1
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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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2
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Colloc'h N, Dhaussy AC, Girard E. Exploring the structural dynamics of proteins by pressure perturbation using macromolecular crystallography. Methods Enzymol 2023; 688:349-381. [PMID: 37748831 DOI: 10.1016/bs.mie.2023.06.007] [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] [Indexed: 09/27/2023]
Abstract
High pressure is a convenient thermodynamic parameter to probe the dynamics of proteins as it is intimately related to volume which is essential for protein function. To be biologically active, a protein fluctuates between different substates. Pressure perturbation can promote some hidden substates by modifying the population between them. High pressure macromolecular crystallography (HPMX) is a perfect tool to capture and to characterize such substates at a molecular level providing new insights on protein dynamics. The present chapter describes the use of the diamond anvil cell to perform HPMX experiments. It also provides tips on sample preparation and optimal data collection as well as on efficient analysis of the resulting high-pressure structures.
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Affiliation(s)
- Nathalie Colloc'h
- Imagerie et stratégies thérapeutiques pour les cancers et tissus cérébraux (ISTCT), CNRS Université de Caen Normandie, Centre Cyceron, Caen, France
| | | | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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3
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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4
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Nagaoka S, Sugiyama N, Yatsunami R, Nakamura S. Characterization of 3-isopropylmalate dehydrogenase from extremely halophilic archaeon Haloarcula japonica. Biosci Biotechnol Biochem 2021; 85:1986-1994. [PMID: 34215877 DOI: 10.1093/bbb/zbab122] [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: 04/11/2021] [Accepted: 06/21/2021] [Indexed: 11/12/2022]
Abstract
3-Isopropylmalate dehydrogenase (IPMDH) catalyzes oxidative decarboxylation of (2R, 3S)-3-isopropylmalate to 2-oxoisocaproate in leucine biosynthesis. In this study, recombinant IPMDH (HjIPMDH) from an extremely halophilic archaeon, Haloarcula japonica TR-1, was characterized. Activity of HjIPMDH increased as KCl concentration increased, and the maximum activity was observed at 3.0 m KCl. Analytical ultracentrifugation revealed that HjIPMDH formed a homotetramer at high KCl concentrations, and it dissociated to a monomer at low KCl concentrations. Additionally, HjIPMDH was thermally stabilized by higher KCl concentrations. This is the first report on haloarchaeal IPMDH.
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Affiliation(s)
- Shintaro Nagaoka
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Noriko Sugiyama
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Rie Yatsunami
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.,National Institute of Technology (KOSEN), Numazu College, Numazu, Shizuoka, Japan
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5
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Glutamate optimizes enzymatic activity under high hydrostatic pressure in Desulfovibrio species: effects on the ubiquitous thioredoxin system. Extremophiles 2021; 25:385-392. [PMID: 34196828 DOI: 10.1007/s00792-021-01236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
In piezophilic microorganisms, enzymes are optimized to perform under high hydrostatic pressure. The two major reported mechanisms responsible for such adaptation in bacterial species are changes in amino acids in the protein structure, favoring their activity and stability under high-pressure conditions, and the possible accumulation of micromolecular co-solutes in the cytoplasm. Recently, the accumulation of glutamate in the cytoplasm of piezophilic Desulfovibrio species has been reported under high-pressure growth conditions. In this study, analysis of the effect of glutamate on the enzymatic activity of the thioredoxin reductase/thioredoxin enzymatic complex of either a piezosensitive or a piezophilic microorganism confirms its role as a protective co-solute. Analysis of the thioredoxin structures suggests an adaptation both to the presence of glutamate and to high hydrostatic pressure in the enzyme from the piezophilic strain. Indeed, the presence of large surface pockets could counterbalance the overall compression that occurs at high hydrostatic pressure to maintain enzymatic activity. A lower isoelectric point and a greater dipolar moment than that of thioredoxin from the piezosensitive strain would allow the protein from the piezophilic strain to compensate for the presence of the charged amino acid glutamate to interact with its partner.
