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Yasuda S, Hayashi T, Murata T, Kinoshita M. Physical pictures of rotation mechanisms of F 1- and V 1-ATPases: Leading roles of translational, configurational entropy of water. Front Mol Biosci 2023; 10:1159603. [PMID: 37363397 PMCID: PMC10288849 DOI: 10.3389/fmolb.2023.1159603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
We aim to develop a theory based on a concept other than the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex. Experimental results conflicting with the chemo-mechanical coupling have recently emerged. We claim that the system comprises not only the protein complex but also the aqueous solution in which the protein complex is immersed and the system performs essentially no mechanical work. We perform statistical-mechanical analyses on V1-ATPase (the A3B3DF complex) for which crystal structures in more different states are experimentally known than for F1-ATPase (the α3β3γ complex). Molecular and atomistic models are employed for water and the structure of V1-ATPase, respectively. The entropy originating from the translational displacement of water molecules in the system is treated as a pivotal factor. We find that the packing structure of the catalytic dwell state of V1-ATPase is constructed by the interplay of ATP bindings to two of the A subunits and incorporation of the DF subunit. The packing structure represents the nonuniformity with respect to the closeness of packing of the atoms in constituent proteins and protein interfaces. The physical picture of rotation mechanism of F1-ATPase recently constructed by Kinoshita is examined, and common points and differences between F1- and V1-ATPases are revealed. An ATP hydrolysis cycle comprises binding of ATP to the protein complex, hydrolysis of ATP into ADP and Pi in it, and dissociation of ADP and Pi from it. During each cycle, the chemical compounds bound to the three A or β subunits and the packing structure of the A3B3 or α3β3 complex are sequentially changed, which induces the unidirectional rotation of the central shaft for retaining the packing structure of the A3B3DF or α3β3γ complex stabilized for almost maximizing the water entropy. The torque driving the rotation is generated by water with no input of chemical free energy. The presence of ATP is indispensable as a trigger of the torque generation. The ATP hydrolysis or synthesis reaction is tightly coupled to the rotation of the central shaft in the normal or inverse direction through the water-entropy effect.
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Affiliation(s)
- Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba, Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology and Art and Sports Sciences, Faculty of Engineering, Niigata University, Niigata, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba, Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
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Microenvironmental innate immune signaling and cell mechanical responses promote tumor growth. Dev Cell 2021; 56:1884-1899.e5. [PMID: 34197724 DOI: 10.1016/j.devcel.2021.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 05/01/2021] [Accepted: 06/09/2021] [Indexed: 01/08/2023]
Abstract
Tissue homeostasis is achieved by balancing stem cell maintenance, cell proliferation and differentiation, as well as the purging of damaged cells. Elimination of unfit cells maintains tissue health; however, the underlying mechanisms driving competitive growth when homeostasis fails, for example, during tumorigenesis, remain largely unresolved. Here, using a Drosophila intestinal model, we find that tumor cells outcompete nearby enterocytes (ECs) by influencing cell adhesion and contractility. This process relies on activating the immune-responsive Relish/NF-κB pathway to induce EC delamination and requires a JNK-dependent transcriptional upregulation of the peptidoglycan recognition protein PGRP-LA. Consequently, in organisms with impaired PGRP-LA function, tumor growth is delayed and lifespan extended. Our study identifies a non-cell-autonomous role for a JNK/PGRP-LA/Relish signaling axis in mediating death of neighboring normal cells to facilitate tumor growth. We propose that intestinal tumors "hijack" innate immune signaling to eliminate enterocytes in order to support their own growth.
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Yoshida K, Uchiyama H, Yamaguchi T. Structure and dynamical properties of hydrated F-actin investigated by X-ray scattering. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Okumura H, Higashi M, Yoshida Y, Sato H, Akiyama R. Theoretical approaches for dynamical ordering of biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:212-228. [PMID: 28988931 DOI: 10.1016/j.bbagen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. SCOPE OF REVIEW We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. MAJOR CONCLUSIONS The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. GENERAL SIGNIFICANCE These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. 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)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
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Amano KI, Iwaki M, Hashimoto K, Fukami K, Nishi N, Takahashi O, Sakka T. Number Density Distribution of Small Particles around a Large Particle: Structural Analysis of a Colloidal Suspension. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:11063-11070. [PMID: 27683951 DOI: 10.1021/acs.langmuir.6b02628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Some colloidal suspensions contain two types of particles-small and large particles-to improve the lubricating ability, light absorptivity, and so forth. Structural and chemical analyses of such colloidal suspensions are often performed to understand their properties. In a structural analysis study, the observation of the number density distribution of small particles around a large particle (gLS) is difficult because these particles are randomly moving within the colloidal suspension by Brownian motion. We obtain gLS using the data from a line optical tweezer (LOT) that can measure the potential of mean force between two large colloidal particles (ΦLL). We propose a theory that transforms ΦLL into gLS. The transform theory is explained in detail and tested. We demonstrate for the first time that LOT can be used for the structural analysis of a colloidal suspension. LOT combined with the transform theory will facilitate structural analyses of the colloidal suspensions, which is important for both understanding colloidal properties and developing colloidal products.
