1
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Antila HS, Dixit S, Kav B, Madsen JJ, Miettinen MS, Ollila OHS. Evaluating Polarizable Biomembrane Simulations against Experiments. J Chem Theory Comput 2024; 20:4325-4337. [PMID: 38718349 PMCID: PMC11137822 DOI: 10.1021/acs.jctc.3c01333] [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: 12/06/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Owing to the increase of available computational capabilities and the potential for providing a more accurate description, polarizable molecular dynamics force fields are gaining popularity in modeling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with increasing cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models─the CHARMM-Drude and the AMOEBA-based parameters─against high-fidelity experimental data and compare them to the top-performing nonpolarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best nonpolarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for the further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.
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Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Department
of Biomedicine, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Sneha Dixit
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
| | - Batuhan Kav
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jïulich 52428, Germany
| | - Jesper J. Madsen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, Global and Planetary
Health, College of Public Health, University
of South Florida, Tampa, Florida 33612, United States of America
| | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department
of Chemistry, University of Bergen, Bergen 5007, Norway
| | - O. H. Samuli Ollila
- VTT Technical
Research Centre of Finland, Espoo 02044, Finland
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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2
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Kastinen T, Batys P, Tolmachev D, Laasonen K, Sammalkorpi M. Ion-Specific Effects on Ion and Polyelectrolyte Solvation. Chemphyschem 2024:e202400244. [PMID: 38712639 DOI: 10.1002/cphc.202400244] [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: 03/05/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
Ion-specific effects on aqueous solvation of monovalent counter ions, Na+ ${^+ }$ , K+ ${^+ }$ , Cl- ${^- }$ , and Br- ${^- }$ , and two model polyelectrolytes (PEs), poly(styrene sulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA) were here studied with ab initio molecular dynamics (AIMD) and classical molecular dynamics (MD) simulations based on the OPLS-aa force-field which is an empirical fixed point-charge force-field. Ion-specific binding to the PE charge groups was also characterized. Both computational methods predict similar response for the solvation of the PEs but differ notably in description of ion solvation. Notably, AIMD captures the experimentally observed differences in Cl- ${^- }$ and Br- ${^- }$ anion solvation and binding with the PEs, while the classical MD simulations fail to differentiate the ion species response. Furthermore, the findings show that combining AIMD with the computationally less costly classical MD simulations allows benefiting from both the increased accuracy and statistics reach.
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Affiliation(s)
- Tuuva Kastinen
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076, Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076, Aalto, Finland
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere University, Finland
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239, Krakow, Poland
| | - Dmitry Tolmachev
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076, Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076, Aalto, Finland
| | - Kari Laasonen
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076, Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076, Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076, Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076, Aalto, Finland
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3
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Mantha S, Glisman A, Yu D, Wasserman EP, Backer S, Wang ZG. Adsorption Isotherm and Mechanism of Ca 2+ Binding to Polyelectrolyte. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6212-6219. [PMID: 38497336 DOI: 10.1021/acs.langmuir.3c03640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Polyelectrolytes, such as poly(acrylic acid) (PAA), can effectively mitigate CaCO3 scale formation. Despite their success as antiscalants, the underlying mechanism of binding of Ca2+ to polyelectrolyte chains remains unresolved. Through all-atom molecular dynamics simulations, we constructed an adsorption isotherm of Ca2+ binding to sodium polyacrylate (NaPAA) and investigated the associated binding mechanism. We find that the number of calcium ions adsorbed [Ca2+]ads to the polymer saturates at moderately high concentrations of free calcium ions [Ca2+]aq in the solution. This saturation value is intricately connected with the binding modes accessible to Ca2+ ions when they bind to the polyelectrolyte chain. We identify two dominant binding modes: the first involves binding to at most two carboxylate oxygens on a polyacrylate chain, and the second, termed the high binding mode, involves binding to four or more carboxylate oxygens. As the concentration of free calcium ions [Ca2+]aq increases from low to moderate levels, the polyelectrolyte chain undergoes a conformational transition from an extended coil to a hairpin-like structure, enhancing the accessibility to the high binding mode. At moderate concentrations of [Ca2+]aq, the high binding mode accounts for at least one-third of all binding events. The chain's conformational change and its consequent access to the high binding mode are found to increase the overall Ca2+ ion binding capacity of the polyelectrolyte chain.
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Affiliation(s)
- Sriteja Mantha
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Alec Glisman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Decai Yu
- Core R&D, The Dow Chemical Company, 633 Washington St., Midland, Michigan 48674, United States
| | - Eric P Wasserman
- Consumer Solutions R&D, The Dow Chemical Company, 400 Arcola Road, Collegeville, Pennsylvania 19426, United States
| | - Scott Backer
- Consumer Solutions R&D, The Dow Chemical Company, 400 Arcola Road, Collegeville, Pennsylvania 19426, United States
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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4
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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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5
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Hu X, Amin KS, Schneider M, Lim C, Salahub D, Baldauf C. System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1448-1464. [PMID: 38279917 PMCID: PMC10867808 DOI: 10.1021/acs.jctc.3c01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/29/2024]
Abstract
The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.
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Affiliation(s)
- Xiaojuan Hu
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kazi S. Amin
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Markus Schneider
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Dennis Salahub
- Centre
for Molecular Simulation and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Carsten Baldauf
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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6
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Nencini R, Regnier MLG, Backlund SM, Mantzari E, Dunn CD, Ollila OHS. Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations. Commun Chem 2024; 7:28. [PMID: 38351219 PMCID: PMC10864328 DOI: 10.1038/s42004-024-01115-4] [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: 08/24/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.
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Affiliation(s)
- Ricky Nencini
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Cory D Dunn
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
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7
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Riopedre-Fernandez M, Biriukov D, Dračínský M, Martinez-Seara H. Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity. Carbohydr Polym 2024; 325:121568. [PMID: 38008475 DOI: 10.1016/j.carbpol.2023.121568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/01/2023] [Accepted: 11/05/2023] [Indexed: 11/28/2023]
Abstract
Hyaluronan is a natural carbohydrate polymer with a negative charge that fosters gel-like conditions crucial for its cellular functions and industrial applications. As a recognized ligand for proteins, understanding their mutual interactions provides solid ground to tune hyaluronan's gel properties using biocompatible peptides. This work employs NMR and molecular dynamics simulations to identify molecular motifs relevant to hyaluronan-peptide interactions using arginine, lysine, and glycine oligopeptides. Arginine-rich peptides exhibit the strongest binding to hyaluronan according to chemical shift perturbation measurements, followed distantly by the similarly charged lysine. This difference highlights the significance of electrostatics and the peculiarities of the guanidinium side chain in arginine, capable of non-polar interactions that further stabilize the binding. Additional nuclear Overhauser effect measurements do not show stable interaction partners, precluding strong and well-defined complexes. Finally, molecular simulations support our findings and show an extended but significant interaction region, especially for arginine, responsible for the observed enhanced binding, which can also promote cross-linking of hyaluronan polymers. Our findings pave the way for optimizing biocompatible peptides to alter hyaluronan gels' properties efficiently and also explain why hyaluronan-protein interaction typically involves positively charged arginine-rich regions also capable of forming hydrogen bonds and non-polar interactions.
