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Li F, Lv K, Liu X, Zhou Y, Liu K. Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models. J Chem Inf Model 2024; 64:5535-5546. [PMID: 38962905 DOI: 10.1021/acs.jcim.4c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
For quickly predicting the rational arrangement of catalysts and substrates, we previously proposed a method to calculate the interacted volumes of molecules over their 3D point cloud models. However, the nonuniform density in molecular point clouds may lead to incomplete contours in some slices, reducing the accuracy of the previous method. In this paper, we propose a two-step method for more accurately computing molecular interacted volumes. First, by employing a prematched mesh slicing method, we layer the 3D triangular mesh models of the electrostatic potential isosurfaces of two molecules globally, transforming the volume calculation into finding the intersecting areas in each layer. Next, by subdividing polygonal edges, we accurately identify intersecting parts within each layer, ensuring precise calculation of interacted volumes. In addition, we present a concise overview for computing intersecting areas in cases of multiple contour intersections and for improving computational efficiency by incorporating bounding boxes at three stages. Experimental results demonstrate that our method maintains high accuracy in different experimental data sets, with an average relative error of 0.16%. On the same experimental setup, our average relative error is 0.07%, which is lower than the previous algorithm's 1.73%, improving the accuracy and stability in calculating interacted volumes.
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Affiliation(s)
- Fangting Li
- College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Kun Lv
- College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xiaohua Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuqiao Zhou
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kai Liu
- College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
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2
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Chiangraeng N, Nakano H, Nimmanpipug P, Yoshida N. Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[ n]uril of Different Sizes. J Phys Chem B 2023; 127:3651-3662. [PMID: 37071755 DOI: 10.1021/acs.jpcb.3c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The role of water in host-ligand binding was investigated using a combination of molecular dynamics simulation and three-dimensional reference interaction site model theory. Three different hosts were selected (CB6, CB7, and CB8). Six organic molecules were used as representative ligands: dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF), acetone, 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO), cyclopentanone (CPN), and pyrrole. From the binding free energy and its components, we divided the ligands into two groups: those with relatively small molecular size (DMSO, DMF, acetone, and pyrrole) and those with relatively large molecular size (DBO and CPN). We established that the solvent water in the CB6 cavity can be completely displaced by small ligands, resulting in a greater binding affinity compared with larger CBs, except in the case of the small pyrrole ligand, due to outstanding intrinsic properties such as the relatively high hydrophobicity and low dipole moment. In the case of the large ligands, the solvent water can be displaced by DBO and CPN in both CB6 and CB7; there were similar tendencies in their binding affinities, with the greatest affinity in the CB7 complexes. However, the tendencies of the binding affinity components are completely different due to the difference between the complex structure and the solvation structure when a ligand binds with a CB structure. The binding affinities suggest that the size fit between the ligand and CB cannot guarantee the greatest binding affinity gain because the binding structure and intrinsic properties of CB and ligand equally play a crucial role.
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Affiliation(s)
- Natthiti Chiangraeng
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Piyarat Nimmanpipug
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Norio Yoshida
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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3
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Kawama K, Fukushima Y, Ikeguchi M, Ohta M, Yoshidome T. gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins. J Chem Inf Model 2022; 62:4460-4473. [PMID: 36068974 DOI: 10.1021/acs.jcim.2c00987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water site distribution function around the protein, is crucial. The typical methods for computing the distribution functions, including molecular dynamics simulations and the three-dimensional reference interaction site model (3D-RISM) theory, require a long computation time ranging from hours to tens of hours. Here, we propose a deep learning (DL) model that rapidly estimates the distribution functions around proteins obtained using the 3D-RISM theory from the protein 3D structure. The distribution functions predicted using our DL model are in good agreement with those obtained using the 3D-RISM theory. Particularly, the coefficient of determination between the distribution function obtained by the DL model and that obtained using the 3D-RISM theory is approximately 0.98. Furthermore, using a graphics processing unit, the prediction by the DL model is completed in less than 1 min, more than 2 orders of magnitude faster than the calculation time of the 3D-RISM theory. The position of water molecules around the protein was estimated based on the distribution function obtained by our DL model, and the position of waters estimated by our DL model was in good agreement with that of water molecules estimated using the 3D-RISM theory and of crystallographic waters. Therefore, our DL model provides a practical and efficient way to calculate the three-dimensional water site distribution functions and to estimate the position of water molecules around the protein. The program called "gr Predictor" is available under the GNU General Public License from https://github.com/YoshidomeGroup-Hydration/gr-predictor.
