1
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Kaffash M, Tolou-Shikhzadeh-Yazdi S, Soleimani S, Hoseinpoor S, Saberi MR, Chamani J. Spectroscopy and molecular simulation on the interaction of Nano-Kaempferol prepared by oil-in-water with two carrier proteins: An investigation of protein-protein interaction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123815. [PMID: 38154302 DOI: 10.1016/j.saa.2023.123815] [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: 10/03/2023] [Revised: 11/28/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
In this work, the interaction of human serum albumin (HSA) and human holo-transferrin (HTF) with the prepared Nano-Kaempferol (Nano-KMP) through oil-in-water procedure was investigated in the form of binary and ternary systems by the utilization of different spectroscopy techniques along with molecular simulation and cancer cell experiments. According to fluorescence spectroscopy outcomes, Nano-KMP is capable of quenching both proteins as binary systems by a static mechanism, while in the form of (HSA-HTF) Nano-KMP as the ternary system, an unlinear Stern-Volmer plot was elucidated with the occurrence of both dynamic and static fluorescence quenching mechanisms in the binding interaction. In addition, the two acquired Ksv values in the ternary system signified the existence of two sets of binding sites with two different interaction behaviors. The binding constant values of HSA-Nano KMP, HTF-Nano-KMP, and (HSA-HTF) Nano-KMP complexes formation were (2.54 ± 0.03) × 104, (2.15 ± 0.02) × 104 and (1.43 ± 0.04) × 104M-1at the first set of binding sites and (4.68 ± 0.05) × 104 M-1 at the second set of binding sites, respectively. The data of thermodynamic parameters confirmed the major roles of hydrogen binding and van der Waals forces in the formation of HSA-Nano KMP and HTF-Nano KMP complexes. The thermodynamic parameter values of (HSA-HTF) Nano KMP revealed the dominance of hydrogen binding and van der Waals forces in the first set of binding sites and hydrophobic forces for the second set of binding sites. Resonance light scattering (RLS) analysis displayed the existence of a different interaction behavior for HSA-HTF complex in the presence of Nano-KMP as the ternary system. Moreover, circular dichroism (CD) technique affirmed the conformational changes of the secondary structure of proteins as binary and ternary systems. Molecular docking and molecular dynamics simulations (for 100 ns) were performed to investigate the mechanism of KMP binding to HSA, HTF, and HSA-HTF. Next to observing a concentration and time-dependent cytotoxicity, the down regulation of PI3K/AkT/mTOR pathway resulted in cell cycle arrest in SW480 cells.
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Affiliation(s)
- Maryam Kaffash
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Samane Soleimani
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Saeideh Hoseinpoor
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
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2
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Broser M, Andruniów T, Kraskov A, Palombo R, Katz S, Kloz M, Dostál J, Bernardo C, Kennis JTM, Hegemann P, Olivucci M, Hildebrandt P. Experimental Assessment of the Electronic and Geometrical Structure of a Near-Infrared Absorbing and Highly Fluorescent Microbial Rhodopsin. J Phys Chem Lett 2023; 14:9291-9295. [PMID: 37815402 DOI: 10.1021/acs.jpclett.3c02167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The recently discovered Neorhodopsin (NeoR) exhibits absorption and emission maxima in the near-infrared spectral region, which together with the high fluorescence quantum yield makes it an attractive retinal protein for optogenetic applications. The unique optical properties can be rationalized by a theoretical model that predicts a high charge transfer character in the electronic ground state (S0) which is otherwise typical of the excited state S1 in canonical retinal proteins. The present study sets out to assess the electronic structure of the NeoR chromophore by resonance Raman (RR) spectroscopy since frequencies and relative intensities of RR bands are controlled by the ground and excited state's properties. The RR spectra of NeoR differ dramatically from those of canonical rhodopsins but can be reliably reproduced by the calculations carried out within two different structural models. The remarkable agreement between the experimental and calculated spectra confirms the consistency and robustness of the theoretical approach.
