1
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Ishizuka R. Martini 3D-OZ: A Theoretical Investigation of Solvation Shell Structures and Solvation Free Energies of Martini Coarse-Grained Proteins. J Phys Chem B 2024; 128:8522-8529. [PMID: 39180742 DOI: 10.1021/acs.jpcb.4c03897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
We investigate the properties of aqueous solutions using integral equation theories and molecular dynamics (MD) simulations within the framework of the MARTINI coarse-grained force field. The integral equation theory used in the present work is based on the Ornstein-Zernike equation coupled with the hypernetted chain (HNC) and Kovalenko-Hirata (KH) closures. Overall, the solvation shell structures and solvation thermodynamics in the HNC approximation are shown to be in better agreement with those from the MD simulation than the KH results. Especially, through the analysis of spatial distribution functions of water around a protein, we have demonstrated that the HNC approximation can provide the highly anisotropic structure of the solvation shell of the protein. On the other hand, the KH approximation works well for simple particle solutes, but the results for highly hydrated proteins deviate quite significantly from the MD results. We further explore in detail the reason underlying the deviation caused by the KH approximation. Lastly, a potential application of the integral equation theory with the MARTINI model is outlined.
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Affiliation(s)
- Ryosuke Ishizuka
- Zkanics F.P.S., Side-6 Senriyama-West, Suita, Osaka 565-0851, Japan
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2
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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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3
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Bursik B, Eller J, Gross J. Predicting Solvation Free Energies from the Minnesota Solvation Database Using Classical Density Functional Theory Based on the PC-SAFT Equation of State. J Phys Chem B 2024; 128:3677-3688. [PMID: 38579126 DOI: 10.1021/acs.jpcb.3c07447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
We critically assess the capabilities of classical density functional theory (DFT) based on the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state to predict the solvation free energies of small molecules in various hydrocarbon solvents. We compare DFT results with experimental data from the Minnesota solvation database and utilize statistical methods to analyze the accuracy of our approach, as well as its weaknesses. The mean absolute error of the solvation free energies is 3.7 kJ mol-1 for n-alkane solvents, ranging from pentane to hexadecane, with 473 solute-solvent systems. For solvents consisting of cyclic hydrocarbons (cyclohexane, benzene, toluene, and ethylbenzene) with 245 solute-solvent systems, we report a slightly larger mean absolute error of 4.2 kJ mol-1. We identify three possible sources of errors: (i) the neglect of solute-solvent and solvent-solvent Coulomb interactions, which limits the applicability of PC-SAFT DFT to nonpolar and weakly polar molecules; (ii) the solute's Lennard-Jones parameters supplied by the general AMBER force field, which are not parametrized toward solvation free energies; and (iii) the application of the Lorentz-Berthelot combining rules to the dispersive interactions between a segment of the PC-SAFT solvent and a Lennard-Jones interaction site of the solute. The approach is more accurate than standard implementations of phenomenological models in common chemistry software packages, which exhibit mean absolute errors larger than 9.12 kJ mol-1, even though newer phenomenological models achieve a mean absolute error of about 2 kJ mol-1. PC-SAFT DFT is more computationally efficient than state of the art explicit molecular simulations in combination with free energy perturbation methods. It is predictive with respect to solvation free energies, i.e., the input for the model is the (element-specific) molecular force field, the solute configuration from molecular dynamics simulations, and the (substance-specific) PC-SAFT parameters. The PC-SAFT parametrization uses pure-component data and does not require experimental solvation free energies. The PC-SAFT equation of state, without applying a DFT formalism, can also be used to calculate solvation free energies, provided that the PC-SAFT parameters for the solute are available. A large number of substances was recently parametrized by members of our group (Esper, T.; Bauer, G.; Rehner, P.; Gross, J. Ind. Eng. Chem. Res. 2023, 62), which enables a comparison to the DFT approach for 103 substances. Accurate results are obtained from the PC-SAFT equation of state with an MAE below 2.51 kJ mol-1. The DFT approach does not require PC-SAFT parameters for the solute and can be applied to all solutes that can be represented by the molecular force field.