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Affiliation(s)
- Kosuke Kawama
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Yusaku Fukushima
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Mitsunori Ikeguchi
- AI-Driven Drug Discovery Collaborative Unit, HPC- and AI-Driven Drug Development Platform Division, Center for Computational Science, RIKEN, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masateru Ohta
- AI-Driven Drug Discovery Collaborative Unit, HPC- and AI-Driven Drug Development Platform Division, Center for Computational Science, RIKEN, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Yoshidome
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
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4
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Kadtsyn ED, Nichiporenko VA, Medvedev NN. Volumetric properties of solutions on the perspective of Voronoi tessellation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Aggarwal L, Biswas P. Hydration Thermodynamics of Familial Parkinson's Disease-Linked Mutants of α-Synuclein. J Chem Inf Model 2021; 61:1850-1858. [PMID: 33749266 DOI: 10.1021/acs.jcim.1c00034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The hydration thermodynamics of different mutants of α-synuclein (α-syn) related to familial Parkinson's disease (PD) is explored using a computational approach that combines both molecular dynamics simulations in water and integral equation theory of molecular liquids. This analysis focuses on the change in conformational entropy, hydration free energy (HFE), and partial molar volume of α-syn upon mutation. The results show that A53T, A30P, E46K, and H50Q mutants aggregate more readily and display increased HFE and less negative interaction volume than the wild-type α-syn. In contrast, an opposite trend is observed for the G51D mutant with a lower experimental aggregation rate. The residuewise decomposition analysis of the HFE highlights that the dehydration/hydration of the hydrophilic residue-rich N- and C-termini of α-syn majorly contributes to the change upon mutation. The hydration shell contributions of different residues to the interaction volume are consistent with its increase/decrease upon mutation. This work shows that both HFE and interaction volume determine the aggregation kinetics of α-syn upon mutation and may serve as an appropriate benchmark for the treatment of PD.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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Sugita M, Onishi I, Irisa M, Yoshida N, Hirata F. Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory. Molecules 2021; 26:E271. [PMID: 33430461 PMCID: PMC7826681 DOI: 10.3390/molecules26020271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022] Open
Abstract
There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.
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Affiliation(s)
- Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1, Ookayama Meguro-ku, Tokyo 152-8550, Japan;
| | - Itaru Onishi
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Masayuki Irisa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Norio Yoshida
- Department of Chemistry, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan;
| | - Fumio Hirata
- Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
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Aggarwal L, Biswas P. Interaction Volume Is a Measure of the Aggregation Propensity of Amyloid-β. J Phys Chem Lett 2020; 11:3993-4000. [PMID: 32352786 DOI: 10.1021/acs.jpclett.0c00922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study highlights the significance of the partial molar volume of amino acids in predicting the aggregation propensity of an intrinsically disordered protein, amyloid-β (Aβ), and its mutants in aqueous solution. The change in the interaction volume of the protein or mutant is quantitatively correlated with its calculated experimental aggregation propensity. This method also reveals how the interaction volume may be tuned by changing the charge and hydrophobicity of Aβ. While a positive change in the interaction volume and a higher aggregation propensity are observed for mutants with a decrease in the overall charge and/or an increase in hydrophobicity, a reverse trend is observed for the mutants with a decrease in the hydrophobicity and/or an increase in its charge. Hence, the interaction volume may be considered as a key parameter for monitoring protein aggregation that bridges the gap between the experimental aggregation kinetics and solvation thermodynamics.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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8
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Tanimoto S, Yoshida N, Yamaguchi T, Ten-no SL, Nakano H. Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory. J Chem Inf Model 2019; 59:3770-3781. [DOI: 10.1021/acs.jcim.9b00330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shoichi Tanimoto
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tsuyoshi Yamaguchi
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Seiichiro L. Ten-no
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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9
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Abstract
Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Å water-carbon cutoff and a 4 Å water-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Å2 which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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10
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Yoshida N, Higashi M, Motoki H, Hirota S. Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach. J Chem Phys 2018; 148:025102. [DOI: 10.1063/1.5009785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishiku, Fukuoka 819-0395, Japan
| | - Masahiro Higashi
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Hideyoshi Motoki
- Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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11
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Sugita M, Hirata F. Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:384002. [PMID: 27452185 DOI: 10.1088/0953-8984/28/38/384002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A protocol to calculate the binding free energy of a host-guest system is proposed based on the MM/3D-RISM method, taking cyclodextrin derivatives and their ligands as model systems. The protocol involves the procedure to identify the most probable binding mode (MPBM) of receptors and ligands by means of the umbrella sampling method. The binding free energies calculated by the MM/3D-RISM method for the complexes of the seven ligands with the MPBM of the cyclodextrin, and with the fluctuated structures around it, are in agreement with the corresponding experimental data in a semi-quantitative manner. It suggests that the protocol proposed here is promising for predicting the binding affinity of a small ligand to a relatively rigid receptor such as cyclodextrin.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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12
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Partial molar volume of nonionic surfactants in aqueous solution studied by the KB/3D-RISM–KH theory. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Voloshin VP, Medvedev NN, Smolin N, Geiger A, Winter R. Disentangling Volumetric and Hydrational Properties of Proteins. J Phys Chem B 2015; 119:1881-90. [DOI: 10.1021/jp510891b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vladimir P. Voloshin
- Institute of Chemical
Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
| | - Nikolai N. Medvedev
- Institute of Chemical
Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolai Smolin
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
| | - Alfons Geiger
- Physikalische
Chemie, Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Roland Winter
- Physikalische
Chemie, Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
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14
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Abstract
The partial specific (or molar) volume, expansibility, and compressibility of a protein are fundamental thermodynamic quantities for characterizing its structure in solution. We review the definitions, measurements, and implications of these volumetric quantities in relation to protein structural biology. The partial specific volumes under constant molality (isomolal) and chemical potential (isopotential) conditions of the cosolvent (multicomponent systems) are explained in terms of preferential solvent interactions relevant to the solubility and stability of proteins. The partial expansibility is briefly discussed in terms of the effects of temperature on protein-solvent interactions (hydration) and internal packing defects (cavities). We discuss the compressibility-structure-function relationships of proteins based on analyses of the correlations between the partial adiabatic compressibilities and the structures or functions of various globular proteins (including mutants), focusing on the roles of the internal cavities in structural fluctuations. The volume and compressibility changes associated with various conformational transitions are also discussed in terms of the changes in hydration and cavities in order to elucidate the nonnative structures and the transition mechanisms, especially those associated with pressure denaturation.
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15
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Distinct configurations of cations and water in the selectivity filter of the KcsA potassium channel probed by 3D-RISM theory. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.03.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Yoshida N. Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method. J Chem Phys 2014; 140:214118. [DOI: 10.1063/1.4879795] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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17
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Phongphanphanee S, Yoshida N, Oiki S, Hirata F. Probing “ambivalent” snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The potassium channel is highly selective for K+ over Na+, and the mechanism underlying this selectivity remains unclear. We show the three-dimensional distribution functions (3D-DFs) of small cations (Li+, Na+, and K+) and the free energy profile of ions inside the open selectivity filter (SF) of the KcsA channel. Our previous results [S. Phongphanphanee, N. Yoshida, S. Oiki, F. Hirata. Abstract Book of 5th International Symposium on Molecular Science of Fluctuations toward Biological Functions, P062 (2012)] indicate that the 3D-DF for K+ exhibits distinct peaks at the sites formed by the eight carbonyl oxygen atoms belonging to the surrounding peptide-backbone and residues (the cage site). Li+ has sharp distributions in the 3D-DF at the center of a quadruplex composed of four carbonyl oxygen atoms (the plane site). Na+ has a rather diffuse distribution throughout the SF region with peaks both in the plane and in cage sites. The results provide microscopic evidence of the phenomenological findings that Li+ and Na+ are not excluded from the SF region and that the binding affinity alone does not cause the ion selectivity of KcsA. In the present study, with an ion placed explicitly along the pore axis, the free energy profiles of the ions inside the SF were calculated; from these profiles we suggest a new mechanism for selective K+ permeation. According to the model, a K+ ion must overcome a free energy barrier that is approximately half that of Na+ to exit from either of the SF mouths due to the existence of an intermediate local minimum along the route for climbing the barriers.
