1
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Zhu J, Xu P, Zhao E, Zhang X, Li X, Li J. The impacts of net charge on the water dispersity of nanoparticles. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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2
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Jin J, Han Y, Pak AJ, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model. J Chem Phys 2021; 154:044104. [PMID: 33514116 PMCID: PMC7826168 DOI: 10.1063/5.0026651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander J. Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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3
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Chechko VE, Gotsulskiy VY, Malomuzh NP. Similarity degrees and differences of argon, hydrogen sulphide, water, methanol and ethanol on their coexistence curves. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Mason PE, Tavagnacco L, Saboungi ML, Hansen T, Fischer HE, Neilson GW, Ichiye T, Brady JW. Molecular Dynamics and Neutron Scattering Studies of Potassium Chloride in Aqueous Solution. J Phys Chem B 2019; 123:10807-10813. [PMID: 31769976 DOI: 10.1021/acs.jpcb.9b08422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Neutron diffraction with isotopic substitution (NDIS) experiments were done on both natural abundance potassium and isotopically labeled 41KCl heavy water solutions to characterize the solvent structuring around the potassium ion in water. Preliminary measurements suggested that the literature value for the coherent neutron scattering length (2.69 fm) for 41K was significantly in error. This value was remeasured using a neutron powder diffractometer and found to be 2.40 fm. This revision increases significantly the contrast between the natural abundance K and 41K by about 30% (from 1.0 to 1.3 fm). The experimentally determined structure factor of the potassium ion was then compared to that calculated from molecular dynamics (MD) simulations. Previous neutron scattering measurements of potassium gave a solvation number of 5.5 (see below). In this study, the NDIS and MD results are in good agreement and allowed us to derive a coordination number of 6.1 for water molecules and 0.8 for chloride ions around each K+ ion in 4 molal aqueous KCl solution.
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Affiliation(s)
- Philip E Mason
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic & Center for Biomolecules and Complex Molecular Systems , 16610 Prague 6 , Czech Republic
| | - Letizia Tavagnacco
- Department of Food Science , Cornell University , Ithaca , New York 14853 , United States
| | - Marie-Louise Saboungi
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie , UMR 7590 CNRS - Sorbonne Université, Campus Pierre et Marie Curie , 4, Place Jussieu , 75005 Paris , France
| | - Thomas Hansen
- Institut Laue-Langevin , 71 Avenue des Martyrs , 38042 Grenoble Cedex 9 , France
| | - Henry E Fischer
- Institut Laue-Langevin , 71 Avenue des Martyrs , 38042 Grenoble Cedex 9 , France
| | - George W Neilson
- H.H. Wills Physics Laboratory , University of Bristol , BS8 1TL Bristol , U.K
| | - Toshiko Ichiye
- Department of Chemistry , Georgetown University , Box 571227, Washington , DC 20057 , United States
| | - John W Brady
- Department of Food Science , Cornell University , Ithaca , New York 14853 , United States
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5
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Schneider J, Korshunova K, Musiani F, Alfonso-Prieto M, Giorgetti A, Carloni P. Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations. Biochem Biophys Res Commun 2018; 498:366-374. [PMID: 29409902 DOI: 10.1016/j.bbrc.2018.01.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/21/2022]
Abstract
Membrane receptors constitute major targets for pharmaceutical intervention. Drug design efforts rely on the identification of ligand binding poses. However, the limited experimental structural information available may make this extremely challenging, especially when only low-resolution homology models are accessible. In these cases, the predictions may be improved by molecular dynamics simulation approaches. Here we review recent developments of multiscale, hybrid molecular mechanics/coarse-grained (MM/CG) methods applied to membrane proteins. In particular, we focus on our in-house MM/CG approach. It is especially tailored for G-protein coupled receptors, the largest membrane receptor family in humans. We show that our MM/CG approach is able to capture the atomistic details of the receptor/ligand binding interactions, while keeping the computational cost low by representing the protein frame and the membrane environment in a highly simplified manner. We close this review by discussing ongoing improvements and challenges of the current implementation of our MM/CG code.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany; VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Viet Nam.