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Affiliation(s)
- Benjamin Bursik
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Johannes Eller
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
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4
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Fedotova MV, Chuev GN. The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands. Int J Mol Sci 2024; 25:3697. [PMID: 38612508 PMCID: PMC11011341 DOI: 10.3390/ijms25073697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat. Scientists around the world are making enormous efforts to solve these problems. In silico methods, which allow quite rapid obtention of, in many cases, accurate information in this field, are effective tools for the description of various aspects of virus activity, including virus-host cell interactions, and, thus, can provide a molecular insight into the mechanism of virus functioning. The three-dimensional reference interaction site model (3D-RISM) seems to be one of the most effective and inexpensive methods to compute hydrated viruses, since the method allows us to provide efficient calculations of hydrated viruses, remaining all molecular details of the liquid environment and virus structure. The pandemic challenge has resulted in a fast increase in the number of 3D-RISM calculations devoted to hydrated viruses. To provide readers with a summary of this literature, we present a systematic overview of the 3D-RISM calculations, covering the period since 2010. We discuss various biophysical aspects of the 3D-RISM results and demonstrate capabilities, limitations, achievements, and prospects of the method using examples of viruses such as influenza, hepatitis, and SARS-CoV-2 viruses.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics, The Russian Academy of Sciences, Institutskaya St., 142290 Pushchino, Russia
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5
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Cao S, Kalin ML, Huang X. EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. J Comput Chem 2023; 44:1536-1549. [PMID: 36856731 DOI: 10.1002/jcc.27088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/24/2022] [Accepted: 01/29/2023] [Indexed: 03/02/2023]
Abstract
Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL.
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Affiliation(s)
- Siqin Cao
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael L Kalin
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Reimann M, Kaupp M. Reaction Entropies in Solution from Analytical Three-Dimensional Reference Interaction Site Model Derivatives with Application to Redox and Spin-Crossover Processes. J Phys Chem A 2022; 126:3708-3716. [PMID: 35652546 DOI: 10.1021/acs.jpca.2c02317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An analytical approach to compute the excess entropy of solvation at constant pressure in three-dimensional reference interaction site model (3D-RISM) calculations is presented. It includes the changes in the macroscopic dielectric constant of the solvent upon variation of temperature and density. The approach is exact within the framework of force-field descriptions of the solute and gives reasonable results for self-consistently determined electrostatics as used in the 3D-RISM-self-consistent field approach, particularly for entropy differences. The new method is applied to simple examples of reaction entropies of iron complexes in aqueous solution, for which simple gas-phase calculations and many other approaches give unreliable estimates. For both redox half-reactions and spin-crossover processes, (semi)quantitative agreement with experimental reaction entropies can be achieved out of the box.
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Affiliation(s)
- Marc Reimann
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17.Juni 135, Berlin D-10623, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17.Juni 135, Berlin D-10623, Germany
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7
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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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8
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Ganyecz Á, Kállay M. Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges. J Phys Chem A 2022; 126:2417-2429. [PMID: 35394778 PMCID: PMC9036516 DOI: 10.1021/acs.jpca.1c07904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
implemented the embedded cluster reference interaction
site model (EC-RISM) originally developed by Kloss, Heil, and Kast
(J. Phys. Chem. B2008, 112, 4337–4343).
This method combines quantum mechanical calculations with the 3D reference
interaction site model (3D-RISM). Numerous options, such as buffer,
grid space, basis set, charge model, water model, closure relation,
and so forth, were investigated to find the best settings. Additionally,
the small point charges, which are derived from the solvent distribution
from the 3D-RISM solution to represent the solvent in the QM calculation,
were neglected to reduce the overhead without the loss of accuracy.
