1
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Maruyama Y, Yoshida N. RISMiCal: A software package to perform fast RISM/3D-RISM calculations. J Comput Chem 2024; 45:1470-1482. [PMID: 38472097 DOI: 10.1002/jcc.27340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.
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Affiliation(s)
- Yutaka Maruyama
- Data Science Center for Creative Design and Manufacturing, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki-shi, Kanagawa, Japan
| | - Norio Yoshida
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Japan
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2
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Gilson MK, Kurtzman T. Free Energy Density of a Fluid and Its Role in Solvation and Binding. J Chem Theory Comput 2024; 20:2871-2887. [PMID: 38536144 PMCID: PMC11197885 DOI: 10.1021/acs.jctc.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. First, we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, f(R), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, fbulk, near a solute but should asymptotically approach fbulk with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential. Second, we use statistical thermodynamics to formulate a definition of the free energy density that satisfies these desiderata. Third, we show how any free energy density satisfying the desiderata may be used to analyze molecular processes in solution. In particular, because the spatial integral of f(R) equals the free energy of the system, it can be used to compute free energy changes that result from the rearrangement of solutes as well as the forces exerted on the solutes by the solvent. This enables the use of a thermodynamic analysis of water in protein binding sites to inform ligand design. Finally, we discuss related literature and address published concerns regarding the thermodynamic plausibility of a position-dependent free energy density. The theory presented here has applications in theoretical and computational chemistry and may be further generalizable beyond fluids, such as to solids and macromolecules.
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Affiliation(s)
- Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, and Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA, 92093, USA
| | - Tom Kurtzman
- PhD Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, 10016, USA; Department of Chemistry, Lehman College, The City University of New York, Bronx, New York, 10468, USA
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3
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Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating in vivo drug efficacy. More recently, the rise of deep-learning approaches has led to new tools for predicting RNA-small molecule binding. In this review, we present an overview of the recently developed computational methods for RNA-ligand docking and their advantages and disadvantages.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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4
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Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory. Int J Mol Sci 2021; 22:ijms22105061. [PMID: 34064655 PMCID: PMC8151972 DOI: 10.3390/ijms22105061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé-Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.
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5
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Tanimoto S, Tamura K, Hayashi S, Yoshida N, Nakano H. A computational method to simulate global conformational changes of proteins induced by cosolvent. J Comput Chem 2021; 42:552-563. [PMID: 33433010 DOI: 10.1002/jcc.26481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/09/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022]
Abstract
A computational method to investigate the global conformational change of a protein is proposed by combining the linear response path following (LRPF) method and three-dimensional reference interaction site model (3D-RISM) theory, which is referred to as the LRPF/3D-RISM method. The proposed method makes it possible to efficiently simulate protein conformational changes caused by either solutions of varying concentrations or the presence of cosolvent species by taking advantage of the LRPF and 3D-RISM. The proposed method is applied to the urea-induced denaturation of ubiquitin. The LRPF/3D-RISM trajectories successfully simulate the early stage of the denaturation process within the simulation time of 300 ns, whereas no significant structural change is observed even in the 1 μs standard MD simulation. The obtained LRPF/3D-RISM trajectories reproduce the mechanism of the urea denaturation of ubiquitin reported in previous studies, and demonstrate the high efficiency of the method.
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Affiliation(s)
- Shoichi Tanimoto
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Koichi Tamura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
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6
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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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7
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Kobryn AE, Maruyama Y, Velázquez-Martínez CA, Yoshida N, Gusarov S. Modeling the interaction of SARS-CoV-2 binding to the ACE2 receptor via molecular theory of solvation. NEW J CHEM 2021. [DOI: 10.1039/d1nj02015c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The angiotensin-converting enzyme 2 (ACE2) protein is a cell gate receptor for the SARS-CoV-2 virus, responsible for the development of symptoms associated with the Covid-19 disease.
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Affiliation(s)
- Alexander E. Kobryn
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive NW, Edmonton, Alberta, T6G 2M9, Canada
| | - Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Carlos A. Velázquez-Martínez
- 2142-L Katz Group Centre for Research, University of Alberta, 11315-87 Avenue NW, Edmonton, Alberta, T6G 2H5, Canada
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Sergey Gusarov
- Nanotechnology Research Centre, National Research Council Canada, 11421 Saskatchewan Drive NW, Edmonton, Alberta, T6G 2M9, Canada
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Maldonado AM, Basdogan Y, Berryman JT, Rempe SB, Keith JA. First-principles modeling of chemistry in mixed solvents: Where to go from here? J Chem Phys 2020; 152:130902. [PMID: 32268733 DOI: 10.1063/1.5143207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents.
