1
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Yasuda S, Hayashi T, Kajiwara Y, Murata T, Kinoshita M. Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability. J Chem Phys 2019; 150:055101. [DOI: 10.1063/1.5082217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Satoshi Yasuda
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuta Kajiwara
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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2
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Hayashi T, Inoue M, Yasuda S, Petretto E, Škrbić T, Giacometti A, Kinoshita M. Universal effects of solvent species on the stabilized structure of a protein. J Chem Phys 2018; 149:045105. [PMID: 30068177 DOI: 10.1063/1.5042111] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the effects of solvent specificities on the stability of the native structure (NS) of a protein on the basis of our free-energy function (FEF). We use CPB-bromodomain (CBP-BD) and apoplastocyanin (apoPC) as representatives of the protein universe and water, methanol, ethanol, and cyclohexane as solvents. The NSs of CBP-BD and apoPC consist of 66% α-helices and of 35% β-sheets and 4% α-helices, respectively. In order to assess the structural stability of a given protein immersed in each solvent, we contrast the FEF of its NS against that of a number of artificially created, misfolded decoys possessing the same amino-acid sequence but significantly different topology and α-helix and β-sheet contents. In the FEF, we compute the solvation entropy using the morphometric approach combined with the integral equation theories, and the change in electrostatic (ES) energy upon the folding is obtained by an explicit atomistic but simplified calculation. The ES energy change is represented by the break of protein-solvent hydrogen bonds (HBs), formation of protein intramolecular HBs, and recovery of solvent-solvent HBs. Protein-solvent and solvent-solvent HBs are absent in cyclohexane. We are thus able to separately evaluate the contributions to the structural stability from the entropic and energetic components. We find that for both CBP-BD and apoPC, the energetic component dominates in methanol, ethanol, and cyclohexane, with the most stable structures in these solvents sharing the same characteristics described as an association of α-helices. In particular, those in the two alcohols are identical. In water, the entropic component is as strong as or even stronger than the energetic one, with a large gain of translational, configurational entropy of water becoming crucially important so that the relative contents of α-helix and β-sheet and the content of total secondary structures are carefully selected to achieve sufficiently close packing of side chains. If the energetic component is excluded for a protein in water, the priority is given to closest side-chain packing, giving rise to the formation of a structure with very low α-helix and β-sheet contents. Our analysis, which requires minimal computational effort, can be applied to any protein immersed in any solvent and provides robust predictions that are quite consistent with the experimental observations for proteins in different solvent environments, thus paving the way toward a more detailed understanding of the folding process.
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Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masao Inoue
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Emanuele Petretto
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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3
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Hayashi T, Yasuda S, Škrbić T, Giacometti A, Kinoshita M. Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail. J Chem Phys 2017; 147:125102. [DOI: 10.1063/1.4999376] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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4
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Yasuda S, Kajiwara Y, Toyoda Y, Morimoto K, Suno R, Iwata S, Kobayashi T, Murata T, Kinoshita M. Hot-Spot Residues to be Mutated Common in G Protein-Coupled Receptors of Class A: Identification of Thermostabilizing Mutations Followed by Determination of Three-Dimensional Structures for Two Example Receptors. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b02997] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Satoshi Yasuda
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular
Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Institute
of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuta Kajiwara
- Graduate
School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yosuke Toyoda
- Graduate
School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazushi Morimoto
- Graduate
School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryoji Suno
- Graduate
School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- Graduate
School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Graduate
School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takeshi Murata
- Graduate
School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular
Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- JST, PRESTO, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Masahiro Kinoshita
- Institute
of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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5
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Kajiwara Y, Yasuda S, Takamuku Y, Murata T, Kinoshita M. Identification of thermostabilizing mutations for a membrane protein whose three-dimensional structure is unknown. J Comput Chem 2016; 38:211-223. [DOI: 10.1002/jcc.24673] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/24/2016] [Accepted: 10/30/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Yuta Kajiwara
- Department of Fundamental Energy Science, Graduate School of Energy Science; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science; Chiba University; 1-33 Yayoi-cho Inage Chiba 263-8522 Japan
- Molecular Chirality Research Center; Chiba University; 1-33 Yayoi-cho Inage Chiba 263-8522 Japan
- Laboratory for Complex Energy Processes Section, Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Yuuki Takamuku
- Department of Chemistry, Graduate School of Science; Chiba University; 1-33 Yayoi-cho Inage Chiba 263-8522 Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science; Chiba University; 1-33 Yayoi-cho Inage Chiba 263-8522 Japan
- Molecular Chirality Research Center; Chiba University; 1-33 Yayoi-cho Inage Chiba 263-8522 Japan
