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Sugita M, Hirata F. Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis. J Comput Chem 2023; 44:1031-1039. [PMID: 36594509 DOI: 10.1002/jcc.27062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 01/04/2023]
Abstract
A new theoretical method, referred to as Generalized Langevin Mode Analysis (GLMA), is proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The method combines the two theories in the statistical mechanics, or the Generalized Langevin theory and the RISM/3D-RISM theory, to calculate the second derivative, or the Hessian matrix, of the free energy surface of a biomolecule in aqueous solution, which consists of the intramolecular interaction among atoms in the biomolecule and the solvation free energy. The method is applied to calculate the wave-number spectrum of an alanine dipeptide in water for which the optical heterodyne-detected Raman-induced spectroscopy (RIKES) spectrum is available to compare with. The theoretical analysis reproduced the main features of the experimental spectrum with respect to the peak positions of the four bands around ~90 cm-1 , ~240 cm-1 , ~370 cm-1 , and 400 cm-1 , observed in the experimental spectrum, in spite that the physics involved in the two spectrum was not exactly the same: the experimental spectrum includes the contributions from the dipeptide and the water molecules interacting with the solute, while the theoretical one is just concerned with the solute molecule, influenced by solvation. Two major discrepancies between the theoretical and experimental spectra, one in the band intensity around ~100 cm-1 , and the other in the peak positions around ~370 cm-1 , are discussed in terms of the fluctuation mode of water molecules interacting with the dipeptide, which is not taken explicitly into account in the theoretical analysis.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan
| | - Fumio Hirata
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan
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Blue Light Sensing BlsA-Mediated Modulation of Meropenem Resistance and Biofilm Formation in Acinetobacter baumannii. mSystems 2023; 8:e0089722. [PMID: 36622157 PMCID: PMC9948694 DOI: 10.1128/msystems.00897-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The presence or absence of BlsA, a protein with a blue light-sensing flavin domain in the genomes of Acinetobacter species has aroused curiosity about its roles in the regulation of bacterial lifestyle under light. Genomic and transcriptomic analyses revealed the loss of BlsA in several multidrug-resistant (MDR) A. baumannii strains as well as the light-mediated induction of blsA, along with a possible BlsA-interacting partner BipA. Their direct in vivo interactions were verified using a bacterial two-hybrid system. The results demonstrated that the C-terminal region of BipA could bind to the C-terminal residues of BlsA under blue light at 23°C but not at 37°C. Genetic manipulations of blsA and bipA revealed that the coexistence of BlsA and BipA was required to induce the light-dependent expression of ompA in A. baumannii ATCC 17978 at 23°C. The same phenomenon occurred in the BlsA-deficient MDR strain in our functional complementation assay; however, the underlying molecular mechanism remains poorly understood. BlsA-modulated amounts of OmpA, the most abundant porin, in the outer membrane affected the membrane integrity and permeability of small molecules. Dark conditions or the deletion of ompA made the membrane more permeable to lipophilic ethidium bromide (EtBr) but not to meropenem. Interestingly, light illumination and low temperature conditions made the cells more sensitive to meropenem; however, this bactericidal effect was not noted in the blsA mutant or in the BlsA-deficient MDR strains. Light-mediated cell death and the reduction of biofilm formation at 23°C were abolished in the blsA mutant strain, suggesting multifaceted roles of BlsA in A. baumannii strains. IMPORTANCE Little is known about the functional roles of BlsA and its interacting partners in Acinetobacter species. Intriguingly, no BlsA homolog was found in several clinical isolates, suggesting that BlsA was not required inside the host because of the lack of blue light and the warm temperature conditions. As many chromophore-harboring proteins interact with various partners to control light-dependent cellular behaviors, the maintenance of blsA in the genomes of many Acinetobacter species during their evolution may be beneficial when fluctuations occur in two important environmental factors: light and temperature. Our study is the first to report the novel protein partner of BlsA, namely, BipA, and its contribution to multiple phenotypic changes, including meropenem resistance and biofilm formation. Rapid physiological acclimation to changing light or temperature conditions may be possible in the presence of the light-sensing BlsA protein, which may have more interacting partners than expected.