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18
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Medvedev NN, Voloshin VP, Kim AV, Anikeenko AV, Geiger A. Culation of partial molar volume and its components for molecular dynamics models of dilute solutions. J STRUCT CHEM+ 2014. [DOI: 10.1134/s0022476613080088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Shek YL, Noudeh GD, Nazari M, Heerklotz H, Abu-Ghazalah RM, Dubins DN, Chalikian TV. Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex. Biopolymers 2013; 101:216-27. [DOI: 10.1002/bip.22317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Yuen Lai Shek
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Golamreza Dehghan Noudeh
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Mozhgan Nazari
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Heiko Heerklotz
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Rashid M. Abu-Ghazalah
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - David N. Dubins
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
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20
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Makarov A, LoBrutto R, Karpinski P. Effect of pressure on secondary structure of proteins under ultra high pressure liquid chromatographic conditions. J Chromatogr A 2013; 1318:112-21. [DOI: 10.1016/j.chroma.2013.09.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/14/2013] [Accepted: 09/18/2013] [Indexed: 11/28/2022]
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21
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Sindhikara DJ, Hirata F. Analysis of biomolecular solvation sites by 3D-RISM theory. J Phys Chem B 2013; 117:6718-23. [PMID: 23675899 DOI: 10.1021/jp4046116] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.
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Affiliation(s)
- Daniel J Sindhikara
- Department of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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22
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Sindhikara DJ, Yoshida N, Hirata F. Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase. J Comput Chem 2012; 33:1536-43. [PMID: 22522665 DOI: 10.1002/jcc.22984] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/10/2012] [Accepted: 03/10/2012] [Indexed: 01/16/2023]
Abstract
We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three-dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D-RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI-272 bound form of HIV-1 protease and predicting both sodium ions and water molecules near the rotor ring of F-adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39-0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D-RISM output within minutes. It is extremely useful for examining multiple specific solvent-solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel J Sindhikara
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan
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23
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Makarov A, LoBrutto R, Karpinski P, Kazakevich Y, Christodoulatos C, Ganguly AK. INVESTIGATION OF THE EFFECT OF PRESSURE AND LIOPHILIC MOBILE PHASE ADDITIVES ON RETENTION OF SMALL MOLECULES AND PROTEINS USING REVERSED-PHASE ULTRAHIGH PRESSURE LIQUID CHROMATOGRAPHY. J LIQ CHROMATOGR R T 2012. [DOI: 10.1080/10826076.2011.601494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Alexey Makarov
- a Novartis Pharmaceuticals Corporation , East Hanover , New Jersey , USA
| | - Rosario LoBrutto
- a Novartis Pharmaceuticals Corporation , East Hanover , New Jersey , USA
| | - Paul Karpinski
- a Novartis Pharmaceuticals Corporation , East Hanover , New Jersey , USA
| | | | | | - A. K. Ganguly
- c Stevens Institute of Technology, Castle Point on Hudson , Hoboken , New Jersey , USA
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24
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Mimura S, Yamato T, Kamiyama T, Gekko K. Nonneutral evolution of volume fluctuations in lysozymes revealed by normal-mode analysis of compressibility. Biophys Chem 2012; 161:39-45. [DOI: 10.1016/j.bpc.2011.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 11/25/2011] [Indexed: 11/28/2022]
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25
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Size dependence of cavity volume: A molecular dynamics study. Biophys Chem 2012; 161:46-9. [DOI: 10.1016/j.bpc.2011.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/14/2011] [Accepted: 10/16/2011] [Indexed: 11/18/2022]
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26
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Mehta CM, White ET, Litster JD. Correlation of second virial coefficient with solubility for proteins in salt solutions. Biotechnol Prog 2011; 28:163-70. [PMID: 22002946 DOI: 10.1002/btpr.724] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/30/2011] [Indexed: 11/08/2022]