- JST, PRESTO; 1-33 Yayoi-cho Inage Chiba 263-8522 Japan
| | - Masahiro Kinoshita
- Laboratory for Complex Energy Processes Section, Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
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6
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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: 0.9] [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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7
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Urquiza-Carvalho GA, Fragoso WD, Rocha GB. Assessment of semiempirical enthalpy of formation in solution as an effective energy function to discriminate native-like structures in protein decoy sets. J Comput Chem 2016; 37:1962-72. [DOI: 10.1002/jcc.24415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/29/2016] [Accepted: 05/11/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Gabriel Aires Urquiza-Carvalho
- Departamento De QúImica; CCEN, Universidade Federal Da ParáIba; Jõao, Pessoa/PB, Caixa Postal: 5093 CEP: 58051-970 Brazil
| | - Wallace Duarte Fragoso
- Departamento De QúImica; CCEN, Universidade Federal Da ParáIba; Jõao, Pessoa/PB, Caixa Postal: 5093 CEP: 58051-970 Brazil
| | - Gerd Bruno Rocha
- Departamento De QúImica; CCEN, Universidade Federal Da ParáIba; Jõao, Pessoa/PB, Caixa Postal: 5093 CEP: 58051-970 Brazil
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8
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Yasuda S, Kajiwara Y, Takamuku Y, Suzuki N, Murata T, Kinoshita M. Identification of Thermostabilizing Mutations for Membrane Proteins: Rapid Method Based on Statistical Thermodynamics. J Phys Chem B 2016; 120:3833-43. [DOI: 10.1021/acs.jpcb.6b01405] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | | | - Takeshi Murata
- JST, PRESTO, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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9
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Ikebe J, Umezawa K, Higo J. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction. Biophys Rev 2016; 8:45-62. [PMID: 28510144 PMCID: PMC5425738 DOI: 10.1007/s12551-015-0189-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023] Open
Abstract
Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.
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Affiliation(s)
- Jinzen Ikebe
- Molecular Modeling and Simulation Group, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Koji Umezawa
- Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo, 169-8555, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
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10
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Murakami S, Oshima H, Hayashi T, Kinoshita M. On the physics of thermal-stability changes upon mutations of a protein. J Chem Phys 2015; 143:125102. [DOI: 10.1063/1.4931814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shota Murakami
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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11
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Kamo F, Ishizuka R, Matubayasi N. Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent. Protein Sci 2015; 25:56-66. [PMID: 26189564 DOI: 10.1002/pro.2754] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022]
Abstract
Energetics was analyzed for Trp-cage miniprotein in water to elucidate the solvation effect in heat denaturation. The solvation free energy was computed for a set of protein structures at room and high temperatures with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were investigated against the intramolecular (structural) energy of the protein and the average interaction energy of the protein with the solvent water. It was observed both at room and high temperatures that the solvation free energy is anticorrelated to the structural energy and varies in parallel to the electrostatic component of the protein-water interaction energy without correlations to the van der Waals and excluded-volume components. When the set of folded structures sampled at room temperature was compared with the set of unfolded ones at high temperature, it was found that the preference order of the two sets is in correspondence to the van der Waals and excluded-volume components in the sum of the protein intramolecular and protein-water intermolecular interactions and is not distinguished by the electrostatic component.
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Affiliation(s)
- Fumitaka Kamo
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
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12
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Oda K, Kinoshita M. Physicochemical origin of high correlation between thermal stability of a protein and its packing efficiency: a theoretical study for staphylococcal nuclease mutants. Biophys Physicobiol 2015; 12:1-12. [PMID: 27493849 PMCID: PMC4736840 DOI: 10.2142/biophysico.12.0_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/18/2015] [Indexed: 12/01/2022] Open
Abstract
There is an empirical rule that the thermal stability of a protein is related to the packing efficiency or core volume of the folded state and the protein tends to exhibit higher stability as the backbone and side chains are more closely packed. Previously, the wild type and its nine mutants of staphylococcal nuclease were compared by examining their folded structures. The results obtained were as follows: The stability was not correlated with the number of intramolecular hydrogen bonds, intramolecular electrostatic interaction energy, or degree of burial of the hydrophobic surface; though the empirical rule mentioned above held, it was not the proximate cause of higher stability; and the number of van der Waals contacts N vdW, or equivalently, the intramolecular van der Waals interaction energy was an important factor governing the stability. Here we revisit the wild type and its nine mutants of staphylococcal nuclease using our statistical-mechanical theory for hydration of a protein. A molecular model is employed for water. We show that the pivotal factor is the magnitude of the water-entropy gain upon folding. The gain originates from an increase in the total volume available to the translational displacement of water molecules coexisting with the protein in the system. The magnitude is highly correlated with the denaturation temperature T m. Moreover, the apparent correlation between N vdW and T m as well as the empirical rule is interpretable (i.e., their physicochemical meanings can be clarified) on the basis of the water-entropy effect.