On the MNSOL[a], MNSOL, and FreeSolv databases, our implemented and
optimized method provides solvation free energies in water with 5.70,
6.32, and 6.44 kJ/mol root-mean-square deviations, respectively, but
with different settings, 5.22, 6.08, and 6.63 kJ/mol can also be achieved.
Only solvent models containing fitting parameters, like COSMO-RS and
EC-RISM with universal correction and directly used electrostatic
potential, perform better than our EC-RISM implementation with atomic
charges.
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Affiliation(s)
- Ádám Ganyecz
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest P.O. Box 91, H-1521 Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest P.O. Box 91, H-1521 Hungary
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9
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HAGIWARA S, HARUYAMA J, OTANI M, UMEMURA Y, TAKEUCHI T, SAKAEBE H. Theoretical Consideration of Side Reactions between the VS<sub>4</sub> Electrode and Carbonate Solvents in Lithium–metal Polysulfide Batteries. ELECTROCHEMISTRY 2022. [DOI: 10.5796/electrochemistry.22-00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Satoshi HAGIWARA
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST)
| | - Jun HARUYAMA
- The Institute for Solid State Physics, The University of Tokyo
| | - Minoru OTANI
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yuki UMEMURA
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomonari TAKEUCHI
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hikari SAKAEBE
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST)
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10
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Kruchinin SE, Fedotova MV. Ion Pairing of the Neurotransmitters Acetylcholine and Glutamate in Aqueous Solutions. J Phys Chem B 2021; 125:11219-11231. [PMID: 34597044 DOI: 10.1021/acs.jpcb.1c05117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neurotransmitters (NTs) play an important role in neural communication, regulating a variety of functions such as motivation, learning, memory, and muscle contraction. Their intermolecular interactions in biological media are an important factor affecting their biological activity. However, the available information on the features of these interactions is scarce and contradictory, especially, in an estimation of possible ion binding. In this paper, we present the results of a study for two well-known NTs, acetylcholine (ACh) and glutamate (Glu), with relation to the NT-inorganic ion and the NT-NT binding in a water environment. The features of NT pairing are investigated in aqueous AChCl and NaGlu solutions over a wide concentration range using the integral equation method in 1D- and 3D- reference interaction site model (RISM) approaches. The data for ACh are given for its two bioactive TG (trans, gauche) and TT (trans, trans) conformers. As was found, for both NTs, the results indicate the NT-inorganic counterion contact pair to be the predominant associate type in the concentrated solutions. In this case, the counterions occupy the vacated "water" space in the hydration shell of the onium moiety (ACh) or carboxylate groups (Glu). For ACh, the "unfolded" TT conformer demonstrates a slightly greater possibility for counterion pairing in comparison with the "folded" TG conformer. For Glu, the probability of its binding with a counterion is slightly stronger for the "side-chain" carboxylate group than for the "backbone" group. The obtained results also revealed an insignificant probability of Glu--Glu- pairing. Namely, the RISM data indicate Glu--Glu- binding by NH3+-COO- interactions. A link between the ion binding of NTs and their biological activity is discussed. This contribution adds new knowledge to our understanding of the interactions between the NTs and their molecular environment, providing further insights into the behavior of these compounds in biological media.
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Affiliation(s)
- Sergey E Kruchinin
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
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11
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Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Accurate prediction of hydration free energies and solvation structures using molecular density functional theory with a simple bridge functional. J Chem Phys 2021; 155:024117. [PMID: 34266282 DOI: 10.1063/5.0057506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper assesses the ability of molecular density functional theory to predict efficiently and accurately the hydration free energies of molecular solutes and the surrounding microscopic water structure. A wide range of solutes were investigated, including hydrophobes, water as a solute, and the FreeSolv database containing 642 drug-like molecules having a variety of shapes and sizes. The usual second-order approximation of the theory is corrected by a third-order, angular-independent bridge functional. The overall functional is parameter-free in the sense that the only inputs are bulk water properties, independent of the solutes considered. These inputs are the direct correlation function, compressibility, liquid-gas surface tension, and excess chemical potential of the solvent. Compared to molecular simulations with the same force field and the same fixed solute geometries, the present theory is shown to describe accurately the solvation free energy and structure of both hydrophobic and hydrophilic solutes. Overall, the method yields a precision of order 0.5 kBT for the hydration free energies of the FreeSolv database, with a computer speedup of 3 orders of magnitude. The theory remains to be improved for a better description of the H-bonding structure and the hydration free energy of charged solutes.
