1
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Nencini R, Tempra C, Biriukov D, Riopedre-Fernandez M, Cruces Chamorro V, Polák J, Mason PE, Ondo D, Heyda J, Ollila OHS, Jungwirth P, Javanainen M, Martinez-Seara H. Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field. J Chem Theory Comput 2024; 20:7546-7559. [PMID: 39186899 PMCID: PMC11391585 DOI: 10.1021/acs.jctc.4c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physically rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems─lipid membranes, proteins (including peptides and amino acids), and saccharides─without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.
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Affiliation(s)
- Ricky Nencini
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland
| | - Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Miguel Riopedre-Fernandez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
| | - Victor Cruces Chamorro
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Philip E Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
| | - Daniel Ondo
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic
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2
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Riopedre-Fernandez M, Kostal V, Martinek T, Martinez-Seara H, Biriukov D. Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions. J Chem Inf Model 2024. [PMID: 39250601 DOI: 10.1021/acs.jcim.4c00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity of GAGs is largely attributed to varied sulfation patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks to their unmatched microscopic resolution, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics force fields used in biosimulations to accurately capture sulfation-specific interactions is not well established, partly due to the intrinsic properties of GAGs that pose challenges for most experimental techniques. In this work, we evaluate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca2+ to sulfated moieties─N-methylsulfamate and methylsulfate─that resemble N- and O-sulfation found in GAGs, respectively. We tested available nonpolarizable (CHARMM36 and GLYCAM06) and explicitly polarizable (Drude and AMOEBA) force fields, and derived new implicitly polarizable models through charge scaling (prosECCo75 and GLYCAM-ECC75) that are consistent with our developed "charge-scaling" framework. The calcium-sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations, which serve as a robust alternative to experiments. AIMD simulations indicate that the preferential Ca2+ binding mode to sulfated GAG groups is solvent-shared pairing. Only our scaled-charge models agree satisfactorily with the AIMD data, while all other force fields exhibit poorer agreement, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields display a notable disagreement with the AIMD data, likely attributed to difficulties in their optimization and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, which qualitatively disagrees with our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.
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Affiliation(s)
- Miguel Riopedre-Fernandez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Vojtech Kostal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Tomas Martinek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
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3
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Marien J, Prévost C, Sacquin-Mora S. nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat. J Chem Inf Model 2024; 64:6570-6582. [PMID: 39092904 DOI: 10.1021/acs.jcim.4c00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.
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Affiliation(s)
- Jules Marien
- Laboratoire de Biochimie Théorique, Université Paris-Cité, CNRS, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, Université Paris-Cité, CNRS, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, Université Paris-Cité, CNRS, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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4
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Kastinen T, Batys P, Tolmachev D, Laasonen K, Sammalkorpi M. Ion-Specific Effects on Ion and Polyelectrolyte Solvation. Chemphyschem 2024; 25: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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5
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Wilson C, Karttunen M, de Groot BL, Gapsys V. Accurately Predicting Protein p Ka Values Using Nonequilibrium Alchemy. J Chem Theory Comput 2023; 19:7833-7845. [PMID: 37820376 PMCID: PMC10653114 DOI: 10.1021/acs.jctc.3c00721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 10/13/2023]
Abstract
The stability, solubility, and function of a protein depend on both its net charge and the protonation states of its individual residues. pKa is a measure of the tendency for a given residue to (de)protonate at a specific pH. Although pKa values can be resolved experimentally, theory and computation provide a compelling alternative. To this end, we assess the applicability of a nonequilibrium (NEQ) alchemical free energy method to the problem of pKa prediction. On a data set of 144 residues that span 13 proteins, we report an average unsigned error of 0.77 ± 0.09, 0.69 ± 0.09, and 0.52 ± 0.04 pK for aspartate, glutamate, and lysine, respectively. This is comparable to current state-of-the-art predictors and the accuracy recently reached using free energy perturbation methods (e.g., FEP+). Moreover, we demonstrate that our open-source, pmx-based approach can accurately resolve the pKa values of coupled residues and observe a substantial performance disparity associated with the lysine partial charges in Amber14SB/Amber99SB*-ILDN, for which an underused fix already exists.