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Affiliation(s)
- Miguel Riopedre-Fernandez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 16000, Czech Republic
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 16000, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 16000, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 16000, Czech Republic.
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8
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Mason PE, Martinek T, Fábián B, Vazdar M, Jungwirth P, Tichacek O, Duboué-Dijon E, Martinez-Seara H. Hydration of biologically relevant tetramethylammonium cation by neutron scattering and molecular dynamics. Phys Chem Chem Phys 2024; 26:3208-3218. [PMID: 38193286 PMCID: PMC10806622 DOI: 10.1039/d3cp05449g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Neutron scattering and molecular dynamics studies were performed on a concentrated aqueous tetramethylammonium (TMA) chloride solution to gain insight into the hydration shell structure of TMA, which is relevant for understanding its behavior in biological contexts of, e.g., properties of phospholipid membrane headgroups or interactions between DNA and histones. Specifically, neutron diffraction with isotopic substitution experiments were performed on TMA and water hydrogens to extract the specific correlation between hydrogens in TMA (HTMA) and hydrogens in water (HW). Classical molecular dynamics simulations were performed to help interpret the experimental neutron scattering data. Comparison of the hydration structure and simulated neutron signals obtained with various force field flavors (e.g. overall charge, charge distribution, polarity of the CH bonds and geometry) allowed us to gain insight into how sensitive the TMA hydration structure is to such changes and how much the neutron signal can capture them. We show that certain aspects of the hydration, such as the correlation of the hydrogen on TMA to hydrogen on water, showed little dependence on the force field. In contrast, other correlations, such as the ion-ion interactions, showed more marked changes. Strikingly, the neutron scattering signal cannot discriminate between different hydration patterns. Finally, ab initio molecular dynamics was used to examine the three-dimensional hydration structure and thus to benchmark force field simulations. Overall, while neutron scattering has been previously successfully used to improve force fields, in the particular case of TMA we show that it has only limited value to fully determine the hydration structure, with other techniques such as ab initio MD being of a significant help.
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Affiliation(s)
- Philip E Mason
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 160 00 Praha 6, Czech Republic.
| | - Tomas Martinek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 160 00 Praha 6, Czech Republic.
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 160 00 Praha 6, Czech Republic.
| | - Mario Vazdar
- Department of Mathematics, Informatics, and Cybernetics, University of Chemistry and Technology Prague, Technická 5, 16628 Prague, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 160 00 Praha 6, Czech Republic.
| | - Ondrej Tichacek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 160 00 Praha 6, Czech Republic.
| | - Elise Duboué-Dijon
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542, 160 00 Praha 6, Czech Republic.
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9
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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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10
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Kostal V, Jungwirth P, Martinez-Seara H. Nonaqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations. J Phys Chem Lett 2023; 14:8691-8696. [PMID: 37733610 PMCID: PMC10561266 DOI: 10.1021/acs.jpclett.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge-charge interactions in solution may become severely overestimated, leading to unrealistically strong bindings of ions to biomolecules. The electronic continuum correction introduces electronic polarization in a mean-field way via scaling of charges by the reciprocal of the square root of the high-frequency dielectric constant of the solvent environment. Here, we use ab initio molecular dynamics simulations to quantify the effect of electronic polarization on pairs of like-charged ions in a model nonaqueous environment where electronic polarization is the only dielectric response. Our findings confirm the conceptual validity of this approach, underlining its applicability to complex aqueous biomolecular systems. Simultaneously, the results presented here justify the potential employment of weaker charge scaling factors in force field development.
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Affiliation(s)
- Vojtech Kostal
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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11
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Biriukov D, Javanainen M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J Chem Theory Comput 2023; 19:6332-6341. [PMID: 37651714 PMCID: PMC10537000 DOI: 10.1021/acs.jctc.3c00614] [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: 06/08/2023] [Indexed: 09/02/2023]
Abstract
The routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the flat-bottom approach to lipid bilayers with various compositions and solvent environments, covering ions and cationic peptides to validate the approach in a realistic use case. We also discuss the possible limitations of the method as well as its computational efficiency and provide a step-by-step guide on how to set up such simulations in a straightforward manner.
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Affiliation(s)
- Denys Biriukov
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the
Czech Republic, Flemingovo
nam. 2, Prague 6 CZ-16610, Czech Republic
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno CZ-62500, Czech Republic
| | - Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the
Czech Republic, Flemingovo
nam. 2, Prague 6 CZ-16610, Czech Republic
- Institute
of Biotechnology, University of Helsinki, Helsinki FI-00790, Finland
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12
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Rezaei M, Sakong S, Groß A. Molecular Modeling of Water-in-Salt Electrolytes: A Comprehensive Analysis of Polarization Effects and Force Field Parameters in Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:5712-5730. [PMID: 37528639 DOI: 10.1021/acs.jctc.3c00171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Accurate modeling of highly concentrated aqueous solutions, such as water-in-salt (WiS) electrolytes in battery applications, requires proper consideration of polarization contributions to atomic interactions. Within the force field molecular dynamics (MD) simulations, the atomic polarization can be accounted for at various levels. Nonpolarizable force fields implicitly account for polarization effects by incorporating them into their van der Waals interaction parameters. They can additionally mimic electron polarization within a mean-field approximation through ionic charge scaling. Alternatively, explicit polarization description methods, such as the Drude oscillator model, can be selectively applied to either a subset of polarizable atoms or all polarizable atoms to enhance simulation accuracy. The trade-off between simulation accuracy and computational efficiency highlights the importance of determining an optimal level of accounting for atomic polarization. In this study, we analyze different approaches to include polarization effects in MD simulations of WiS electrolytes, with an example of a Na-OTF solution. These approaches range from a nonpolarizable to a fully polarizable force field. After careful examination of computational costs, simulation stability, and feasibility of controlling the electrolyte properties, we identify an efficient combination of force fields: the Drude polarizable force field for salt ions and non-polarizable models for water. This cost-effective combination is sufficiently flexible to reproduce a broad range of electrolyte properties, while ensuring simulation stability over a relatively wide range of force field parameters. Furthermore, we conduct a thorough evaluation of the influence of various force field parameters on both the simulation results and technical requirements, with the aim of establishing a general framework for force field optimization and facilitating parametrization of similar systems.
