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Aguilar-Pineda J, González-Melchor M. Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models. J Chem Theory Comput 2024; 20:6369-6387. [PMID: 38991114 PMCID: PMC11270832 DOI: 10.1021/acs.jctc.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024]
Abstract
G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.
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Affiliation(s)
- Jorge
Alberto Aguilar-Pineda
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
| | - Minerva González-Melchor
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
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Cruces Chamorro V, Jungwirth P, Martinez-Seara H. Building Water Models Compatible with Charge Scaling Molecular Dynamics. J Phys Chem Lett 2024; 15:2922-2928. [PMID: 38451169 PMCID: PMC10945568 DOI: 10.1021/acs.jpclett.4c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Charge scaling has proven to be an efficient way to account in a mean-field manner for electronic polarization by aqueous ions in force field molecular dynamics simulations. However, commonly used water models with dielectric constants over 50 are not consistent with this approach leading to "overscaling", i.e., generally too weak ion-ion interactions. Here, we build water models fully compatible with charge scaling, i.e., having the correct low-frequency dielectric constant of about 45. To this end, we employ advanced optimization and machine learning schemes in order to explore the vast parameter space of four-site water models efficiently. As an a priori unwarranted positive result, we find a sizable range of force field parameters that satisfy the above dielectric constant constraint providing at the same time accuracy with respect to experimental data comparable with the best existing four-site water models such as TIP4P/2005, TIP4P-FB, or OPC. The present results thus open the way to the development of a consistent charge scaling force field for modeling ions in aqueous solutions.
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Affiliation(s)
- Victor Cruces Chamorro
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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3
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Shock CJ, Stevens MJ, Frischknecht AL, Nakamura I. Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents. J Chem Phys 2023; 159:134507. [PMID: 37795785 DOI: 10.1063/5.0165481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
We develop a Stockmayer fluid model that accounts for the dielectric responses of polar solvents (water, MeOH, EtOH, acetone, 1-propanol, DMSO, and DMF) and NaCl solutions. These solvent molecules are represented by Lennard-Jones (LJ) spheres with permanent dipole moments and the ions by charged LJ spheres. The simulated dielectric constants of these liquids are comparable to experimental values, including the substantial decrease in the dielectric constant of water upon the addition of NaCl. Moreover, the simulations predict an increase in the dielectric constant when considering the influence of ion translations in addition to the orientation of permanent dipoles.
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Affiliation(s)
- Cameron J Shock
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Issei Nakamura
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA
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Zhang D, Li Y, Lu H, Zhao F, Cheng J, Zhang J. Influence of conversion on dielectric constant of Dicyandiamide cured epoxy resin:a molecular dynamic simulation and experiment study. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Kolafa J. Pressure in Molecular Simulations with Scaled Charges. 1. Ionic Systems. J Phys Chem B 2020; 124:7379-7390. [PMID: 32790401 DOI: 10.1021/acs.jpcb.0c02641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge scaling, rationalized as MDEC (molecular dynamics in electronic continuum) or ECC (electronic continuum correction), has become a widely used simple approach to how to avoid self-consistent induced dipoles yet approximately take into account the effects of electronic polarizability. It has been assumed that the continuum permittivity does not depend on density; in turn, pressure is calculated by standard formulas. In this work, we elaborate a complementary approximation of density-independent molecular polarizability and derive formulas for pressure corrections within the MDEC framework; real behavior lies between these two extremes. The pressure corrections for test ionic systems are huge and negative, leading to sizable densities in constant-pressure MDEC simulations. A comparison of MDEC results with equivalent polarizable systems gives a good pressure match for a crystal but very low MDEC pressures for ionic liquids. These results witness about the importance of a correct density dependence not only of continuum permittivity in MDEC simulations but also of polarizability in polarizable simulations.
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Affiliation(s)
- Jiří Kolafa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
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Wexler AD, Fuchs EC, Woisetschläger J, Vitiello G. Electrically induced liquid-liquid phase transition in water at room temperature. Phys Chem Chem Phys 2019; 21:18541-18550. [PMID: 31397450 DOI: 10.1039/c9cp03192h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we expand on findings previously reported [Wexler et al., Phys. Chem. Chem. Phys., 2016, 18, 16281] on the experimental observation of a phase transition in a hydrogen bonded liquid manifesting in long range dipole-dipole interactions. The studied system, liquid water stressed by an electric field, exhibits collective oscillations brought about through spontaneous breakdown of symmetry. Raman spectroscopy identifies the primary excitation of the emergent phase as transverse optically active phonon-like sidebands that appear on the hydrogen bonded asymmetric stretch mode. The phase transition is observed throughout the entire volume of liquid. The system also exhibits a self-similarity relation between the scattered Raman intensity and the electric field strength which further supports the conclusion that collective behavior persists against thermal disruption. The experimental findings are discussed in terms of a quantum field theory for macroscopic quantum systems.
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Affiliation(s)
- Adam D Wexler
- Arie Zwijnenburg Laboratory for Advanced Microscopy and Optical Metrology, Wetsus - European Center of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911MA Leeuwarden, The Netherlands.
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Vokáčová ZS, Pluhařová E. Understanding structure and dynamics of organic liquid mixtures by molecular simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Qiu Y, Nerenberg PS, Head-Gordon T, Wang LP. Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data. J Phys Chem B 2019; 123:7061-7073. [DOI: 10.1021/acs.jpcb.9b05455] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yudong Qiu
- Chemistry Department, University of California, Davis, Davis, California 95616, United States
| | - Paul S. Nerenberg
- Departments of Physics & Astronomy and Biological Sciences, California State University, Los Angeles, California 90032, United States
| | - Teresa Head-Gordon
- Pitzer Theory Center and Departments of Chemistry, Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lee-Ping Wang
- Chemistry Department, University of California, Davis, Davis, California 95616, United States
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Wei W, Luo J, Waldispühl J, Moitessier N. Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes. J Chem Inf Model 2019; 59:2941-2951. [PMID: 30998377 DOI: 10.1021/acs.jcim.9b00163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past two decades, interests in DNA and RNA as drug targets have been growing rapidly. Following the trends observed with protein drug targets, computational approaches for drug design have been developed for this new class of molecules. Our efforts toward the development of a universal docking program, Fitted, led us to focus on nucleic acids. Throughout the development of this docking program, efforts were directed toward displaceable water molecules which must be accurately located for optimal docking-based drug discovery. However, although there is a plethora of methods to place water molecules in and around protein structures, there is, to the best of our knowledge, no such fully automated method for nucleic acids, which are significantly more polar and solvated than proteins. We report herein a new method, Splash'Em (Solvation Potential Laid around Statistical Hydration on Entire Macromolecules) developed to place water molecules within the binding cavity of nucleic acids. This fast method was shown to have high agreement with water positions in crystal structures and will therefore provide essential information to medicinal chemists.
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Jorge M, Lue L. The dielectric constant: Reconciling simulation and experiment. J Chem Phys 2019; 150:084108. [DOI: 10.1063/1.5080927] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Miguel Jorge
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Leo Lue
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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