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6
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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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7
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Gerringer ME, Yancey PH, Tikhonova OV, Vavilov NE, Zgoda VG, Davydov DR. Pressure tolerance of deep-sea enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes. FEBS J 2020; 287:5394-5410. [PMID: 32250538 PMCID: PMC7818408 DOI: 10.1111/febs.15317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 03/15/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
We explore the principles of pressure tolerance in enzymes of deep-sea fishes using lactate dehydrogenases (LDH) as a case study. We compared the effects of pressure on the activities of LDH from hadal snailfishes Notoliparis kermadecensis and Pseudoliparis swirei with those from a shallow-adapted Liparis florae and an abyssal grenadier Coryphaenoides armatus. We then quantified the LDH content in muscle homogenates using mass-spectrometric determination of the LDH-specific conserved peptide LNLVQR. Existing theory suggests that adaptation to high pressure requires a decrease in volume changes in enzymatic catalysis. Accordingly, evolved pressure tolerance must be accompanied with an important reduction in the volume change associated with pressure-promoted alteration of enzymatic activity ( Δ V PP ∘ ). Our results suggest an important revision to this paradigm. Here, we describe an opposite effect of pressure adaptation-a substantial increase in the absolute value of Δ V PP ∘ in deep-living species compared to shallow-water counterparts. With this change, the enzyme activities in abyssal and hadal species do not substantially decrease their activity with pressure increasing up to 1-2 kbar, well beyond full-ocean depth pressures. In contrast, the activity of the enzyme from the tidepool snailfish, L. florae, decreases nearly linearly from 1 to 2500 bar. The increased tolerance of LDH activity to pressure comes at the expense of decreased catalytic efficiency, which is compensated with increased enzyme contents in high-pressure-adapted species. The newly discovered strategy is presumably used when the enzyme mechanism involves the formation of potentially unstable excited transient states associated with substantial changes in enzyme-solvent interactions.
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8
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Okai M, Onoue C, Tsuda R, Ishigami C, Yoshida-Mishima C, Urano N, Kato C, Ishida M. Q301P mutant of Vibrio PR protease affects activities under low-temperature and high-pressure conditions. J Biosci Bioeng 2020; 130:341-346. [PMID: 32611521 DOI: 10.1016/j.jbiosc.2020.05.011] [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: 03/30/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 10/24/2022]
Abstract
We characterized a protease of the M4 family from the cold-adapted Vibrio sp. Pr21 that was isolated from seawater at 320-m deep in Sagami Bay, Japan, and named it as PR protease based on the strain name Pr21. The PR protease had activities at 10-60 °C and 0.1-350 MPa, with the optimal temperature and pressure at 40 °C and 250 MPa. The mutant 10C9 (Q301P) obtained by error-prone PCR had higher activities than the wild-type enzyme at 10-60 °C, and the Q301P mutation contributed to the increase of the activity. The specific activity value of 10C9 was also higher than that of the wild-type enzyme at 0.1-200 MPa, but the specific activity ratios (1.28-1.59) of 10C9/wild-type enzyme at 50-200 MPa at 30 °C were smaller than those at 10-60 °C (1.73-4.39) at 0.1 MPa. The catalytic efficiency value of 10C9 was lower than that of the wild-type enzyme at 200 MPa. The homology models of PR protease suggested that the side chain of Q301 was hydrogen-bonded with the carbonyl oxygen atom of the main chain of N234 in the wild-type enzyme, and P301 had no contact with N234 in 10C9. The break of the hydrogen bond in 10C9 might strengthen the increase of the flexibility of the β-sheet near the substrate binding pocket under high-temperature conditions, whereas the flexibility of the β-sheet in 10C9 might be moderately increased compared to that in the wild-type enzyme under high-pressure conditions.
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Affiliation(s)
- Masahiko Okai
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chiori Onoue
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Ryo Tsuda
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chihiro Ishigami
- School of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chie Yoshida-Mishima
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Naoto Urano
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Masami Ishida
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
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9
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Ugur I, Schroft M, Marion A, Glaser M, Antes I. Predicting the bioactive conformations of macrocycles: a molecular dynamics-based docking procedure with DynaDock. J Mol Model 2019; 25:197. [PMID: 31222506 DOI: 10.1007/s00894-019-4077-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
Macrocyclic compounds are of growing interest as a new class of therapeutics, especially as inhibitors binding to protein-protein interfaces. As molecular modeling is a well-established complimentary tool in modern drug design, the number of attempts to develop reliable docking strategies and algorithms to accurately predict the binding mode of macrocycles is rising continuously. Standard molecular docking approaches need to be adapted to this application, as a comprehensive yet efficient sampling of all ring conformations of the macrocycle is necessary. To overcome this issue, we designed a molecular dynamics-based docking protocol for macrocycles, in which the challenging sampling step is addressed by conventional molecular dynamics (750 ns) simulations performed at moderately high temperature (370 K). Consecutive flexible docking with the DynaDock approach based on multiple, pre-sampled ring conformations yields highly accurate poses with ligand RMSD values lower than 1.8 Å. We further investigated the value of molecular dynamics-based complex stability estimations for pose selection and discuss its applicability in combination with standard binding free energy estimations for assessing the quality of poses in future blind docking studies.