Abstract
In this work, osmotic second virial coefficients (B(22)) were determined and correlated with the measured solubilities for the proteins, α-amylase, ovalbumin, and lysozyme. The B(22) values and solubilities were determined in similar solution conditions using two salts, sodium chloride and ammonium sulfate in an acidic pH range. An overall decrease in the solubility of the proteins (salting out) was observed at high concentrations of ammonium sulfate and sodium chloride solutions. However, for α-amylase, salting-in behavior was also observed in low concentration sodium chloride solutions. In ammonium sulfate solutions, the B(22) are small and close to zero below 2.4 M. As the ammonium sulfate concentrations were further increased, B(22) values decreased for all systems studied. The effect of sodium chloride on B(22) varies with concentration, solution pH, and the type of protein studied. Theoretical models show a reasonable fit to the experimental derived data of B(22) and solubility. B(22) is also directly proportional to the logarithm of the solubility values for individual proteins in salt solutions, so the log-linear empirical models developed in this work can also be used to rapidly predict solubility and B(22) values for given protein-salt systems.
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Affiliation(s)
- Chirag M Mehta
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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27
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Lucent D, Snow CD, Aitken CE, Pande VS. Non-bulk-like solvent behavior in the ribosome exit tunnel. PLoS Comput Biol 2010; 6:e1000963. [PMID: 20975935 PMCID: PMC2958802 DOI: 10.1371/journal.pcbi.1000963] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/17/2010] [Indexed: 11/19/2022] Open
Abstract
As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.
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Affiliation(s)
- Del Lucent
- Biophysics Program, Stanford University, Stanford, California, USA
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28
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Yu I, Tasaki T, Nakada K, Nagaoka M. Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume: Time-Resolved Surficial Kirkwood-Buff Approach. J Phys Chem B 2010; 114:12392-7. [DOI: 10.1021/jp1043267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Isseki Yu
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 229-8558, Japan, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan, and CREST, Japan Science and Technology Agency, Japan
| | - Tomohiro Tasaki
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 229-8558, Japan, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan, and CREST, Japan Science and Technology Agency, Japan
| | - Kyoko Nakada
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 229-8558, Japan, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan, and CREST, Japan Science and Technology Agency, Japan
| | - Masataka Nagaoka
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Sagamihara, Kanagawa 229-8558, Japan, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan, and CREST, Japan Science and Technology Agency, Japan
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29
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Awile O, Krisko A, Sbalzarini IF, Zagrovic B. Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. PLoS Comput Biol 2010; 6:e1000854. [PMID: 20657662 PMCID: PMC2904767 DOI: 10.1371/journal.pcbi.1000854] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 06/04/2010] [Indexed: 12/22/2022] Open
Abstract
The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity.
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Affiliation(s)
- Omar Awile
- Mediterranean Institute for Life Sciences, Split, Croatia
- Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Anita Krisko
- Faculte de Medecine Paris Descartes, INSERM U1001, Paris, France
| | - Ivo F. Sbalzarini
- Mediterranean Institute for Life Sciences, Split, Croatia
- Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Bojan Zagrovic
- Mediterranean Institute for Life Sciences, Split, Croatia
- Department of Physics, University of Split, Split, Croatia
- University of Vienna, Department of Structural & Computational Biology, Max F. Perutz Laboratories, Vienna, Austria
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30
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Phongphanphanee S, Yoshida N, Hirata F. The potential of mean force of water and ions in aquaporin channels investigated by the 3D-RISM method. J Mol Liq 2009. [DOI: 10.1016/j.molliq.2008.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Yoshida N, Imai T, Phongphanphanee S, Kovalenko A, Hirata F. Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids. J Phys Chem B 2009; 113:873-86. [PMID: 19105732 DOI: 10.1021/jp807068k] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.