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Affiliation(s)
- Majid Rezaei
- Institute of Theoretical Chemistry, Ulm University, Oberberghof 7, 89081 Ulm, Germany
| | - Sung Sakong
- Institute of Theoretical Chemistry, Ulm University, Oberberghof 7, 89081 Ulm, Germany
| | - Axel Groß
- Institute of Theoretical Chemistry, Ulm University, Oberberghof 7, 89081 Ulm, Germany
- Helmholtz Institute Ulm (HIU) for Electrochemical Energy Storage, Helmholtzstraße 11, 89069 Ulm, Germany
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13
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Herman CE, Valiya Parambathu A, Asthagiri DN, Lenhoff AM. Polarizability Plays a Decisive Role in Modulating Association between Molecular Cations and Anions. J Phys Chem Lett 2023; 14:7020-7026. [PMID: 37523856 DOI: 10.1021/acs.jpclett.3c01566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Electrostatic interactions involving proteins depend on not only the ionic charges involved but also their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of different pairs of monovalent molecular ions that are relevant to protein-protein and protein-ligand interactions. Cationic analogues of the basic amino acid side chains are simulated, along with oxyanionic analogues of cation-exchange ligands and acidic amino acids. Experimentally observed association trends with respect to the cations, but not anions, are captured by a nonpolarizable model. An effective continuum correction to account for electronic polarizability can capture both trends better but at the expense of fidelity to the underlying free energy landscape for ion-pair association. A polarizable model proves decisive in capturing experimentally suggested trends with respect to both cations and anions; critically, the free energy landscape for ion-pair association is itself altered, thus altering configurational sampling.
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Affiliation(s)
- Chase E Herman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Arjun Valiya Parambathu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Dilipkumar N Asthagiri
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
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14
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Baltrukevich H, Bartos P. RNA-protein complexes and force field polarizability. Front Chem 2023; 11:1217506. [PMID: 37426330 PMCID: PMC10323139 DOI: 10.3389/fchem.2023.1217506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
Molecular dynamic (MD) simulations offer a way to study biomolecular interactions and their dynamics at the atomistic level. There are only a few studies of RNA-protein complexes in MD simulations, and here we wanted to study how force fields differ when simulating RNA-protein complexes: 1) argonaute 2 with bound guide RNA and a target RNA, 2) CasPhi-2 bound to CRISPR RNA and 3) Retinoic acid-inducible gene I C268F variant in complex with double-stranded RNA. We tested three non-polarizable force fields: Amber protein force fields ff14SB and ff19SB with RNA force field OL3, and the all-atom OPLS4 force field. Due to the highly charged and polar nature of RNA, we also tested the polarizable AMOEBA force field and the ff19SB and OL3 force fields with a polarizable water model O3P. Our results show that the non-polarizable force fields lead to compact and stable complexes. The polarizability in the force field or in the water model allows significantly more movement from the complex, but in some cases, this results in the disintegration of the complex structure, especially if the protein contains longer loop regions. Thus, one should be cautious when running long-scale simulations with polarizability. As a conclusion, all the tested force fields can be used to simulate RNA-protein complexes and the choice of the optimal force field depends on the studied system and research question.
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Affiliation(s)
| | - Piia Bartos
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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15
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Tetteh J, Kubelka J, Piri M. Effect of oil carboxylate hydrophobicity on calcite wettability and its reversal by cationic surfactants: An experimental and molecular dynamics simulation investigation. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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16
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Yesylevskyy S, Martinez-Seara H, Jungwirth P. Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers. J Phys Chem B 2023; 127:4523-4531. [PMID: 37191140 DOI: 10.1021/acs.jpcb.3c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this work, the influence of membrane curvature on the Ca2+ binding to phospholipid bilayers is investigated by means of molecular dynamics simulations. In particular, we compared Ca2+ binding to flat, elastically buckled, or uniformly bent zwitterionic and anionic phospholipid bilayers. We demonstrate that Ca2+ ions bind preferably to the concave membrane surfaces in both types of bilayers. We also show that the membrane curvature leads to pronounced changes in Ca2+ binding including differences in free ion concentrations, lipid coordination distributions, and the patterns of ion binding to different chemical groups of lipids. Moreover, these effects differ substantially for the concave and convex membrane monolayers. Comparison between force fields with either full or scaled charges indicates that charge scaling results in reduction of the Ca2+ binding to curved phosphatidylserine bilayers, while for phosphatidylcholine membranes, calcium binds only weakly for both force fields.
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Affiliation(s)
- Semen Yesylevskyy
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Nauky Avenue 46, 03038 Kyiv, Ukraine
- Receptor.AI Incorporated, 20-22 Wenlock Road, N1 7GU London, U.K
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
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17
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [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] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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18
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Melse O, Antes I, Kaila VRI, Zacharias M. Benchmarking biomolecular force field-based Zn 2+ for mono- and bimetallic ligand binding sites. J Comput Chem 2023; 44:912-926. [PMID: 36495007 DOI: 10.1002/jcc.27052] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Zn2+ is one of the most versatile biologically available metal ions, but accurate modeling of Zn2+ -containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn2+ models are parameterized in bulk solvent, in-depth knowledge about their performance in a protein environment is limited. Thus, we systematically investigate here the behavior of non-polarizable Zn2+ models for their ability to reproduce experimentally determined metal coordination and ligand binding in metalloproteins. The benchmarking is performed in challenging environments, including mono- (carbonic anhydrase II) and bimetallic (metallo-β-lactamase VIM-2) ligand binding sites. We identify key differences in the performance between the Zn2+ models with regard to the preferred ligating atoms (charged/non-charged), attraction of water molecules, and the preferred coordination geometry. Based on these results, we suggest suitable simulation conditions for varying Zn2+ site geometries that could guide the further development of biomolecular Zn2+ models.
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Affiliation(s)
- Okke Melse
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.,SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Iris Antes
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.,SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany
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19
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Subasinghege Don V, Kim L, David R, Nauman JA, Kumar R. Adsorption Studies at the Graphene Oxide-Liquid Interface: A Molecular Dynamics Study. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:5920-5930. [PMID: 37025926 PMCID: PMC10069394 DOI: 10.1021/acs.jpcc.2c07080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/08/2023] [Indexed: 06/19/2023]
Abstract
The adsorption of organic aromatic molecules, namely aniline, onto graphene oxide is investigated using molecular simulations. The effect of the oxidation level of the graphene oxide sheet as well as the presence of two different halide salts, sodium chloride and sodium iodide, were examined. The aniline molecule in the more-reduced graphene oxide case, in the absence of added salt, showed a slightly greater affinity for the graphene oxide-water interface as compared to the oxidized form. The presence of the iodide ion increased the affinity of the aniline molecule in the reduced case but had the opposite effect for the more-oxidized form. The effect of oxidation and added salt on the interfacial water layer was also examined.
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Affiliation(s)
- Visal Subasinghege Don
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, United States
| | - Lukas Kim
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, United States
| | - Rolf David
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, United States
| | - Julia A. Nauman
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, United States
| | - Revati Kumar
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, United States
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20
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Blazquez S, Conde MM, Vega C. Scaled charges for ions: An improvement but not the final word for modeling electrolytes in water. J Chem Phys 2023; 158:054505. [PMID: 36754806 DOI: 10.1063/5.0136498] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
In this work, we discuss the use of scaled charges when developing force fields for NaCl in water. We shall develop force fields for Na+ and Cl- using the following values for the scaled charge (in electron units): ±0.75, ±0.80, ±0.85, and ±0.92 along with the TIP4P/2005 model of water (for which previous force fields were proposed for q = ±0.85 and q = ±1). The properties considered in this work are densities, structural properties, transport properties, surface tension, freezing point depression, and maximum in density. All the developed models were able to describe quite well the experimental values of the densities. Structural properties were well described by models with charges equal to or larger than ±0.85, surface tension by the charge ±0.92, maximum in density by the charge ±0.85, and transport properties by the charge ±0.75. The use of a scaled charge of ±0.75 is able to reproduce with high accuracy the viscosities and diffusion coefficients of NaCl solutions for the first time. We have also considered the case of KCl in water, and the results obtained were fully consistent with those of NaCl. There is no value of the scaled charge able to reproduce all the properties considered in this work. Although certainly scaled charges are not the final word in the development of force fields for electrolytes in water, its use may have some practical advantages. Certain values of the scaled charge could be the best option when the interest is to describe certain experimental properties.