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Affiliation(s)
- Ilke Ugur
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Maja Schroft
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Antoine Marion
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Manuel Glaser
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Iris Antes
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany.
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10
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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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11
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Li XG, Zhang WJ, Xiao X, Jian HH, Jiang T, Tang HZ, Qi XQ, Wu LF. Pressure-Regulated Gene Expression and Enzymatic Activity of the Two Periplasmic Nitrate Reductases in the Deep-Sea Bacterium Shewanella piezotolerans WP3. Front Microbiol 2018; 9:3173. [PMID: 30622525 PMCID: PMC6308320 DOI: 10.3389/fmicb.2018.03173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/07/2018] [Indexed: 01/06/2023] Open
Abstract
Shewanella species are widely distributed in marine environments, from the shallow coasts to the deepest sea bottom. Most Shewanella species possess two isoforms of periplasmic nitrate reductases (NAP-α and NAP-β) and are able to generate energy through nitrate reduction. However, the contributions of the two NAP systems to bacterial deep-sea adaptation remain unclear. In this study, we found that the deep-sea denitrifier Shewanella piezotolerans WP3 was capable of performing nitrate respiration under high hydrostatic pressure (HHP) conditions. In the wild-type strain, NAP-β played a dominant role and was induced by both the substrate and an elevated pressure, whereas NAP-α was constitutively expressed at a relatively lower level. Genetic studies showed that each NAP system alone was sufficient to fully sustain nitrate-dependent growth and that both NAP systems exhibited substrate and pressure inducible expression patterns when the other set was absent. Biochemical assays further demonstrated that NAP-α had a higher tolerance to elevated pressure. Collectively, we report for the first time the distinct properties and contributions of the two NAP systems to nitrate reduction under different pressure conditions. The results will shed light on the mechanisms of bacterial HHP adaptation and nitrogen cycling in the deep-sea environment.
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Affiliation(s)
- Xue-Gong Li
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/CAS, Sanya, China
| | - Wei-Jia Zhang
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/CAS, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua-Hua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Jiang
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Tang
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Qing Qi
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/CAS, Sanya, China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/CAS, Sanya, China.,Aix Marseille Université, CNRS, LCB, Marseille, France
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12
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Abstract
The discovery of microbial communities in extreme conditions that would seem hostile to life leads to the question of how the molecules making up these microbes can maintain their structure and function. While microbes that live under extremes of temperature have been heavily studied, those that live under extremes of pressure, or "piezophiles", are now increasingly being studied because of advances in sample collection and high-pressure cells for biochemical and biophysical measurements. Here, adaptations of enzymes in piezophiles against the effects of pressure are discussed in light of recent experimental and computational studies. However, while concepts from studies of enzymes from temperature extremophiles can provide frameworks for understanding adaptations by piezophile enzymes, the effects of temperature and pressure on proteins differ in significant ways. Thus, the state of the knowledge of adaptation in piezophile enzymes is still in its infancy and many more experiments and computational studies on different enzymes from a variety of piezophiles are needed.
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Affiliation(s)
- Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, 20057, United States
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13
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Nagae T, Yamada H, Watanabe N. High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP . Acta Crystallogr D Struct Biol 2018; 74:895-905. [PMID: 30198899 PMCID: PMC6130465 DOI: 10.1107/s2059798318009397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP+ cofactor and the hydration structure. In the crystal form with the closed conformation the M20 loop moved as the pressure changed, with accompanying conformational changes around the active site, including NADP+ and folate. These movements were consistent with the suggested hypothesis that movement of the M20 loop was necessary for ecDHFR to catalyze the reaction. In the crystal form with the open conformation the nicotinamide ring of the NADP+ cofactor undergoes a large flip as an intermediate step in the reaction, despite being in a crystalline state. Furthermore, observation of the water molecules between Arg57 and folate elucidated an early step in the substrate-binding pathway. These results demonstrate the possibility of using high-pressure protein crystallography as a method to capture high-energy substates or transient structures related to the protein reaction cycle.
