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Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions. J 2022. [DOI: 10.3390/j5010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thermodynamics and kinetics are two important scientific fields when studying chemical reactions. Thermodynamics characterize the nature of the material. Kinetics, mostly based on spectroscopy, have been used to determine reaction schemes and identify intermediate species. They are certainly important fields, but they are almost independent. In this review, our attempts to elucidate protein reaction kinetics and mechanisms by monitoring thermodynamic properties, including diffusion in the time domain, are described. The time resolved measurements are performed mostly using the time resolved transient grating (TG) method. The results demonstrate the usefulness and powerfulness of time resolved studies on protein reactions. The advantages and limitations of this TG method are also discussed.
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Zhang H, Sun H, Shen K, Hu J, Hu J, Jiang Z, Song F. Recent Progress with In Situ Characterization of Interfacial Structures under a Solid-Gas Atmosphere by HP-STM and AP-XPS. MATERIALS 2019; 12:ma12223674. [PMID: 31703436 PMCID: PMC6888168 DOI: 10.3390/ma12223674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 11/16/2022]
Abstract
: Surface science is an interdisciplinary field involving various subjects such as physics, chemistry, materials, biology and so on, and it plays an increasingly momentous role in both fundamental research and industrial applications. Despite the encouraging progress in characterizing surface/interface nanostructures with atomic and orbital precision under ultra-high-vacuum (UHV) conditions, investigating in situ reactions/processes occurring at the surface/interface under operando conditions becomes a crucial challenge in the field of surface catalysis and surface electrochemistry. Promoted by such pressing demands, high-pressure scanning tunneling microscopy (HP-STM) and ambient pressure X-ray photoelectron spectroscopy (AP-XPS), for example, have been designed to conduct measurements under operando conditions on the basis of conventional scanning tunneling microscopy (STM) and photoemission spectroscopy, which are proving to become powerful techniques to study various heterogeneous catalytic reactions on the surface. This report reviews the development of HP-STM and AP-XPS facilities and the application of HP-STM and AP-XPS on fine investigations of heterogeneous catalytic reactions via evolutions of both surface morphology and electronic structures, including dehydrogenation, CO oxidation on metal-based substrates, and so on. In the end, a perspective is also given regarding the combination of in situ X-ray photoelectron spectroscopy (XPS) and STM towards the identification of the structure-performance relationship.
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Affiliation(s)
- Huan Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- University of Chinese Academy of Sciences, Beijing 101000, China
| | - Haoliang Sun
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- University of Chinese Academy of Sciences, Beijing 101000, China
| | - Kongchao Shen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- University of Chinese Academy of Sciences, Beijing 101000, China
| | - Jinping Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- University of Chinese Academy of Sciences, Beijing 101000, China
| | - Jinbang Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- University of Chinese Academy of Sciences, Beijing 101000, China
| | - Zheng Jiang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Chinese Academy of Sciences, Shanghai 201204, China
| | - Fei Song
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; (H.Z.); (H.S.); (K.S.); (J.H.); (J.H.); (Z.J.)
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Chinese Academy of Sciences, Shanghai 201204, China
- Correspondence:
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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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Nakajima T, Kuroi K, Nakasone Y, Okajima K, Ikeuchi M, Tokutomi S, Terazima M. Anomalous pressure effects on the photoreaction of a light-sensor protein from Synechocystis, PixD (Slr1694), and the compressibility change of its intermediates. Phys Chem Chem Phys 2018; 18:25915-25925. [PMID: 27711633 DOI: 10.1039/c6cp05091c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
SyPixD (Slr1694) is a blue-light receptor that contains a BLUF (blue-light sensor using a flavin chromophore) domain for the function of phototaxis. The key reaction of this protein is a light-induced conformational change and subsequent dissociation reaction from the decamer to the dimer. In this study, anomalous effects of pressure on this reaction were discovered, and changes in the compressibility of its short-lived intermediates were investigated. While the absorption spectra of the dark and light states are not sensitive to pressure, the formation yield of the first intermediate decreases with pressure to about 40% at 150 MPa. Upon blue-light illumination with a sufficiently strong intensity, the transient grating signal, which represents the dissociation of the SyPixD decamer, was observed at 0.1 MPa, and the signal intensity significantly decreased with increasing pressure. This behavior shows that the dissociation of the decamer from the second intermediate state is suppressed by pressure. However, while the decamer undergoes no dissociation upon excitation of one monomer unit at 0.1 MPa, dissociation is gradually induced with increasing pressure. For solving this strange behavior, the compressibility changes of the intermediates were measured as a function of pressure at weak light intensity. Interestingly, the compressibility change was negative at low pressure, but became positive with increasing pressure. Because the compressibility is related to the volume fluctuation, this observation suggests that the driving force for this reaction is fluctuation of the protein. The relationship between the cavities at the interfaces of the monomer units and the reactivity was also discussed.