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Affiliation(s)
- Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Tadeusz Andruniów
- Department of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anastasia Kraskov
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Miroslav Kloz
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - Jakub Dostál
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - César Bernardo
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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3
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Ahmadi Oskooei F, Mehrzad J, Asoodeh A, Motavalizadehkakhky A. Olive oil-based quercetin nanoemulsion (QuNE)'s interactions with human serum proteins (HSA and HTF) and its anticancer activity. J Biomol Struct Dyn 2023; 41:778-791. [PMID: 34919017 DOI: 10.1080/07391102.2021.2012514] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The current study produced Quercetin nanoemulsions (QuNEs) for the purpose of improving Quercetin solubility in an aqueous polar condition and to analyze QuNE-protein formation (QuNE-human serum albumin (HSA) and QuNE-holo-transferrin (HTF)).QuNE was produced by utilizing an ultrasound-based emulsification method and was characterized by DLS, TEM, and SEM. Its interaction with HSA and HTF proteins was studied by analyzing the results of FRET and RLS spectroscopy, Stern-Volmer plotting, the Van't Hoff equation, CD spectroscopy, and molecular docking methods. Finally, QuNE's cytotoxic impact, cell death type induction, and antioxidant properties were evaluated by applying an MTT assay on a human hepatocyte cancer cell (HepG2), measuring Cas-3 gene expression, and conducting a DPPH antioxidant test, respectively. Compared to the non-entrapped Quercetin, Quercetin-entrapped nano-emulsions formed stable complexes with HSA and HTF by improving hydrophilic-hydrophobic interactions. The binding constant (BC), ΔH0, and ΔS0 indices for both the QuNE-HSA and QuNE-HTF complexes were measured at (4.92 × 105 and 11.99 × 104 M-1), (170.96 and -131.19 KJ.mol-1), and (-464.86 and 342.83J.mol-1K-1), respectively.QuNE lowered the HepG2 viability by up-regulating Cas-3 gene expression and thus inducing apoptosis. Moreover, a notable antioxidant impact on the QuNE was detected. Due to its ability in delivering Quercetin to HSA and HTF proteins and stabilizing their protein complexes, QuNE can be used as a suitable primary transporting agent whose formation of stable bio-accessible QuNE-HSA and -HTF protein complexes creates a safe and natural secondary delivery system, which has potential to be used as an efficient anticancer compound.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Farnaz Ahmadi Oskooei
- Department of Biochemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Jamshid Mehrzad
- Department of Biochemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Ahmad Asoodeh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alireza Motavalizadehkakhky
- Department of Chemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran.,Advanced Research Center for Chemistry, Biochemistry & Nanomaterial, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
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4
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Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin. Nat Commun 2022; 13:6652. [PMID: 36333283 PMCID: PMC9636224 DOI: 10.1038/s41467-022-33953-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
The understanding of how the rhodopsin sequence can be modified to exactly modulate the spectroscopic properties of its retinal chromophore, is a prerequisite for the rational design of more effective optogenetic tools. One key problem is that of establishing the rules to be satisfied for achieving highly fluorescent rhodopsins with a near infrared absorption. In the present paper we use multi-configurational quantum chemistry to construct a computer model of a recently discovered natural rhodopsin, Neorhodopsin, displaying exactly such properties. We show that the model, that successfully replicates the relevant experimental observables, unveils a geometrical and electronic structure of the chromophore featuring a highly diffuse charge distribution along its conjugated chain. The same model reveals that a charge confinement process occurring along the chromophore excited state isomerization coordinate, is the primary cause of the observed fluorescence enhancement.
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5
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Barneschi L, Marsili E, Pedraza-González L, Padula D, De Vico L, Kaliakin D, Blanco-González A, Ferré N, Huix-Rotllant M, Filatov M, Olivucci M. On the fluorescence enhancement of arch neuronal optogenetic reporters. Nat Commun 2022; 13:6432. [PMID: 36307417 PMCID: PMC9616920 DOI: 10.1038/s41467-022-33993-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.