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6
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Vaiwala R, Jadhav S, Thaokar R. Four-to-one coarse-grained polarisable water model for dissipative particle dynamics. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1405159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sameer Jadhav
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rochish Thaokar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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7
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Lee BL, Kuczera K. Simulating the free energy of passive membrane permeation for small molecules. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1407029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brent L. Lee
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas , Lawrence, KS, USA
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8
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John ST, Csányi G. Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. J Phys Chem B 2017; 121:10934-10949. [PMID: 29117675 DOI: 10.1021/acs.jpcb.7b09636] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials. Though slower than the latter, our model can still be faster than all-atom simulations for solvent-free CG models commonly used in biomolecular simulations.
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Affiliation(s)
- S T John
- Department of Physics, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, United Kingdom.,PROWLER.io , 66-68 Hills Road, Cambridge CB2 1LA, United Kingdom
| | - Gábor Csányi
- Department of Engineering, University of Cambridge , Cambridge CB2 1PZ, United Kingdom
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9
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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: 208] [Impact Index Per Article: 29.7] [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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10
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Affiliation(s)
- Mingsen Deng
- Guizhou Provincial Key Laboratory
of Computational Nano-material Science, Guizhou Education University, No.115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Hujun Shen
- Guizhou Provincial Key Laboratory
of Computational Nano-material Science, Guizhou Education University, No.115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
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11
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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12
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Rana MK, Chandra A. Solvation of narrow pores of graphene-like plates in simple dipolar liquids: Wetting and dewetting behavior and solvent dynamics for varying pore width and solute–solvent interaction. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Qi R, Wang LP, Wang Q, Pande VS, Ren P. United polarizable multipole water model for molecular mechanics simulation. J Chem Phys 2015; 143:014504. [PMID: 26156485 PMCID: PMC4499046 DOI: 10.1063/1.4923338] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/21/2015] [Indexed: 11/14/2022] Open
Abstract
We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3-5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.
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Affiliation(s)
- Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lee-Ping Wang
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Qiantao Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Vijay S Pande
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
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14
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15
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Shen H, Li Y, Xu P, Li X, Chu H, Zhang D, Li G. An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model. J Comput Chem 2015; 36:1103-13. [DOI: 10.1002/jcc.23895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/08/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Hujun Shen
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
| | - Yan Li
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
| | - Peijun Xu
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
| | - Xiaofang Li
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
| | - Dinglin Zhang
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian 116023, Liaoning Province Peoples Republic of China
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16
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Izadi S, Anandakrishnan R, Onufriev AV. Building Water Models: A Different Approach. J Phys Chem Lett 2014; 5:3863-3871. [PMID: 25400877 PMCID: PMC4226301 DOI: 10.1021/jz501780a] [Citation(s) in RCA: 626] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/16/2014] [Indexed: 05/19/2023]
Abstract
Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than the symmetry. Instead, we optimize the distribution of point charges to best describe the "electrostatics" of the water molecule. The resulting "optimal" 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures. The improvements in the proposed model extend beyond bulk properties: compared to common rigid models, predicted hydration free energies of small molecules using OPC are uniformly closer to experiment, with root-mean-square error <1 kcal/mol.
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Affiliation(s)
- Saeed Izadi
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer
Science and Physics, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ramu Anandakrishnan
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer
Science and Physics, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Alexey V. Onufriev
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer
Science and Physics, Virginia Tech, Blacksburg, Virginia 24060, United States
- E-mail:
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19
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Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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20
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Lee SH. Molecular Dynamics Simulation Study for Shear Viscosity of Water at High Temperatures using SPC/E Water Model. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.2.644] [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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21
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Shen H, Li Y, Ren P, Zhang D, Li G. An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials. J Chem Theory Comput 2014; 10:731-750. [PMID: 24659927 PMCID: PMC3958967 DOI: 10.1021/ct400974z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Gay–Berne
anisotropic potential has been widely used to
evaluate the nonbonded interactions between coarse-grained particles
being described as elliptical rigid bodies. In this paper, we are
presenting a coarse-grained model for twenty kinds of amino acids
and proteins, based on the anisotropic Gay–Berne and point
electric multipole (EMP) potentials. We demonstrate that the anisotropic
coarse-grained model, namely GBEMP model, is able to reproduce many
key features observed from experimental protein structures (Dunbrack
Library), as well as from atomistic force field simulations (using
AMOEBA, AMBER, and CHARMM force fields), while saving the computational
cost by a factor of about 10–200 depending on specific cases
and atomistic models. More importantly, unlike other coarse-grained
approaches, our framework is based on the fundamental intermolecular
forces with explicit treatment of electrostatic and repulsion-dispersion
forces. As a result, the coarse-grained protein model presented an
accurate description of nonbonded interactions (particularly electrostatic
component) between hetero/homodimers (such as peptide–peptide,
peptide–water). In addition, the encouraging performance of
the model was reflected by the excellent correlation between GBEMP
and AMOEBA models in the calculations of the dipole moment of peptides.