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Affiliation(s)
- S Blazquez
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M M Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - C Vega
- Dpto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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21
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Pandey MP, Sasidharan S, Raghunathan VA, Khandelia H. Molecular Mechanism of Hydrotropic Properties of GTP and ATP. J Phys Chem B 2022; 126:8486-8494. [PMID: 36251789 DOI: 10.1021/acs.jpcb.2c06077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrotropes are small amphiphilic compounds that increase the aqueous solubility of hydrophobic molecules. Recent evidence suggests that adenosine triphosphate (ATP), which is the primary energy carrier in cells, also assumes hydrotropic properties to prevent the aggregation of hydrophobic proteins, but the mechanism of hydrotropy is unknown. Here, we compare the hydrotropic behavior of all four biological nucleoside triphosphates (NTPs) using molecular dynamics (MD) simulations. We launch all atom MD simulations of aqueous solutions of NTPs [ATP, guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)] with pyrene, which acts both as a model hydrophobic compound and as a spectroscopic reporter for aggregation. GTP prevents pyrene aggregation effectively. Dissolution is not achieved in the presence of CTP and UTP. The higher stability of the base stacking in guanine is responsible for the higher hydrotropic efficiency of GTP. Consistent with the simulations, spectroscopic measurements also suggest that the hydrotropic activity of GTP is higher than ATP. Stacking of aromatic pyrene with the aromatic base of NTPs is a characteristic feature of this hydrotropic property. Both ATP and GTP also dissolve clusters of di- and tripeptides containing tryptophan but with equal potency. Importantly, the presence of aromatic amino acids is a necessary condition for the hydrotropic potency of ATP and GTP. Our results can have broad implications for hydrotrope design in the pharmaceutical industry, as well as the possibility of cells employing GTP as a hydrotrope to regulate the hydrophobic protein aggregation in membrane-less biological condensates.
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Affiliation(s)
- Mayank Prakash Pandey
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense5230, Denmark
| | | | | | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense5230, Denmark
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22
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Falginella FL, Kravec M, Drabinová M, Paclíková P, Bryja V, Vácha R. Binding of DEP domain to phospholipid membranes: More than just electrostatics. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183983. [PMID: 35750206 DOI: 10.1016/j.bbamem.2022.183983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Over the past decades an extensive effort has been made to provide a more comprehensive understanding of Wnt signaling, yet many regulatory and structural aspects remain elusive. Among these, the ability of Dishevelled (DVL) protein to relocalize at the plasma membrane is a crucial step in the activation of all Wnt pathways. The membrane binding of DVL was suggested to be mediated by the preferential interaction of its C-terminal DEP domain with phosphatidic acid (PA). However, due to the scarcity and fast turnover of PA, we investigated the role on the membrane association of other more abundant phospholipids. The combined results from computational simulations and experimental measurements with various model phospholipid membranes, demonstrate that the membrane binding of DEP/DVL constructs is governed by the concerted action of generic electrostatics and finely-tuned intermolecular interactions with individual lipid species. In particular, while we confirmed the strong preference for PA lipid, we also observed a weak but non-negligible affinity for phosphatidylserine, the most abundant anionic phospholipid in the plasma membrane, and phosphatidylinositol 4,5-bisphosphate. The obtained molecular insight into DEP-membrane interaction helps to elucidate the relation between changes in the local membrane composition and the spatiotemporal localization of DVL and, possibly, other DEP-containing proteins.
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Affiliation(s)
- Francesco L Falginella
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marek Kravec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Martina Drabinová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Vítĕzslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno 612 65, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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23
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Pluhařová E, Stirnemann G, Laage D. On water reorientation dynamics in cation hydration shells. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Nguyen MT, Biriukov D, Tempra C, Baxova K, Martinez-Seara H, Evci H, Singh V, Šachl R, Hof M, Jungwirth P, Javanainen M, Vazdar M. Ionic Strength and Solution Composition Dictate the Adsorption of Cell-Penetrating Peptides onto Phosphatidylcholine Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11284-11295. [PMID: 36083171 PMCID: PMC9494944 DOI: 10.1021/acs.langmuir.2c01435] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Adsorption of arginine-rich positively charged peptides onto neutral zwitterionic phosphocholine (PC) bilayers is a key step in the translocation of those potent cell-penetrating peptides into the cell interior. In the past, we have shown both theoretically and experimentally that polyarginines adsorb to the neutral PC-supported lipid bilayers in contrast to polylysines. However, comparing our results with previous studies showed that the results often do not match even at the qualitative level. The adsorption of arginine-rich peptides onto 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) may qualitatively depend on the actual experimental conditions where binding experiments have been performed. In this work, we systematically studied the adsorption of R9 and K9 peptides onto the POPC bilayer, aided by molecular dynamics (MD) simulations and fluorescence cross-correlation spectroscopy (FCCS) experiments. Using MD simulations, we tested a series of increasing peptide concentrations, in parallel with increasing Na+ and Ca2+ salt concentrations, showing that the apparent strength of adsorption of R9 decreases upon the increase of peptide or salt concentration in the system. The key result from the simulations is that the salt concentrations used experimentally can alter the picture of peptide adsorption qualitatively. Using FCCS experiments with fluorescently labeled R9 and K9, we first demonstrated that the binding of R9 to POPC is tighter by almost 2 orders of magnitude compared to that of K9. Finally, upon the addition of an excess of either Na+ or Ca2+ ions with R9, the total fluorescence correlation signal is lost, which implies the unbinding of R9 from the PC bilayer, in agreement with our predictions from MD simulations.
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Affiliation(s)
- Man Thi
Hong Nguyen
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Denys Biriukov
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Carmelo Tempra
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Katarina Baxova
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Hüseyin Evci
- J.
Heyrovský Institute of Physical Chemistry of the Czech Academy
of Sciences, Dolejškova
2155/3, CZ-18223 Prague 8, Czech Republic
- Department
of Chemistry, Faculty of Science, University
of South Bohemia in Ceske Budejovice, 370 05 Ceske Budejovice, Czech
Republic
| | - Vandana Singh
- J.
Heyrovský Institute of Physical Chemistry of the Czech Academy
of Sciences, Dolejškova
2155/3, CZ-18223 Prague 8, Czech Republic
- Faculty
of Mathematics and Physics at Charles University, 110 00 Prague, Czech Republic
| | - Radek Šachl
- J.
