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Avelar M, Coppola C, d’Ettorre A, Ienco A, Parisi ML, Basosi R, Santucci A, Olivucci M, Sinicropi A. In Silico Study of a Bacteriorhodopsin/TiO 2 Hybrid System at the Molecular Level. J Chem Theory Comput 2025; 21:3231-3245. [PMID: 40037620 PMCID: PMC11948329 DOI: 10.1021/acs.jctc.4c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Revised: 01/27/2025] [Accepted: 02/07/2025] [Indexed: 03/06/2025]
Abstract
Bacteriorhodopsin (bR) is a light-harvesting membrane protein that represents a promising sensitizer of TiO2 for photovoltaic and photoelectrochemical devices. However, despite numerous experimental studies, the molecular-level understanding of the bR/TiO2 hybrid system is still unsatisfactory. In this contribution, we report the construction and analysis of an atomistic model of such a system. To do so, both steered molecular dynamics-molecular dynamics and quantum mechanics/molecular mechanics computations are applied to four different bR orientations on the anatase TiO2 surface. The resulting bR/TiO2 models are then used to compute the light absorption maxima changes relative to those of bR. We show that all four models reproduce the experimentally observed blue-shift value induced by bR binding on TiO2 and could be used to study the binding and binding-induced protein modifications. We conclude that the constructed models could provide a basis for future studies aiming to simulate the complex long-range electron transfer mechanism in bR/TiO2-based solar energy conversion devices as well as in engineering bR to achieve enhanced efficiencies.
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Affiliation(s)
- Mayra Avelar
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Carmen Coppola
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Alessio d’Ettorre
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Andrea Ienco
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
| | - Maria Laura Parisi
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Riccardo Basosi
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Annalisa Santucci
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Department
of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Adalgisa Sinicropi
- R2ES
Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Italian
National Council for Research - Institute for the Chemistry of OrganoMetallic
Compounds (CNR-ICCOM), 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi
a Grande Interfase, 50019 Sesto Fiorentino, Italy
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Kaçar C, Erden PE, Kılıç E. Graphene/Poly(vinylferrocene) Composite Based Amperometric Biosensor for L-lysine Determination. ELECTROANAL 2017. [DOI: 10.1002/elan.201700207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ceren Kaçar
- Ankara University; Faculty of Science, Department of Chemistry, Tandoğan; 06100 Ankara Turkey
| | - Pınar Esra Erden
- Ankara University; Faculty of Science, Department of Chemistry, Tandoğan; 06100 Ankara Turkey
| | - Esma Kılıç
- Ankara University; Faculty of Science, Department of Chemistry, Tandoğan; 06100 Ankara Turkey
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Bóka B, Korózs M, Nánási M, Adányi N. Novel Amperometric Tri-Enzyme Biosensor for Lysine Determination in Pharmaceutical Products and Food Samples. ELECTROANAL 2015. [DOI: 10.1002/elan.201400600] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Shervedani RK, Foroushani MS. Direct electrochemistry of cytochrome c immobilized on gold electrode surface via Zr(IV) ion glue and its activity for ascorbic acid. Bioelectrochemistry 2014; 98:53-63. [DOI: 10.1016/j.bioelechem.2014.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/26/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
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Chauhan N, Narang J, Sunny, Pundir C. Immobilization of lysine oxidase on a gold–platinum nanoparticles modified Au electrode for detection of lysine. Enzyme Microb Technol 2013; 52:265-71. [DOI: 10.1016/j.enzmictec.2013.01.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 01/13/2013] [Accepted: 01/15/2013] [Indexed: 11/30/2022]
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Shervedani RK, Akrami Z. Gold-deferrioxamine nanometric interface for selective recognition of Fe(III) using square wave voltammetry and electrochemical impedance spectroscopy methods. Biosens Bioelectron 2012; 39:31-6. [PMID: 22796024 DOI: 10.1016/j.bios.2012.06.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/30/2012] [Accepted: 06/14/2012] [Indexed: 11/25/2022]
Abstract
Deferrioxamine, a bacterial hydroxamic siderophore having high binding affinity for Fe(III), is used in its immobilized form, as self-assembled monolayer on Au, for accumulation and recognition of Fe(III) from the solution phase. The accumulated Fe(III) is detected via both active mode based on faradaic reduction current of Fe(III), and inactive mode based on impedimetric effect of accumulated Fe(III) against redox reaction of a suitable probe. Appropriate electrochemical techniques, square wave voltammetry and electrochemical impedance spectroscopy, are used for the transduction of analytical signals obtained by this sensor. Then, the parameters influencing the sensor response are optimized. In the best conditions, a linear response, from 1.0×10(-10) to 1.0×10(-7)M Fe(III) in logarithmic scale with a detection limit of 2.0×10(-11)M, and mean relative standard deviation of 1.7% for n=4 is observed. The results show that the sensor can be used for determination of Fe(III) in the presence of various inorganic ions and biological species. Validity of the method and applicability of the sensor are successfully tested by determination of Fe(III) in various real samples including plant tissue (corn leaves), industrial alloy (Ferrotitanium), and pharmaceutical samples (Venofer(®) ampoule, Ironorm(®) capsule, and V.M. Protein(®) powder).
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Affiliation(s)
- Reza Karimi Shervedani
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Islamic Republic of Iran.
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Shervedani RK, Amini A. Direct electrochemistry of dopamine on gold—Agaricus bisporus laccase enzyme electrode: Characterization and quantitative detection. Bioelectrochemistry 2012; 84:25-31. [DOI: 10.1016/j.bioelechem.2011.10.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/21/2011] [Accepted: 10/24/2011] [Indexed: 12/01/2022]
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Chauhan N, Singh A, Narang J, Dahiya S, Pundir CS. Development of amperometric lysine biosensors based on Au nanoparticles/multiwalled carbon nanotubes/polymers modified Au electrodes. Analyst 2012; 137:5113-22. [DOI: 10.1039/c2an35629e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mazloum-Ardakani M, Beitollahi H, Amini MK, Mirkhalaf F, Mirjalili BF, Akbari A. Application of 2-(3,4-dihydroxyphenyl)-1,3-dithialone self-assembled monolayer on gold electrode as a nanosensor for electrocatalytic determination of dopamine and uric acid. Analyst 2011; 136:1965-70. [DOI: 10.1039/c0an00823k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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