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Copper–Ruthenium Composite as Perspective Material for Bioelectrodes: Laser-Assisted Synthesis, Biocompatibility Study, and an Impedance-Based Cellular Biosensor as Proof of Concept. BIOSENSORS 2022; 12:bios12070527. [PMID: 35884330 PMCID: PMC9313201 DOI: 10.3390/bios12070527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Copper is an inexpensive material that has found wide application in electronics due to its remarkable electric properties. However, the high toxicity of both copper and copper oxide imposes restrictions on the application of this metal as a material for bioelectronics. One way to increase the biocompatibility of pure copper while keeping its remarkable properties is to use copper-based composites. In the present study, we explored a new copper–ruthenium composite as a potential biocompatible material for bioelectrodes. Sample electrodes were obtained by subsequent laser deposition of copper and ruthenium on glass plates from a solution containing salts of these metals. The fabricated Cu–Ru electrodes exhibit high effective area and their impedance properties can be described by simple R-CPE equivalent circuits that make them perspective for sensing applications. Finally, we designed a simple impedance cell-based biosensor using this material that allows us to distinguish between dead and alive HeLa cells.
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2
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Nikolaev DM, Shtyrov AA, Mereshchenko AS, Panov MS, Tveryanovich YS, Ryazantsev MN. An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins' first spectral absorption band maxima. Phys Chem Chem Phys 2020; 22:18114-18123. [PMID: 32761024 DOI: 10.1039/d0cp02638g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) models are a widely used tool to obtain detailed insight into the properties and functioning of proteins. The outcome of QM/MM studies heavily depends on the quality of the applied QM/MM model. Prediction and right placement of internal water molecules in protein cavities is one of the critical parts of any QM/MM model construction. Herein, we performed a systematic study of four protein hydration algorithms. We tested these algorithms for their ability to predict X-ray-resolved water molecules for a set of membrane photosensitive rhodopsin proteins, as well as the influence of the applied water placement algorithms on the QM/MM calculated absorption maxima (λmax) of these proteins. We used 49 rhodopsins and their intermediates with available X-ray structures as the test set. We found that a proper choice of hydration algorithms and setups is needed to predict functionally important water molecules in the chromophore-binding cavity of rhodopsins, such as the water cluster in the N-H region of bacteriorhodopsin or two water molecules in the binding pocket of bovine visual rhodopsin. The QM/MM calculated λmax of rhodopsins is also quite sensitive to the applied protein hydration protocols. The best methodology allows obtaining an 18.0 nm average value for the absolute deviation of the calculated λmax from the experimental λmax. Although the major effect of water molecules on λmax originates from the water molecules located in the binding pocket, the water molecules outside the binding pocket also affect the calculated λmax mainly by causing a reorganization of the protein structure. The results reported in this study can be used for the evaluation and further development of hydration methodologies, in general, and rhodopsin QM/MM models, in particular.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia.
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3
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Laser-Induced Synthesis of Composite Materials Based on Iridium, Gold and Platinum for Non-Enzymatic Glucose Sensing. MATERIALS 2020; 13:ma13153359. [PMID: 32751164 PMCID: PMC7436056 DOI: 10.3390/ma13153359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022]
Abstract
A simple approach for in situ laser-induced modification of iridium-based materials to increase their electrocatalytic activity towards enzyme-free glucose sensing was proposed. For this purpose, we deposited gold and platinum separately and as a mixture on the surface of pre-synthesized iridium microstructures upon laser irradiation at a wavelength of 532 nm. Then, we carried out the comparative investigation of their morphology, elemental and phase composition as well as their electrochemical properties. The best morphology and, as a result, the highest sensitivity (~9960 µA/mM cm2) with respect to non-enzymatic determination of D-glucose were demonstrated by iridium-gold-platinum microstructures also showing low limit of detection (~0.12 µM), a wide linear range (0.5 µM–1 mM) along with good selectivity, reproducibility and stability.
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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Park S, Shin J, Yoon H, Pak Y, Lim M. Complete photodissociation dynamics of CF2I2in solution. Phys Chem Chem Phys 2019; 21:6859-6867. [DOI: 10.1039/c9cp00507b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoexcited CF2I2in c-C6H12undergoes various secondary reactions including complex and isomer formation, after ultrafast two- or three-body dissociations.
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Affiliation(s)
- Seongchul Park
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Juhyang Shin
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Hojeong Yoon
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Youngshang Pak
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 46241
- Korea
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6
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Mereshchenko AS, Myasnikova OS, Olshin PK, Matveev SM, Panov MS, Kochemirovsky VA, Skripkin MY, Tarnovsky AN. Ultrafast Excited-State Dynamics of Ligand-Field and Ligand-to-Metal Charge-Transfer States of CuCl42– in Solution: A Detailed Transient Absorption Study. J Phys Chem B 2018; 122:10558-10571. [DOI: 10.1021/acs.jpcb.8b06901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Andrey S. Mereshchenko
- Saint-Petersburg State University, University Embankment 7/9, St. Petersburg 199034, Russia
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Olesya S. Myasnikova
- Saint-Petersburg State University, University Embankment 7/9, St. Petersburg 199034, Russia
| | - Pavel K. Olshin
- Saint-Petersburg State University, University Embankment 7/9, St. Petersburg 199034, Russia
| | - Sergey M. Matveev
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Maxim S. Panov
- Saint-Petersburg State University, University Embankment 7/9, St. Petersburg 199034, Russia
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Mikhail Yu. Skripkin
- Saint-Petersburg State University, University Embankment 7/9, St. Petersburg 199034, Russia
| | - Alexander N. Tarnovsky
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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Nikolaev D, Shtyrov AA, Panov MS, Jamal A, Chakchir OB, Kochemirovsky VA, Olivucci M, Ryazantsev MN. A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction. ACS OMEGA 2018; 3:7555-7566. [PMID: 30087916 PMCID: PMC6068592 DOI: 10.1021/acsomega.8b00721] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.
