without tryptophan shows dominant non-specific ET dynamics, leading to an ion pair formation, whereas peptides with tryptophans have weak non-specific ET and intensified directed electron transfer. By different excitation wavelengths, we can conclude that the corresponding ion pair state of flavin within the peptide environment has to be energetically located between the S1 and S4 states, whereas the directed electron transfer to tryptophan occurs directly from the S1 state. These photochemical results have fundamental significance for proteins with flavin as redoxactive cofactor.
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Affiliation(s)
- Samantha Wörner
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Julia Leier
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Nadine C. Michenfelder
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Andreas‐Neil Unterreiner
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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14
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Leanse LG, Goh XS, Cheng JX, Hooper DC, Dai T. Dual-wavelength photo-killing of methicillin-resistant Staphylococcus aureus. JCI Insight 2020; 5:134343. [PMID: 32493838 DOI: 10.1172/jci.insight.134343] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/23/2020] [Indexed: 12/20/2022] Open
Abstract
With the effectiveness of antimicrobials declining as antimicrobial resistance continues to threaten public health, we must look to alternative strategies for the treatment of infections. In this study, we investigated an innovative, drug-free, dual-wavelength irradiation approach that combines 2 wavelengths of light, 460 nm and 405 nm, against methicillin-resistant Staphylococcus aureus (MRSA). MRSA was initially irradiated with 460-nm light (90-360 J/cm2) and subsequently irradiated with aliquots of 405-nm light (54-324 J/cm2). For in vivo studies, mouse skin was abraded and infected with approximately 107 CFUs of MRSA and incubated for 3 hours before irradiating with 460 nm (360 J/cm2) and 405 nm (342 J/cm2). Naive mouse skin was also irradiated to investigate apoptosis. We found that staphyloxanthin, the carotenoid pigment in MRSA cells, promoted resistance to the antimicrobial effects of 405-nm light. In addition, we found that the photolytic effect of 460-nm light on staphyloxanthin attenuated resistance of MRSA to 405-nm light killing. Irradiation of 460 nm alone did not elicit any antimicrobial effect on MRSA. In a proof-of-principle mouse skin abrasion infection model, we observed significant killing of MRSA using the dual-wavelength irradiation approach. However, when either wavelength of light was administered alone, no significant decrease in bacterial viability was observed. Moreover, exposure of the dual-wavelength irradiation to naive mouse skin did not result in any visible apoptosis. In conclusion, a dual-wavelength irradiation strategy may offer an innovative, effective, and safe approach for the treatment of skin infections caused by MRSA.
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Affiliation(s)
- Leon G Leanse
- Wellman Center for Photomedicine.,Vaccine and Immunotherapy Center, and
| | | | - Ji-Xin Cheng
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tianhong Dai
- Wellman Center for Photomedicine.,Vaccine and Immunotherapy Center, and
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15
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Segarra-Martí J, Segatta F, Mackenzie TA, Nenov A, Rivalta I, Bearpark MJ, Garavelli M. Modeling multidimensional spectral lineshapes from first principles: application to water-solvated adenine. Faraday Discuss 2020; 221:219-244. [DOI: 10.1039/c9fd00072k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We theoretically describe spectral lineshape from first principles, providing insight into solvent–solute interactions in terms of static and dynamic disorder and how these shape experimental signals in linear and non-linear optical spectroscopies.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Tristan A. Mackenzie
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
- Univ Lyon
| | - Michael J. Bearpark
- Department of Chemistry
- Molecular Sciences Research Hub
- Imperial College London
- London
- UK
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università degli studi di Bologna
- 40136 Bologna
- Italy
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16
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Mondal P, Schwinn K, Huix-Rotllant M. Impact of the redox state of flavin chromophores on the UV–vis spectra, redox and acidity constants and electron affinities. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2019.112164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Pompe N, Chen J, Illarionov B, Panter S, Fischer M, Bacher A, Weber S. Methyl groups matter: Photo-CIDNP characterizations of the semiquinone radicals of FMN and demethylated FMN analogs. J Chem Phys 2019; 151:235103. [PMID: 31864274 DOI: 10.1063/1.5130557] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this contribution, the relative hyperfine couplings are determined for the 1H nuclei of the flavin mononucleotide (FMN) radical in an aqueous environment. In addition, three structural analogs with different methylation patterns are characterized and the influence of the substituents at the isoalloxazine moiety on the electronic structure of the radicals is explored. By exploiting nuclear hyperpolarization generated via the photo-CIDNP (chemically induced dynamic nuclear polarization) effect, it is possible to study the short-lived radical species generated by in situ light excitation. Experimental data are extracted by least-squares fitting and supported by quantum chemical calculations and published values from electron paramagnetic resonance and electron-nuclear double resonance. Furthermore, mechanistic details of the photoreaction of the investigated flavin analogs with l-tryptophan are derived from the photo-CIDNP spectra recorded at different pH values. Thereby, the neutral and anionic radicals of FMN and three structural analogs are, for the first time, characterized in terms of their electronic structure in an aqueous environment.