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Affiliation(s)
- Alex M Maldonado
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yasemin Basdogan
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Joshua T Berryman
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Susan B Rempe
- Center for Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - John A Keith
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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9
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Sugita M, Hamano M, Kasahara K, Kikuchi T, Hirata F. New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory. J Chem Theory Comput 2020; 16:2864-2876. [PMID: 32176492 DOI: 10.1021/acs.jctc.9b01069] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An efficient algorithm to find the binding position and mode of small ligands bound at an active site of protein is proposed based on the spatial distribution function (SDF) obtained from the three-dimensional reference interaction site model (3D-RISM) theory with the Kovalenko-Hirata (KH) closure relation. The ligand examined includes hydrophobic, acidic, and basic molecules and zwitterions. Eighteen different types of proteins, which serve as targets for those ligands, are selected to examine the robustness of the algorithm. An imaginary atom, referred to as an "anchor site", is defined at the center of geometry of a ligand molecule that serves as a center for searching the binding position and mode of the ligand molecule in the translational and rotational spaces. The probable binding sites (PBSs) are identified based on the SDFs of the ligand molecules around the protein, and the PBS is ranked according to the peak height of SDF. The deviations from the mean height of the peak values of SDFs for 50 PBSs are analyzed based on the z-score, which is a measure of prominence of the site. The PBS found at the closest distance from the anchor site of the crystal structure is referred to as the "nearest site". The orientation of the ligand molecule at each PBS is explored by changing the Euler angles, and the most probable binding mode is determined based on the superposition approximation. The binding position of ligand molecules is successfully predicted as one of the distinct peaks in SDF of the anchor site, with a few exceptions. The binding mode of the ligand molecule predicted based on the superposition approximation is consistent with the X-ray crystal structure in nine systems, a half of the systems investigated. The significance of the results is discussed in detail. An application of the new protocol to fragment-based drug discovery is suggested.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masataka Hamano
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Kota Kasahara
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Fumio Hirata
- Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
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10
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Yoshida N, Yamaguchi T. Development of a solvent-polarizable three-dimensional reference interaction-site model theory. J Chem Phys 2020; 152:114108. [DOI: 10.1063/5.0004173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishiku, Fukuoka 819-0395, Japan
| | - Tsuyoshi Yamaguchi
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464–8603, Japan
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11
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Yoshida N. The Reference Interaction Site Model Integrated Calculator (RISMiCal) program package for nano- and biomaterials design. ACTA ACUST UNITED AC 2020. [DOI: 10.1088/1757-899x/773/1/012062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Onishi I, Sunaba S, Yoshida N, Hirata F, Irisa M. Role of Mg 2+ Ions in DNA Hydrolysis by EcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics. J Phys Chem B 2018; 122:9061-9075. [PMID: 30117741 DOI: 10.1021/acs.jpcb.7b12555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of Mg2+ ions during precursor formation in DNA hydrolysis by the homodimeric restriction enzyme EcoRV was elucidated based on the 3D-reference interaction site model (RISM) theory and the molecular dynamics (MD) simulation. From an analysis of the spatial distribution of Mg2+ in an active site using 3D-RISM, we identified a new position for Mg2+ in the X-ray EcoRV-DNA complex structure ( 1rvb ). We refer to the position as site IV†. Site IV† is almost at the same position as that of a Ca2+ ion in the superimposed X-ray crystallographic active-site structure of the PvuII-DNA complex ( 1f0o ). 3D-RISM was also used to locate the position of water molecules, including the water nucleophile at the active site. MD simulations were carried out with the initial structure having two Mg2+ ions at site IV† and at site I*, experimentally identified by Horton et al., to find a stable complex structure in which the DNA fragment was rearranged to orient the scissile bond direction toward the water nucleophile. The equilibrium active-site structure of the EcoRV-DNA complex obtained from the MD simulation was similar to the superimposed X-ray crystallographic structure of the BamHI-DNA complex ( 2bam ). In the active-site structure, two metal ions have almost the same position (≤1.0 Å) as that of 2bam , and the scissile phosphate is twisted to orient the scissile bond toward the water nucleophile, as is the case in 2bam . We propose the equilibrium active-site structure obtained in this study as a precursor for the hydrolysis reaction of EcoRV.