In brief, the GBEMP model given here is general and transferable,
suitable for simulating complex biomolecular systems.
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Affiliation(s)
- Hujun Shen
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
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Zhang N, Zhang P, Kang W, Bluestein D, Deng Y. Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma. JOURNAL OF COMPUTATIONAL PHYSICS 2014; 257:726-736. [PMID: 24910470 PMCID: PMC4045626 DOI: 10.1016/j.jcp.2013.09.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.
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Affiliation(s)
- Na Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, NY 11794, United States
| | - Peng Zhang
- Department of Biomedical Engineering, Stony Brook University, NY 11790, United States
| | - Wei Kang
- Center for Applied Physics and Technology, and College of Engineering, Peking University, Beijing 100871, China
| | - Danny Bluestein
- Department of Biomedical Engineering, Stony Brook University, NY 11790, United States
| | - Yuefan Deng
- Department of Applied Mathematics and Statistics, Stony Brook University, NY 11794, United States
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23
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Lee SH. Temperature Dependence on Structure and Self-Diffusion of Water: A Molecular Dynamics Simulation Study using SPC/E Model. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.12.3800] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Affiliation(s)
- Mario Orsi
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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25
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Wikfeldt KT, Batista ER, Vila FD, Jónsson H. A transferable H2O interaction potential based on a single center multipole expansion: SCME. Phys Chem Chem Phys 2013; 15:16542-56. [DOI: 10.1039/c3cp52097h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Shkurti A, Orsi M, Macii E, Ficarra E, Acquaviva A. Acceleration of coarse grain molecular dynamics on GPU architectures. J Comput Chem 2012; 34:803-18. [DOI: 10.1002/jcc.23183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 10/19/2012] [Accepted: 10/25/2012] [Indexed: 02/01/2023]
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27
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Ohba T, Hata K, Kanoh H. Significant Hydration Shell Formation Instead of Hydrogen Bonds in Nanoconfined Aqueous Electrolyte Solutions. J Am Chem Soc 2012; 134:17850-3. [DOI: 10.1021/ja307338t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Tomonori Ohba
- Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522,
Japan
| | - Kenji Hata
- Nanotube Research
Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi Tsukuba, Ibaraki 305-8565, Japan
| | - Hirofumi Kanoh
- Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522,
Japan
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28
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Riniker S, Eichenberger AP, van Gunsteren WF. Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:647-61. [PMID: 22797564 DOI: 10.1007/s00249-012-0837-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/18/2012] [Accepted: 06/25/2012] [Indexed: 11/29/2022]
Abstract
Simulation of the dynamics of a protein in aqueous solution using an atomic model for both the protein and the many water molecules is still computationally extremely demanding considering the time scale of protein motions. The use of supra-atomic or supra-molecular coarse-grained (CG) models may enhance the computational efficiency, but inevitably at the cost of reduced accuracy. Coarse-graining solvent degrees of freedom is likely to yield a favourable balance between reduced accuracy and enhanced computational speed. Here, the use of a supra-molecular coarse-grained water model that largely preserves the thermodynamic and dielectric properties of atomic level fine-grained (FG) water in molecular dynamics simulations of an atomic model for four proteins is investigated. The results of using an FG, a CG, an implicit, or a vacuum solvent environment of the four proteins are compared, and for hen egg-white lysozyme a comparison to NMR data is made. The mixed-grained simulations do not show large differences compared to the FG atomic level simulations, apart from an increased tendency to form hydrogen bonds between long side chains, which is due to the reduced ability of the supra-molecular CG beads that represent five FG water molecules to make solvent-protein hydrogen bonds. But, the mixed-grained simulations are at least an order of magnitude faster than the atomic level ones.