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Affiliation(s)
- Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Hiroyuki Yamada
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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Ohmae E, Hamajima Y, Nagae T, Watanabe N, Kato C. Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:680-691. [PMID: 29630970 DOI: 10.1016/j.bbapap.2018.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/01/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022]
Abstract
We previously found that the enzymatic activity of 3-isopropylmalate dehydrogenase from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 (SbIPMDH) was pressure-tolerant up to 100 MPa, but that from its atmospheric congener S. oneidensis strain MR-1 (SoIPMDH) was pressure-sensitive. Such characteristics were determined by only one amino acid residue at position 266, serine (SoIPMDH) or alanine (SbIPMDH) [Y. Hamajima et al. Extremophiles 20: 177, 2016]. In this study, we investigated the structural stability of these enzymes. At pH 7.6, SoIPMDH was slightly more stable against hydrostatic pressure than SbIPMDH, contrary to the physiological pressures of their normal environments. Pressure unfolding of these IPMDHs followed a two-state unfolding model between a native dimer and two unfolded monomers, and the dimer structure was pressure-tolerant up to 200 MPa, employing a midpoint pressure of 245.3 ± 0.1 MPa and a volume change of -225 ± 24 mL mol-1 for the most unstable mutant, SbIPMDH A266S. Thus, their pressure-dependent activity did not originate from structural perturbations such as unfolding or dimer dissociation. Conversely, urea-induced unfolding of these IPMDHs followed a three-state unfolding model, including a dimer intermediate. Interestingly, the first transition was strongly pH-dependent but pressure-independent; however, the second transition showed the opposite pattern. Obtained volume changes due to urea-induced unfolding were almost equal for both IPMDHs, approximately +10 and -30 mL mol-1 for intermediate formation and dimer dissociation, respectively. These results indicated that both IPMDHs have similar structural stability, and a pressure-adaptation mechanism was provided for only the enzymatic activity of SbIPMDH.
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Affiliation(s)
- Eiji Ohmae
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Yuki Hamajima
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan; Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi 464-8603, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
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15
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Fujii S, Masanari-Fujii M, Kobayashi S, Kato C, Nishiyama M, Harada Y, Wakai S, Sambongi Y. Commonly stabilized cytochromes c from deep-sea Shewanella and Pseudomonas. Biosci Biotechnol Biochem 2018; 82:1-8. [PMID: 29540113 DOI: 10.1080/09168451.2018.1448255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/23/2018] [Indexed: 10/17/2022]
Abstract
Two cytochromes c5 (SBcytc and SVcytc) have been derived from Shewanella living in the deep-sea, which is a high pressure environment, so it could be that these proteins are more stable at high pressure than at atmospheric pressure, 0.1 MPa. This study, however, revealed that SBcytc and SVcytc were more stable at 0.1 MPa than at higher pressure. In addition, at 0.1-150 MPa, the stability of SBcytc and SVcytc was higher than that of homologues from atmospheric-pressure Shewanella, which was due to hydrogen bond formation with the heme in the former two proteins. This study further revealed that cytochrome c551 (PMcytc) of deep-sea Pseudomonas was more stable than a homologue of atmospheric-pressure Pseudomonas aeruginosa, and that specific hydrogen bond formation with the heme also occurred in the former. Although SBcytc and SVcytc, and PMcytc are phylogenetically very distant, these deep-sea cytochromes c are commonly stabilized through hydrogen bond formation.