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Affiliation(s)
- Leonardo Barneschi
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Emanuele Marsili
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.8250.f0000 0000 8700 0572University of Durham, Department of Chemistry, South Road, Durham, DH1 3LE United Kingdom ,grid.5337.20000 0004 1936 7603Present Address: Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Laura Pedraza-González
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.5395.a0000 0004 1757 3729Present Address: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Daniele Padula
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Danil Kaliakin
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Alejandro Blanco-González
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Nicolas Ferré
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Miquel Huix-Rotllant
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Michael Filatov
- grid.258803.40000 0001 0661 1556Department of Chemistry, Kyungpook National University, Daegu, 702-701 South Korea
| | - Massimo Olivucci
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA ,grid.11843.3f0000 0001 2157 9291University of Strasbourg Institute for Advanced Studies, 5, alleé duGeń eŕ al Rouvillois, F-67083 Strasbourg, France
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6
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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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7
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Lin CY, Boxer SG. Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore. J Am Chem Soc 2020; 142:11032-11041. [PMID: 32453950 DOI: 10.1021/jacs.0c02796] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferred for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found that the color of the neutral chromophore can be more sensitive to protein electrostatics than can the anionic counterpart. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model as compared to that of the anionic state, which requires only two forms ( J. Am. Chem. Soc. 2019, 141, 15250-15265). Specifically, an underlying zwitterionic charge-transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to excited-state proton transfer (ESPT) of the protonated chromophore, we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The three-form model could also be applied to similar biological and nonbiological dyes and complements the failure of the two-form model for donor-acceptor systems with localized ground-state electronic distributions.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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8
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Mokaberi P, Babayan-Mashhadi F, Amiri Tehrani Zadeh Z, Saberi MR, Chamani J. Analysis of the interaction behavior between Nano-Curcumin and two human serum proteins: combining spectroscopy and molecular stimulation to understand protein-protein interaction. J Biomol Struct Dyn 2020; 39:3358-3377. [DOI: 10.1080/07391102.2020.1766570] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Fatemeh Babayan-Mashhadi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehrani Zadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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9
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Manathunga M, Yang X, Olivucci M. Electronic State Mixing Controls the Photoreactivity of a Rhodopsin with all- trans Chromophore Analogues. J Phys Chem Lett 2018; 9:6350-6355. [PMID: 30336038 PMCID: PMC6261349 DOI: 10.1021/acs.jpclett.8b02550] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rhodopsins hosting synthetic retinal protonated Schiff base analogues are important for developing tools for optogenetics and high-resolution imaging. The ideal spectroscopic properties of such analogues include long-wavelength absorption/emission and fast/hindered photoisomerization. While the former may be achieved, for instance, by elongating the chromophore π-system, the latter requires a detailed understanding of the substituent effects (i.e., steric or electronic) on the chromophore light-induced dynamics. In the present letter we compare the results of quantum mechanics/molecular mechanics excited-state trajectories of native and analogue-hosting microbial rhodopsins from the eubacterium Anabaena. The results uncover a relationship between the nature of the substituent on the analogue (i.e., electron-donating (a Me group) or electron-withdrawing (a CF3 group)) and rhodopsin excited-state lifetime. Most importantly, we show that electron-donating or -withdrawing substituents cause a decrease or an increase in the electronic mixing of the first two excited states which, in turn, controls the photoisomerization speed.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry, Bowling Green State
University, Bowling Green, OH 43403, USA
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State
University, Bowling Green, OH 43403, USA
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State
University, Bowling Green, OH 43403, USA
- Dipartimento di Biotecnologie, Chimica e Farmacia,
Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Institut de Physique et Chimie des Matériaux
de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg,
France
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10
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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11
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Orozco-Gonzalez Y, Manathunga M, Marín MDC, Agathangelou D, Jung KH, Melaccio F, Ferré N, Haacke S, Coutinho K, Canuto S, Olivucci M. An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. J Chem Theory Comput 2017; 13:6391-6404. [DOI: 10.1021/acs.jctc.7b00860] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoelvis Orozco-Gonzalez