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Affiliation(s)
- Norio Yoshida
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
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32
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Yu I, Takayanagi M, Nagaoka M. Intrinsic Alterations in the Partial Molar Volume on the Protein Denaturation: Surficial Kirkwood−Buff Approach. J Phys Chem B 2009; 113:3543-7. [DOI: 10.1021/jp808575k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Isseki Yu
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masayoshi Takayanagi
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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33
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Imai T, Hisadomi Y, Sawamura S, Taniguchi Y. Uncovering the physical origin of the difference between aliphatic chain and aromatic ring in the “hydrophobic” effects on partial molar volume. J Chem Phys 2008; 128:044502. [DOI: 10.1063/1.2828768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Yu I, Jindo Y, Nagaoka M. Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration. J Phys Chem B 2007; 111:10231-8. [PMID: 17676787 DOI: 10.1021/jp068367z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ectoine, a zwitterionic compatible solute (CS), acts as an effective stabilizer of protein function. Using molecular dynamics simulation, solvent spatial distributions around both met-enkephalin (M-Enk) and chymotrypsin inhibitor 2 (CI2) were investigated at the molecular level in ectoine aqueous solution. An unexpected finding was that ectoine exhibits preferential binding, as an overall tendency, around both peptides. However, with the aid of the surficial Kirkwood-Buff parameter, it was clearly shown that the preferential exclusion of ectoine from the peptide surface was weaker in the smaller M-Enk than in the larger CI2. It is concluded that a denser and more structured hydration layer, such as that developed on the surface of CI2, is an important factor in the exclusion of ectoine.
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Affiliation(s)
- Isseki Yu
- Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan
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35
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Imai T, Ohyama S, Kovalenko A, Hirata F. Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin. Protein Sci 2007; 16:1927-33. [PMID: 17660257 PMCID: PMC2206979 DOI: 10.1110/ps.072909007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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36
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Imai T, Isogai H, Seto T, Kovalenko A, Hirata F. Theoretical study of volume changes accompanying xenon-lysozyme binding: implications for the molecular mechanism of pressure reversal of anesthesia. J Phys Chem B 2007; 110:12149-54. [PMID: 16800529 DOI: 10.1021/jp056346j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The change in partial molar volume (PMV) accompanying the xenon-lysozyme binding was investigated for elucidating the molecular mechanism of the pressure reversal of general anesthesia, using the three-dimensional reference interaction site model theory of molecular solvation. An increase of the PMV from xenon binding to the substrate binding site of lysozyme was found, and the binding is suppressed by pressure, while the internal site binding did not change the PMV. The PMV change was analyzed by decomposing it into several contributions from geometry and hydration. We also analyzed the hydration change due to the binding. From the results, we draw a molecular picture of the PMV change accompanying xenon-lysozyme binding, which gives a possible mechanism of pressure reversal of anesthesia.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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37
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Imai T, Harano Y, Kinoshita M, Kovalenko A, Hirata F. Theoretical analysis on changes in thermodynamic quantities upon protein folding: Essential role of hydration. J Chem Phys 2007; 126:225102. [PMID: 17581082 DOI: 10.1063/1.2743962] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The free energy change associated with the coil-to-native structural transition of protein G in aqueous solution is calculated by using the molecular theory of solvation, also known as the three-dimensional reference interaction site model theory, to uncover the molecular mechanism of protein folding. The free energy is decomposed into the protein intramolecular energy, the hydration energy, and the hydration entropy. The folding is accompanied with a large gain in the protein intramolecular energy. However, it is almost canceled by the correspondingly large loss in the hydration energy due to the dehydration, resulting in the total energy gain about an order of magnitude smaller than might occur in vacuum. The hydration entropy gain is found to be a substantial driving force in protein folding. It is comparable with or even larger than the total energy gain. The total energy gain coupled with the hydration entropy gain is capable of suppressing the conformational entropy loss in the folding. Based on careful analysis of the theoretical results, the authors present a challenging physical picture of protein folding where the overall folding process is driven by the water entropy effect.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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38