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Affiliation(s)
- Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- Universié Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
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12
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Miyata T, Yabuki N, Leung J. Transferability of Sigma Enlarging Bridge Function for Lennard-Jones Diatomic Solute Using Monatomic Solvent Correlation Obtained from Molecular Dynamics Simulation. CHEM LETT 2020. [DOI: 10.1246/cl.200521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tatsuhiko Miyata
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| | - Naoya Yabuki
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| | - Jackie Leung
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
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14
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Miyata T. Sigma enlarging bridge function for heteronuclear Lennard-Jones diatomic solute solvated in a Lennard-Jones monatomic solvent in terms of the parameter transferability. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Abstract
The electrostatic response underlying the 3D-RISM theory and its general relationship to models in which the solvent is represented in terms of a dielectric continuum are examined. It is found that the theory provides a coherent picture of solvation, although its behavior is not entirely consistent with the trends that are expected in the limit of a large solute. The electrostatic discrepancy is due to the nature of the isotropic pair additive site-site correlation function associated with the susceptibility response of the uniform fluid. The influence of the discrepancy in the magnitude of the solvation free energy is negligible for a solvent with a large dielectric constant.
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Affiliation(s)
- Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637-1454, United States
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16
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Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Simple Parameter-Free Bridge Functionals for Molecular Density Functional Theory. Application to Hydrophobic Solvation. J Phys Chem B 2020; 124:6885-6893. [DOI: 10.1021/acs.jpcb.0c04496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91191, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, Paris, F-75005, France
- Réseau sur le Stockage Électrochimique de l’Énergie, CNRS FR3459, 33 rue Saint Leu, Amiens, Cedex 80039, France
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18
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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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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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20
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Luukkonen S, Levesque M, Belloni L, Borgis D. Hydration free energies and solvation structures with molecular density functional theory in the hypernetted chain approximation. J Chem Phys 2020; 152:064110. [DOI: 10.1063/1.5142651] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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21
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Chuev GN, Fedotova MV, Valiev M. Chemical bond effects in classical site density functional theory of inhomogeneous molecular liquids. J Chem Phys 2020; 152:041101. [PMID: 32007044 DOI: 10.1063/1.5139619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Intra-molecular interactions or chemical bonds represent one of the main distinguishing characteristics of molecular fluids. Development of accurate and practical methods to treat these effects is one of the long standing problems in classical site density functional theory (SDFT). One particular instance when these issues become particularly severe is the case of classical interaction potentials with auxiliary sites or dummy atoms. In this situation, current SDFT implementations, such as the three-dimensional reference interaction site model, lead to nonphysical results. We re-examine this issue in this work using our recent reformulation of SDFT (Valiev and Chuev, J. Stat. Mech.: Theory Exp. 2018, 093201). We put forward a simple practical solution to this problem and illustrate its utility for the case of spherical solutes in diatomic liquids.
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Affiliation(s)
- Gennady N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Marat Valiev
- Molecular Sciences Software Group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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22
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Fedotova MV, Kruchinin SE, Chuev GN. Features of local ordering of biocompatible ionic liquids: The case of choline-based amino acid ionic liquids. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.112081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Maruyama Y, Takano H, Mitsutake A. Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory. Biophys Physicobiol 2019; 16:407-429. [PMID: 31984194 PMCID: PMC6975981 DOI: 10.2142/biophysico.16.0_407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023] Open
Abstract
Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.