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Affiliation(s)
- Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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29
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Darré L, Tek A, Baaden M, Pantano S. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. J Chem Theory Comput 2012; 8:3880-94. [DOI: 10.1021/ct3001816] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
| | - Alex Tek
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
- Université Pierre et Marie
Curie, UPMC Sorbonne Universités, 4 place Jussieu 75005 Paris,
France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergio Pantano
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
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30
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Darré L, Machado MR, Pantano S. Coarse-grained models of water. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1097] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Shen H, Xia Z, Li G, Ren P. A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY VOLUME 8 2012. [DOI: 10.1016/b978-0-444-59440-2.00005-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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32
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Orsi M, Essex JW. The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One 2011; 6:e28637. [PMID: 22194874 PMCID: PMC3241685 DOI: 10.1371/journal.pone.0028637] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 11/11/2011] [Indexed: 02/05/2023] Open
Abstract
A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r) = 1). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
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Affiliation(s)
- Mario Orsi
- School of Chemistry, University of Southampton, Southampton, United Kingdom.
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33
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Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Force Field for Membrane–Peptide Simulations. J Chem Theory Comput 2011; 7:3793-802. [DOI: 10.1021/ct200593t] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zhe Wu
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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34
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Abstract
Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical∕molecular mechanical (QM∕MM) calculations at the MP2∕aug-cc-pVQZ level on a B3LYP∕aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM∕MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM∕MM multipoles is much closer than that from the site models to the potential from the QM∕MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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35
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Kamerlin SCL, Vicatos S, Dryga A, Warshel A. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu Rev Phys Chem 2011; 62:41-64. [PMID: 21034218 DOI: 10.1146/annurev-physchem-032210-103335] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent years have witnessed an explosion in computational power, leading to attempts to model ever more complex systems. Nevertheless, there remain cases for which the use of brute-force computer simulations is clearly not the solution. In such cases, great benefit can be obtained from the use of physically sound simplifications. The introduction of such coarse graining can be traced back to the early usage of a simplified model in studies of proteins. Since then, the field has progressed tremendously. In this review, we cover both key developments in the field and potential future directions. Additionally, particular emphasis is given to two general approaches, namely the renormalization and reference potential approaches, which allow one to move back and forth between the coarse-grained (CG) and full models, as these approaches provide the foundation for CG modeling of complex systems.
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Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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36
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Orsi M, Noro MG, Essex JW. Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes. J R Soc Interface 2011; 8:826-41. [PMID: 21131331 PMCID: PMC3104353 DOI: 10.1098/rsif.2010.0541] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/09/2010] [Indexed: 11/12/2022] Open
Abstract
Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel 'dual-resolution' molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup-glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a 'destabilizing' tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed.
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Affiliation(s)
- Mario Orsi
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Massimo G. Noro
- Unilever R&D Port Sunlight, Quarry Road East, Bebington, Wirral, CH63 3JW, UK
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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37
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Abstract
Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.
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38
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Riniker S, van Gunsteren WF. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. J Chem Phys 2011; 134:084110. [DOI: 10.1063/1.3553378] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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39
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Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. J Phys Chem B 2010; 114:10524-9. [DOI: 10.1021/jp1019763] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhe Wu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706
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40
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Te JA, Ichiye T. Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model. J Chem Phys 2010; 132:114511. [PMID: 20331309 DOI: 10.1063/1.3359432] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The soft-sticky dipole-quadrupole-octupole (SSDQO) potential energy function for a coarse-grained single-site water model has Lennard-Jones interactions and an approximate multipole expansion for the electrostatics. Here, the Lennard-Jones parameters and multipole moments of SSDQO were optimized so that the structural, thermodynamic, dynamic, and dielectric properties agreed with experimental values of liquid water at ambient conditions. Using these parameters, the temperature and pressure dependence of various properties were shown to be in good agreement with experiment, including a temperature of maximum density at approximately 260 K. This new parametrization, referred to as SSDQO1, is both computationally faster and generally more accurate over a wide range of conditions than traditional three-site water models, which demonstrates that a model with a single dipole, quadrupole, and octupole on each water molecule can reproduce the tetrahedral hydrogen bonded network of water.
