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Wang YR, Wang SL, Luo RM. Evaluation of key aroma compounds and protein secondary structure in the roasted Tan mutton during the traditional charcoal process. Front Nutr 2022; 9:1003126. [PMID: 36330139 PMCID: PMC9622931 DOI: 10.3389/fnut.2022.1003126] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/20/2022] [Indexed: 09/11/2023] Open
Abstract
The traditional charcoal technique was used to determine the changes in the key aroma compounds of Tan mutton during the roasting process. The results showed that the samples at the different roasting time were distinguished using GC-MS in combination with PLS-DA. A total of 26 volatile compounds were identified, among which 14 compounds, including (E)-2-octenal, 1-heptanol, hexanal, 1-hexanol, heptanal, 1-octen-3-ol, 1-pentanol, (E)-2-nonenal, octanal, 2-undecenal, nonanal, pentanal, 2-pentylfuran and 2-methypyrazine, were confirmed as key aroma compounds through the odor activity values (OAV) and aroma recombination experiments. The OAV and contribution rate of the 14 key aroma compounds were maintained at high levels, and nonanal had the highest OAV (322.34) and contribution rate (27.74%) in the samples after roasting for 10 min. The content of α-helix significantly decreased (P < 0.05), while the β-sheet content significantly increased (P < 0.05) during the roasting process. The content of random coils significantly increased in the samples roasted for 0-8 min (P < 0.05), and then no obvious change was observed. At the same time, β-turn content had no obvious change. Correlation analysis showed that the 14 key aroma compounds were all positively correlated with the content of α-helix and negatively correlated with the contents of β-sheet and random coil, and also positively correlated with the content of β-turn, except hexanal and 2-methypyrazine. The results are helpful to promoting the industrialization of roasted Tan mutton.
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Affiliation(s)
- Yong-Rui Wang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Song-Lei Wang
- College of Food and Wine, Ningxia University, Yinchuan, China
| | - Rui-Ming Luo
- College of Food and Wine, Ningxia University, Yinchuan, China
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2
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Lee S, Jo K, Jeong HG, Choi YS, Kyoung H, Jung S. Freezing-induced denaturation of myofibrillar proteins in frozen meat. Crit Rev Food Sci Nutr 2022; 64:1385-1402. [PMID: 36052640 DOI: 10.1080/10408398.2022.2116557] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Freezing is commonly used to extend the shelf life of meat and meat products but may impact the overall quality of those products by inducing structural changes in myofibrillar proteins (MPs) through denaturation, chemical modification, and encouraging protein aggregation. This review covers the effect of freezing on the denaturation of MPs in terms of the effects of ice crystallization on solute concentrations, cold denaturation, and protein oxidation. Freezing-induced denaturation of MPs begins with ice crystallization in extracellular spaces and changes in solute concentrations in the unfrozen water fraction. At typical temperatures for freezing meat (lower than -18 °C), cold denaturation of proteins occurs, accompanied by an alteration in their secondary and tertiary structure. Moreover, the disruption of muscle cells triggers the release of cellular enzymes, accelerating protein degradation and oxidation. To minimize severe deterioration during the freezing and frozen storage of meat, there is a vital need to use an appropriate freezing temperature below the glass transition temperature and to avoid temperature fluctuations during storage to prevent recrystallization. Such an understanding of MP denaturation can be applied to determine the optimum freezing conditions for meat products with highly retained sensory, nutritional, and functional qualities.
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Affiliation(s)
- Seonmin Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Kyung Jo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Hyun Gyung Jeong
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Yun-Sang Choi
- Research Group of Food Processing, Korea Food Research Institute, Wanju, Korea
| | - Hyunjin Kyoung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Samooel Jung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
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3
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Chen Y, Mutukuri TT, Wilson NE, Zhou QT. Pharmaceutical protein solids: Drying technology, solid-state characterization and stability. Adv Drug Deliv Rev 2021; 172:211-233. [PMID: 33705880 PMCID: PMC8107147 DOI: 10.1016/j.addr.2021.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 01/30/2023]
Abstract
Despite the boom in biologics over the past decade, the intrinsic instability of these large molecules poses significant challenges to formulation development. Almost half of all pharmaceutical protein products are formulated in the solid form to preserve protein native structure and extend product shelf-life. In this review, both traditional and emerging drying techniques for producing protein solids will be discussed. During the drying process, various stresses can impact the stability of protein solids. However, understanding the impact of stress on protein product quality can be challenging due to the lack of reliable characterization techniques for biological solids. Both conventional and advanced characterization techniques are discussed including differential scanning calorimetry (DSC), solid-state Fourier transform infrared spectrometry (ssFTIR), solid-state fluorescence spectrometry, solid-state hydrogen deuterium exchange (ssHDX), solid-state nuclear magnetic resonance (ssNMR) and solid-state photolytic labeling (ssPL). Advanced characterization tools may offer mechanistic investigations into local structural changes and interactions at higher resolutions. The continuous exploration of new drying techniques, as well as a better understanding of the effects caused by different drying techniques in solid state, would advance the formulation development of biological products with superior quality.
