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Fujii S, Sakaguchi R, Oki H, Kawahara K, Ohkubo T, Fujiyoshi S, Sambongi Y. Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'. J Struct Biol 2023; 215:108031. [PMID: 37758155 DOI: 10.1016/j.jsb.2023.108031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/05/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023]
Abstract
Two homologous cytochromes c', SBCP and SVCP, from deep-sea Shewanella benthica and Shewanella violacea respectively exhibit only nine surface amino acid substitutions, along with one at the N-terminus. Despite the small sequence difference, SBCP is thermally more stable than SVCP. Here, we examined the thermal stability of SBCP variants, each containing one of the nine substituted residues in SVCP, and found that the SBCP K87V variant was the most destabilized. We then determined the X-ray crystal structure of the SBCP K87V variant at a resolution of 2.1 Å. The variant retains a four-helix bundle structure similar to the wild-type, but notable differences are observed in the hydration structure around the mutation site. Instead of forming of the intrahelical salt bridge between Lys-87 and Asp-91 in the wild-type, a clathrate-like hydration around Val-87 through a hydrogen bond network with the nearby amino acid residues is observed. This network potentially enhances the ordering of surrounding water molecules, leading to an entropic destabilization of the protein. These results suggest that the unfavorable hydrophobic hydration environment around Val-87 and the inability to form the Asp-91-mediated salt bridge contribute to the observed difference in stability between SBCP and SVCP. These findings will be useful in future protein engineering for controlling protein stability through the manipulation of surface intrahelical salt bridges.
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Affiliation(s)
- Sotaro Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK.
| | - Riku Sakaguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroya Oki
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan; Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Kazuki Kawahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - So Fujiyoshi
- The IDEC Institute, Hiroshima University, Higashi-Hiroshima, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Higashi-Hiroshima, Japan.
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Yamaguchi Y, Nishiyama M, Kai H, Kaneko T, Kaihara K, Iribe G, Takai A, Naruse K, Morimatsu M. High hydrostatic pressure induces slow contraction in mouse cardiomyocytes. Biophys J 2022; 121:3286-3294. [PMID: 35841143 PMCID: PMC9463647 DOI: 10.1016/j.bpj.2022.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Cardiomyocytes are contractile cells that regulate heart contraction. Ca2+ flux via Ca2+ channels activates actomyosin interactions, leading to cardiomyocyte contraction, which is modulated by physical factors (e.g., stretch, shear stress, and hydrostatic pressure). We evaluated the mechanism triggering slow contractions using a high-pressure microscope to characterize changes in cell morphology and intracellular Ca2+ concentration ([Ca2+]i) in mouse cardiomyocytes exposed to high hydrostatic pressures. We found that cardiomyocytes contracted slowly without an acute transient increase in [Ca2+]i, while a myosin ATPase inhibitor interrupted pressure-induced slow contractions. Furthermore, transmission electron microscopy showed that, although the sarcomere length was shortened upon the application of 20 MPa, this pressure did not collapse cellular structures such as the sarcolemma and sarcomeres. Our results suggest that pressure-induced slow contractions in cardiomyocytes are driven by the activation of actomyosin interactions without an acute transient increase in [Ca2+]i.
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Affiliation(s)
- Yohei Yamaguchi
- Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Department of Physiology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan
| | - Hiroaki Kai
- Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Toshiyuki Kaneko
- Department of Physiology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Keiko Kaihara
- Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Gentaro Iribe
- Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Department of Physiology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Akira Takai
- Department of Physiology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Keiji Naruse
- Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masatoshi Morimatsu
- Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
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Morikawa TJ, Nishiyama M, Yoshizawa K, Fujita H, Watanabe TM. Glycine insertion modulates the fluorescence properties of Aequorea victoria green fluorescent protein and its variants in their ambient environment. Biophys Physicobiol 2021; 18:145-158. [PMID: 34178565 PMCID: PMC8214926 DOI: 10.2142/biophysico.bppb-v18.016] [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: 02/02/2021] [Accepted: 04/27/2021] [Indexed: 12/04/2022] Open
Abstract
The green fluorescent protein (GFP) derived from Pacific Ocean jellyfish is an essential tool in biology. GFP-solvent interactions can modulate the fluorescent property of GFP. We previously reported that glycine insertion is an effective mutation in the yellow variant of GFP, yellow fluorescent protein (YFP). Glycine insertion into one of the β-strands comprising the barrel structure distorts its structure, allowing water molecules to invade near the chromophore, enhancing hydrostatic pressure or solution hydrophobicity sensitivity. However, the underlying mechanism of how glycine insertion imparts environmental sensitivity to YFP has not been elucidated yet. To unveil the relationship between fluorescence and β-strand distortion, we investigated the effects of glycine insertion on the dependence of the optical properties of GFP variants named enhanced-GFP (eGFP) and its yellow (eYFP) and cyan (eCFP) variants with respect to pH, temperature, pressure, and hydrophobicity. Our results showed that the quantum yield decreased depending on the number of inserted glycines in all variants, and the dependence on pH, temperature, pressure, and hydrophobicity was altered, indicating the invasion of water molecules into the β-barrel. Peak shifts in the emission spectrum were observed in glycine-inserted eGFP, suggesting a change of the electric state in the excited chromophore. A comparative investigation of the spectral shift among variants under different conditions demonstrated that glycine insertion rearranged the hydrogen bond network between His148 and the chromophore. The present results provide important insights for further understanding the fluorescence mechanism in GFPs and suggest that glycine insertion could be a potent approach for investigating the relationship between water molecules and the intra-protein chromophore.