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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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Time-resolved detection of association/dissociation reactions and conformation changes in photosensor proteins for application in optogenetics. Biophys Rev 2021; 13:1053-1059. [DOI: 10.1007/s12551-021-00868-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 11/27/2022] Open
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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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Terazima M. Spectrally Silent Protein Reaction Dynamics Revealed by Time-Resolved Thermodynamics and Diffusion Techniques. Acc Chem Res 2021; 54:2238-2248. [PMID: 33886281 DOI: 10.1021/acs.accounts.1c00113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biological functions essentially consist of a series of chemical reactions, including intermolecular interactions, and also involve the cooperation of a number of biological molecules performing these reactions. To understand this function at the molecular level, all steps of the reactions must be elucidated. However, since the biosystems including the surrounding environment are notably large, the reactions have to be elucidated from several different approaches. A variety of techniques have been developed to obtain structural information, and the knowledge of the three-dimensional structure of biomolecules has increased dramatically. Contrarily, the current information on reaction dynamics, which is essential for understanding reactions, is still not enough. Although frequently used techniques, such as spectroscopy, have revealed several important processes of reactions, there are various hidden dynamics that are not detected by these methods (silent dynamics). For example, although water molecules are essential for bioreactions, dynamics of the protein-water interaction are very difficult to trace and spectrally silent. Transient association/dissociations of proteins with partner proteins are difficult to observe. Another important property to understand the reaction of proteins is fluctuations, which are random movements that do not change the average structure and energy. The importance of fluctuations has been pointed out in order to explain enzymatic activity; however, it is extremely difficult to detect changes in fluctuation during a reaction. In this Account, unique time-resolved methods, time-resolved thermodynamics, and time-resolved diffusion methods, both of which are able to detect silent dynamics in solution at physiological temperature, are described.Thermodynamic properties are important for characterizing materials, in particular, macromolecules such as biomolecules. Therefore, the data available regarding these properties, for several stable proteins, is abundant. However, it is almost impossible to characterize short-lived intermediate species in irreversible reactions using traditional thermodynamic techniques. Similarly, although the translational diffusion coefficient is a useful property to determine the protein size and intermolecular interactions, there have been no reports revealing reaction dynamics. The transient grating (TG) method enables us to measure these quantities in a time-resolved manner for a variety of irreversible reactions. With this method, it is now possible to study biomolecule reactions from the viewpoint of thermodynamic properties and diffusion, and to elucidate reaction dynamics that cannot be detected by other spectroscopic methods.Here, the principles of the methodologies used, their characteristic advantages, and their applications to protein reactions are described. The TG measurements of octopus rhodopsin revealed a spectrally hidden intermediate and determined an energetic profile along the reaction coordinate. This emphasizes that the measurement in solution, not for trapped intermediates, is important to characterize the reaction intermediates. The application of these methods to a blue light sensor PixD revealed many spectrally silent dynamics as well as the importance of fluctuation for the reaction. As an example of the time-resolved heat capacity change and transient thermal expansion measurements, the reaction of PYP was briefly described. The reaction scheme of another blue light sensor protein, phototropins, and a spectrally silent DNA binding process of EL222 were fully elucidated by the time-resolved diffusion method.
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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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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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Kuroi K, Kamijo M, Ueki M, Niwa Y, Hiramatsu H, Nakabayashi T. Time-resolved FTIR study on the structural switching of human galectin-1 by light-induced disulfide bond formation. Phys Chem Chem Phys 2020; 22:1137-1144. [DOI: 10.1039/c9cp04881b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The light-induced disulfide bond technique, which we have previously developed, has enabled the time-resolved measurement of the disulfide-induced conformational switching of the lectin protein human galectin-1.