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Affiliation(s)
- Yuan Chen
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Tarun Tejasvi Mutukuri
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Nathan E Wilson
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA.
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4
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Wang G, Li J. Review, analysis, and optimization of the CRISPR Streptococcus pyogenes Cas9 system. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2021.100080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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5
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Comparison based on statistical thermodynamics between globule-to-coil transition of poly(N-isopropylacrylamide) and cold denaturation of a protein. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Yasuda S, Kazama K, Akiyama T, Kinoshita M, Murata T. Elucidation of cosolvent effects thermostabilizing water-soluble and membrane proteins. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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7
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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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] [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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9
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Zhou CY, Cao JX, Zhuang XB, Bai Y, Li CB, Xu XL, Zhou GH. Evaluation of the secondary structure and digestibility of myofibrillar proteins in cooked ham. CYTA - JOURNAL OF FOOD 2019. [DOI: 10.1080/19476337.2018.1554704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Chang-Yu Zhou
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, P.R. China
| | - Jin-Xuan Cao
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, P.R. China
| | - Xin-Bo Zhuang
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
| | - Yun Bai
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
| | - Chun-Bao Li
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
| | - Xing-Lian Xu
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
| | - Guang-Hong Zhou
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
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10
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Hayashi T, Matsuda T, Nagata T, Katahira M, Kinoshita M. Mechanism of protein-RNA recognition: analysis based on the statistical mechanics of hydration. Phys Chem Chem Phys 2019; 20:9167-9180. [PMID: 29560998 DOI: 10.1039/c8cp00155c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We investigate the RBD1-r(GUAGU) binding as a case study using all-atom models for the biomolecules, molecular models for water, and the currently most reliable statistical-mechanical method. RBD1 is one of the RNA-binding domains of mammalian Musashi1 (Msi1), and r(GUAGU) contains the minimum recognition sequence for Msi1, r(GUAG). We show that the binding is driven by a large gain of configurational entropy of water in the entire system. It is larger than the sum of conformational-entropy losses for RBD1 and r(GUAGU). The decrease in RBD1-r(GUAGU) interaction energy upon binding is largely cancelled out by the increase in the sum of RBD1-water, r(GUAGU)-water, and water-water interaction energies. We refer to this increase as "energetic dehydration". The decrease is larger than the increase for the van der Waals component, whereas the opposite is true for the electrostatic component. We give a novel reason for the empirically known fact that protein residues possessing side chains with positive charges and with flat moieties frequently appear within protein-RNA binding interfaces. A physical picture of the general protein-RNA binding mechanism is then presented. To achieve a sufficiently large water-entropy gain, shape complementarity at the atomic level needs to be constructed by utilizing the stacking and sandwiching of flat moieties (aromatic rings of the protein and nucleobases of RNA) as fundamental motifs. To compensate for electrostatic energetic dehydration, charge complementarity becomes crucial within the binding interface. We argue the reason why the RNA recognition motif (RRM) is the most ubiquitous RNA binding domain.
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Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Tomoaki Matsuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Masato Katahira
- 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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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: 15] [Impact Index Per Article: 2.5] [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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12
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13
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Tavagnacco L, Zaccarelli E, Chiessi E. On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water. Phys Chem Chem Phys 2018; 20:9997-10010. [PMID: 29619464 PMCID: PMC5932979 DOI: 10.1039/c8cp00537k] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cooperativity of PNIPAM coil-to-globule transition in water arises from the structuring of solvent in proximity to hydrophobic groups.
By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain.
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Affiliation(s)
- L Tavagnacco
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
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14
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Tokunaga Y, Yamamori Y, Matubayasi N. Probabilistic analysis for identifying the driving force of protein folding. J Chem Phys 2018; 148:125101. [PMID: 29604891 DOI: 10.1063/1.5019410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.