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Madushanka Manathunga
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Damianos Agathangelou
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kwang-Hwan Jung
- Department
of Life Science and Institute of Biological Interfaces, Sogang University 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Massimo Olivucci
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
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12
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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13
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Dokukina I, Marian CM, Weingart O. New Perspectives on an Old Issue: A Comparative MS-CASPT2 and OM2-MRCI Study of Polyenes and Protonated Schiff Bases. Photochem Photobiol 2017; 93:1345-1355. [PMID: 28833170 DOI: 10.1111/php.12833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/13/2017] [Indexed: 11/29/2022]
Abstract
Polyenic systems are involved in light perception of numerous living organisms. Although a π-conjugated backbone is a common feature of all polyenes, their photophysics may vary. We provide a comparative quantum mechanical study of low-lying S1 and S2 excited states in short (3-5 double bonds) symmetric all-trans linear polyenes and corresponding protonated Schiff bases. In our investigation, we use the well-established ab initio multireference CASPT2 approach and benchmark the efficient semiempirical OM2-MRCI approach against it. For all protonated Schiff bases, MS-CASPT2 results in two distinct S1 minima with inverted and noninverted bond length pattern, respectively. We find that OM2-MRCI is a computationally affordable and reliable alternative to MS-CASPT2 for investigations of polyenic systems, particularly when highly demanding calculations (e.g. excited-state dynamics) need to be performed.
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Affiliation(s)
- Irina Dokukina
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Christel M Marian
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
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14
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El-Tahawy MMT, Nenov A, Garavelli M. Photoelectrochromism in the Retinal Protonated Schiff Base Chromophore: Photoisomerization Speed and Selectivity under a Homogeneous Electric Field at Different Operational Regimes. J Chem Theory Comput 2016; 12:4460-75. [DOI: 10.1021/acs.jctc.6b00558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohsen M. T. El-Tahawy
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
- Chemistry
Department, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Artur Nenov
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica “G. Ciamician″, Universita’ degli Studi di Bologna, Via Selmi, 2 I - 40126 Bologna, Italy
- Université
de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, Centre
Nationale de Recherche Scientifique, 46 allée d’Italie, 69007 Lyon Cedex 07, France
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15
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Schapiro I. The Origin of Bond Selectivity and Excited-State Reactivity in Retinal Analogues. J Phys Chem A 2016; 120:3353-65. [DOI: 10.1021/acs.jpca.6b00701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Igor Schapiro
- Fritz Haber
Center for Molecular
Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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16
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Ockenfels A, Schapiro I, Gärtner W. Rhodopsins carrying modified chromophores--the 'making of', structural modelling and their light-induced reactivity. Photochem Photobiol Sci 2016; 15:297-308. [PMID: 26860474 DOI: 10.1039/c5pp00322a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A series of vitamin-A aldehydes (retinals) with modified alkyl group substituents (9-demethyl-, 9-ethyl-, 9-isopropyl-, 10-methyl, 10-methyl-13-demethyl-, and 13-demethyl retinal) was synthesized and their 11-cis isomers were used as chromophores to reconstitute the visual pigment rhodopsin. Structural changes were selectively introduced around the photoisomerizing C11=C12 bond. The effect of these structural changes on rhodopsin formation and bleaching was determined. Global fit of assembly kinetics yielded lifetimes and spectral features of the assembly intermediates. Rhodopsin formation proceeds stepwise with prolonged lifetimes especially for 9-demethyl retinal (longest lifetime τ3 = 7500 s, cf., 3500 s for retinal), and for 10-methyl retinal (τ3 = 7850 s). These slowed-down processes are interpreted as either a loss of fixation (9dm) or an increased steric hindrance (10me) during the conformational adjustment within the protein. Combined quantum mechanics and molecular mechanics (QM/MM) simulations provided structural insight into the retinal analogues-assembled, full-length rhodopsins. Extinction coefficients, quantum yields and kinetics of the bleaching process (μs-to-ms time range) were determined. Global fit analysis yielded lifetimes and spectral features of bleaching intermediates, revealing remarkably altered kinetics: whereas the slowest process of wild-type rhodopsin and of bleached and 11-cis retinal assembled rhodopsin takes place with lifetimes of 7 and 3.8 s, respectively, this process for 10-methyl-13-demethyl retinal was nearly 10 h (34670 s), coming to completion only after ca. 50 h. The structural changes in retinal derivatives clearly identify the precise interactions between chromophore and protein during the light-induced changes that yield the outstanding efficiency of rhodopsin.