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Affiliation(s)
- Nils Pompe
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Jing Chen
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Sabrina Panter
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Adelbert Bacher
- Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
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18
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Richert S, Chen J, Pompe N, Radtke V, Lllarionov B, Fischer M, Bacher A, Weber S. Influence of the cofactor structure on the photophysical processes initiating signal transduction in a phototropin-derived LOV domain. J Chem Phys 2019; 151:235102. [PMID: 31864253 DOI: 10.1063/1.5131856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Due to their biological importance, the photochemistry of blue-light photoreceptor proteins has been studied extensively over the last few decades. Most blue-light photoreceptors, such as cryptochromes and phototropins, utilize flavin chromophores as their cofactors. After irradiation with light, the chromophore undergoes electron transfer with nearby redox-active amino-acid residues within the protein, whereby this first step of signal transduction may be initiated either from the flavin's excited singlet or triplet state. Despite the collective effort of theoreticians and experimentalists to characterize and understand the photochemistry of flavoproteins, the mechanistic details of the excited state processes initiating signal transduction are yet to be revealed. Here, we use a light-oxygen-voltage-sensing domain from Avena sativa phototropin to get additional insight into the excited state photochemistry of flavoproteins. The influence of structural variations of the cofactor flavin mononucleotide (FMN) is explored by varying the methyl substitution pattern in positions 7 and 8 of the flavin core. The photophysical properties of the FMN derivatives, in the absence and presence of the protein environment, are investigated by UV-vis absorption, fluorescence, and electron paramagnetic resonance spectroscopies as well as cyclic voltammetry. The comparison of the properties of the modified flavin cofactors with those of FMN shows that the rates of the different excited state reactions, and therefore also the singlet/triplet yields, can be modulated substantially by only minor structural modifications of the flavin core.
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Affiliation(s)
- Sabine Richert
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Jing Chen
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Nils Pompe
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Valentin Radtke
- Institute of Inorganic and Analytical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Boris Lllarionov
- Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Adelbert Bacher
- Institute of Organic Chemistry and Biochemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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19
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Characterization and Testing of a Novel Sprayable Crosslinked Edible Coating Based on Salmon Gelatin. COATINGS 2019. [DOI: 10.3390/coatings9100595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of this study was to develop and characterize a sprayable edible coating using salmon gelatin (SG) and its stabilization by photopolymerization using riboflavin (Rf). Suspensions of SG with Rf at pH values of 5.0 and 8.5 were exposed for 2 min to visible light (VL) and ultraviolet (UV) light and further characterized to determine structural changes of the different gelatin formulations. Rheology analysis showed that at pH 5, the loss modulus (G’’) was higher that the storage modulus (G’) for crosslinked samples (VL and UV light). However, at pH 8.5 G’ values increased over G’’, showing a strong crosslinking effect. Interestingly both moduli did not intersect at any point and their maximum values did not change upon cooling with respect to the gelatin suspension without light exposure, demonstrating that triple helix formation was not affected by the reaction. In fact, neither the gelation temperature nor the enthalpy values were significantly affected. Viscosity measurements confirmed the hydrogel formation using VL, showing higher viscosity values after exposure at increasing temperatures. Transmittance (T%) measurements showed an increase in T% in the suspensions after VL exposure, with only a 10% decrease compared to SG without riboflavin. For validation, the coating was sprayed in fresh salmon fillets, showing a 37% delay in spoilage and reduced weight loss. Therefore, photopolymerization of low viscosity gelatins would allow to manage viscoelasticity of the biomaterial stabilizing it as coating and preventing the deterioration of salmon fillets.