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Affiliation(s)
- Ken-Ichi Amano
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
| | - Mitsuhiro Iwaki
- Quantitative Biology Center, RIKEN , Suita, Osaka 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University , Suita, Osaka 565-0874, Japan
| | - Kota Hashimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
| | - Kazuhiro Fukami
- Department of Materials Science and Engineering, Graduate School of Engineering, Kyoto University , Kyoto 606-8501, Japan
| | - Naoya Nishi
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University , Sendai 981-8558, Japan
| | - Tetsuo Sakka
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
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Suzuki M, Imao A, Mogami G, Chishima R, Watanabe T, Yamaguchi T, Morimoto N, Wazawa T. Strong Dependence of Hydration State of F-Actin on the Bound Mg(2+)/Ca(2+) Ions. J Phys Chem B 2016; 120:6917-28. [PMID: 27332748 DOI: 10.1021/acs.jpcb.6b02584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding of the hydration state is an important issue in the chemomechanical energetics of versatile biological functions of polymerized actin (F-actin). In this study, hydration-state differences of F-actin by the bound divalent cations are revealed through precision microwave dielectric relaxation (DR) spectroscopy. G- and F-actin in Ca- and Mg-containing buffer solutions exhibit dual hydration components comprising restrained water with DR frequency f2 (<fw: DR frequency of bulk solvent, 17 GHz at 20 °C) and hypermobile water (HMW) with DR frequency f1 (>fw). The hydration state of F-actin is strongly dependent on the ionic composition. In every buffer tested, the HMW signal Dhyme (≡ (f1 - fw)δ1/(fwδw)) of F-actin is stronger than that of G-actin, where δw is DR-amplitude of bulk solvent and δ1 is that of HMW in a fixed-volume ellipsoid containing an F-actin and surrounding water in solution. Dhyme value of F-actin in Ca2.0-buffer (containing 2 mM Ca(2+)) is markedly higher than in Mg2.0-buffer (containing 2 mM Mg(2+)). Moreover, in the presence of 2 mM Mg(2+), the hydration state of F-actin is changed by adding a small fraction of Ca(2+) (∼0.1 mM) and becomes closer to that of the Ca-bound form in Ca2.0-buffer. This is consistent with the results of the partial specific volume and the Cotton effect around 290 nm in the CD spectra, indicating a change in the tertiary structure and less apparent change in the secondary structure of actin. The number of restrained water molecules per actin (N2) is estimated to be 1600-2100 for Ca2.0- and F-buffer and ∼2500 for Mg2.0-buffer at 10-15 °C. These numbers are comparable to those estimated from the available F-actin atomic structures as in the first water layer. The number of HMW molecules is roughly explained by the volume between the equipotential surface of -kT/2e and the first water layer of the actin surface by solving the Poisson-Boltzmann equation using UCSF Chimera.
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Affiliation(s)
- Makoto Suzuki
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Asato Imao
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - George Mogami
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Ryotaro Chishima
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Takahiro Watanabe
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Takaya Yamaguchi
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Nobuyuki Morimoto
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , 6-6-02 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Tetsuichi Wazawa
- Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University , Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Suzuki M. What is “hypermobile” water?: detected in alkali halide, adenosine phosphate, and F-actin solutions by high-resolution microwave dielectric spectroscopy. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Experimental observation by high-resolution microwave dielectric spectroscopy of hydration properties of alkali halide ions, adenosine phosphate ions, and F-actin revealed the existence of hypermobile water (HMW) molecules around those solutes. To understand the molecular process of HMW, two theoretical approaches are reviewed here. One is based on a statistical mechanical approach to analyze the rotational freedom of water molecules around a charged particle. Another approach reports direct calculation of dielectric relaxation process of water molecules around an ion. Experimentally observed HMW molecules are theoretically explained with the significance of multi-correlations among an ion and water molecules.
