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Yamamoto T, Yasuda S, Kasai RS, Nakano R, Hikiri S, Sugaya K, Hayashi T, Ogasawara S, Shiroishi M, Fujiwara TK, Kinoshita M, Murata T. A methodology for creating mutants of G-protein coupled receptors stabilized in active state by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022; 31:e4425. [PMID: 36173170 PMCID: PMC9490800 DOI: 10.1002/pro.4425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 09/28/2023]
Abstract
We challenged the stabilization of a G-protein coupled receptor (GPCR) in the active state solely by multiple amino-acid mutations without the agonist binding. For many GPCRs, the free energy of the active state is higher than that of the inactive state. When the inactive state is stabilized through the lowering of its free energy, the apparent midpoint temperature of thermal denaturation Tm exhibits a significant increase. However, this is not always the case for the stabilization of the active state. We constructed a modified version of our methodology combining statistical thermodynamics and evolutionary molecular engineering, which was recently developed for the inactive state. First, several residues to be mutated are determined using our statistical-thermodynamics theory. Second, a gene (mutant) library is constructed using Escherichia coli cells to efficiently explore most of the mutational space. Third, for the mutant screening, the mutants prepared in accordance with the library are expressed in engineered Saccharomyces cerevisiae YB14 cells which can grow only when a GPCR mutant stabilized in the active state has signaling function. For the adenosine A2A receptor tested, the methodology enabled us to sort out two triple mutants and a double mutant. It was experimentally corroborated that all the mutants exhibit much higher binding affinity for G protein than the wild type. Analyses indicated that the mutations make the structural characteristics shift toward those of the active state. However, only slight increases in Tm resulted from the mutations, suggesting the unsuitability of Tm to the stability measure for the active state.
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Affiliation(s)
- Taisei Yamamoto
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
| | - Rinshi S. Kasai
- Institute for Glyco‐core Research (iGCORE)Gifu UniversityGifuJapan
- Institute for Life and Medical SciencesKyoto UniversityKyotoJapan
| | - Ryosuke Nakano
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Simon Hikiri
- Graduate School of Engineering ScienceOsaka UniversityOsakaJapan
| | - Kanna Sugaya
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of EngineeringNiigata UniversityNiigataJapan
- Institute of Advanced EnergyKyoto UniversityKyotoJapan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
- Institute for Advanced Academic ResearchChiba UniversityChibaJapan
| | - Mitsunori Shiroishi
- Department of Biological Science and TechnologyTokyo University of ScienceTokyoJapan
| | - Takahiro K. Fujiwara
- Institute for Integrated Cell‐Material Sciences (WPI‐iCeMS)Kyoto UniversityKyotoJapan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Institute of Advanced EnergyKyoto UniversityKyotoJapan
- Center for the Promotion of Interdisciplinary Education and ResearchKyoto UniversityKyoto‐shiJapan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of ScienceChiba UniversityChibaJapan
- Membrane Protein Research CenterChiba UniversityChibaJapan
- Molecular Chirality Research CenterChiba UniversityChibaJapan
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Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M. Hydration properties of a protein at low and high pressures: Physics of pressure denaturation. J Chem Phys 2020; 152:065103. [PMID: 32061219 DOI: 10.1063/1.5140499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Using experimentally determined structures of ubiquitin at 1 and 3000 bar, we generate sufficiently large ensembles of model structures in the native and pressure-induced (denatured) states by means of molecular dynamics simulations with explicit water. We calculate the values of a free-energy function (FEF), which comprises the hydration free energy (HFE) and the intramolecular (conformational) energy and entropy, for the two states at 1 and 3000 bar. The HFE and the conformational entropy, respectively, are calculated using our statistical-mechanical method, which has recently been shown to be accurate, and the Boltzmann-quasi-harmonic method. The HFE is decomposed into a variety of physically insightful components. We show that the FEF of the native state is lower than that of the denatured state at 1 bar, whereas the opposite is true at 3000 bar, thus being successful in reproducing the pressure denaturation. We argue that the following two quantities of hydration play essential roles in the denaturation: the WASA-dependent term in the water-entropy loss upon cavity creation for accommodating the protein (WASA is the water-accessible surface area of the cavity) and the protein-water Lennard-Jones interaction energy. At a high pressure, the mitigation of the serious water crowding in the system is the most important, and the WASA needs to be sufficiently enlarged with the increase in the excluded-volume being kept as small as possible. The denatured structure thus induced is characterized by the water penetration into the protein interior. The pressure denaturation is accompanied by a significantly large gain of water entropy.