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Affiliation(s)
- Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Takano
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
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24
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Fedotova MV. Compatible osmolytes - bioprotectants: Is there a common link between their hydration and their protective action under abiotic stresses? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Maruyama Y. Correction terms for the solvation free energy functional of three-dimensional reference interaction site model based on the reference-modified density functional theory. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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An assessment of the sigma enlarging bridge function for a Lennard-Jones solution using a solvent-solvent correlation function obtained from molecular dynamics simulation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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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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28
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Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site. PLoS One 2019; 14:e0219473. [PMID: 31291328 PMCID: PMC6619770 DOI: 10.1371/journal.pone.0219473] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/25/2022] Open
Abstract
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site.
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Affiliation(s)
- Crystal Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | | | - Andriy Kovalenko
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - David A. Case
- Department of Chemistry, Lehman College, The City University of New York, Bronx, New York, United States of America
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tom Kurtzman
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Tyler Luchko
- Department of Physics and Astronomy, California State University, Northridge, California, United States of America
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29
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Cao S, Konovalov KA, Unarta IC, Huang X. Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute–Solvent Interface. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Siqin Cao
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Kirill A. Konovalov
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Ilona Christy Unarta
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuhui Huang
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- HKUST‐Shenzhen Research Institute Hi‐Tech Park, Nanshan Shenzhen 518057 China
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30
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Kido K. A noniterative mean‐field QM/MM‐type approach with a linear response approximation toward an efficient free‐energy evaluation. J Comput Chem 2019; 40:2072-2085. [DOI: 10.1002/jcc.25844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 01/23/2023]
Affiliation(s)
- Kentaro Kido
- Nuclear Safety Research CenterJapan Atomic Energy Agency 2‐4 Shirane, Shirakata, Tokai‐mura Ibaraki 319‐1195 Naka‐gun Japan
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31
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Sosnin S, Misin M, Palmer DS, Fedorov MV. 3D matters! 3D-RISM and 3D convolutional neural network for accurate bioaccumulation prediction. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:32LT03. [PMID: 29964270 DOI: 10.1088/1361-648x/aad076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, we present a new method for predicting complex physical-chemical properties of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) that uses solvent spatial distributions around solutes as input. These spatial distributions are obtained by a molecular theory called three-dimensional reference interaction site model. We have shown that the method allows one to achieve a good accuracy of prediction of bioconcentration factor which is difficult to predict by direct application of methods of molecular theory or simulations. Our research demonstrates that combination of molecular theories with modern machine learning approaches can be effectively used for predicting properties that are otherwise inaccessible to purely theory-based models.
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Affiliation(s)
- Sergey Sosnin
- Center for Computational and Data-intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobelya Ulitsa 3 Moscow, 121205, Russia
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32
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Matter H, Güssregen S. Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands. Bioorg Med Chem Lett 2018; 28:2343-2352. [PMID: 29880400 DOI: 10.1016/j.bmcl.2018.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022]
Abstract
Water is an essential part of protein binding sites and mediates interactions to ligands. Its displacement by ligand parts affects the free binding energy of resulting protein-ligand complexes. Therefore the characterization of solvation properties is important for design. Of particular interest is the propensity of localized water to be favorably displaced by a ligand. This review discusses two popular computational approaches addressing these questions, namely WaterMap based on statistical mechanics analysis of MD simulations and 3D RISM based on integral equation theory of liquids. The theoretical background and recent applications in structure-based design will be presented.
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Affiliation(s)
- Hans Matter
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany.