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Affiliation(s)
- Kunisato Kuroi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
- Faculty of Pharmaceutical Sciences
| | - Mana Kamijo
- Faculty of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Mutsuki Ueki
- Faculty of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yusuke Niwa
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao Tung University
- Hsinchu 30010
- Taiwan
- Center for Emergent Functional Matter Science
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
- Faculty of Pharmaceutical Sciences
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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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10
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Bencivenga F, Mincigrucci R, Capotondi F, Foglia L, Naumenko D, Maznev AA, Pedersoli E, Simoncig A, Caporaletti F, Chiloyan V, Cucini R, Dallari F, Duncan RA, Frazer TD, Gaio G, Gessini A, Giannessi L, Huberman S, Kapteyn H, Knobloch J, Kurdi G, Mahne N, Manfredda M, Martinelli A, Murnane M, Principi E, Raimondi L, Spampinati S, Spezzani C, Trovò M, Zangrando M, Chen G, Monaco G, Nelson KA, Masciovecchio C. Nanoscale transient gratings excited and probed by extreme ultraviolet femtosecond pulses. SCIENCE ADVANCES 2019; 5:eaaw5805. [PMID: 31360768 PMCID: PMC6660206 DOI: 10.1126/sciadv.aaw5805] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/20/2019] [Indexed: 05/27/2023]
Abstract
Advances in developing ultrafast coherent sources operating at extreme ultraviolet (EUV) and x-ray wavelengths allow the extension of nonlinear optical techniques to shorter wavelengths. Here, we describe EUV transient grating spectroscopy, in which two crossed femtosecond EUV pulses produce spatially periodic nanoscale excitations in the sample and their dynamics is probed via diffraction of a third time-delayed EUV pulse. The use of radiation with wavelengths down to 13.3 nm allowed us to produce transient gratings with periods as short as 28 nm and observe thermal and coherent phonon dynamics in crystalline silicon and amorphous silicon nitride. This approach allows measurements of thermal transport on the ~10-nm scale, where the two samples show different heat transport regimes, and can be applied to study other phenomena showing nontrivial behaviors at the nanoscale, such as structural relaxations in complex liquids and ultrafast magnetic dynamics.
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Affiliation(s)
- F. Bencivenga
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - R. Mincigrucci
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - F. Capotondi
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - L. Foglia
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - D. Naumenko
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - A. A. Maznev
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - E. Pedersoli
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - A. Simoncig
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - F. Caporaletti
- Department of Physics, University of Trento, Via Sommarive 14, Povo (TN), Italy
| | - V. Chiloyan
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - R. Cucini
- IOM-CNR, Strada Statale 14, km 163.5, in Area Science Park, I-34012 Basovizza (TS), Italy
| | - F. Dallari
- Department of Physics, University of Trento, Via Sommarive 14, Povo (TN), Italy
| | - R. A. Duncan
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - T. D. Frazer
- JILA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
| | - G. Gaio
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - A. Gessini
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - L. Giannessi
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - S. Huberman
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - H. Kapteyn
- JILA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
| | - J. Knobloch
- JILA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
| | - G. Kurdi
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - N. Mahne
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
- IOM-CNR, Strada Statale 14, km 163.5, in Area Science Park, I-34012 Basovizza (TS), Italy
| | - M. Manfredda
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - A. Martinelli
- Department of Physics, University of Trento, Via Sommarive 14, Povo (TN), Italy
| | - M. Murnane
- JILA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
| | - E. Principi
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - L. Raimondi
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - S. Spampinati
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - C. Spezzani
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - M. Trovò
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
| | - M. Zangrando
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
- IOM-CNR, Strada Statale 14, km 163.5, in Area Science Park, I-34012 Basovizza (TS), Italy
| | - G. Chen
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - G. Monaco
- Department of Physics, University of Trento, Via Sommarive 14, Povo (TN), Italy
| | - K. A. Nelson
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C. Masciovecchio
- Elettra Sincrotrone Trieste S.C.p.A., Strada Statale 14, km 163.5, 34149 Basovizza (TS), Italy
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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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12
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Iwata K, Terazima M, Masuhara H. Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation. Biochim Biophys Acta Gen Subj 2017; 1862:335-357. [PMID: 29108958 DOI: 10.1016/j.bbagen.2017.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 10/18/2022]
Abstract
Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Koichi Iwata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroshi Masuhara
- Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsueh Rd., Hsinchu 30010, Taiwan.