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Affiliation(s)
- Jerez A Te
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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41
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Te JA, Tan ML, Ichiye T. Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model. Chem Phys Lett 2010; 491:218-223. [PMID: 21072255 PMCID: PMC2975465 DOI: 10.1016/j.cplett.2010.04.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a "lone-pair" orientation for the water accepting the sugar hydroxyl hydrogen bond that is more consistent with the limited experimental data than the "dipole" orientation in SPC/E, which has important implications for studies of the cryoprotectant properties of sugars.
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Affiliation(s)
- Jerez A. Te
- Department of Chemistry, Georgetown University, Washington, DC, 20057
| | - Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, DC, 20057
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, 20057
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42
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van Zon R, Schofield J. Constructing smooth potentials of mean force, radial distribution functions, and probability densities from sampled data. J Chem Phys 2010; 132:154110. [DOI: 10.1063/1.3366523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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43
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Orsi M, Michel J, Essex JW. Coarse-grain modelling of DMPC and DOPC lipid bilayers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:155106. [PMID: 21389551 DOI: 10.1088/0953-8984/22/15/155106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Our recently developed coarse-grain model for dimyristoylphosphatidylcholine (DMPC) has been improved and extended to dioleylphosphatidylcholine (DOPC), a more typical constituent of real biological membranes. Single-component DMPC and DOPC bilayers have been simulated using microsecond-long molecular dynamics. We investigated properties that are difficult or impossible to access experimentally, such as the pressure distribution, the spontaneous curvature and the diffusion pattern of individual lipid molecules. Moreover, we studied the dipole potential, a basic physical feature of paramount biological importance that cannot be currently modelled by other coarse-grain approaches. In fact, a complete representation of the system electrostatics and a realistic description of the water component make our method unique amongst the existing coarse-grain membrane models. The spontaneous permeation of water, a phenomenon out of reach of standard atomistic models, was also observed and quantified; this was possible thanks to the efficiency of our model, which is about two orders of magnitude less computationally expensive than atomic-level counterparts. Results are generally in good agreement with the literature data. Further model extensions and future applications are proposed.
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Affiliation(s)
- Mario Orsi
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
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44
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Orsi M, Sanderson WE, Essex JW. Permeability of small molecules through a lipid bilayer: a multiscale simulation study. J Phys Chem B 2009; 113:12019-29. [PMID: 19663489 DOI: 10.1021/jp903248s] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transmembrane permeation of eight small (molecular weight <100) organic molecules across a phospholipid bilayer is investigated by multiscale molecular dynamics simulation. The bilayer and hydrating water are represented by simplified, efficient coarse-grain models, whereas the permeating molecules are described by a standard atomic-level force-field. Permeability properties are obtained through a refined version of the z-constraint algorithm. By constraining each permeant at selected depths inside the bilayer, we have sampled free energy differences and diffusion coefficients across the membrane. These data have been combined, according to the inhomogeneous solubility-diffusion model, to yield the permeability coefficients. The results are generally consistent with previous atomic-level calculations and available experimental data. Computationally, our multiscale approach proves 2 orders of magnitude faster than traditional atomic-level methods.
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Affiliation(s)
- Mario Orsi
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
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45
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Conde MM, Vega C, Tribello GA, Slater B. The phase diagram of water at negative pressures: Virtual ices. J Chem Phys 2009; 131:034510. [DOI: 10.1063/1.3182727] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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46
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Walsh TR, Liang T. A multipole-based water potential with implicit polarization for biomolecular simulations. J Comput Chem 2009; 30:893-9. [PMID: 18785240 DOI: 10.1002/jcc.21111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly sampled from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force-field is also shown to work compatibly with existing polarizable multipole-based force-fields for biomolecules.