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39
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Imai T, Hiraoka R, Kovalenko A, Hirata F. Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. Proteins 2007; 66:804-13. [PMID: 17186526 DOI: 10.1002/prot.21311] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Water molecules confined in protein cavities are of great importance in understanding the protein structure and functions. However, it is a nontrivial task to locate such water molecules in protein by the ordinary molecular simulation and modeling techniques as well as experimental methods. The present study proves that the three-dimensional reference interaction site model (3D-RISM) theory, a recently developed statistical-mechanical theory of molecular solvation, has an outstanding advantage in locating such water molecules. In this paper, we demonstrate that the 3D-RISM theory is able to reproduce the structure and the number of water molecules in cavities of hen egg-white lysozyme observed commonly in the X-ray structures of different resolutions and conditions. Furthermore, we show that the theory successfully identified a water molecule in a cavity, the existence of which has been ambiguous even from the X-ray results. In contrast, we confirmed that molecular dynamics simulation is helpless at present to find such water molecules because the results substantially depend on the initial coordinates of water molecules. Possible applications of the theory to problems in the fields of biochemistry and biophysics are also discussed.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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40
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Yamazaki T, Imai T, Hirata F, Kovalenko A. Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation. J Phys Chem B 2007; 111:1206-12. [PMID: 17266276 DOI: 10.1021/jp064615f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We explain the molecular mechanism of the effect of urea and glycerol cosolvents on the partial molar volume (PMV) change associated with the pressure denaturation of staphylococcal nuclease (SNase) protein recently observed in experiments. Native and denatured conformations of SNase are produced by using molecular dynamics simulations in water, and the PMV is obtained from the integral equation theory of molecular liquids called 3D-RISM, which is based on statistical mechanics. The PMV of the native SNase in water predicted by 3D-RISM theory is in good agreement with experiment. The PMV changes associated with pressure denaturation in water and in water-urea and water-glycerol mixtures are qualitatively reproduced. By analyzing the results obtained, we found two interesting cosolvent effects on the PMV: (1) both urea and glycerol cosolvents increase the PMVs of both native and denatured SNase compared to those in water and (2) both urea and glycerol cosolvents increase the PMV of denatured SNase more than that of native SNase. We also showed that these two observations can be explained in terms of the thermal volume, which is related to the packing effect of solvent molecules.
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Affiliation(s)
- Takeshi Yamazaki
- Department of Mechanical Engineering, University of Alberta, and National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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41
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Salamanca C, Contreras M, Gamboa C. Partial molar volume of anionic polyelectrolytes in aqueous solution. J Colloid Interface Sci 2007; 309:435-9. [PMID: 17350646 DOI: 10.1016/j.jcis.2006.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 11/21/2006] [Accepted: 11/21/2006] [Indexed: 11/25/2022]
Abstract
In this work the partial molar volumes (V) of different anionic polyelectrolytes and hydrophobically modified polyelectrolytes (PHM) were measured. Polymers like polymaleic acid-co-styrene, polymaleic acid-co-1-olefin, polymaleic acid-co-vinyl-2-pyrrolidone, and polyacrylic acid (abbreviated as MAS-n, PA-n-K2, AMVP, and PAA, respectively) were employed. These materials were investigated by density measurements in highly dilute aqueous solutions. The molar volume results allow us to discuss the effect of the carboxylic groups and the contributions from the comonomeric principal chain. The PAA presents the smaller V, while the largest V value was for AMVP. The V of PHM shows a linear relationship with the number of methylene groups in the lateral chain. It is found that the magnitude of the contribution per methylene group decreases as the hydrophobic character of the environment increases.