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Affiliation(s)
- Itaru Onishi
- Department of Bioscience and Bioinformatics , Kyushu Institute of Technology , Iizuka 820-8502 , Japan
| | - Shunya Sunaba
- Department of Bioscience and Bioinformatics , Kyushu Institute of Technology , Iizuka 820-8502 , Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science , Kyushu University , Fukuoka 819-0395 , Japan
| | - Fumio Hirata
- Toyota Physical & Chemical Research Institute , Aichi 480-1192 , Japan.,Institute for Molecular Science , Okazaki 444-8585 , Japan
| | - Masayuki Irisa
- Department of Bioscience and Bioinformatics , Kyushu Institute of Technology , Iizuka 820-8502 , Japan
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13
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Kasahara K, Sato H. Time-dependent pair distribution functions based on Smoluchowski equation and application to an electrolyte solution. J Comput Chem 2018; 39:1491-1497. [DOI: 10.1002/jcc.25219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/28/2018] [Accepted: 03/14/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Kento Kasahara
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Hirofumi Sato
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB); Kyoto University, Nishikyo-ku; Kyoto 615-8520 Japan
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14
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Iwasaki H, Yamaguchi S, Miura S. Comparative study of 3D-RISM theory and molecular dynamics calculations for the free-energy landscape of a hydrated dipeptide. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1342128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hiroshi Iwasaki
- Faculty of Mathematics and Physics, Kanazawa University, Kanazawa, Japan
| | - Satoshi Yamaguchi
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - Shinichi Miura
- Faculty of Mathematics and Physics, Kanazawa University, Kanazawa, Japan
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15
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Yoshida N. Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids. J Chem Inf Model 2017; 57:2646-2656. [DOI: 10.1021/acs.jcim.7b00389] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norio Yoshida
- Department of Chemistry,
Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 Japan
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16
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Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev 2017; 117:12385-12414. [PMID: 28949513 PMCID: PMC5639468 DOI: 10.1021/acs.chemrev.7b00259] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 11/29/2022]
Abstract
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.
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Affiliation(s)
- Emiliano Brini
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher J. Fennell
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Marivi Fernandez-Serra
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Barbara Hribar-Lee
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Ken A. Dill
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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17
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Kasahara K, Sato H. Dynamics theory for molecular liquids based on an interaction site model. Phys Chem Chem Phys 2017; 19:27917-27929. [DOI: 10.1039/c7cp05423h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamics theories for molecular liquids based on an interaction site model have been developed over the past few decades and proved to be powerful tools to investigate various dynamical phenomena.
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Affiliation(s)
- Kento Kasahara
- Department of Molecular Engineering
- Kyoto University
- Japan
| | - Hirofumi Sato
- Department of Molecular Engineering and Elements Strategy for Catalysts and Batteries (ESICB)
- Kyoto University
- Japan
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18
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Kasahara K, Sato H. A theory of diffusion controlled reactions in polyatomic molecule system. J Chem Phys 2016; 145:194502. [DOI: 10.1063/1.4967400] [Citation(s) in RCA: 6] [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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19
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Munaò G, Costa D, Caccamo C. Development of molecular closures for the reference interaction site model theory with application to square-well and Lennard-Jones homonuclear diatomics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:414007. [PMID: 27548461 DOI: 10.1088/0953-8984/28/41/414007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Inspired by significant improvements obtained for the performances of the polymer reference interaction site model (PRISM) theory of the fluid phase when coupled with 'molecular closures' (Schweizer and Yethiraj 1993 J. Chem. Phys. 98 9053), we exploit a matrix generalization of this concept, suitable for the more general RISM framework. We report a preliminary test of the formalism, as applied to prototype square-well homonuclear diatomics. As for the structure, comparison with Monte Carlo shows that molecular closures are slightly more predictive than their 'atomic' counterparts, and thermodynamic properties are equally accurate. We also devise an application of molecular closures to models interacting via continuous, soft-core potentials, by using well established prescriptions in liquid state perturbation theories. In the case of Lennard-Jones dimers, our scheme definitely improves over the atomic one, providing semi-quantitative structural results, and quite good estimates of internal energy, pressure and phase coexistence. Our finding paves the way to a systematic employment of molecular closures within the RISM framework to be applied to more complex systems, such as molecules constituted by several non-equivalent interaction sites.
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Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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20
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Mrugalla F, Kast SM. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:344004. [PMID: 27366935 DOI: 10.1088/0953-8984/28/34/344004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.