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Mishima H, Oshima H, Yasuda S, Amano KI, Kinoshita M. On the physics of multidrug efflux through a biomolecular complex. J Chem Phys 2013; 139:205102. [DOI: 10.1063/1.4832896] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kinoshita M. A new theoretical approach to biological self-assembly. Biophys Rev 2013; 5:283-293. [PMID: 28510109 DOI: 10.1007/s12551-013-0100-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/02/2013] [Indexed: 11/25/2022] Open
Abstract
Upon biological self-assembly, the number of accessible translational configurations of water in the system increases considerably, leading to a large gain in water entropy. It is important to calculate the solvation entropy of a biomolecule with a prescribed structure by accounting for the change in water-water correlations caused by solute insertion. Modeling water as a dielectric continuum is not capable of capturing the physical essence of the water entropy effect. As a reliable tool, we propose a hybrid of the angle-dependent integral equation theory combined with a multipolar water model and a morphometric approach. Using our methods wherein the water entropy effect is treated as the key factor, we can elucidate a variety of processes such as protein folding, cold, pressure, and heat denaturating of a protein, molecular recognition, ordered association of proteins such as amyloid fibril formation, and functioning of ATP-driven proteins.
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Affiliation(s)
- Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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Okazaki KI, Sato T, Takano M. Temperature-enhanced association of proteins due to electrostatic interaction: a coarse-grained simulation of actin-myosin binding. J Am Chem Soc 2012; 134:8918-25. [PMID: 22559201 DOI: 10.1021/ja301447j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Association of protein molecules constitutes the basis for the interaction network in a cell. Despite its fundamental importance, the thermodynamic aspect of protein-protein binding, particularly the issues relating to the entropy change upon binding, remains elusive. The binding of actin and myosin, which are vital proteins in motility, is a typical example, in which two different binding mechanisms have been argued: the binding affinity increases with increasing temperature and with decreasing salt-concentration, indicating the entropy-driven binding and the enthalpy-driven binding, respectively. How can these thermodynamically different binding mechanisms coexist? To address this question, which is of general importance in understanding protein-protein bindings, we conducted an in silico titration of the actin-myosin system by molecular dynamics simulation using a residue-level coarse-grained model, with particular focus on the role of the electrostatic interaction. We found a good agreement between in silico and in vitro experiments on the salt-concentration dependence and the temperature dependence of the binding affinity. We then figured out how the two binding mechanisms can coexist: the enthalpy (due to electrostatic interaction between actin and myosin) provides the basal binding affinity, and the entropy (due to the orientational disorder of water molecules) enhances it at higher temperatures. In addition, we analyzed the actin-myosin complex structures observed during the simulation and obtained a variety of weak-binding complex structures, among which were found an unusual binding mode suggested by an earlier experiment and precursor structures of the strong-binding complex proposed by electron microscopy. These results collectively indicate the potential capability of a residue-level coarse-grained model to simulate the association-dissociation dynamics (particularly for transient weak-bindings) exhibited by larger and more complicated systems, as in a cell.
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Affiliation(s)
- Kei-ichi Okazaki
- Department of Pure and Applied Physics, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, Japan
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Yoshidome T. Importance of water entropy in rotation mechanism of F 1-ATPase. Biophysics (Nagoya-shi) 2011; 7:113-122. [PMID: 27857599 PMCID: PMC5036781 DOI: 10.2142/biophysics.7.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/21/2011] [Indexed: 12/01/2022] Open
Abstract
We briefly review our theoretical study on the rotation scheme of F1-ATPase. In the scheme, the key factor is the water entropy which has been shown to drive a variety of self-assembly processes in biological systems. We decompose the crystal structure of F1-ATPase into three sub-complexes each of which is composed of the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in the sub-complexes I, II, and III, respectively. We calculate the hydration entropy of each sub-complex using a hybrid of the integral equation theory for molecular liquids and the morphometric approach. It is found that the absolute value of the hydration entropy follows the order, sub-complex I > sub-complex II > sub-complex III. Moreover, the differences are quite large, which manifests highly asymmetrical packing of F1-ATPase. In our picture, this asymmetrical packing plays crucially important roles in the rotation of the γ subunit. We discuss how the rotation is induced by the water-entropy effect coupled with such chemical processes as ATP binding, ATP hydrolysis, and release of the products.
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Affiliation(s)
- Takashi Yoshidome
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Amano KI, Oshima H, Kinoshita M. Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system. J Chem Phys 2011; 135:185101. [DOI: 10.1063/1.3657856] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Amano KI, Kinoshita M. Model of insertion and release of a large solute into and from a biopolymer complex. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.01.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Yoshidome T, Ito Y, Ikeguchi M, Kinoshita M. Rotation Mechanism of F1-ATPase: Crucial Importance of the Water Entropy Effect. J Am Chem Soc 2011; 133:4030-9. [PMID: 21348521 DOI: 10.1021/ja109594y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Yoshidome
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuko Ito
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly. ENTROPY 2010. [DOI: 10.3390/e12061632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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