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Affiliation(s)
- Koji Oda
- Taisho Pharmaceutical Co., Ltd., Yoshino-cho 1-403, Kita-ku, Saitama 331-9530, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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13
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Yoshidome T, Ekimoto T, Matubayasi N, Harano Y, Kinoshita M, Ikeguchi M. An accurate and efficient computation method of the hydration free energy of a large, complex molecule. J Chem Phys 2015; 142:175101. [DOI: 10.1063/1.4919636] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Takashi Yoshidome
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Yuichi Harano
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamino, Himeji-shi, Hyogo 670-8524, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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14
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Yasuda S, Hayashi T, Kinoshita M. Physical origins of the high structural stability of CLN025 with only ten residues. J Chem Phys 2014; 141:105103. [DOI: 10.1063/1.4894753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Satoshi Yasuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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15
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Oshima H, Kinoshita M. Effects of sugars on the thermal stability of a protein. J Chem Phys 2014; 138:245101. [PMID: 23822280 DOI: 10.1063/1.4811287] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is experimentally known that the heat-denaturation temperature of a protein is raised (i.e., its thermal stability is enhanced) by sugar addition. In earlier works, we proposed a physical picture of thermal denaturation of proteins in which the measure of the thermal stability is defined as the solvent-entropy gain upon protein folding at 298 K normalized by the number of residues. A multipolar-model water was adopted as the solvent. The polyatomic structures of the folded and unfolded states of a protein were taken into account in the atomic detail. A larger value of the measure implies higher thermal stability. First, we show that the measure remains effective even when the model water is replaced by the hard-sphere solvent whose number density and molecular diameter are set at those of real water. The physical picture is then adapted to the elucidation of the effects of sugar addition on the thermal stability of a protein. The water-sugar solution is modeled as a binary mixture of hard spheres. The thermal stability is determined by a complex interplay of the diameter of sugar molecules dC and the total packing fraction of the solution η: dC is estimated from the volume per molecule in the sugar crystal and η is calculated using the experimental data of the solution density. We find that the protein is more stabilized as the sucrose or glucose concentration becomes higher and the stabilization effect is stronger for sucrose than for glucose. These results are in accord with the experimental observations. Using a radial-symmetric integral equation theory and the morphometric approach, we decompose the change in the measure upon sugar addition into two components originating from the protein-solvent pair and protein-solvent many-body correlations, respectively. Each component is further decomposed into the excluded-volume and solvent-accessible-surface terms. These decompositions give physical insights into the microscopic origin of the thermal-stability enhancement by sugar addition. As an example, the higher stability of the native state relative to that of the unfolded state is found to be attributable primarily to an increase in the solvent crowding caused by sugar addition. Due to the hydrophilicity of sugar molecules, the addition of sugar by a larger amount or that with a larger molecular size leads to an increase in η which is large enough to make the solvent crowding more serious.