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Affiliation(s)
- Yoshihiko Tokunaga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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15
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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: 2.0] [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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16
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Oshima H, Hayashi T, Kinoshita M. Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects. Biophys J 2017; 110:2496-2506. [PMID: 27276267 DOI: 10.1016/j.bpj.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 01/01/2023] Open
Abstract
Actomyosin is an important molecular motor, and the binding of actin and myosin is an essential research target in biophysics. Nevertheless, the physical factors driving or opposing the binding are still unclear. Here, we investigate the role of water in actin-myosin binding using the most reliable statistical-mechanical method currently available for assessing biomolecules immersed in water. This method is characterized as follows: water is treated not as a dielectric continuum but as an ensemble of molecules; the polyatomic structures of proteins are taken into consideration; and the binding free energy is decomposed into physically insightful entropic and energetic components by accounting for the hydration effect to its full extent. We find that the actin-myosin binding brings large gains of electrostatic and Lennard-Jones attractive interactions. However, these gains are accompanied by even larger losses of actin-water and myosin-water electrostatic and LJ attractive interactions. Although roughly half of the energy increase due to the losses is cancelled out by the energy decrease arising from structural reorganization of the water released upon binding, the remaining energy increase is still larger than the energy decrease brought by the gains mentioned above. Hence, the net change in system energy is positive, which opposes binding. Importantly, the binding is driven by a large gain of configurational entropy of water, which surpasses the positive change in system energy and the conformational entropy loss occurring for actin and myosin. The principal physical origin of the large water-entropy gain is as follows: the actin-myosin interface is closely packed with the achievement of high shape complementarity on the atomic level, leading to a large increase in the total volume available to the translational displacement of water molecules in the system and a resultant reduction of water crowding (i.e., entropic correlations among water molecules).
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Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
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17
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Murakami S, Hayashi T, Kinoshita M. Effects of salt or cosolvent addition on solubility of a hydrophobic solute in water: Relevance to those on thermal stability of a protein. J Chem Phys 2017; 146:055102. [DOI: 10.1063/1.4975165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Merlino A, Pontillo N, Graziano G. A driving force for polypeptide and protein collapse. Phys Chem Chem Phys 2017; 19:751-756. [DOI: 10.1039/c6cp07397b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Polypeptide collapse is driven by the solvent-excluded volume decrease, the presence of nonpolar side chains is not so important.
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Affiliation(s)
- Antonello Merlino
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- Complesso Universitario di Monte Sant'Angelo
- 80126 Napoli
- Italy
| | - Nicola Pontillo
- Dipartimento di Scienze Chimiche
- Università degli Studi di Napoli Federico II
- Complesso Universitario di Monte Sant'Angelo
- 80126 Napoli
- Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie
- Università del Sannio
- 82100 Benevento
- Italy
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19
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Kinoshita M, Hayashi T. Unified elucidation of the entropy-driven and -opposed hydrophobic effects. Phys Chem Chem Phys 2017; 19:25891-25904. [DOI: 10.1039/c7cp05160c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The association of nonpolar solutes is generally believed to be entropy driven, which has been shown to be true for the contact of small molecules, ellipsoids, and plates.
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Hayashi T, Oshima H, Harano Y, Kinoshita M. Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:344003. [PMID: 27366886 DOI: 10.1088/0953-8984/28/34/344003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For neutral hard-sphere solutes, we compare the reduced density profile of water around a solute g(r), solvation free energy μ, energy U, and entropy S under the isochoric condition predicted by the two theories: dielectrically consistent reference interaction site model (DRISM) and angle-dependent integral equation (ADIE) theories. A molecular model for water pertinent to each theory is adopted. The hypernetted-chain (HNC) closure is employed in the ADIE theory, and the HNC and Kovalenko-Hirata (K-H) closures are tested in the DRISM theory. We also calculate g(r), U, S, and μ of the same solute in a hard-sphere solvent whose molecular diameter and number density are set at those of water, in which case the radial-symmetric integral equation (RSIE) theory is employed. The dependences of μ, U, and S on the excluded volume and solvent-accessible surface area are analyzed using the morphometric approach (MA). The results from the ADIE theory are in by far better agreement with those from computer simulations available for g(r), U, and μ. For the DRISM theory, g(r) in the vicinity of the solute is quite high and becomes progressively higher as the solute diameter d U increases. By contrast, for the ADIE theory, it is much lower and becomes further lower as d U increases. Due to unphysically positive U and significantly larger |S|, μ from the DRISM theory becomes too high. It is interesting that μ, U, and S from the K-H closure are worse than those from the HNC closure. Overall, the results from the DRISM theory with a molecular model for water are quite similar to those from the RSIE theory with the hard-sphere solvent. Based on the results of the MA analysis, we comparatively discuss the different theoretical methods for cases where they are applied to studies on the solvation of a protein.