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Affiliation(s)
- Masao Inoue
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Simon Hikiri
- 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 230-0045, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Nagata T, Yamada T, Hayashi T, Hikiri S, Kobayashi N, Ikeguchi M, Katahira M, Kinoshita M, Yanagawa H. Structural and Physical Basis for the Higher Affinity to Oncoprotein MDM2 of a Peptide Selected with MRNA Display Over Tumor Suppressor p53. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M. Mechanism of globule-to-coil transition of poly(N-isopropylacrylamide) in water: Relevance to cold denaturation of a protein. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Yamada T, Hayashi T, Hikiri S, Kobayashi N, Yanagawa H, Ikeguchi M, Katahira M, Nagata T, Kinoshita M. How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2? J Chem Inf Model 2019; 59:3533-3544. [PMID: 31282659 DOI: 10.1021/acs.jcim.9b00226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An oncoprotein MDM2 binds to the extreme N-terminal peptide region of a tumor suppressor protein p53 (p53NTD) and inhibits its anticancer activity. We recently discovered a peptide named MIP which exhibits much higher binding affinity for MDM2 than p53NTD. Experiments showed that the binding free energy (BFE) of MDM2-MIP is lower than that of MDM2-p53NTD by approximately -4 kcal/mol. Here, we develop a theoretical method which is successful in reproducing this quantitative difference and elucidating its physical origins. It enables us to decompose the BFE into a variety of energetic and entropic components, evaluate their relative magnitudes, and identify the physical factors driving or opposing the binding. It should be applicable also to the assessment of differences among ligands in the binding affinity for a particular receptor, which is a central issue in modern chemistry. In the MDM2 case, the higher affinity of MIP is ascribed to a larger gain of translational, configurational entropy of water upon binding. This result is useful to the design of a peptide possessing even higher affinity for MDM2 as a reliable drug against a cancer.
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Affiliation(s)
- Tatsuya Yamada
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Simon Hikiri
- 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
| | - Naohiro Kobayashi
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Hiroshi Yanagawa
- Y-Lab. of IDAC Theranostics, Inc. , 1-1-48 Suehiro-cho , Tsurumi, Yokohama 230-0045 , Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science , Yokohama City University , 1-7-29, Suehiro-cho , Tsurumi-ku, Yokohama 230-0045 , Japan.,RIKEN Medical Sciences Innovation Hub Program , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama 230-0045 , Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University , Uji , Kyoto 611-0011 , Japan
| | - Takashi Nagata
- 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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Hikiri S, Hayashi T, Inoue M, Ekimoto T, Ikeguchi M, Kinoshita M. An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins. J Chem Phys 2019; 150:175101. [DOI: 10.1063/1.5093110] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Simon Hikiri
- 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
| | - 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
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22 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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Hikiri S, Hayashi T, Ikeguchi M, Kinoshita M. Statistical thermodynamics for the unexpectedly large difference between disaccharide stereoisomers in terms of solubility in water. Phys Chem Chem Phys 2018; 20:23684-23693. [PMID: 30191211 DOI: 10.1039/c8cp04377a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We unravel the physical origins of the large difference between cellobiose and maltose, which consist of two β-1,4 and α-1,4 linked d-glucose units, respectively, in terms of the solubility in water. We construct a thermodynamic theory where the chemical-potential difference between disaccharides in water and in vacuum is identified as the key free-energy function. Its energetic and entropic components are calculated for cellobiose and maltose by statistical-mechanical theories for solute hydration. The disaccharide structures are taken into account at the atomic level and a molecular model is adopted for water. Molecular dynamics simulations are used to account for the conformational fluctuation of a disaccharide molecule, which also enables us to estimate the conformational entropy. We show that the cellobiose/maltose solubility ratio calculated is in good agreement with the experimental value. The solubility becomes much lower for cellobiose due to conformational-entropy and water-entropy effects. The former effect is relevant to higher stability of the intramolecular hydrogen bond between oxygen atoms in the six-membered ring and in the neighboring hydroxyl group: the hydration alters the fluctuation of a molecular conformation to a larger or less regular one, but the degree of this alteration is smaller. The latter effect is attributed to more separation of two hydroxymethyl groups in a molecule, causing lower probability of the overlap of excluded volumes generated by the groups for water molecules. We suggest that physicochemical properties of disaccharides in water become variable depending on the stereoisomerism through hydration effects and the origins of the variety are entropic.
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Affiliation(s)
- Simon Hikiri
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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Kajiwara Y, Yasuda S, Hikiri S, Hayashi T, Ikeguchi M, Murata T, Kinoshita M. Physical Origin of Thermostabilization by a Quadruple Mutation for the Adenosine A2a Receptor in the Active State. J Phys Chem B 2018; 122:4418-4427. [DOI: 10.1021/acs.jpcb.8b00443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yuta Kajiwara
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - 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
| | - Simon Hikiri
- Graduate School of Science, 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
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, 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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Hikiri S, Yoshidome T, Ikeguchi M. Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates. J Chem Theory Comput 2016; 12:5990-6000. [DOI: 10.1021/acs.jctc.6b00563] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Hikiri
- Graduate School of Medical
Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Yoshidome
- Graduate School of Medical
Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical
Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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