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Affiliation(s)
- Carter
J. Wilson
- Department
of Mathematics, The University of Western
Ontario, N6A 5B7 London, Canada
- Centre
for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, N6A 5B7 London, Canada
| | - Mikko Karttunen
- Centre
for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, N6A 5B7 London, Canada
- Department
of Physics & Astronomy, The University
of Western Ontario, N6A
5B7 London, Canada
- Department
of Chemistry, The University of Western
Ontario, N6A 5B7 London, Canada
| | - Bert L. de Groot
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, 37077 Göttingen, Germany
| | - Vytautas Gapsys
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, 37077 Göttingen, Germany
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
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6
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Huang C, Pettitt BM. Parameter Dependence of the Solubility Limit for Disodium Phosphate. J Phys Chem B 2023; 127:8690-8696. [PMID: 37788371 PMCID: PMC10913426 DOI: 10.1021/acs.jpcb.3c05343] [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] [Indexed: 10/05/2023]
Abstract
The solubility limit was calculated for supersaturated solutions of disodium phosphate in water as a function of the sodium-oxygen Lennard-Jones radius parameter Rmin. We found that changes in the sodium-oxygen Rmin were clearly exponentially related to the concentration of the solubility limit. Starting from standard force fields more suited to nucleic acids and phospholipids, only relatively small changes were required to achieve the experimentally known solubility limit. Simultaneously, we found that it was possible to achieve the solubility limit and the osmotic pressure with the same model parameters. Based on transferability, the adjusted Rmin parameter can be used to more accurately model phosphorylated proteins.
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Affiliation(s)
- Caleb Huang
- Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
| | - B Montgomery Pettitt
- Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
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7
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Mohammadi E, Joshi SY, Deshmukh SA. Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models. Biomacromolecules 2023; 24:4078-4092. [PMID: 37603467 DOI: 10.1021/acs.biomac.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Interactions between amino acids and water play an important role in determining the stability and folding/unfolding, in aqueous solution, of many biological macromolecules, which affects their function. Thus, understanding the molecular-level interactions between water and amino acids is crucial to tune their function in aqueous solutions. Herein, we have developed nonbonded interaction parameters between the coarse-grained (CG) models of 20 amino acids and the one-site CG water model. The nonbonded parameters, represented using the 12-6 Lennard Jones (LJ) potential form, have been optimized using an artificial neural network (ANN)-assisted particle swarm optimization (PSO) (ANN-assisted PSO) method. All-atom (AA) molecular dynamics (MD) simulations of dipeptides in TIP3P water molecules were performed to calculate the Gibbs hydration free energies. The nonbonded force-field (FF) parameters between CG amino acids and the one-site CG water model were developed to accurately reproduce these energies. Furthermore, to test the transferability of these newly developed parameters, we calculated the hydration free energies of the analogues of the amino acid side chains, which showed good agreement with reported experimental data. Additionally, we show the applicability of these models by performing self-assembly simulations of peptide amphiphiles. Overall, these models are transferable and can be used to study the self-assembly of various biomaterials and biomolecules to develop a mechanistic understanding of these processes.
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Affiliation(s)
- Esmat Mohammadi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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8
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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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9
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Shen K, Nguyen M, Sherck N, Yoo B, Köhler S, Speros J, Delaney KT, Shell MS, Fredrickson GH. Predicting surfactant phase behavior with a molecularly informed field theory. J Colloid Interface Sci 2023; 638:84-98. [PMID: 36736121 DOI: 10.1016/j.jcis.2023.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
HYPOTHESIS The computational study of surfactants and self-assembly is challenging because 1) models need to reflect chemistry-specific interactions, and 2) self-assembled structures are difficult to equilibrate with conventional molecular dynamics. We propose to overcome these challenges with a multiscale simulation approach where relative entropy minimization transfers chemically-detailed information from all-atom (AA) simulations to coarse-grained (CG) models that can be simulated using field-theoretic methods. Field-theoretic simulations are not limited by intrinsic physical time scales like diffusion and allow for rigorous equilibration via free energy minimization. This approach should enable the study of properties that are difficult to obtain by particle-based simulations. SIMULATION WORK We apply this workflow to sodium dodecylsulfate. To ensure chemical fidelity we present an AA force field calibrated against interfacial tension experiments. We generate CG models from AA simulation trajectories and show that particle-based and field-theoretic simulations of the CG model reproduce AA simulations and experimental measurements. FINDINGS The workflow captures the complex balance of interactions in a multicomponent system ultimately described by an atomistic model. The resulting CG models can study complex 3D phases like double or alternating gyroids, and reproduce salt effects on properties like aggregation number and shape transitions.