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42
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Imai T, Kovalenko A, Hirata F. Hydration structure, thermodynamics, and functions of protein studied by the 3D-RISM theory. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020600779376] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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43
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Imai T, Harano Y, Kinoshita M, Kovalenko A, Hirata F. A theoretical analysis on hydration thermodynamics of proteins. J Chem Phys 2006; 125:24911. [PMID: 16848615 DOI: 10.1063/1.2213980] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recently developed integral equation theory of molecular solvation. The HFE is decomposed into the energetic and entropic components under the isochoric condition. The former comprises the protein-water interaction energy and the water reorganization energy arising from the structural changes induced in water. Each component is further decomposed into the nonelectrostatic and electrostatic contributions. It is found that the HFE is governed by the nonelectrostatic hydration entropy and the electrostatic hydration energy. The nonelectrostatic hydration entropy is almost exclusively ascribed to the translational entropy loss of water upon the protein insertion. It asymptotically becomes proportional to the excluded volume (EV) for water molecules as the protein size increases. The hydration energy is determined by the protein-water interaction energy which is half compensated by the water reorganization energy. These energy terms are approximately proportional to the water-accessible surface area (ASA). The energetic and entropic contributions are balanced with each other and the HFE has no apparent linear relation with the EV and ASA.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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44
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Takekiyo T, Imai T, Kato M, Taniguchi Y. Understanding high pressure stability of helical conformation of oligopeptides and helix bundle protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:355-63. [PMID: 16478681 DOI: 10.1016/j.bbapap.2005.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 11/13/2005] [Accepted: 11/18/2005] [Indexed: 11/27/2022]
Abstract
The pressure effect on conformational equilibria of simple organic compounds and the pressure denaturation of proteins have been well investigated by using vibrational spectroscopy. However, there was no systematic investigation of the pressure effect on conformational equilibria of oligopeptides, which are located between the simple organic compounds and proteins. Here, we review the recent vibrational spectroscopic and theoretical studies of the pressure effect on conformational equilibria of model oligopeptides and helix bundle protein in aqueous solution.
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Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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45
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Imai T, Hiraoka R, Kovalenko A, Hirata F. Water molecules in a protein cavity detected by a statistical-mechanical theory. J Am Chem Soc 2006; 127:15334-5. [PMID: 16262373 DOI: 10.1021/ja054434b] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four water molecules confined in a small cavity of hen egg-white lysozyme were detected by means of the three-dimensional (3D) RISM theory, a statistical-mechanical theory of molecular solutions. This is the first theoretical realization of confined molecules in a protein without making nonsense tricks, such as placing the molecules in the space a priori. Possible impacts which the result may have on biochemistry and biophysics, including the molecular recognition, enzymatic reactions, etc., are discussed.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Imai T, Takekiyo T, Kovalenko A, Hirata F, Kato M, Taniguchi Y. Theoretical study of volume changes associated with the helix-coil transition of an alanine-rich peptide in aqueous solution. Biopolymers 2005; 79:97-105. [PMID: 16001396 DOI: 10.1002/bip.20337] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The changes in the partial molar volume (PMV) associated with the conformational transition of an alanine-rich peptide AK16 from the alpha-helix structure to various random coil structures are calculated by the three-dimensional interaction site model (3D-RISM) theory coupled with the Kirkwood-Buff theory. The volume change is analyzed by decomposing it into contributions from geometry and hydration: the changes in the van der Waals, void, thermal, and interaction volume. The total change in the PMV is positive. This is primarily due to the growth of void space within the peptide, which is canceled in part by the volume reduction resulting from the increase in the electrostatic interaction between the peptide and water molecules. The changes in the void and thermal volume of the coil structures are widely distributed and tend to compensate each other. Additionally, the relations between the hydration volume components and the surface properties are investigated. We categorize coil structures into extended coils with the PMV smaller than helix and general coils with the PMV larger than helix. The pressure therefore can both stabilize and destabilize the coil structures. The latter seems to be a more proper model of random coil structures of the peptide.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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Graziano G. Comment on “Hydrophobic effects on partial molar volume” [J. Chem. Phys. 122, 094509 (2005)]. J Chem Phys 2005; 123:167103; author reply 167104. [PMID: 16268729 DOI: 10.1063/1.2085028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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