Heyrovský Institute of Physical Chemistry of the Czech Academy
of Sciences, Dolejškova
2155/3, CZ-18223 Prague 8, Czech Republic
| | - Martin Hof
- J.
Heyrovský Institute of Physical Chemistry of the Czech Academy
of Sciences, Dolejškova
2155/3, CZ-18223 Prague 8, Czech Republic
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Institute
of Biotechnology, University of Helsinki, FI-00014 University
of Helsinki, Finland
| | - Mario Vazdar
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Department
of Mathematics, University of Chemistry
and Technology, 166 28 Prague, Czech Republic
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25
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Nencini R, Ollila OHS. Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments. J Phys Chem B 2022; 126:6955-6963. [PMID: 36063117 PMCID: PMC9483918 DOI: 10.1021/acs.jpcb.2c05024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions of charged molecules with biomembranes regulate many of their biological activities, but their binding affinities to lipid bilayers are difficult to measure experimentally and model theoretically. Classical molecular dynamics (MD) simulations have the potential to capture the complex interactions determining how charged biomolecules interact with membranes, but systematic overbinding of sodium and calcium cations in standard MD simulations raises the question of how accurately force fields capture the interactions between lipid membranes and charged biomolecules. Here, we evaluate the binding of positively charged small molecules, etidocaine, and tetraphenylphosphonium to a phosphatidylcholine (POPC) lipid bilayer using the changes in lipid head-group order parameters. We observed that these molecules behave oppositely to calcium and sodium ions when binding to membranes: (i) their binding affinities are not overestimated by standard force field parameters, (ii) implicit inclusion of electronic polarizability increases their binding affinity, and (iii) they penetrate into the hydrophobic membrane core. Our results can be explained by distinct binding mechanisms of charged small molecules with hydrophobic moieties and monoatomic ions. The binding of the former is driven by hydrophobic effects, while the latter has direct electrostatic interactions with lipids. In addition to elucidating how different kinds of charged biomolecules bind to membranes, we deliver tools for further development of MD simulation parameters and methodology.
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Affiliation(s)
- Ricky Nencini
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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26
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Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
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27
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The lung surfactant activity probed with molecular dynamics simulations. Adv Colloid Interface Sci 2022; 304:102659. [PMID: 35421637 DOI: 10.1016/j.cis.2022.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 01/17/2023]
Abstract
The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.
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28
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Basit A, Yadav AK, Bandyopadhyay P. Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation. J Chem Inf Model 2022; 62:2821-2834. [PMID: 35608259 DOI: 10.1021/acs.jcim.2c00428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of calcium ions (Ca2+) to the calcium-binding proteins (CBPs) controls a plethora of regulatory processes. Among the roles played by CBPs in several diseases, the onset and progress of some cardiovascular diseases are caused by mutations in calmodulin (CaM), an important member of CBPs. Rationalization and prediction of the binding affinity of Ca2+ ions to the CaM can play important roles in understanding the origin of cardiovascular diseases. However, there is no robust structure-based computational method for predicting the binding affinity of Ca2+ ions to the different forms of CBPs in general and CaM in particular. In the current work, we have devised a fast yet accurate computational technique to accurately calculate the binding affinity of Ca2+ to the different forms of CaM. This method combines the well-known molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method and a charge scaling approach developed by previous authors that takes care of the polarization of CaM and Ca2+ ions. Our detailed analysis of the different components of binding free energy shows that subtle changes in electrostatics and van der Waals contribute to the difference in the binding affinity of mutants from that of the wild type (WT), and the charge scaling approach is superior in calculating these subtle changes in electrostatics as compared to the nonpolarizable force field used in this work. A statistically significant regression model made from our binding free energy calculations gives a correlation coefficient close to 0.8 to the experimental results. This structure-based predictive model can open up a new strategy to understand and predict the binding of Ca2+ to the mutants of CBPs, in general.
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Affiliation(s)
- Abdul Basit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ajeet Kumar Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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29
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Puyo-Fourtine J, Juillé M, Hénin J, Clavaguéra C, Duboué-Dijon E. Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J Phys Chem B 2022; 126:4022-4034. [PMID: 35608554 DOI: 10.1021/acs.jpcb.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca2+ than Mg2+, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg2+). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.
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Affiliation(s)
- Julie Puyo-Fourtine
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Marie Juillé
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Jérôme Hénin
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Elise Duboué-Dijon
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
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30
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Biriukov D, Wang HW, Rampal N, Tempra C, Kula P, Neuefeind JC, Stack AG, Předota M. The "good," the "bad," and the "hidden" in neutron scattering and molecular dynamics of ionic aqueous solutions. J Chem Phys 2022; 156:194505. [PMID: 35597655 DOI: 10.1063/5.0093643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We characterize a concentrated 7.3 m CaCl2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca2+-Cl- interactions were primarily "hidden" in the Ca-NDIS signal due to overlapping with Ca2+-Ow and Ca2+-Hw contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models "on average," the question "which model is the best" has not been answered but replaced by the question "which model is better for a given research." An overall "good" model can still be inappropriate or, in some instances, "bad" and, unfortunately, produce erroneous results. The accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.
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Affiliation(s)
- Denys Biriukov
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Hsiu-Wen Wang
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Nikhil Rampal
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Patrik Kula
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Joerg C Neuefeind
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Andrew G Stack
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Milan Předota
- Department of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
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31
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Phan LX, Lynch CI, Crain J, Sansom MS, Tucker SJ. Influence of effective polarization on ion and water interactions within a biomimetic nanopore. Biophys J 2022; 121:2014-2026. [DOI: 10.1016/j.bpj.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/25/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
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32
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Sedano LF, Blazquez S, Noya EG, Vega C, Troncoso J. Maximum in density of electrolyte solutions: Learning about ion-water interactions and testing the Madrid-2019 force field. J Chem Phys 2022; 156:154502. [PMID: 35459318 DOI: 10.1063/5.0087679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we studied the effect of Li+, Na+, K+, Mg2+, and Ca2+ chlorides and sulfates on the temperature of maximum density (TMD) of aqueous solutions at room pressure. Experiments at 1 molal salt concentration were carried out to determine the TMD of these solutions. We also performed molecular dynamics simulations to estimate the TMD at 1 and 2 m with the Madrid-2019 force field, which uses the TIP4P/2005 water model and scaled charges for the ions, finding an excellent agreement between experiment and simulation. All the salts studied in this work shift the TMD of the solution to lower temperatures and flatten the density vs temperature curves (when compared to pure water) with increasing salt concentration. The shift in the TMD depends strongly on the nature of the electrolyte. In order to explore this dependence, we have evaluated the contribution of each ion to the shift in the TMD concluding that Na+, Ca2+, and SO4 2- seem to induce the largest changes among the studied ions. The volume of the system has been analyzed for salts with the same anion and different cations. These curves provide insight into the effect of different ions upon the structure of water. We claim that the TMD of electrolyte solutions entails interesting physics regarding ion-water and water-water interactions and should, therefore, be considered as a test property when developing force fields for electrolytes. This matter has been rather unnoticed for almost a century now and we believe it is time to revisit it.