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Affiliation(s)
- Andreas Ockenfels
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany.
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17
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Valsson O, Filippi C, Casida ME. Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory. J Chem Phys 2015; 142:144104. [DOI: 10.1063/1.4916354] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Dokukina I, Weingart O. Spectral properties and isomerisation path of retinal in C1C2 channelrhodopsin. Phys Chem Chem Phys 2015; 17:25142-50. [DOI: 10.1039/c5cp02650d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computed torsion profiles along the reactive coordinate in S1reveal a two-path deactivation mechanism for retinal in C1C2 channelrhodopsin.
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Affiliation(s)
- I. Dokukina
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - O. Weingart
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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19
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Walczak E, Andruniów T. Impacts of retinal polyene (de)methylation on the photoisomerization mechanism and photon energy storage of rhodopsin. Phys Chem Chem Phys 2015; 17:17169-81. [DOI: 10.1039/c5cp01939g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Similar to native rhodopsin, a two-mode space-saving isomerization mechanism drives the photoreaction in (de)methylated rhodopsin analogues.
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Affiliation(s)
- Elżbieta Walczak
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw
- Poland
| | - Tadeusz Andruniów
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw
- Poland
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20
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21
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Directed evolution of Gloeobacter violaceus rhodopsin spectral properties. J Mol Biol 2014; 427:205-20. [PMID: 24979679 DOI: 10.1016/j.jmb.2014.06.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/05/2014] [Accepted: 06/22/2014] [Indexed: 01/01/2023]
Abstract
Proton-pumping rhodopsins (PPRs) are photoactive retinal-binding proteins that transport ions across biological membranes in response to light. These proteins are interesting for light-harvesting applications in bioenergy production, in optogenetics applications in neuroscience, and as fluorescent sensors of membrane potential. Little is known, however, about how the protein sequence determines the considerable variation in spectral properties of PPRs from different biological niches or how to engineer these properties in a given PPR. Here we report a comprehensive study of amino acid substitutions in the retinal-binding pocket of Gloeobacter violaceus rhodopsin (GR) that tune its spectral properties. Directed evolution generated 70 GR variants with absorption maxima shifted by up to ±80nm, extending the protein's light absorption significantly beyond the range of known natural PPRs. While proton-pumping activity was disrupted in many of the spectrally shifted variants, we identified single tuning mutations that incurred blue and red shifts of 42nm and 22nm, respectively, that did not disrupt proton pumping. Blue-shifting mutations were distributed evenly along the retinal molecule while red-shifting mutations were clustered near the residue K257, which forms a covalent bond with retinal through a Schiff base linkage. Thirty eight of the identified tuning mutations are not found in known microbial rhodopsins. We discovered a subset of red-shifted GRs that exhibit high levels of fluorescence relative to the WT (wild-type) protein.
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22
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Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M. Learning from photobiology how to design molecular devices using a computer. Chem Soc Rev 2014; 43:4019-36. [DOI: 10.1039/c4cs00037d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Learning how to model photo-responsive proteins may open the way to the design of lightpowered biomimetic molecular devices.