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Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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21
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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: 2.8] [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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22
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Sanfelice D, Morandi E, Pastore A, Niccolai N, Temussi PA. Cold Denaturation Unveiled: Molecular Mechanism of the Asymmetric Unfolding of Yeast Frataxin. Chemphyschem 2015; 16:3599-602. [PMID: 26426928 PMCID: PMC4676917 DOI: 10.1002/cphc.201500765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/01/2015] [Indexed: 11/11/2022]
Abstract
What is the mechanism that determines the denaturation of proteins at low temperatures, which is, by now, recognized as a fundamental property of all proteins? We present experimental evidence that clarifies the role of specific interactions that favor the entrance of water into the hydrophobic core, a mechanism originally proposed by Privalov but never proved experimentally. By using a combination of molecular dynamics simulation, molecular biology, and biophysics, we identified a cluster of negatively charged residues that represents a preferential gate for the entrance of water molecules into the core. Even single-residue mutations in this cluster, from acidic to neutral residues, affect cold denaturation much more than heat denaturation, suppressing cold denaturation at temperatures above zero degrees. The molecular mechanism of the cold denaturation of yeast frataxin is intrinsically different from that of heat denaturation.
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Affiliation(s)
- Domenico Sanfelice
- Department of Basic and Clinical Neurosciences, Kings College London, London, SE5 9RX, UK
| | - Edoardo Morandi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Annalisa Pastore
- Department of Basic and Clinical Neurosciences, Kings College London, London, SE5 9RX, UK.
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Piero Andrea Temussi
- Department of Basic and Clinical Neurosciences, Kings College London, London, SE5 9RX, UK.
- Department of Chemical Sciences, Università di Napoli Federico II, via Cinthia, 80126, Napoli, Italy.
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23
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Hayashi T, Oshima H, Yasuda S, Kinoshita M. Mechanism of One-to-Many Molecular Recognition Accompanying Target-Dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example. J Phys Chem B 2015; 119:14120-9. [PMID: 26421917 DOI: 10.1021/acs.jpcb.5b08513] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The new type of molecular recognition, in which an intrinsically disordered region (IDR) of a protein binds to many different target proteins with target-dependent structure formation, is indispensable to the expression of life phenomena and also implicated in a number of diseases. According to the prevailing view, the physicochemical factors responsible for the binding are also target dependent. Here we consider an IDR of the tumor suppressor p53 protein, p53CTD, as an important example related to carcinogenesis and analyze its binding to four targets accompanying the formation of target-dependent structures (i.e., helix, sheet, and two different coils) using our statistical-mechanical method combined with molecular models for water. We find that all of the seemingly different binding processes are driven by a large gain of the translational, configurational entropy of water in the system. The gain originates from sufficiently high shape complementarity on the atomic level within the p53CTD-target interface. It is also required that the electrostatic complementarity be ensured as much as possible to compensate for the dehydration. Such complementarities are achieved in harmony with the portion of the target to which p53CTD binds, leading to a large diversity of structures of p53CTD formed upon binding: If they are not achievable, the binding does not occur. This finding is made possible only by calculating the changes in thermodynamic quantities upon binding and decomposing them into physically insightful components.
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Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Hiraku Oshima
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- 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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24
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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: 1.2] [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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25
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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: 1.1] [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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26
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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: 0.7] [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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27
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Oshima H, Kinoshita M. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water. J Chem Phys 2015; 142:145103. [DOI: 10.1063/1.4917075] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hiraku Oshima
- 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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28
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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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29
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Abstract
A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy.
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30
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Koda R, Koyama A, Fukami K, Nishi N, Sakka T, Abe T, Kitada A, Murase K, Kinoshita M. Effect of cation species on surface-induced phase transition observed for platinum complex anions in platinum electrodeposition using nanoporous silicon. J Chem Phys 2014; 141:074701. [DOI: 10.1063/1.4892596] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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31
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Kinoshita M, Oshima H. Changes in hydrophobic and hydrophilic hydration properties caused by raising the pressure or by lowering the temperature. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Kumar A, Rani A, Venkatesu P, Kumar A. Quantitative evaluation of the ability of ionic liquids to offset the cold-induced unfolding of proteins. Phys Chem Chem Phys 2014; 16:15806-10. [DOI: 10.1039/c4cp01001a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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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: 33] [Impact Index Per Article: 3.3] [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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34
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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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35
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Fukami K, Koda R, Sakka T, Ogata Y, Kinoshita M. Electrochemical deposition of platinum within nanopores on silicon: Drastic acceleration originating from surface-induced phase transition. J Chem Phys 2013; 138:094702. [DOI: 10.1063/1.4793526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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36
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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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