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Affiliation(s)
- T R Walsh
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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47
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van Zon R, Schofield J. Event-driven dynamics of rigid bodies interacting via discretized potentials. J Chem Phys 2008; 128:154119. [DOI: 10.1063/1.2901173] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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48
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Orsi M, Haubertin DY, Sanderson WE, Essex JW. A quantitative coarse-grain model for lipid bilayers. J Phys Chem B 2007; 112:802-15. [PMID: 18085766 DOI: 10.1021/jp076139e] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simplified particle-based computer model for hydrated phospholipid bilayers has been developed and applied to quantitatively predict the major physical features of fluid-phase biomembranes. Compared with available coarse-grain methods, three novel aspects are introduced. First, the main electrostatic features of the system are incorporated explicitly via charges and dipoles. Second, water is accurately (yet efficiently) described, on an individual level, by the soft sticky dipole model. Third, hydrocarbon tails are modeled using the anisotropic Gay-Berne potential. Simulations are conducted by rigid-body molecular dynamics. Our technique proves 2 orders of magnitude less demanding of computational resources than traditional atomic-level methodology. Self-assembled bilayers quantitatively reproduce experimental observables such as electron density, compressibility moduli, dipole potential, lipid diffusion, and water permeability. The lateral pressure profile has been calculated, along with the elastic curvature constants of the Helfrich expression for the membrane bending energy; results are consistent with experimental estimates and atomic-level simulation data. Several of the results presented have been obtained for the first time using a coarse-grain method. Our model is also directly compatible with atomic-level force fields, allowing mixed systems to be simulated in a multiscale fashion.
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Affiliation(s)
- Mario Orsi
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
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49
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Ichiye T, Tan ML. Soft sticky dipole-quadrupole-octupole potential energy function for liquid water: an approximate moment expansion. J Chem Phys 2007; 124:134504. [PMID: 16613458 DOI: 10.1063/1.2161201] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new, efficient potential energy function for liquid water is presented here. The new model, which is referred here as the soft sticky dipole-quadrupole-octupole (SSDQO) model, describes a water molecule as a Lennard-Jones sphere with point dipole, quadrupole, and octupole moments. It is a single-point model and resembles the hard-sphere sticky dipole potential model for water by Bratko et al. [J. Chem. Phys. 83, 6367 (1985)] and the soft sticky dipole model by Ichiye and Liu [J. Phys. Chem. 100, 2723 (1996)] except now the sticky potential consists of an approximate moment expansion for the dimer interaction potential, which is much faster than the true moment expansion. The object here is to demonstrate that the SSDQO potential energy function can accurately mimic the potential energy function of a multipoint model using the moments of that model. First, the SSDQO potential energy function using the dipole, quadruple, and octupole moments from SPC/E, TIP3P, or TIP5P is shown to reproduce the dimer potential energy functions of the respective multipoint model. In addition, in Monte Carlo simulations of the pure liquid at room temperature, SSDQO reproduces radial distribution functions of the respective model. However, the Monte Carlo simulations using the SSDQO model are about three times faster than those using the three-point models and the long-range interactions decay faster for SSDQO (1/r(3) and faster) than for multipoint models (1/r). Moreover, the contribution of each moment to the energetics and other properties can be determined. Overall, the simplicity, efficiency, and accuracy of the SSDQO potential energy function make it potentially very useful for studies of aqueous solvation by computer simulations.
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Affiliation(s)
- Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
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Tan ML, Lucan L, Ichiye T. Study of multipole contributions to the structure of water around ions in solution using the soft sticky dipole-quadrupole-octupole (SSDQO) model of water. J Chem Phys 2007; 124:174505. [PMID: 16689581 DOI: 10.1063/1.2177240] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvation of ions in the soft sticky dipole-quadrupole-octupole (SSDQO) model for liquid water is presented here. This new potential energy function for liquid water describes water-water interactions by a Lennard-Jones term plus a sticky potential consisting of an approximate moment expansion with point dipole, quadrupole, and octupole moments. The SSDQO potential energy function using the moments from extended simple point charge (SPC/E), TIP3P, or TIP5P reproduces the pair potential energy functions and radial distribution functions of the respective multipoint model but it is much faster than even the three-point models. Here, the solvation of ions in SSDQO water is studied using ion-water potential energy functions consisting of moment expansions up to the charge-quadrupole term, up to the charge-octupole term, and up to an approximate charge-hexadecapole term using the moments of SPC/E water. The radial distributions from Monte Carlo simulations show the best agreement with the results for ions in SPC/E water for the expansion up to the charge-hexadecapole term. Thus, the best results are obtained when the water-water and ion-water potentials are exact up to the 1r(4) term and also contain an approximate 1r(5) term. Overall, the simplicity, efficiency, and accuracy of the SSDQO potential make it potentially very useful for computer simulations of aqueous solvation.
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Affiliation(s)
- Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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