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Affiliation(s)
- Tsubasa Nakajima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Kunisato Kuroi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Koji Okajima
- Research Institute for Advanced Science and Technology, Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Satoru Tokutomi
- Research Institute for Advanced Science and Technology, Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Kuroi K, Sato F, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Time-resolved fluctuation during the photochemical reaction of a photoreceptor protein: phototropin1LOV2-linker. Phys Chem Chem Phys 2017; 18:6228-38. [PMID: 26854261 DOI: 10.1039/c5cp07472j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although the relationship between structural fluctuations and reactions is important for elucidating reaction mechanisms, experimental data describing such fluctuations of reaction intermediates are sparse. In order to investigate structural fluctuations during a protein reaction, the compressibilities of intermediate species after photoexcitation of a phot1LOV2-linker, which is a typical LOV domain protein with the C-terminal linker including the J-α helix and used recently for optogenetics, were measured in the time-domain by the transient grating and transient lens methods with a high pressure optical cell. The yield of covalent bond formation between the chromophore and a Cys residue (S state formation) relative to that at 0.1 MPa decreased very slightly with increasing pressure. The fraction of the reactive species that yields the T state (linker-unfolded state) decreased almost proportionally with pressure (0.1-200 MPa) to about 65%. Interestingly, the volume change associated with the reaction was much more pressure sensitive. By combining these data, the compressibility changes for the short lived intermediate (S state) and the final product (T state) formation were determined. The compressibility of the S state was found to increase compared with the dark (D) state, and the compressibility decreased during the transition from the S state to the T state. The compressibility change is discussed in terms of cavities inside the protein. By comparing the crystal structures of the phot1LOV2-linker at dark and light states, we concluded that the cavity volumes between the LOV domain and the linker domain increase in the S state, which explains the enhanced compressibility.
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Affiliation(s)
- Kunisato Kuroi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Francielle Sato
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Kazunori Zikihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Kuroi K, Okajima K, Ikeuchi M, Tokutomi S, Kamiyama T, Terazima M. Pressure-Sensitive Reaction Yield of the TePixD Blue-Light Sensor Protein. J Phys Chem B 2015; 119:2897-907. [DOI: 10.1021/jp511946u] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kunisato Kuroi
- Department of Chemistry, Graduate School
of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Koji Okajima
- Department of Life Sciences (Biology),
Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai,
Osaka 599-8531, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology),
Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Satoru Tokutomi
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai,
Osaka 599-8531, Japan
| | - Tadashi Kamiyama
- Department of Chemistry, School of Science and Engineering, Kinki University, Higashi-Osaka, Osaka 577-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School
of Science, Kyoto University, Kyoto 606-8502, Japan
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Abstract
Movement is a fundamental characteristic of all living things. This biogenic function is carried out by various nanometer-sized molecular machines. Molecular motor is a typical molecular machinery in which the characteristic features of proteins are integrated; these include enzymatic activity, energy conversion, molecular recognition and self-assembly. These biologically important reactions occur with the association of water molecules that surround the motors. Applied pressures can alter the intermolecular interactions between the motors and water. In this chapter we describe the development of a high-pressure microscope and a new motility assay that enables the visualization of the motility of molecular motors under conditions of high-pressure. Our results demonstrate that applied pressure dynamically changes the motility of molecular motors such as kinesin, F1-ATPase and bacterial flagellar motors.
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Affiliation(s)
- Masayoshi Nishiyama
- The Hakubi Center for Advanced Research/Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan,
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Abstract
Knowledge of the dynamical behavior of proteins, and in particular their conformational fluctuations, is essential to understanding the mechanisms underlying their reactions. Here, transient enhancement of the isothermal partial molar compressibility, which is directly related to the conformational fluctuation, during a chemical reaction of a blue light sensor protein from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) was investigated in a time-resolved manner. The UV-Vis absorption spectrum of TePixD did not change with the application of high pressure. Conversely, the transient grating signal intensities representing the volume change depended significantly on the pressure. This result implies that the compressibility changes during the reaction. From the pressure dependence of the amplitude, the compressibility change of two short-lived intermediate (I1 and I2) states were determined to be +(5.6 ± 0.6) × 10(-2) cm(3) ⋅ mol(-1) ⋅ MPa(-1) for I1 and +(6.6 ± 0.7) × 10(-2) cm(3) ⋅ mol(-1) ⋅ MPa(-1) for I2. This result showed that the structural fluctuation of intermediates was enhanced during the reaction. To clarify the relationship between the fluctuation and the reaction, the compressibility of multiply excited TePixD was investigated. The isothermal compressibility of I1 and I2 intermediates of TePixD showed a monotonic decrease with increasing excitation laser power, and this tendency correlated with the reactivity of the protein. This result indicates that the TePixD decamer cannot react when its structural fluctuation is small. We concluded that the enhanced compressibility is an important factor for triggering the reaction of TePixD. To our knowledge, this is the first report showing enhanced fluctuations of intermediate species during a protein reaction, supporting the importance of fluctuations.
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Nishiyama M, Kimura Y, Nishiyama Y, Terazima M. Pressure-induced changes in the structure and function of the kinesin-microtubule complex. Biophys J 2009; 96:1142-50. [PMID: 19186149 PMCID: PMC2716646 DOI: 10.1016/j.bpj.2008.10.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 10/21/2008] [Indexed: 11/26/2022] Open
Abstract
Kinesin-1 is an ATP-driven molecular motor that "walks" along a microtubule by working two heads in a "hand-over-hand" fashion. The stepping motion is well-coordinated by intermolecular interactions between the kinesin head and microtubule, and is sensitively changed by applied forces. We demonstrate that hydrostatic pressure works as an inhibitory action on kinesin motility. We developed a high-pressure microscope that enables the application of hydrostatic pressures of up to 200 MPa (2000 bar). Under high-pressure conditions, taxol-stabilized microtubules were shortened from both ends at the same speed. The sliding velocity of kinesin motors was reversibly changed by pressure, and reached half-maximal value at approximately 100 MPa. The pressure-velocity relationship was very close to the force-velocity relationship of single kinesin molecules, suggesting a similar inhibitory mechanism on kinesin motility. Further analysis showed that the pressure mainly affects the stepping motion, but not the ATP binding reaction. The application of pressure is thought to enhance the structural fluctuation and/or association of water molecules with the exposed regions of the kinesin head and microtubule. These pressure-induced effects could prevent kinesin motors from completing the stepping motion.
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Affiliation(s)
- Masayoshi Nishiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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