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Affiliation(s)
- Kevin Shen
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara 93106, CA, United States; Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara 93106, CA, United States.
| | - My Nguyen
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara 93106, CA, United States
| | - Nicholas Sherck
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara 93106, CA, United States
| | - Brian Yoo
- BASF Corporation, Tarrytown 10591, NY, United States
| | | | - Joshua Speros
- California Research Alliance (CARA) by BASF, Berkeley 94720, CA, United States
| | - Kris T Delaney
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara 93106, CA, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara 93106, CA, United States.
| | - Glenn H Fredrickson
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara 93106, CA, United States; Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara 93106, CA, United States; Department of Materials Engineering, University of California, Santa Barbara, Santa Barbara 93106, CA, United States.
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10
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Fedotova VS, Sokolova MP, Vorobiov VK, Sivtsov EV, Lukasheva NV, Smirnov MA. Water Influence on the Physico-Chemical Properties and 3D Printability of Choline Acrylate-Bacterial Cellulose Inks. Polymers (Basel) 2023; 15:polym15092156. [PMID: 37177302 PMCID: PMC10181127 DOI: 10.3390/polym15092156] [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: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The aim of this work was to study the influence of water as a co-solvent on the interaction between a polymerizable ionic liquid-choline acrylate (ChA)-and bacterial cellulose. Bacterial cellulose dispersed in ChA is a new type of UV-curable biopolymer-based ink that is a prospective material for the 3D printing of green composite ion-gels. Higher cellulose content in inks is beneficial for the ecological and mechanical properties of materials, and leads to increased viscosity and the yield stress of such systems and hampers printability. It was found that the addition of water results in (1) a decrease in the solvent viscosity and yield stress; and (2) a decrease in the stability of dispersion toward phase separation under stress. In this work, an optimal composition in the range of 30-40 wt% water content demonstrating 97-160 Pa of yield stress was found that ensures the printability and stability of inks. The rheological properties of inks and mechanical characteristics (0.7-0.8 MPa strength and 1.1-1.2 MPa Young's modulus) were obtained. The mechanism of influence of the ratio ChA/water on the properties of ink was revealed with atomic force microscopy, wide-angle X-ray diffraction studies of bacterial cellulose after regeneration from solvent, and computer simulation of ChA/water mixtures and their interaction with the cellulose surface.
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Affiliation(s)
- Veronika S Fedotova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, V.O. Bolshoi Pr. 31, 199004 St. Petersburg, Russia
| | - Maria P Sokolova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, V.O. Bolshoi Pr. 31, 199004 St. Petersburg, Russia
| | - Vitaly K Vorobiov
- Institute of Macromolecular Compounds, Russian Academy of Sciences, V.O. Bolshoi Pr. 31, 199004 St. Petersburg, Russia
| | - Eugene V Sivtsov
- Saint Petersburg State Institute of Technology, Moskovsky Prospekt 24-26/49, 190013 St. Petersburg, Russia
| | - Natalia V Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, V.O. Bolshoi Pr. 31, 199004 St. Petersburg, Russia
| | - Michael A Smirnov
- Institute of Macromolecular Compounds, Russian Academy of Sciences, V.O. Bolshoi Pr. 31, 199004 St. Petersburg, Russia
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11
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Phan LX, Chamorro VC, Martinez-Seara H, Crain J, Sansom MSP, Tucker SJ. Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin. Biophys J 2023; 122:1548-1556. [PMID: 36945777 PMCID: PMC10147828 DOI: 10.1016/j.bpj.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 [c36] fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in chloride-pumping rhodopsin. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and can yield results comparable with more accurate and computationally demanding methods.
