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Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach. J 2022. [DOI: 10.3390/j5010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of a protein in a protein folding system. We plotted the various energies against the root mean square deviation, required as a reference structure. Herein, we replotted the various energies against the end-to-end distance between the N- and C-termini, which is not a required reference and is experimentally measurable. The solvation free energies for all proteins tend to be low as the end-to-end distance increases, whereas the conformational energies tend to be low as the end-to-end distance decreases. The end-to-end distance is one of interesting measures to study the behavior of proteins.
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Isogai Y, Imamura H, Nakae S, Sumi T, Takahashi KI, Shirai T. Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals. iScience 2021; 24:102920. [PMID: 34430810 PMCID: PMC8374505 DOI: 10.1016/j.isci.2021.102920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/04/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Myoglobin (Mb) is highly concentrated in the myocytes of diving mammals such as whales and seals, in comparison with land animals, and its molecular evolution has played a crucial role in their deep-sea adaptation. We previously resurrected ancestral whale Mbs and demonstrated the evolutional strategies for higher solubility under macromolecular crowding conditions. Pinnipeds, such as seals and sea lions, are also expert diving mammals with Mb-rich muscles. In the present study, we resurrected ancestral pinniped Mbs and investigated their biochemical and structural properties. Comparisons between pinniped and whale Mbs revealed the common and distinctive strategies for the deep-sea adaptation. The overall evolution processes, gaining precipitant tolerance and improving thermodynamic stability, were commonly observed. However, the strategies for improving the folding stability differed, and the pinniped Mbs exploited the shielding of hydrophobic surfaces more effectively than the whale Mbs.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
- Corresponding author
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Setsu Nakae
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Ken-ichi Takahashi
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga 526-0829, Japan
- Corresponding author
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Sumi T, Imamura H. Water-mediated interactions destabilize proteins. Protein Sci 2021; 30:2132-2143. [PMID: 34382697 PMCID: PMC8442971 DOI: 10.1002/pro.4168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/29/2023]
Abstract
Proteins are folded to avoid exposure of the nonpolar groups to water because water‐mediated interactions between nonpolar groups are a promising factor in the thermodynamic stabilities of proteins—which is a well‐accepted view as one of the unique effects of hydrophobic interactions. This article poses a critical question for this classical view by conducting an accurate solvation free‐energy calculation for a thermodynamic cycle of a protein folding using a liquid‐state density functional theory. Here, the solvation‐free energy for a leucine zipper formation was examined in the coiled‐coil protein GCN4‐p1, a typical model for hydrophobic interactions, which demonstrated that water‐mediated interactions were unfavorable for the association of nonpolar groups in the native state, while the dispersion forces between them were, instead, responsible for the association. Furthermore, the present analysis well predicted the isolated helical state stabilized by pressure, which was previously observed in an experiment. We reviewed the problems in the classical concept and semiempirical presumption that the energetic cost of the hydration of nonpolar groups is a driving force of folding.
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Affiliation(s)
- Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Kita-ku, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Kita-ku, Japan
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
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Ohgi H, Imamura H, Sumi T, Nishikawa K, Koga Y, Westh P, Morita T. Two different regimes in alcohol-induced coil-helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations. Phys Chem Chem Phys 2021; 23:5760-5772. [PMID: 33481971 DOI: 10.1039/d0cp05103a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inhomogeneous distribution of constituent molecules in a mixed solvent has been known to give remarkable effects on the solute, e.g., conformational changes of biomolecules in an alcohol-water mixture. We investigated the general effects of 2,2,2-trifluoroethanol (TFE) on proteins/peptides in a mixture of water and TFE using melittin as a model protein. Fluctuations and Kirkwood-Buff integrals (KBIs) in the TFE-H2O mixture, quantitative descriptions of inhomogeneity, were determined by small-angle X-ray scattering investigation and compared with those in the aqueous solutions of other alcohols. The concentration fluctuation for the mixtures ranks as methanol < ethanol ≪ TFE < tert-butanol < 1-propanol, indicating that the inhomogeneity of molecular distribution in the TFE-H2O mixture is unexpectedly comparable to those in the series of mono-ols. On the basis of the concentration dependence of KBIs between the TFE molecules, it was found that a strong attraction between the TFE molecules is not necessarily important to induce helix conformation, which is inconsistent with the previously proposed mechanism. To address this issue, by combining the KBIs and the helix contents reported by the experimental spectroscopic studies, we quantitatively evaluated the change in the preferential binding parameter of TFE to melittin attributed to the coil-helix transition. As a result, we found two different regimes on TFE-induced helix formation. In the dilute concentration region of TFE below ∼2 M, where the TFE molecules are not aggregated among themselves, the excess preferential binding of TFE to the helix occurs due to the direct interaction between them, namely independent of the solvent fluctuation. In the higher concentration region above ∼2 M, in addition to the former effect, the excess preferential binding is significantly enhanced by the solvent fluctuation. This scheme should be held as general cosolvent effects of TFE on proteins/peptides.
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Affiliation(s)
- Hiroyo Ohgi
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.
| | - Keiko Nishikawa
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan. and Toyota Physical & Chemical Research Institute, Nagakute, Aichi 480-1192, Japan
| | - Yoshikata Koga
- Department of Chemistry, The University of British Columbia, Vancouver, V6T 1Z1, Canada
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs, Lyngby, Denmark
| | - Takeshi Morita
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
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Maruyama Y. Correction terms for the solvation free energy functional of three-dimensional reference interaction site model based on the reference-modified density functional theory. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Sumi T, Koga K. Theoretical analysis on thermodynamic stability of chignolin. Sci Rep 2019; 9:5186. [PMID: 30914684 PMCID: PMC6435801 DOI: 10.1038/s41598-019-41518-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/11/2019] [Indexed: 11/28/2022] Open
Abstract
Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann’s hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores.
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Affiliation(s)
- Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan. .,Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
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Wang N, Huang X, Gong H, Zhou Y, Li X, Li F, Bao Y, Xie C, Wang Z, Yin Q, Hao H. Thermodynamic mechanism of selective cocrystallization explored by MD simulation and phase diagram analysis. AIChE J 2019. [DOI: 10.1002/aic.16570] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Na Wang
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Hao Gong
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical TechnologyTianjin University Tianjin China
| | - Yanan Zhou
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Xin Li
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Fei Li
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Ying Bao
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Chuang Xie
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Zhao Wang
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Qiuxiang Yin
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
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Budkov Y, Kolesnikov A, Ivlev D, Kalikin N, Kiselev M. Possibility of pressure crossover prediction by classical DFT for sparingly dissolved compounds in scCO2. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Isogai Y, Imamura H, Nakae S, Sumi T, Takahashi KI, Nakagawa T, Tsuneshige A, Shirai T. Tracing whale myoglobin evolution by resurrecting ancient proteins. Sci Rep 2018; 8:16883. [PMID: 30442991 PMCID: PMC6237822 DOI: 10.1038/s41598-018-34984-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/29/2018] [Indexed: 11/24/2022] Open
Abstract
Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan.
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Setsu Nakae
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Ken-Ichi Takahashi
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Taro Nakagawa
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Antonio Tsuneshige
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan.
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