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Affiliation(s)
- S. Gozem
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - F. Melaccio
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - H. L. Luk
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - S. Rinaldi
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - M. Olivucci
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
- Dipartimento di Chimica
- Università di Siena
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23
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Cheminal A, Léonard J, Kim S, Jung KH, Kandori H, Haacke S. Steady state emission of the fluorescent intermediate of Anabaena Sensory Rhodopsin as a function of light adaptation conditions. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Walczak E, Szefczyk B, Andruniów T. Geometries and Vertical Excitation Energies in Retinal Analogues Resolved at the CASPT2 Level of Theory: Critical Assessment of the Performance of CASSCF, CC2, and DFT Methods. J Chem Theory Comput 2013; 9:4915-27. [DOI: 10.1021/ct400423u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elżbieta Walczak
- Wroclaw University of Technology, Institute of Physical & Theoretical Chemistry, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Borys Szefczyk
- Wroclaw University of Technology, Institute of Physical & Theoretical Chemistry, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Wroclaw University of Technology, Institute of Physical & Theoretical Chemistry, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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25
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Alexiev U, Farrens DL. Fluorescence spectroscopy of rhodopsins: insights and approaches. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:694-709. [PMID: 24183695 DOI: 10.1016/j.bbabio.2013.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Ulrike Alexiev
- Physics Department, Freie Universität Berlin, Berlin, Germany.
| | - David L Farrens
- Departments of Biochemistry and Molecular Biology, Oregon Health Sciences University, USA
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26
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Gozem S, Melaccio F, Lindh R, Krylov AI, Granovsky AA, Angeli C, Olivucci M. Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods. J Chem Theory Comput 2013; 9:4495-506. [DOI: 10.1021/ct400460h] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Federico Melaccio
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, I-53100 Siena, Italy
| | - Roland Lindh
- Department
of Chemistry, Ångström, the Theoretical Chemistry Programme, POB 518, SE-751 20 Uppsala, Sweden
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | - Celestino Angeli
- Dipartimento
di Chimica, Università di Ferrara, via Borsari 46, I-44121 Ferrara, Italy
| | - Massimo Olivucci
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, I-53100 Siena, Italy
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27
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Huntress MM, Gozem S, Malley KR, Jailaubekov AE, Vasileiou C, Vengris M, Geiger JH, Borhan B, Schapiro I, Larsen DS, Olivucci M. Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics. J Phys Chem B 2013; 117:10053-70. [DOI: 10.1021/jp305935t] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark M. Huntress
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Samer Gozem
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Konstantin R. Malley
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Askat E. Jailaubekov
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Mikas Vengris
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
- Faculty of
Physics, Vilnius University, Sauletekio
10 LT10223 Vilnius,
Lithuania
| | - James H. Geiger
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Igor Schapiro
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
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28
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Hernández-Rodríguez EW, Montero-Alejo AL, López R, Sánchez-García E, Montero-Cabrera LA, García de la Vega JM. Electron density deformations provide new insights into the spectral shift of rhodopsins. J Comput Chem 2013; 34:2460-71. [DOI: 10.1002/jcc.23414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 11/08/2022]
Affiliation(s)
| | - Ana Lilian Montero-Alejo
- Laboratorio de Química Computacional y Teórica; Departamento de Química Física; Universidad de La Habana; Havana; 10400; Cuba
| | - Rafael López
- Departamento de Química Física Aplicada; Facultad de Ciencias, Universidad Autónoma de Madrid; Madrid; 28049; Spain
| | - Elsa Sánchez-García
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1; Mülheim an der Ruhr; 45470; Germany
| | - Luis Alberto Montero-Cabrera
- Laboratorio de Química Computacional y Teórica; Departamento de Química Física; Universidad de La Habana; Havana; 10400; Cuba
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29
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Gozem S, Krylov AI, Olivucci M. Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods. J Chem Theory Comput 2012; 9:284-92. [DOI: 10.1021/ct300759z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Anna I. Krylov
- Department of Chemistry, University
of Southern California, Los Angeles, California 90089-0482, United
States
| | - Massimo Olivucci
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica,
Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
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