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Affiliation(s)
- Linda X Phan
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Victor Cruces Chamorro
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Jason Crain
- Department of Biochemistry, University of Oxford, Oxford, UK; IBM Research Europe, Hartree Centre, Daresbury, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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12
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Tolmachev D, Nazarychev V, Fedotova V, Vorobiov V, Lukasheva N, Smirnov M, Karttunen M. Investigation of structure and properties of polymerizable deep eutectic solvent based on choline chloride and acrylic acid. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Liu H, Fu H, Chipot C, Shao X, Cai W. Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects. J Chem Inf Model 2022; 62:3863-3873. [PMID: 35920605 DOI: 10.1021/acs.jcim.2c00678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The strength of salt bridges resulting from the interaction of cations and anions is modulated by their environment. However, polarization of the solvent molecules by the charged moieties makes the accurate description of cation-anion interactions in an aqueous solution by means of a pairwise additive potential energy function and classical combination rules particularly challenging. In this contribution, aiming at improving the representation of solvent-exposed salt-bridge interactions with an all-atom non-polarizable force field, we put forth here a parametrization strategy. First, the interaction of a cation and an anion is characterized by hybrid quantum mechanical/molecular mechanics (QM/MM) potential of mean force (PMF) calculations, whereby constantly exchanging solvent molecules around the ions are treated at the quantum mechanical level. The Lennard-Jones (LJ) parameters describing the salt-bridge ion pairs are then optimized to match the reference QM/MM PMFs through the so-called nonbonded FIX, or NBFIX, feature of the CHARMM force field. We apply the new set of parameters, coined CHARMM36m-SBFIX, to the calculation of association constants for the ammonium-acetate and guanidinium-acetate complexes, the osmotic pressures for glycine zwitterions, guanidinium, and acetate ions, and to the simulation of both folded and intrinsically disordered proteins. Our findings indicate that CHARMM36m-SBFIX improves the description of solvent-exposed salt-bridge interactions, both structurally and thermodynamically. However, application of this force field to the standard binding free-energy calculation of a protein-ligand complex featuring solvent-excluded salt-bridge interactions leads to a poor reproduction of the experimental value, suggesting that the parameters optimized in an aqueous solution cannot be readily transferred to describe solvent-excluded salt-bridge interactions. Put together, owing to their sensitivity to the environment, modeling salt-bridge interactions by means of a single, universal set of LJ parameters remains a daunting theoretical challenge.
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Affiliation(s)
- Han Liu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Haohao Fu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR n°7019, Université de Lorraine, F-54506 Vandœuvre-lès-Nancy, France.,Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana 61801, Illinois, United States.,Department of Biochemistry and Molecular Biology and Gordon Center for Integrative Science, The University of Chicago, Chicago 60637, Illinois, United States
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Wensheng Cai
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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14
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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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15
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Bernhardt MP, Nagata Y, van der Vegt NFA. Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion-Water Pair Potentials Based on Ab Initio Molecular Dynamics Data. J Phys Chem Lett 2022; 13:3712-3717. [PMID: 35439420 DOI: 10.1021/acs.jpclett.2c00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The use of the Lennard-Jones (LJ) potential in computer simulations of aqueous electrolyte solutions is widespread. The standard approach is to parametrize LJ potential parameters against thermodynamic solution properties, but problems in representing the local structural and dynamic properties of ion hydration shells remain. The r-12-term in the LJ potential is responsible for this as it leads to overly repulsive ion-water interactions at short range. As a result, the LJ potential predicts blue-shifted vibrational peaks of the cations' rattling mode and too large negative ion hydration entropies. We demonstrate that cation-water effective pair potentials derived from ab initio MD data have softer short-range repulsions and represent hydration shell properties significantly better. Our findings indicate that replacing the LJ potential with these effective pair potentials offers a promising route to represent thermodynamic solution properties and local interactions of specific ions with nonpolarizable force field models.
