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Zhu X, Xu Y, Zhao C, Jia C, Guo X. Recent Advances in Photochemical Reactions on Single-Molecule Electrical Platforms. Macromol Rapid Commun 2022; 43:e2200017. [PMID: 35150177 DOI: 10.1002/marc.202200017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/05/2022] [Indexed: 11/08/2022]
Abstract
The photochemical reaction is a very important type of chemical reactions. Visualizing and controlling photo-mediated reactions is a long-standing goal and challenge. In this regard, single-molecule electrical detection with label-free, real-time and in situ characteristics has unique advantages in monitoring the dynamic process of photoreactions at the single-molecule level. In this Review, we provide a valuable summary of the latest process of single-molecule photochemical reactions based on single-molecule electrical platforms. The single-molecule electrical detection platforms for monitoring photoreactions are displayed, including their fundamental principles, construction methods and practical applications. The single-molecule studies of two different types of light-mediated reactions are summarized as below: i) photo-induced reactions, including reversible cyclization, conformational isomerization and other photo-related reactions; ii) plasmon-mediated photoreactions, including reaction mechanisms and concrete examples, such as plasmon-induced photolysis of S-S/O-O bonds and tautomerization of porphycene. In addition, the prospects for future research directions and challenges in this field are also discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xin Zhu
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, P. R. China.,Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
| | - Yanxia Xu
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, P. R. China
| | - Cong Zhao
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin, 300350, P. R. China.,Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing, 100871, P. R. China
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Nakasone Y, Terazima M. A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules. Front Genet 2021; 12:691010. [PMID: 34276791 PMCID: PMC8278059 DOI: 10.3389/fgene.2021.691010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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Affiliation(s)
- Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Terazima M. Studies of photo-induced protein reactions by spectrally silent reaction dynamics detection methods: applications to the photoreaction of the LOV2 domain of phototropin from Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1093-105. [PMID: 21211575 DOI: 10.1016/j.bbapap.2010.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 12/06/2010] [Accepted: 12/22/2010] [Indexed: 01/28/2023]
Abstract
Biological function involves a series of chemical reactions of biological molecules, and during these reactions, there are numerous spectrally silent dynamic events that cannot be monitored by absorption or emission spectroscopic techniques. Such spectrally silent dynamics include changes in conformation, intermolecular interactions (hydrogen bonding, hydrophobic interactions), inter-protein interactions (oligomer formation, dissociation reactions) and conformational fluctuations. These events might be associated with biological function. To understand the molecular mechanisms of reactions, time-resolved detection of such dynamics is essential. Recently, it has been shown that time-resolved detection of the refractive index is a powerful tool for measuring dynamic events. This technique is complementary to optical absorption detection methods and the signal contains many unique properties, which are difficult to obtain by other methods. The advantages and methods for signal analyses are described in detail in this review. A typical example of an application of time-resolved refractive index change detection is given in the second part: The photoreaction of the LOV2 domain of a blue light photoreceptor from Arabidopsis Thaliana (phototropin). This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Losi A, Gensch T, van der Horst MA, Hellingwerf KJ, Braslavsky SE. Hydrogen-bond network probed by time-resolved optoacoustic spectroscopy: photoactive yellow protein and the effect of E46Q and E46A mutations. Phys Chem Chem Phys 2009; 7:2229-36. [PMID: 19791418 DOI: 10.1039/b419079c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enthalpy and structural volume changes (delta Hi and delta Vi) produced upon photoinduced formation and decay of the red-shifted intermediate (pR = I1) in the photoactive yellow protein (WT-PYP) from Halorhodospira halophila and the mutated E46Q-PYP and E46A-PYP, were determined by laser-induced optoacoustic spectroscopy (LIOAS) using the two-temperatures method, at pH 8.5. These mutations alter the hydrogen bond between the phenolate oxygen of the chromophore and the residue at position 46. Hydrogen bonding is still possible in E46Q-PYP via the delta-NH2 group of glutamine, whereas it is no longer possible with the methyl group of alanine in E46A-PYP. In all three proteins, pR decays within hundreds of ns to micros into the next intermediate, pR'. The delta H values for the formation of pR (delta H pR) and for its decay into pR'(delta H pR-->pR') are negligibly affected by the E46Q and the E46A substitution. In all three proteins the large delta H pR value drives the photocycle. Whereas delta V pR is a similar contraction of ca. 15 ml mol(-1) for E46Q-PYP and WT-PYP, attributed to strengthening the hydrogen bond network (between 4 and 5 hydrogen bonds) inside the protein chromophore cavity, an expansion is observed for E46A-PYP, indicating just an enlargement of the chromophore cavity upon chromophore isomerization. The results are discussed in the light of the recent time-resolved room temperature, crystallographic studies with WT-PYP and E46Q-PYP. Formation of pR' is somewhat slower for E46Q-PYP and much slower for E46A-PYP. The structural volume change for this transition, delta V pR-->pR', is relatively small and positive for WT-PYP, slightly larger for E46Q-PYP, and definitely larger for the hydrogen-bond lacking E46A-PYP. This indicates a larger entropic change for this transition in E46A-PYP, reflected in the large pre-exponential factor for the pR to pR' decay rate constant determined in the 5-30 degrees C temperature range. This decay also shows an activation entropy that compensates the larger activation energy in E46A-PYP, as compared to the values for WT-PYP and E46Q-PYP.