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Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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16
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Yasuda S, Oshima H, Kinoshita M. Structural stability of proteins in aqueous and nonpolar environments. J Chem Phys 2013; 137:135103. [PMID: 23039615 DOI: 10.1063/1.4755755] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A protein folds into its native structure with the α-helix and∕or β-sheet in aqueous solution under the physiological condition. The relative content of these secondary structures largely varies from protein to protein. However, such structural variability is not exhibited in nonaqueous environment. For example, there is a strong trend that alcohol induces a protein to form α-helices, and many of the membrane proteins within the lipid bilayer consists of α-helices. Here we investigate the structural stability of proteins in aqueous and nonpolar environments using our recently developed free-energy function F = (Λ - TS)∕(k(B)T(0)) = Λ∕(k(B)T(0)) - S∕k(B) (T(0) = 298 K and the absolute temperature T is set at T(0)) which is based on statistical thermodynamics. Λ∕(k(B)T(0)) and S∕k(B) are the energetic and entropic components, respectively, and k(B) is Boltzmann's constant. A smaller value of the positive quantity, -S, represents higher efficiency of the backbone and side-chain packing promoted by the entropic effect arising from the translational displacement of solvent molecules or the CH(2), CH(3), and CH groups which constitute nonpolar chains of lipid molecules. As for Λ, in aqueous solution, a transition to a more compact structure of a protein accompanies the break of protein-solvent hydrogen bonds: As the number of donors and acceptors buried without protein intramolecular hydrogen bonding increases, Λ becomes higher. In nonpolar solvent, lower Λ simply implies more intramolecular hydrogen bonds formed. We find the following. The α-helix and β-sheet are advantageous with respect to -S as well as Λ and to be formed as much as possible. In aqueous solution, the solvent-entropy effect on the structural stability is so strong that the close packing of side chains is dominantly important, and the α-helix and β-sheet contents are judiciously adjusted to accomplish it. In nonpolar solvent, the solvent-entropy effect is substantially weaker than in aqueous solution. Λ is crucial and the α-helix is more stable than the β-sheet in terms of Λ, which develops a tendency that α-helices are exclusively chosen. For a membrane protein, α-helices are stabilized as fundamental structural units for the same reason, but their arrangement is performed through the entropic effect mentioned above.
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Affiliation(s)
- Satoshi Yasuda
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
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17
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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: 4.8] [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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18
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Yoshidome T, Ito Y, Matubayasi N, Ikeguchi M, Kinoshita M. Structural characteristics of yeast F1-ATPase before and after 16-degree rotation of the γ subunit: theoretical analysis focused on the water-entropy effect. J Chem Phys 2012; 137:035102. [PMID: 22830731 DOI: 10.1063/1.4734298] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have recently proposed a novel picture of the rotation mechanism for F(1)-ATPase [T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)]. In the picture, the asymmetric packing in F(1)-ATPase, originating from the water-entropy effect, plays the key role in the rotation. Here, we analyze the differences between the experimentally determined structures of yeast F(1)-ATPase before and after 16° rotation of the γ subunit with the emphasis on the water-entropy effect. For each of these structures, we calculate the hydration entropies of three sub-complexes comprising the γ subunit, one of the β subunits, and two α subunits adjacent to them. The β(E), β(TP), and β(DP) subunits are involved in sub-complexes I, II, and III, respectively. The calculation is performed using a hybrid of the angle-dependent integral equation theory combined with the molecular model for water and the morphometric approach. The absolute value of the hydration entropy is in the following order: sub-complex I > sub-complex II > sub-complex III. The packing efficiency of the sub-complex follows the opposite order. The rotation gives rise to less efficient packing in sub-complex III and a corresponding water-entropy loss. However, the other two sub-complexes, accompanying water-entropy gains, become more efficiently packed. These results are consistent with our picture of the rotation mechanism, supporting its validity. The water-entropy analysis shows that the interfaces of α(DP)-β(DP) and α(E)-β(E) become more open after the rotation, which is in accord with the experimental observation.
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Affiliation(s)
- Takashi Yoshidome
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Yoshidome T, Kinoshita M. Physical origin of hydrophobicity studied in terms of cold denaturation of proteins: comparison between water and simple fluids. Phys Chem Chem Phys 2012; 14:14554-66. [PMID: 23014986 DOI: 10.1039/c2cp41738c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A clue to the physical origin of the hydrophobicity is in the experimental observations, which show that it is weakened at low temperatures. By considering a solvophobic model protein immersed in water and three species of simple solvents, we analyze the temperature dependence of the changes in free energy, energy, and entropy of the solvent upon protein unfolding. The angle-dependent and radial-symmetric integral equation theories and the morphometric approach are employed in the analysis. Each of the changes is decomposed into two terms, which depend on the excluded volume and on the area and curvature of the solvent-accessible surface, respectively. The excluded-volume term of the entropy change is further decomposed into two components representing the protein-solvent pair correlation and the protein-solvent-solvent triplet and higher-order correlation, respectively. We show that water crowding in the system becomes more serious upon protein unfolding but this effect becomes weaker as the temperature is lowered. If the hydrophobicity originated from the water structuring near a nonpolar solute, it would be strengthened upon lowering of the temperature. Among the three species of simple solvents, considerable weakening of the solvophobicity at low temperatures is observed only for the solvent where the particles interact through a strong attractive potential and the particle size is as small as that of water. Even in the case of this solvent, however, cold denaturation of a protein cannot be reproduced. It would be reproducible if the attractive potential was substantially enhanced, but such enhancement causes the appearance of the metastability limit for a single liquid phase.