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Affiliation(s)
- L F Sedano
- Depto. Química Física I (Unidad Asociada de I+D+i al CSIC), Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - S Blazquez
- Depto. Química Física I (Unidad Asociada de I+D+i al CSIC), Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - E G Noya
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - C Vega
- Depto. Química Física I (Unidad Asociada de I+D+i al CSIC), Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J Troncoso
- Departamento de Física Aplicada, Universidad de Vigo, Facultad de Ciencias del Campus de Ourense, E 32004 Ourense, Spain
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33
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Deng J, Cui Q. Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants. J Am Chem Soc 2022; 144:4594-4610. [PMID: 35239338 PMCID: PMC9616648 DOI: 10.1021/jacs.2c00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Buried charged residues play important roles in the modulation of protein stabilities and conformational dynamics and make crucial contributions to protein functions. Considering the generally nonpolar nature of protein interior, a key question concerns the contribution of electronic polarization to the stabilization and properties of buried charges. We answer this question by conducting free energy simulations using the latest polarizable CHARMM force field based on Drude oscillators for a series of Staphylococcal nuclease mutants that involve a buried Glu-Lys pair in different titration states and orientations. While a nonpolarizable model suggests that the ionized form of the buried Glu-Lys pair is more than 40 kcal/mol less stable than the charge-neutral form, the two titration states are comparable in stability when electronic polarization is included explicitly, a result better reconcilable with available experimental data. Analysis of free energy components suggests that additional stabilization of the ionized Glu-Lys pair has contributions from both the enhanced salt-bridge strength and stronger interaction between the ion-pair and surrounding protein residues and penetrated water. Despite the stronger direct interaction between Glu and Lys, the ion-pair exhibits considerably larger and faster structural fluctuations when polarization is included, due to compensation of interactions in the cavity. Collectively, observations from this work provide compelling evidence that electronic polarization is essential to the stability, hydration, dynamics, and therefore function of buried charges in proteins. Therefore, our study advocates for the explicit consideration of electronic polarization for mechanistic and engineering studies that implicate buried charged residues, such as enzymes and ion transporters.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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34
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Tempra C, Ollila OHS, Javanainen M. Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension. J Chem Theory Comput 2022; 18:1862-1869. [PMID: 35133839 PMCID: PMC8908734 DOI: 10.1021/acs.jctc.1c00951] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lipid monolayers provide our lungs and eyes their functionality and serve as proxy systems in biomembrane research. Therefore, lipid monolayers have been studied intensively including using molecular dynamics simulations, which are able to probe their lateral structure and interactions with, e.g., pharmaceuticals or nanoparticles. However, such simulations have struggled in describing the forces at the air-water interface. Particularly, the surface tension of water and long-range van der Waals interactions have been considered critical, but their importance in monolayer simulations has been evaluated only separately. Here, we combine the recent C36/LJ-PME lipid force field that includes long-range van der Waals forces with water models that reproduce experimental surface tensions to elucidate the importance of these contributions in monolayer simulations. Our results suggest that a water model with correct surface tension is necessary to reproduce experimental surface pressure-area isotherms and monolayer phase behavior. The latter includes the liquid expanded and liquid condensed phases, their coexistence, and the opening of pores at the correct area per lipid upon expansion. Despite these improvements of the C36/LJ-PME with certain water models, the standard cutoff-based CHARMM36 lipid model with the 4-point OPC water model still provides the best agreement with experiments. Our results emphasize the importance of using high-quality water models in applications and parameter development in molecular dynamics simulations of biomolecules.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic.,Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
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35
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Blazquez S, Conde MM, Abascal JLF, Vega C. The Madrid-2019 force field for electrolytes in water using TIP4P/2005 and scaled charges: Extension to the ions F−, Br−, I−, Rb+, and Cs+. J Chem Phys 2022; 156:044505. [DOI: 10.1063/5.0077716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- S. Blazquez
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M. M. Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - J. L. F. Abascal
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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36
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Lukasheva N, Tolmachev D, Martinez-Seara H, Karttunen M. Changes in the Local Conformational States Caused by Simple Na + and K + Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields with and without NBFIX and ECC Corrections. Polymers (Basel) 2022; 14:252. [PMID: 35054659 PMCID: PMC8779100 DOI: 10.3390/polym14020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K+ or Na+ counterions, were investigated using atomistic molecular dynamics (MD) simulations. We performed a comparison of seven popular force fields, namely AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and using two common corrections for overbinding of ions, the non-bonded fix (NBFIX), and electronic continuum corrections (ECC). These corrections were originally introduced to correct for the often-reported problem concerning the overbinding of ions to the charged groups of polyelectrolytes. In this work, a comparison of the simulation results with existing experimental data revealed several differences between the investigated force fields. The data from these simulations and comparisons with previous experimental data were then used to determine the limitations and strengths of these force fields in the context of the structural and dynamic properties of anionic polyamino acids. Physical properties, such as molecular sizes, local structure, and dynamics, were studied using two types of common counterions, namely potassium and sodium. The results show that, in some cases, both the macroion size and dynamics depend strongly on the models (parameters) for the counterions due to strong overbinding of the ions and charged side chain groups. The local structures and dynamics are more sensitive to dihedral angle parameterization, resulting in a preference for defined monomer conformations and the type of correction used. We also provide recommendations based on the results.
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Affiliation(s)
- Natalia Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy Pr. 31, 199004 St. Petersburg, Russia
| | - Dmitry Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy Pr. 31, 199004 St. Petersburg, Russia
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Náměstí 542/2, CZ166 10 Prague 6, Czech Republic
| | - Mikko Karttunen
- Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
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37
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Miranda-Quintana RA, Smiatek J. Specific Ion Effects in Different Media: Current Status and Future Challenges. J Phys Chem B 2021; 125:13840-13849. [PMID: 34918938 DOI: 10.1021/acs.jpcb.1c07957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We discuss the current state of research as well as the future challenges for a deeper understanding of specific ion effects in protic and aprotic solvents as well as various additional media. Despite recent interest in solute or interfacial effects, we focus exclusively on the specific properties of ions in bulk electrolyte solutions. Corresponding results show that many mechanisms remain unknown for these simple media, although theoretical, computational, and experimental studies have provided some insights into explaining individual observations. In particular, the importance of local interactions and electronic properties is emphasized, which enabled a more consistent interpretation of specific ion effects over the past years. Despite current insufficient knowledge, we also discuss future challenges in relation to dynamic properties as well as the influence of different concentrations, different solvents, and solute contributions to gain a deeper understanding of specific ion effects for technological applications.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.,Digitalization Development Biologicals CMC, Boehringer Ingelheim Pharma GmbH & Co. KG, D-88397 Biberach (Riss), Germany
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38
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The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans. Int J Mol Sci 2021; 22:ijms222111529. [PMID: 34768961 PMCID: PMC8583755 DOI: 10.3390/ijms222111529] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
The increasing recognition of the biochemical importance of glycosaminoglycans (GAGs) has in recent times made them the center of attention of recent research investigations. It became evident that subtle conformational factors play an important role in determining the relationship between the chemical composition of GAGs and their activity. Therefore, a thorough understanding of their structural flexibility is needed, which is addressed in this work by means of all-atom molecular dynamics (MD) simulations. Four major GAGs with different substitution patterns, namely hyaluronic acid as unsulphated GAG, heparan-6-sulphate, chondroitin-4-sulphate, and chondroitin-6-sulphate, were investigated to elucidate the influence of sulphation on the dynamical features of GAGs. Moreover, the effects of increasing NaCl and KCl concentrations were studied as well. Different structural parameters were determined from the MD simulations, in combination with a presentation of the free energy landscape of the GAG conformations, which allowed us to unravel the conformational fingerprints unique to each GAG. The largest effects on the GAG structures were found for sulphation at position 6, as well as binding of the metal ions in the absence of chloride ions to the carboxylate and sulphate groups, which both increase the GAG conformational flexibility.