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Affiliation(s)
- Takamitsu J Morikawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, Higashiosaka, Osaka 577-8502, Japan
| | - Keiko Yoshizawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
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High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration. Sci Rep 2020; 10:2351. [PMID: 32047226 PMCID: PMC7012829 DOI: 10.1038/s41598-020-59172-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.
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Hata H, Nishiyama M, Kitao A. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129395. [PMID: 31302180 DOI: 10.1016/j.bbagen.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations. SCOPE OF REVIEW First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure. MAJOR CONCLUSIONS Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening. GENERAL SIGNIFICANCE MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan.
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Response of neutrophilic Shewanella violacea to acid stress: growth rate, organic acid production, and gene expression. Extremophiles 2019; 23:319-326. [DOI: 10.1007/s00792-019-01083-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
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Fujimori K, Fujii S, Lisdiana L, Wakai S, Yagi H, Sambongi Y. Differences in biochemical properties of two 5'-nucleotidases from deep- and shallow-sea Shewanella species under various harsh conditions. Biosci Biotechnol Biochem 2019; 83:1085-1093. [PMID: 30764715 DOI: 10.1080/09168451.2019.1578641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Deep-sea Shewanella violacea 5'-nucleotidase (SVNTase) activity exhibited higher NaCl tolerance than that of a shallow-sea Shewanella amazonensis homologue (SANTase), the sequence identity between them being 70.4%. Here, SVNTase exhibited higher activity than SANTase with various inorganic salts, similar to the difference in their NaCl tolerance. In contrast, SVNTase activity decreased with various organic solvents, while SANTase activity was retained with the same concentrations of the solvents. Therefore, SVNTase is more robust than SANTase with inorganic salts, but more vulnerable with organic solvents. As to protein stability, SANTase was more stable against organic solvents and heat than SVNTase, which correlated with the differences in their enzymatic activities. We also found that SANTase retained higher activity for three weeks than SVNTase did in the presence of glycerol. These findings will facilitate further application of these enzymes as appropriate biological catalysts under various harsh conditions. Abbreviations: NTase: 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase; SVNTase: Shewanella violacea 5'-nucleotidase; CD: circular dichroism.
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Affiliation(s)
- Kiko Fujimori
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Sotaro Fujii
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Lisa Lisdiana
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan.,b Department of Biology , Universitas Negeri Surabaya, Kampus Unesa Ketintang , Surabaya , Indonesia
| | - Satoshi Wakai
- c Graduate School of Science, Technology, and Innovation , Kobe University , Kobe , Japan
| | - Hisashi Yagi
- d Department of Chemistry and Biotechnology, Graduate School of Sustainability Science , Tottori University , Tottori , Japan.,e Center for Research on Green Sustainable Chemistry , Tottori University , Tottori , Japan
| | - Yoshihiro Sambongi
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
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Stability of cytochromes c′ from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure. Extremophiles 2019; 23:239-248. [DOI: 10.1007/s00792-019-01077-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/13/2019] [Indexed: 10/27/2022]
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9
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Wakai S. Biochemical and thermodynamic analyses of energy conversion in extremophiles. Biosci Biotechnol Biochem 2018; 83:49-64. [PMID: 30381012 DOI: 10.1080/09168451.2018.1538769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.
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Affiliation(s)
- Satoshi Wakai
- a Graduate School of Science, Technology and Innovation , Kobe University , Kobe , Japan
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