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Affiliation(s)
- Florian Mrugalla
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
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21
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Sakaki S. Theoretical and Computational Study of a Complex System Consisting of Transition Metal Element(s): How to Understand and Predict Its Geometry, Bonding Nature, Molecular Property, and Reaction Behavior. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150119] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shigeyoshi Sakaki
- Fukui Institute for Fundamental Chemistry, Kyoto University
- CREST, Japan Science and Technology Agency (JST)
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22
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Zhao Q, Wang Q, Zhang C, Du Z, Tian M, Mi J. Effect of Chain Topology of Polyethylenimine on Physisorption and Chemisorption of Carbon Dioxide. Chemphyschem 2015; 16:1480-90. [DOI: 10.1002/cphc.201402865] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/29/2015] [Indexed: 11/09/2022]
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23
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Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Therrien E, Weill N, Tomberg A, Corbeil CR, Lee D, Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy. J Chem Inf Model 2014; 54:3198-210. [DOI: 10.1021/ci500299h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Eric Therrien
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Nathanael Weill
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Anna Tomberg
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Christopher R. Corbeil
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Devin Lee
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street W., Montréal, Québec, Canada H3A 0B8
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25
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Kiyota Y, Takeda-Shitaka M. Molecular Recognition Study on the Binding of Calcium to Calbindin D9k Based on 3D Reference Interaction Site Model Theory. J Phys Chem B 2014; 118:11496-503. [DOI: 10.1021/jp504822r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yasuomi Kiyota
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Mayuko Takeda-Shitaka
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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26
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Iwasaki H, Gyoubu S, Kawatsu T, Miura S. A 3D-RISM integral equation study of a hydrated dipeptide. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Maruyama Y, Yoshida N, Tadano H, Takahashi D, Sato M, Hirata F. Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT. J Comput Chem 2014; 35:1347-55. [PMID: 24771232 DOI: 10.1002/jcc.23619] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/26/2014] [Accepted: 04/06/2014] [Indexed: 01/19/2023]
Abstract
A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems.
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Affiliation(s)
- Yutaka Maruyama
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, 223-8522, Japan
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28
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Chuev GN, Vyalov I, Georgi N. Extraction of site-site bridge functions and effective pair potentials from simulations of polar molecular liquids. J Comput Chem 2014; 35:1010-23. [DOI: 10.1002/jcc.23586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 02/08/2014] [Accepted: 02/13/2014] [Indexed: 01/13/2023]
Affiliation(s)
- Gennady N. Chuev
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science; Pushchino Moscow Region 142290 Russia
| | - Ivan Vyalov
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
| | - Nikolaj Georgi
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
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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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30
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Zheng M, Li Y, Xiong B, Jiang H, Shen J. Water PMF for predicting the properties of water molecules in protein binding site. J Comput Chem 2012; 34:583-92. [DOI: 10.1002/jcc.23170] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 09/04/2012] [Accepted: 09/30/2012] [Indexed: 01/09/2023]
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31
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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32
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Nikolić D, Blinov N, Wishart D, Kovalenko A. 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol. J Chem Theory Comput 2012; 8:3356-72. [PMID: 26605742 DOI: 10.1021/ct300257v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We explore a new approach in the rational design of specificity in molecular recognition of small molecules based on statistical-mechanical integral equation theory of molecular liquids in the form of the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). The numerically stable iterative solution of conventional 3D-RISM equations includes the fragmental decomposition of flexible ligands, which are treated as distinct species in solvent mixtures of arbitrary complexity. The computed density functions for solution (including ligand) molecules are obtained as a set of discrete spatial grids that uniquely describe the continuous solvent-site distribution around the protein solute. Potentials of mean force derived from these distributions define the scoring function interfaced with the AutoDock program for an automated ranking of docked conformations. As a case study in terms of solvent composition, we analyze cooperative interactions encountered in the binding of a flexible thiamine molecule to the prion protein at near-physiological conditions. The predicted location and residency times of computed binding modes are in excellent agreement with the available experimental data.
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Affiliation(s)
- Dragan Nikolić
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
| | - Nikolay Blinov
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada.,Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - David Wishart
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Andriy Kovalenko
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada.,Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
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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: 114] [Impact Index Per Article: 9.5] [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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34
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Yoshida N, Kiyota Y, Phongphanphanee S, Maruyama Y, Imai T, Hirata F. Statistical mechanics theory of molecular recognition and pharmaceutical design. INT REV PHYS CHEM 2011. [DOI: 10.1080/0144235x.2011.648755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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