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Affiliation(s)
- Dmitrii
M. Nikolaev
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Andrey A. Shtyrov
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Maxim S. Panov
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
| | - Adeel Jamal
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Oleg B. Chakchir
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Vladimir A. Kochemirovsky
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry and Pharmacy, Università di Siena, via A. Moro 2, Siena I-53100, Italy
| | - Mikhail N. Ryazantsev
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
- Institute
of Macromolecular Compounds of the Russian Academy of Sciences, 31 Bolshoy pr., St. Petersburg 199004, Russia
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Logunov LS, Panov MS, Myund LA, Tumkin II, Khairullina EM, Ryazantsev MN, Balova IA, Kochemirovsky VA. Influence of the ligand nature on the in situ laser-induced synthesis of the electrocatalytically active copper microstructures. ARAB J CHEM 2018. [DOI: 10.1016/j.arabjc.2017.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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9
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Tanabe I, Suyama A, Sato T, Fukui KI. Systematic analysis of various ionic liquids by attenuated total reflectance spectroscopy (145–450 nm) and quantum chemical calculations. Analyst 2018; 143:2539-2545. [DOI: 10.1039/c8an00563j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Electronic absorption spectra in 140–450 nm were investigated by attenuated total reflectance spectroscopy and quantum chemical calculations.
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Affiliation(s)
- Ichiro Tanabe
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
| | - Aki Suyama
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
| | - Taiki Sato
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
| | - Ken-ichi Fukui
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
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Reid SA. When isomerisation is electron transfer: the intriguing story of the iso-halocarbons. INT REV PHYS CHEM 2014. [DOI: 10.1080/0144235x.2014.942548] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Zhang CP, Chen QY, Guo Y, Xiao JC, Gu YC. Difluoromethylation and trifluoromethylation reagents derived from tetrafluoroethane β-sultone: Synthesis, reactivity and applications. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2013.11.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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12
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Harris SJ, Murdock D, Zhang Y, Oliver TAA, Grubb MP, Orr-Ewing AJ, Greetham GM, Clark IP, Towrie M, Bradforth SE, Ashfold MNR. Comparing molecular photofragmentation dynamics in the gas and liquid phases. Phys Chem Chem Phys 2013; 15:6567-82. [PMID: 23552482 DOI: 10.1039/c3cp50756d] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article explores the extent to which insights gleaned from detailed studies of molecular photodissociations in the gas phase (i.e. under isolated molecule conditions) can inform our understanding of the corresponding photofragmentation processes in solution. Systems selected for comparison include a thiophenol (p-methylthiophenol), a thioanisole (p-methylthioanisole) and phenol, in vacuum and in cyclohexane solution. UV excitation in the gas phase results in RX-Y (X = O, S; Y = H, CH3) bond fission in all cases, but over timescales that vary by ~4 orders of magnitude - all of which behaviours can be rationalised on the basis of the relevant bound and dissociative excited state potential energy surfaces (PESs) accessed by UV photoexcitation, and of the conical intersections that facilitate radiationless transfer between these PESs. Time-resolved UV pump-broadband UV/visible probe and/or UV pump-broadband IR probe studies of the corresponding systems in cyclohexane solution reveal additional processes that are unique to the condensed phase. Thus, for example, the data clearly reveal evidence of (i) vibrational relaxation of the photoexcited molecules prior to their dissociation and of the radical fragments formed upon X-Y bond fission, and (ii) geminate recombination of the RX and Y products (leading to reformation of the ground state parent and/or isomeric adducts). Nonetheless, the data also show that, in each case, the characteristics (and the timescale) of the initial bond fission process that occurs under isolated molecule conditions are barely changed by the presence of a weakly interacting solvent like cyclohexane. These condensed phase studies are then extended to an ether analogue of phenol (allyl phenyl ether), wherein UV photo-induced RO-allyl bond fission constitutes the first step of a photo-Claisen rearrangement.
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Affiliation(s)
- Stephanie J Harris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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El–Khoury PZ, Pal SK, Mereshchenko AS, Tarnovsky AN. Towards Controlling Photochemical Reactivity in Small Polyatomic Molecules in Solution: Difluorodiiodomethane. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134105031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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El-Khoury PZ, George L, Kalume A, Schapiro I, Olivucci M, Tarnovsky AN, Reid SA. Matrix isolation and computational studies of the CF2I radical. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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El-Khoury PZ, Pal SK, Mereshchenko AS, Tarnovsky AN. The formation and back isomerization of iso-H2C–Br–Br on a 100-ps time scale following 255-nm excitation of CH2Br2 in acetonitrile. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.04.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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El-Khoury PZ, George L, Kalume A, Reid SA, Ault BS, Tarnovsky AN. Characterization of iso-CF2I2 in frequency and ultrafast time domains. J Chem Phys 2010; 132:124501. [DOI: 10.1063/1.3357728] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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