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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33
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Yokogawa D. Toward Accurate Solvation Free Energy Calculation with the Reference Interaction Site Model Self-Consistent Field: Introduction of a New Bridge Function. J Chem Theory Comput 2018; 14:3272-3278. [DOI: 10.1021/acs.jctc.8b00314] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- D. Yokogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya UniversityChikusa, Nagoya 464-8602, Japan
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34
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Vyalov I, Rocchia W. Including diverging electrostatic potential in 3D-RISM theory: The charged wall case. J Chem Phys 2018; 148:114106. [PMID: 29566525 DOI: 10.1063/1.5019596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although three-dimensional site-site molecular integral equations of liquids are a powerful tool of the modern theoretical chemistry, their applications to the problem of characterizing the electrical double layer originating at the solid-liquid interface with a macroscopic substrate are severely limited by the fact that an infinitely extended charged plane generates a divergent electrostatic potential. Such potentials cannot be treated within the standard 3D-Reference Interaction Site Model equation solution framework since it leads to functions that are not Fourier transformable. In this paper, we apply a renormalization procedure to overcome this obstacle. We then check the validity and numerical accuracy of the proposed computational scheme on the prototypical gold (111) surface in contact with water/alkali chloride solution. We observe that despite the proposed method requires, to achieve converged charge densities, a higher spatial resolution than that suited to the estimation of biomolecular solvation with either 3D-RISM or continuum electrostatics approaches, it still is computationally efficient. Introducing the electrostatic potential of an infinite wall, which is periodic in 2 dimensions, we avoid edge effects, permit a robust integration of Poisson's equation, and obtain the 3D electrostatic potential profile for the first time in such calculations. We show that the potential within the electrical double layer presents oscillations which are not grasped by the Debye-Hückel and Gouy-Chapman theories. This electrostatic potential deviates from its average of up to 1-2 V at small distances from the substrate along the lateral directions. Applications of this theoretical development are relevant, for example, for liquid scanning tunneling microscopy imaging.
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Affiliation(s)
- Ivan Vyalov
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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35
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Ansari SM, Palmer DS. Comparative Molecular Field Analysis Using Molecular Integral Equation Theory. J Chem Inf Model 2018; 58:1253-1265. [DOI: 10.1021/acs.jcim.7b00600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samiul M. Ansari
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
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36
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Sumi T, Maruyama Y, Mitsutake A, Mochizuki K, Koga K. Application of reference‐modified density functional theory: Temperature and pressure dependences of solvation free energy. J Comput Chem 2017; 39:202-217. [DOI: 10.1002/jcc.25101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Tomonari Sumi
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
- Department of Chemistry, Faculty of ScienceOkayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
| | - Yutaka Maruyama
- Co‐Design Team, FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science, 7‐1‐26, Minatojima‐minami‐machiKobe650‐0047 Japan
| | - Ayori Mitsutake
- Department of PhysicsKeio University, 3‐14‐1 Hiyoshi, Kohoku‐kuYokohama Kanagawa223–8522 Japan
| | - Kenji Mochizuki
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
| | - Kenichiro Koga
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
- Department of Chemistry, Faculty of ScienceOkayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
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37
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Miyata T. A Parameterization of Empirical Sigma Enlarging Bridge Correction of Kovalenko-Hirata Closure in Ornstein-Zernike Theory for Lennard-Jones Fluids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tatsuhiko Miyata
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577
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38
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Hydration and ion-binding of glycine betaine: How they may be involved into protection of proteins under abiotic stresses. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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39
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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40
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Fedotova MV, Kruchinin SE, Chuev GN. Hydration structure of osmolyte TMAO: concentration/pressure-induced response. NEW J CHEM 2017. [DOI: 10.1039/c6nj03296f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of solute concentration/pressure on the TMAO hydration structure was studied to understand its protective action under abiotic stressors.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics
- The Russian Academy of Sciences
- Pushchino
- Russia
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41
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Dmitrieva OA, Fedotova MV, Buchner R. Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline. Phys Chem Chem Phys 2017; 19:20474-20483. [DOI: 10.1039/c7cp04335j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Strongly hydrated l-proline cooperatively binds Na+ and Cl− ions in aqueous solution.