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Affiliation(s)
- Sotaro Fujii
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
- b Global Career Design Center , Hiroshima University , Higashi-Hiroshima , Japan
| | - Misa Masanari-Fujii
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Shinya Kobayashi
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Chiaki Kato
- c Japan Agency for Marine-Earth Science and Technology , Yokosuka , Japan
| | - Masayoshi Nishiyama
- d The HAKUBI Center for Advanced Research , Kyoto University , Kyoto , Japan
| | - Yoshie Harada
- e Institute for Integrated Cell-Material Sciences (WPI-iCeMS) , Kyoto University , Kyoto , Japan
| | - Satoshi Wakai
- f Graduate School of Science Technology and Innovation , Kobe University , Kobe , Japan
| | - Yoshihiro Sambongi
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
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Medvedev KE, Kolchanov NA, Afonnikov DA. Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. J Bioinform Comput Biol 2017; 15:1650036. [DOI: 10.1142/s0219720016500360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The understanding of biological and molecular mechanisms providing survival of cells under extreme temperatures and pressures will help to answer fundamental questions related to the origin of life and to design of biotechnologically important enzymes with new properties. Here, we analyze amino acid sequences of the Nip7 proteins from 35 archaeal species to identify positions containing mutations specific to the hydrostatic pressure and temperature of organism’s habitat. The number of such positions related to pressure change is much lower than related to temperature change. The results suggest that adaptation to temperature changes of the Nip7 protein cause more pronounced modifications in sequence and structure, than to the pressure changes. Structural analysis of residues at these positions demonstrated their involvement in salt-bridge formation, which may reflect the importance of protein structure stabilization by salt-bridges at extreme environmental conditions.
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Affiliation(s)
- Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern, Medical Center, Dallas, Texas 75390, USA
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl., 1, Moscow 123182, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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17
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Masanari M, Fujii S, Kawahara K, Oki H, Tsujino H, Maruno T, Kobayashi Y, Ohkubo T, Wakai S, Sambongi Y. Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea. Biosci Biotechnol Biochem 2016; 80:2365-2370. [DOI: 10.1080/09168451.2016.1232155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
Monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea (SVcytc5) was stable against heat and denaturant compared with the homologous protein from shallow-sea piezo-sensitive Shewanella livingstonensis (SLcytc5). Here, the SVcytc5 crystal structure revealed that the Lys-50 side chain on the flexible loop formed a hydrogen bond with heme whereas that of corresponding hydrophobic Leu-50 could not form such a bond in SLcytc5, which appeared to be one of possible factors responsible for the difference in stability between the two proteins. This structural insight was confirmed by a reciprocal mutagenesis study on the thermal stability of these two proteins. As SVcytc5 was isolated from a deep-sea piezophilic bacterium, the present comparative study indicates that adaptation of monomeric SVcytc5 to high pressure environments results in stabilization against heat.
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Affiliation(s)
- Misa Masanari
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuki Kawahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Hiroya Oki
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Hirofumi Tsujino
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Takahiro Maruno
- Graduate School of Engineering, Osaka University, Suita, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, Suita, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Satoshi Wakai
- Graduate School of Science Technology and Innovation, Kobe University, Kobe, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
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18
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Hayashi M, Nishiyama M, Kazayama Y, Toyota T, Harada Y, Takiguchi K. Reversible Morphological Control of Tubulin-Encapsulating Giant Liposomes by Hydrostatic Pressure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3794-3802. [PMID: 27023063 DOI: 10.1021/acs.langmuir.6b00799] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Liposomes encapsulating cytoskeletons have drawn much recent attention to develop an artificial cell-like chemical-machinery; however, as far as we know, there has been no report showing isothermally reversible morphological changes of liposomes containing cytoskeletons because the sets of various regulatory factors, that is, their interacting proteins, are required to control the state of every reaction system of cytoskeletons. Here we focused on hydrostatic pressure to control the polymerization state of microtubules (MTs) within cell-sized giant liposomes (diameters ∼10 μm). MT is the cytoskeleton formed by the polymerization of tubulin, and cytoskeletal systems consisting of MTs are very dynamic and play many important roles in living cells, such as the morphogenesis of nerve cells and formation of the spindle apparatus during mitosis. Using real-time imaging with a high-pressure microscope, we examined the effects of hydrostatic pressure on the morphology of tubulin-encapsulating giant liposomes. At ambient pressure (0.1 MPa), many liposomes formed protrusions due to tubulin polymerization within them. When high pressure (60 MPa) was applied, the protrusions shrank within several tens of seconds. This process was repeatedly inducible (around three times), and after the pressure was released, the protrusions regenerated within several minutes. These deformation rates of the liposomes are close to the velocities of migrating or shape-changing living cells rather than the shortening and elongation rates of the single MTs, which have been previously measured. These results demonstrate that the elongation and shortening of protrusions of giant liposomes is repeatedly controllable by regulating the polymerization state of MTs within them by applying and releasing hydrostatic pressure.
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Affiliation(s)
- Masahito Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan
| | | | | | | | | | - Kingo Takiguchi
- Division of Biological Science, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan
- Structural Biology Research Center, Nagoya University , Nagoya 464-8601, Japan
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