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39
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Gonzalez MA, Zaragoza A, Lynch CI, Sansom MSP, Valeriani C. Influence of water models on water movement through AQP1. J Chem Phys 2021; 155:154502. [PMID: 34686053 DOI: 10.1063/5.0063986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water permeation through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence, accurate simulations of water permeation are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC, and TIP4P/2005. Bulk diffusion, diffusion permeability, and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems) and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in very good agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behavior within a biological nanopore.
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Affiliation(s)
| | - Alberto Zaragoza
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Charlotte I Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Chantal Valeriani
- Universidad Complutense de Madrid, Facultad de Ciencias Fícias, Departamento de Estructura de la Materia, Física Térmica y Electrónica, 28040 Madrid, Spain
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40
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Chubak I, Scalfi L, Carof A, Rotenberg B. NMR Relaxation Rates of Quadrupolar Aqueous Ions from Classical Molecular Dynamics Using Force-Field Specific Sternheimer Factors. J Chem Theory Comput 2021; 17:6006-6017. [PMID: 34570493 DOI: 10.1021/acs.jctc.1c00690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nuclear magnetic resonance (NMR) relaxation of quadrupolar nuclei is governed by the electric field gradient (EFG) fluctuations at their position. In classical molecular dynamics (MD), the electron cloud contribution to the EFG can be included via the Sternheimer approximation, in which the full EFG at the nucleus that can be computed using quantum density functional theory (DFT) is considered to be proportional to that arising from the external, classical charge distribution. In this work, we systematically assess the quality of the Sternheimer approximation as well as the impact of the classical force field (FF) on the NMR relaxation rates of aqueous quadrupolar ions at infinite dilution. In particular, we compare the rates obtained using an ab initio parametrized polarizable FF, a recently developed empirical FF with scaled ionic charges and a simple empirical nonpolarizable FF with formal ionic charges. Surprisingly, all three FFs considered yield good values for the rates of smaller and less polarizable solutes (Li+, Na+, K+, Cl-), provided that a model-specific Sternheimer parametrization is employed. Yet, the polarizable and scaled charge FFs yield better estimates for divalent and more polarizable species (Mg2+, Ca2+, Cs+). We find that a linear relationship between the quantum and classical EFGs holds well in all of the cases considered; however, such an approximation often leads to quite large errors in the resulting EFG variance, which is directly proportional to the computed rate. We attempted to reduce the errors by including first order nonlinear corrections to the EFG, yet no clear improvement for the resulting variance has been found. The latter result indicates that more refined methods for determining the EFG at the ion position, in particular those that take into account the instantaneous atomic environment around an ion, might be necessary to systematically improve the NMR relaxation rate estimates in classical MD.
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Affiliation(s)
- Iurii Chubak
- Sorbonne Université CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
| | - Laura Scalfi
- Sorbonne Université CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
| | - Antoine Carof
- Universite de Lorraine, CNRS, LPCT, F-54000, Nancy, France
| | - Benjamin Rotenberg
- Sorbonne Université CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
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41
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Smirnov MA, Tolmachev DA, Glova AD, Sokolova MP, Geydt PV, Lukasheva NV, Lyulin SV. Combined Use of Atomic Force Microscopy and Molecular Dynamics in the Study of Biopolymer Systems. POLYMER SCIENCE SERIES C 2021. [DOI: 10.1134/s1811238221020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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42
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Carter-Fenk KA, Dommer AC, Fiamingo ME, Kim J, Amaro RE, Allen HC. Calcium bridging drives polysaccharide co-adsorption to a proxy sea surface microlayer. Phys Chem Chem Phys 2021; 23:16401-16416. [PMID: 34318808 DOI: 10.1039/d1cp01407b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Saccharides comprise a significant mass fraction of organic carbon in sea spray aerosol (SSA), but the mechanisms through which saccharides are transferred from seawater to the ocean surface and eventually into SSA are unclear. It is hypothesized that saccharides cooperatively adsorb to other insoluble organic matter at the air/sea interface, known as the sea surface microlayer (SSML). Using a combination of surface-sensitive infrared reflection-absorption spectroscopy and all-atom molecular dynamics simulations, we demonstrate that the marine-relevant, anionic polysaccharide alginate co-adsorbs to an insoluble palmitic acid monolayer via divalent cationic bridging interactions. Ca2+ induces the greatest extent of alginate co-adsorption to the monolayer, evidenced by the ∼30% increase in surface coverage, whereas Mg2+ only facilitates one-third the extent of co-adsorption at seawater-relevant cation concentrations due to its strong hydration propensity. Na+ cations alone do not facilitate alginate co-adsorption, and palmitic acid protonation hinders the formation of divalent cationic bridges between the palmitate and alginate carboxylate moieties. Alginate co-adsorption is largely confined to the interfacial region beneath the monolayer headgroups, so surface pressure, and thus monolayer surface coverage, only changes the amount of alginate co-adsorption by less than 5%. Our results provide physical and molecular characterization of a potentially significant polysaccharide enrichment mechanism within the SSML.