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Affiliation(s)
- Olga A. Dmitrieva
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
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42
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SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling. J Comput Aided Mol Des 2016; 30:1115-1127. [PMID: 27585474 DOI: 10.1007/s10822-016-9947-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/18/2016] [Indexed: 12/15/2022]
Abstract
Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.
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Sumi T, Maruyama Y, Mitsutake A, Koga K. A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution. J Chem Phys 2016; 144:224104. [DOI: 10.1063/1.4953191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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44
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Proline hydration at low temperatures: its role in the protection of cell from freeze-induced stress. Amino Acids 2016; 48:1685-94. [DOI: 10.1007/s00726-016-2232-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
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45
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Frach R, Heil J, Kast SM. Structure and thermodynamics of nondipolar molecular liquids and solutions from integral equation theory. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1167266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Roland Frach
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund, Germany
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund, Germany
| | - Stefan M. Kast
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund, Germany
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Bešter-Rogač M, Fedotova MV, Kruchinin SE, Klähn M. Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids. Phys Chem Chem Phys 2016; 18:28594-28605. [DOI: 10.1039/c6cp05010g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining MD simulations and RISM calculations with experiments, we demonstrated that the interionic interactions of investigated ILs as model 1,1 electrolytes in water solutions are weak but evidently dependent on the molecular structure.
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Affiliation(s)
| | | | | | - Marco Klähn
- Institute of Chemical and Engineering Sciences
- Agency for Science
- Technology and Research
- Singapore
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47
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Eiberweiser A, Nazet A, Kruchinin SE, Fedotova MV, Buchner R. Hydration and Ion Binding of the Osmolyte Ectoine. J Phys Chem B 2015; 119:15203-11. [PMID: 26565946 DOI: 10.1021/acs.jpcb.5b09276] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ectoine is a widespread osmolyte enabling halophilic bacteria to withstand high osmotic stress that has many potential applications ranging from cosmetics to its use as a therapeutic agent. In this contribution, combining experiment and theory, the hydration and ion-binding of this zwitterionic compound was studied to gain information on the functioning of ectoine in particular and of osmolytes in general. Dielectric relaxation spectroscopy was used to determine the effective hydration number of ectoine and its effective dipole moment in aqueous solutions with and without added NaCl. The obtained experimental data were compared with structural results from 1D-RISM and 3D-RISM calculations. It was found that ectoine is strongly hydrated, even in the presence of high salt concentrations. Upon addition of NaCl, ions are bound to ectoine but the formed complexes are not very stable. Interestingly, this osmolyte strongly rises the static relative permittivity of its solutions, shielding thus effectively long-range Coulomb interactions among ions in ectoine-containing solutions. We believe that via this effect, which should be common to all zwitterionic osmolytes, ectoine protects against excessive ions within the cell in addition to its strong osmotic activity protecting against ions outside.
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Affiliation(s)
- Andreas Eiberweiser
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Andreas Nazet
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
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Oshima H, Kinoshita M. A highly efficient hybrid method for calculating the hydration free energy of a protein. J Comput Chem 2015; 37:712-23. [DOI: 10.1002/jcc.24253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
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49
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Three-dimensional reference interaction site model solvent combined with a quantum mechanical treatment of the solute. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Palmer DS, Mišin M, Fedorov MV, Llinas A. Fast and General Method To Predict the Physicochemical Properties of Druglike Molecules Using the Integral Equation Theory of Molecular Liquids. Mol Pharm 2015. [PMID: 26212723 DOI: 10.1021/acs.molpharmaceut.5b00441] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a method to predict physicochemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D reference interaction site model of the integral equation theory of molecular liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark data sets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction.
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Affiliation(s)
- David S Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde , Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - Maksim Mišin
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, U.K
| | - Maxim V Fedorov
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, U.K
| | - Antonio Llinas
- Respiratory, Inflammation and Autoimmune iMed, AstraZeneca R&D , Pepparedsleden 1, SE-431 83, Mölndal, Sweden
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