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20
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Brisker-Klaiman D, Dreuw A. On the influence of dimerisation of lumiflavin in aqueous solution on its optical spectra – a quantum chemical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1616843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Daria Brisker-Klaiman
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
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21
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Su D, Kabir MP, Orozco-Gonzalez Y, Gozem S, Gadda G. Fluorescence Properties of Flavin Semiquinone Radicals in Nitronate Monooxygenase. Chembiochem 2019; 20:1646-1652. [PMID: 30748074 DOI: 10.1002/cbic.201900016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 11/09/2022]
Abstract
Fluorescent cofactors like flavins can be exploited to probe their local environment with spatial and temporal resolution. Although the fluorescence properties of the oxidized and two-electron-reduced states of flavins have been studied extensively, this is not the case for the one-electron-reduced state. Both the neutral and anionic semiquinones have proven particularly challenging to examine, as they are unstable in solution and are transient, short-lived species in many catalytic cycles. Here, we report that the nitronate monooxygenase (NMO) from Pseudomonas aeruginosa PAO1 is capable of stabilizing both semiquinone forms anaerobically for hours, thus enabling us to study their spectroscopy in a constant protein environment. We found that in the active site of NMO, the anionic semiquinone exhibits no fluorescence, whereas the neutral semiquinone radical shows a relatively strong fluorescence, with a behavior that violates the Kasha-Vavilov rule. These fluorescence properties are discussed in the context of time-dependent density functional theory calculations, which reveal low-lying dark states in both systems.
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Affiliation(s)
- Dan Su
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Samer Gozem
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA.,Department of Biology, Georgia State University, 100 Piedmond Ave., Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 5090, Atlanta, GA, 30303, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302, USA
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22
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Zanetti-Polzi L, Daidone I, Corni S. Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage. J Phys Chem Lett 2019; 10:1450-1456. [PMID: 30855973 DOI: 10.1021/acs.jpclett.9b00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Redox proteins and enzymes are at risk of irreversible oxidative damage from highly oxidizing intermediates generated in the active site in the case of unsuccessful functional reaction. Chains of tyrosine and/or tryptophan residues have been recently proposed to provide protection to the active site and the whole protein by delivering oxidizing equivalents (holes) out of the protein via a multistep hopping mechanism. In the present work we use a hybrid quantum/classical theoretical-computational methodology based on the perturbed matrix method and on molecular dynamics simulations to calculate the oxidation potential difference along a chain of tyrosine and tryptophan residues in a human redox enzyme of major importance, a superoxide dismutase, which acts as antioxidant defense. We show that the hole hopping is thermodynamically favored along such a chain and that the hopping propensity is strongly affected by the protein environment and in particular by the active site and its second coordination sphere.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Stefano Corni
- Department of Chemical Sciences , University of Padova , I-35131 Padova , Italy
- Center S3 , CNR-Institute of Nanoscience , Via Campi 213/A , 41125 Modena , Italy
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23
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Kabir MP, Orozco-Gonzalez Y, Gozem S. Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment. Phys Chem Chem Phys 2019; 21:16526-16537. [DOI: 10.1039/c9cp02230a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This study discusses how UV/vis absorption spectra of flavin in different redox and protonation states are shifted by the nearby electrostatic microenvironment.
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Affiliation(s)
| | | | - Samer Gozem
- Department of Chemistry
- Georgia State University
- Atlanta
- USA
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24
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Zanetti-Polzi L, Del Galdo S, Daidone I, D'Abramo M, Barone V, Aschi M, Amadei A. Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. Phys Chem Chem Phys 2018; 20:24369-24378. [PMID: 30215645 DOI: 10.1039/c8cp04190c] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.