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Affiliation(s)
- Kimberly A Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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43
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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44
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Gresh N, Perahia D. Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry. J Comput Chem 2021; 42:1430-1446. [PMID: 34101861 DOI: 10.1002/jcc.26555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
Dimethyl phosphate (DMP- ) is a model for the phosphodiester backbone of DNA, RNA, and phospholipids. It is central for the binding of divalent cations and water along the backbone of nucleic acids. Significant polarization and charge-transfer contributions and nonadditivity come into play in the multimolecular complexes organized around phosphate. Prior to large-scale molecular dynamics (MD) with advanced polarizable potentials, it is essential to evaluate how well the values and trends of intermolecular interaction energies (ΔE) from ab initio quantum chemistry (QC) and their individual contributions are reproduced in a diversity of such complexes. These differ by the starting binding modes of a divalent cation, Zn(II), namely direct, bi- or mono-dentate to anionic and/or ester oxygens, versus through-water binding. We present first the results from automated refinements of the individual contributions of the SIBFA potential with respect to their QC counterparts using a Zn(II) or a water probe. This is followed by validations on eight relaxed multimolecular complexes of DMP- with Zn(II) or Mg(II) and seven waters, then on sixteen complexes of DMP- with Zn(II) and eight waters in arrangements extracted from MD or energy-minimization on a droplet of sixty-four waters. This monitors the compared evolutions of SIBFA and QC ΔE and their individual contributions in the competing arrangements. Some waters, bridging Zn(II) and DMP- , were found to have exceptionally large dipole moments, of up to 3.8 Debye. The perspectives of extension to a flexible phosphodiester backbone are discussed in the context of the SIBFA potential for DNA and RNA.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, Paris, France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
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45
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Nguyen MTH, Tichacek O, Martinez-Seara H, Mason PE, Jungwirth P. Resolving the Equal Number Density Puzzle: Molecular Picture from Simulations of LiCl(aq) and NaCl(aq). J Phys Chem B 2021; 125:3153-3162. [PMID: 33534574 DOI: 10.1021/acs.jpcb.0c10599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The change in number densities of aqueous solutions of alkali chlorides should be qualitatively predictable. Typically, as cations get larger, the number density of the solution decreases. However, aqueous solutions of lithium and sodium chloride exhibit at ambient conditions practically identical number densities at equal molalities despite different ionic sizes. Here, we provide an atomistic interpretation of this experimentally observed anomalous behavior using molecular dynamics simulations. The obtained results show that the rigidity of the Li+ first and second solvation shells and the associated compromised hydrogen bonding result in practically equal average water densities in the local hydration regions for Li+ and Na+ despite different sizes of the cations. In addition, in more distant regions from the cations, the water densities of these two solutions also coincide. These findings thus provide an atomistic interpretation for matching number densities of LiCl and NaCl solutions. In contrast, the number density differences between NaCl and KCl solutions as well as between LiCl and KCl solutions behave in a regular fashion with lower number densities of solutions observed for larger cations.
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Affiliation(s)
- Man Thi Hong Nguyen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Ondrej Tichacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Philip E Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
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46
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Li Z, Song LF, Li P, Merz KM. Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J Chem Theory Comput 2021; 17:2342-2354. [PMID: 33793233 DOI: 10.1021/acs.jctc.0c01320] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Commonly seen in rare-earth chemistry and materials science, highly charged metal ions play key roles in many chemical processes. Computer simulations have become an important tool for scientific research nowadays. Meaningful simulations require reliable parameters. In the present work, we parametrized 18 M(III) and 6 M(IV) metal ions for four new water models (OPC3, OPC, TIP3P-FB, TIP4P-FB) in conjunction with each of the 12-6 and 12-6-4 nonbonded models. Similar to what was observed previously, issues with the 12-6 model can be fixed by using the 12-6-4 model. Moreover, the four new water models showed comparable performance or considerable improvement over the previous water models (TIP3P, SPC/E, and TIP4PEW) in the same category (3-point or 4-point water models, respectively). Finally, we reported a study of a metalloprotein system demonstrating the capability of the 12-6-4 model to model metalloproteins. The reported parameters will facilitate accurate simulations of highly charged metal ions in aqueous solution.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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47
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Döpke MF, Hartkamp R. The importance of specifically adsorbed ions for electrokinetic phenomena: Bridging the gap between experiments and MD simulations. J Chem Phys 2021; 154:094701. [DOI: 10.1063/5.0038161] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Max F. Döpke
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - Remco Hartkamp
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
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48
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Rao S, Klesse G, Lynch CI, Tucker SJ, Sansom MSP. Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions. J Phys Chem B 2021; 125:981-994. [PMID: 33439645 PMCID: PMC7869105 DOI: 10.1021/acs.jpcb.0c09285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/13/2020] [Indexed: 12/30/2022]
Abstract
Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.
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Affiliation(s)
- Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford, U.K.
| | - Gianni Klesse
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
| | | | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
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49
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Zhu J, Huang J. Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field. J Phys Chem B 2021; 125:393-405. [PMID: 33373260 DOI: 10.1021/acs.jpcb.0c08556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylguanidinium is an important molecular ion, which also serves as the model compound for the arginine side chain. We studied the structure and dynamics of the methylguanidium ion at the air/water interface by molecular dynamics simulations employing the Drude polarizable force field. We found out that methylguanidinium accumulated at the interface, with a majority adopting tilted conformations. We also demonstrated that methylguanidinium and guanidinium ions had different preference toward the air/water interface. Detailed analysis of induced dipole moments showed how ions adjusted their charge distribution at the interface and revealed how the anisotropy in molecular polarizability impacted the orientation of molecular ions. Our results illustrate the importance of explicitly including the electronic polarization effects in modeling interfacial properties.
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Affiliation(s)
- Jian Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
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50
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Dhabal D, Patra T. Molecular simulation of osmometry in aqueous solutions of the BMIMCl ionic liquid: a potential route to force field parameterization of liquid mixtures. Phys Chem Chem Phys 2020; 22:28325-28338. [PMID: 33300529 DOI: 10.1039/d0cp03833d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite widespread development and use of ionic liquids (ILs) in both academic and industrial research, computational force fields (FFs) for most of those are not available for a precise description of inter-species interactions in aqueous environments. In the scope of this study, by means of molecular simulations, the osmotic coefficient of an aqueous solution of an IL is calculated and used as a basis to reparameterize popular IL-FFs existing in the literature. We first calculate the osmotic coefficients (at 298.15 K and 1 atm pressure) of aqueous solutions of 1-butyl-3-methylimidazolium chloride (BMIMCl), a generic IL, popularly used in biomass processing and the subsequent conversion to value-added intermediates. The performance of two popular atomic, nonpolarizable FFs developed for BMIMCl, one by Lopes, Pádua, and coworkers (FF-LP) and the other by Sambasivarao, Acevedo, and coworkers (FF-SA), when mixed with the SPC/E water model, is tested with respect to their ability to reproduce the experimental osmotic coefficient data. Interestingly, the osmotic coefficient is found to be increasing with a gradual increase in IL molality within the concentration range of our investigation, which is contrary to the experimental trend reported in the literature for the same IL-water mixture. Henceforth, necessary corrections to the nonbonded ion-ion and ion-water interactions are made to match the experimental osmotic coefficient. To further assess the reliability of the new FF, we extensively explore the thermodynamic (density, isothermal compressibility, and thermal expansion coefficient), dynamic (diffusivity and viscosity), and association/dissociation properties (rationalized with the help of radial distribution functions) with both the original and reparameterized FF for a wider range of concentrations up to a molality of 18.50 mol kg-1. The calculated quantities are compared against experimental data wherever available. The modified FF parameters exhibit significant improvements in terms of its ability to match experimental solution properties, such as density, viscosity, association/dissociation, etc. We report that excessive dissociation of BMIMCl in water is responsible for the shortcomings observed in the original FFs and improved prediction of physicochemical properties could be achieved using the modified FFs.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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