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Hayakawa D, Yamaotsu N, Nakagome I, Ozawa SI, Yoshida T, Hirono S. In silico analyses of the effects of a point mutation and a pharmacological chaperone on the thermal fluctuation of phenylalanine hydroxylase. Biophys Chem 2017; 228:47-54. [DOI: 10.1016/j.bpc.2017.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
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14
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Shibuta S, Imamura H, Nishikawa K, Morita T. Fluctuational parameters based on the Bhatia–Thornton theory for supercritical solutions: Application to a supercritical aqueous solution of n -pentane. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Park SY, Tame JRH. Seeing the light with BLUF proteins. Biophys Rev 2017; 9:169-176. [PMID: 28510088 DOI: 10.1007/s12551-017-0258-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/05/2017] [Indexed: 10/19/2022] Open
Abstract
First described about 15 years ago, BLUF (Blue Light Using Flavin) domains are light-triggered switches that control enzyme activity or gene expression in response to blue light, remaining activated for seconds or even minutes after stimulation. The conserved, ferredoxin-like fold holds a flavin chromophore that captures the light and somehow triggers downstream events. BLUF proteins are found in both prokaryotes and eukaryotes and have a variety of architectures and oligomeric forms, but the BLUF domain itself seems to have a well-preserved structure and mechanism that have been the focus of intense study for a number of years. Crystallographic and NMR structures of BLUF domains have been solved, but the conflicting models have led to considerable debate about the atomic details of photo-activation. Advanced spectroscopic and computational methods have been used to analyse the early events after photon absorption, but these too have led to widely differing conclusions. New structural models are improving our understanding of the details of the mechanism and may lead to novel tailor-made tools for optogenetics.
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Affiliation(s)
- Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
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16
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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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17
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Kondoh M, Terazima M. Conformational and Intermolecular Interaction Dynamics of Photolyase/Cryptochrome Proteins Monitored by the Time-Resolved Diffusion Technique. Photochem Photobiol 2017; 93:15-25. [DOI: 10.1111/php.12681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Masato Kondoh
- Department of Chemistry; Graduate School of Pure and Applied Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - Masahide Terazima
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku, Kyoto Japan
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18
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Vega-Flick A, Eliason JK, Maznev AA, Khanolkar A, Abi Ghanem M, Boechler N, Alvarado-Gil JJ, Nelson KA. Laser-induced transient grating setup with continuously tunable period. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:123101. [PMID: 26724000 DOI: 10.1063/1.4936767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a modification of the laser-induced transient grating setup enabling continuous tuning of the transient grating period. The fine control of the period is accomplished by varying the angle of the diffraction grating used to split excitation and probe beams. The setup has been tested by measuring dispersion of bulk and surface acoustic waves in both transmission and reflection geometries. The presented modification is fully compatible with optical heterodyne detection and can be easily implemented in any transient grating setup.
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Affiliation(s)
- A Vega-Flick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - J K Eliason
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - A A Maznev
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - A Khanolkar
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - M Abi Ghanem
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - N Boechler
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - J J Alvarado-Gil
- Applied Physics Department, CINVESTAV-Unidad Mérida, Carretera Antigua a Progreso Km 6, Cordemex, Mérida, Yucatán 97310 Mexico
| | - K A Nelson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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19
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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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