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Affiliation(s)
- Takashi Yoshidome
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan
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20
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Application of Hydration Thermodynamics to the Evaluation of Protein Structures and Protein-Ligand Binding. ENTROPY 2012. [DOI: 10.3390/e14081443] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mishima H, Yasuda S, Yoshidome T, Oshima H, Harano Y, Ikeguchi M, Kinoshita M. Characterization of experimentally determined native-structure models of a protein using energetic and entropic components of free-energy function. J Phys Chem B 2012; 116:7776-86. [PMID: 22697465 DOI: 10.1021/jp301541z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We show how to characterize the native-structure models of a protein using our free-energy function F which is based on hydration thermodynamics. Ubiquitin is adopted as an example protein. We consider models determined by the X-ray crystallography and two types of NMR model sets. A model set of type 1 comprises candidate models for a fixed native structure, and that of type 2 forms an ensemble of structures representing the structural variability of the native state. In general, the X-ray models give lower F than the NMR models. There is a trend that, as a model deviates more from the model with the lowest F among the X-ray models, its F becomes higher. Model sets of type 1 and those of type 2, respectively, exhibit two different characteristics with respect to the correlation between the deviation and F. It is argued that the total amount of constraints such as NOEs effectively taken into account in constructing the NMR models can be examined by analyzing the behavior of F. We investigate structural characteristics of the models in terms of the energetic and entropic components of F which are relevant to intramolecular hydrogen bonding and to backbone and side-chain packing, respectively.
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Affiliation(s)
- Hirokazu Mishima
- Graduate School of Energy Science, Kyoto University , Uji, Kyoto 611-0011, Japan
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Koppole S, Schaefer M. A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias. J Comput Chem 2012; 33:791-9. [DOI: 10.1002/jcc.22908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/24/2011] [Accepted: 11/20/2011] [Indexed: 11/12/2022]
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Du S, Harano Y, Kinoshita M, Sakurai M. A scoring function based on solvation thermodynamics for protein structure prediction. Biophysics (Nagoya-shi) 2012; 8:127-38. [PMID: 27493529 PMCID: PMC4629643 DOI: 10.2142/biophysics.8.127] [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: 06/27/2012] [Accepted: 07/31/2012] [Indexed: 12/01/2022] Open
Abstract
We predict protein structure using our recently developed free energy function for describing protein stability, which is focused on solvation thermodynamics. The function is combined with the current most reliable sampling methods, i.e., fragment assembly (FA) and comparative modeling (CM). The prediction is tested using 11 small proteins for which high-resolution crystal structures are available. For 8 of these proteins, sequence similarities are found in the database, and the prediction is performed with CM. Fairly accurate models with average Cα root mean square deviation (RMSD) ∼ 2.0 Å are successfully obtained for all cases. For the rest of the target proteins, we perform the prediction following FA protocols. For 2 cases, we obtain predicted models with an RMSD ∼ 3.0 Å as the best-scored structures. For the other case, the RMSD remains larger than 7 Å. For all the 11 target proteins, our scoring function identifies the experimentally determined native structure as the best structure. Starting from the predicted structure, replica exchange molecular dynamics is performed to further refine the structures. However, we are unable to improve its RMSD toward the experimental structure. The exhaustive sampling by coarse-grained normal mode analysis around the native structures reveals that our function has a linear correlation with RMSDs < 3.0 Å. These results suggest that the function is quite reliable for the protein structure prediction while the sampling method remains one of the major limiting factors in it. The aspects through which the methodology could further be improved are discussed.
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Affiliation(s)
- Shiqiao Du
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yuichi Harano
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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Kodama R, Roth R, Harano Y, Kinoshita M. Morphometric approach to thermodynamic quantities of solvation of complex molecules: Extension to multicomponent solvent. J Chem Phys 2011; 135:045103. [DOI: 10.1063/1.3617247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Oshima H, Yasuda S, Yoshidome T, Ikeguchi M, Kinoshita M. Crucial importance of the water-entropy effect in predicting hot spots in protein–protein complexes. Phys Chem Chem Phys 2011; 13:16236-46. [DOI: 10.1039/c1cp21597c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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