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Affiliation(s)
- Aba Losi
- Max-Planck-Institut für Bioanorganische Chemie (formerly Strahlenchemie), Postfach 101365, D-45413 Mülheim an der Ruhr, Germany
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Kondoh M, Baden N, Terazima M. Photochemical reaction and diffusion of caged calcium studied by the transient grating. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Hazra P, Inoue K, Laan W, Hellingwerf KJ, Terazima M. Energetics and role of the hydrophobic interaction during photoreaction of the BLUF domain of AppA. J Phys Chem B 2008; 112:1494-501. [PMID: 18189382 DOI: 10.1021/jp0767314] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recently developed method for time-resolved thermodynamic measurements was used to study the photochemical reaction(s) of the BLUF domain of AppA (AppA-BLUF), which has a dimeric form in the ground state, in terms of the energetics and heat capacity changes (DeltaC(p)) in different time domains. The enthalpy change (DeltaH) of the first intermediate that forms within 1 ns after photoexcitation was 38 (+/-8) kJ mol(-1) at 298 K. The heat capacity change (DeltaC(p)) upon formation of this intermediate was positive [1.4 (+/-0.3) kJ mol(-1) K(-1)]. This positive DeltaC(p) suggests that the hydrophobic surface area of AppA-BLUF exposed to the bulk solvent increased. After this initial transition, a dimerization reaction with another ground-state dimer (i.e., tetramer formation) takes place. Upon this reaction, the energy was stabilized to 26 (+/-6) kJ mol(-1) at 298 K. Interestingly, the dimer formation was accompanied by a larger but negative DeltaC(p) [-6.0 (+/-1) kJ mol(-1) K(-1)]. This negative DeltaC(p) might indicate buried hydrophobic residues at the interface of the dimer and/or the existence of trapped water at the interface. We suggest that hydrophobic interactions are the main driving force for the formation of the dimer upon photoactivation of AppA-BLUF.
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Affiliation(s)
- Partha Hazra
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Baden N, Hirota S, Takabe T, Funasaki N, Terazima M. Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time domain. J Chem Phys 2007; 127:175103. [PMID: 17994853 DOI: 10.1063/1.2780860] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- N Baden
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Imai T, Kovalenko A, Hirata F. Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory. J Phys Chem B 2007; 109:6658-65. [PMID: 16851748 DOI: 10.1021/jp045667c] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Khan JS, Imamoto Y, Kataoka M, Tokunaga F, Terazima M. Time-Resolved Thermodynamics: Heat Capacity Change of Transient Species during Photoreaction of PYP. J Am Chem Soc 2005; 128:1002-8. [PMID: 16417392 DOI: 10.1021/ja055584p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heat capacity changes of short-lived transient species in different time ranges were measured for the first time by using the thermal component of the transient grating and transient lens signals at various temperatures. This method was applied to the transient intermediates of Photoactive Yellow Protein (PYP). The temperature dependence of the enthalpy change shows that the heat capacity of the short-lived intermediate pR2 (also called I1 or PYP(L)) species is the same as that of the ground state (pG) species within our experimental accuracy, whereas that of the long-lived intermediate pB (I2 or PYP(M)) is much larger (2.7 +/- 0.4 kJ/mol K) than that of pG. The larger heat capacity is interpreted in terms of the conformational change of the pB species such as melted conformation and/or exposure of the nonpolar residues to the aqueous phase. This technique can be used for photochemical reactions in general to investigate the conformational change and the hydrophobic interaction in a time domain.
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Affiliation(s)
- Javaid Shahbaz Khan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Terazima M. Diffusion coefficients as a monitor of reaction kinetics of biological molecules. Phys Chem Chem Phys 2005; 8:545-57. [PMID: 16482296 DOI: 10.1039/b513509e] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For revealing spectrally silent dynamics in chemical reactions, a new method, the time-dependent diffusion coefficient, is presented. Principles and typical examples of this method, in particular applications to biologically related reactions, are reviewed. The pulsed laser induced transient grating signal of the photo-decomposition reaction of caged ATP showed that the diffusion coefficient increases gradually with time reflecting the molecular size decrease by the dissociation. Hence, this rate should be a direct measurement of the photo-dissociation rate of ATP from the caged state. In an application to a protein folding reaction, the time-development of the diffusion coefficient was observed during the folding reaction. This time dependence was interpreted in terms of the intermolecular interaction change; i.e., conversion from the intermolecular hydrogen bonding to intramolecular one. It was found that the change of the hydrogen bonding network occurred by the two state manner in entire refolding process of cytochrome c. The unique feature of this time-dependent diffusion coefficient method is discussed.
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Affiliation(s)
- Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Japan
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