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Affiliation(s)
- Laura Zanetti-Polzi
- Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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25
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Matthews E, Cercola R, Dessent CEH. Protomer-Dependent Electronic Spectroscopy and Photochemistry of the Model Flavin Chromophore Alloxazine. Molecules 2018; 23:molecules23082036. [PMID: 30110962 PMCID: PMC6222404 DOI: 10.3390/molecules23082036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 12/16/2022] Open
Abstract
Flavin chromophores play key roles in a wide range of photoactive proteins, but key questions exist in relation to their fundamental spectroscopic and photochemical properties. In this work, we report the first gas-phase spectroscopy study of protonated alloxazine (AL∙H⁺), a model flavin chromophore. Laser photodissociation is employed across a wide range (2.34⁻5.64 eV) to obtain the electronic spectrum and characterize the photofragmentation pathways. By comparison to TDDFT quantum chemical calculations, the spectrum is assigned to two AL∙H⁺ protomers; an N5 (dominant) and O4 (minor) form. The protomers have distinctly different spectral profiles in the region above 4.8 eV due to the presence of a strong electronic transition for the O4 protomer corresponding to an electron-density shift from the benzene to uracil moiety. AL∙H⁺ photoexcitation leads to fragmentation via loss of HCN and HNCO (along with small molecules such as CO₂ and H₂O), but the photofragmentation patterns differ dramatically from those observed upon collision excitation of the ground electronic state. This reveals that fragmentation is occurring during the excited state lifetime. Finally, our results show that the N5 protomer is associated primarily with HNCO loss while the O4 protomer is associated with HCN loss, indicating that the ring-opening dynamics are dependent on the location of protonation in the ground-state molecule.
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Affiliation(s)
- Edward Matthews
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
| | - Rosaria Cercola
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
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26
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Giacomozzi L, Kjær C, Langeland Knudsen J, Andersen LH, Brøndsted Nielsen S, Stockett MH. Absorption and luminescence spectroscopy of mass-selected flavin adenine dinucleotide mono-anions. J Chem Phys 2018; 148:214309. [PMID: 29884035 DOI: 10.1063/1.5024028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We report the absorption profile of isolated Flavin Adenine Dinucleotide (FAD) mono-anions recorded using photo-induced dissociation action spectroscopy. In this charge state, one of the phosphoric acid groups is deprotonated and the chromophore itself is in its neutral oxidized state. These measurements cover the first four optical transitions of FAD with excitation energies from 2.3 to 6.0 eV (210-550 nm). The S0 → S2 transition is strongly blue shifted relative to aqueous solution, supporting the view that this transition has a significant charge-transfer character. The remaining bands are close to their solution-phase positions. This confirms that the large discrepancy between quantum chemical calculations of vertical transition energies and solution-phase band maxima cannot be explained by solvent effects. We also report the luminescence spectrum of FAD mono-anions in vacuo. The gas-phase Stokes shift for S1 is 3000 cm-1, which is considerably larger than any previously reported for other molecular ions and consistent with a significant displacement of the ground and excited state potential energy surfaces. Consideration of the vibronic structure is thus essential for simulating the absorption and luminescence spectra of flavins.
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Affiliation(s)
- L Giacomozzi
- Department of Physics, Stockholm University, Stockholm, Sweden
| | - C Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - L H Andersen
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - M H Stockett
- Department of Physics, Stockholm University, Stockholm, Sweden
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27
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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28
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Daidone I, Amadei A, Aschi M, Zanetti-Polzi L. On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:451-457. [PMID: 29212059 DOI: 10.1016/j.saa.2017.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/27/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.
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Affiliation(s)
- Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy.
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29
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Zanetti-Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Lett 2017; 591:3265-3275. [PMID: 28881468 DOI: 10.1002/1873-3468.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/21/2017] [Accepted: 08/31/2017] [Indexed: 11/06/2022]
Abstract
We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide I' IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump.
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Affiliation(s)
| | - Caitlin M Davis
- Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA
| | - Martin Gruebele
- Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Italy
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30
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Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein. J Phys Chem Lett 2017; 8:3321-3327. [PMID: 28665138 DOI: 10.1021/acs.jpclett.7b01575] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical-molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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