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Affiliation(s)
- Marvin P Bernhardt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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16
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Chávez-García C, Hénin J, Karttunen M. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. J Chem Inf Model 2022; 62:958-970. [PMID: 35130441 DOI: 10.1021/acs.jcim.1c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The malfunction of the methyl-CpG binding protein 2 (MeCP2) is associated with the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the databases, and only the structure of its MBD domain has been solved. We used this structure to build a full-length model of MeCP2 by completing the rest of the protein via ab initio modeling. Using a combination of all-atom and coarse-grained simulations, we characterized its structure and dynamics as well as the conformational space sampled by the ID and transcriptional repression domain (TRD) domains in the absence of the rest of the protein. The present work is the first computational study of the full-length protein. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. Our all-atom model is in good agreement with the available experimental data, predicting amino acid W104 to be buried, amino acids R111 and R133 to be solvent-accessible, and having a 4.1% α-helix content, compared to the 4% found experimentally. Finally, we compared the model predicted by AlphaFold to our Modeller model. The model was not stable in water and underwent further folding. Together, these simulations provide a detailed (if perhaps incomplete) conformational ensemble of the full-length MeCP2, which is compatible with experimental data and can be the basis of further studies, e.g., on mutants of the protein or its interactions with its biological partners.
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Affiliation(s)
- Cecilia Chávez-García
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique UPR 9080, CNRS and Université de Paris, Paris 75005, France
| | - Mikko Karttunen
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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17
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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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18
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Tolmachev D, Lukasheva N, Ramazanov R, Nazarychev V, Borzdun N, Volgin I, Andreeva M, Glova A, Melnikova S, Dobrovskiy A, Silber SA, Larin S, de Souza RM, Ribeiro MCC, Lyulin S, Karttunen M. Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives. Int J Mol Sci 2022; 23:645. [PMID: 35054840 PMCID: PMC8775846 DOI: 10.3390/ijms23020645] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/13/2022] Open
Abstract
Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can predict and reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.
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Affiliation(s)
- Dmitry Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Natalia Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Ruslan Ramazanov
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Victor Nazarychev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Natalia Borzdun
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Igor Volgin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Maria Andreeva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Artyom Glova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Sofia Melnikova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Alexey Dobrovskiy
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Steven A. Silber
- 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
| | - Sergey Larin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Rafael Maglia de Souza
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo 05508-070, Brazil; (R.M.d.S.); (M.C.C.R.)
| | - Mauro Carlos Costa Ribeiro
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo 05508-070, Brazil; (R.M.d.S.); (M.C.C.R.)
| | - Sergey Lyulin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia; (N.L.); (R.R.); (V.N.); (N.B.); (I.V.); (M.A.); (A.G.); (S.M.); (A.D.); (S.L.); (S.L.)
- 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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19
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González-Fernández C, Bringas E, Oostenbrink C, Ortiz I. In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come? Comput Struct Biotechnol J 2022; 20:5886-5901. [PMID: 36382192 PMCID: PMC9636410 DOI: 10.1016/j.csbj.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Lipopolysaccharide (LPS), a main component of the outer membrane of Gram-negative bacteria, has crucial implications on both antibiotic resistance and the overstimulation of the host innate immune system. Fighting against these global concerns calls for the molecular understanding of the barrier function and immunostimulatory ability of LPS. Molecular dynamics (MD) simulations have become an invaluable tool for uncovering important findings in LPS research. While the reach of MD simulations for investigating the immunostimulatory ability of LPS has been already outlined, little attention has been paid to the role of MD simulations for exploring its barrier function and synthesis. Herein, we give an overview about the impact of MD simulations on gaining insight into the shield role and synthesis pathway of LPS, which have attracted considerable attention to discover molecules able to surmount antibiotic resistance, either circumventing LPS defenses or disrupting its synthesis. We specifically focus on the enhanced sampling and free energy calculation methods that have been combined with MD simulations to address such research. We also highlight the use of special-purpose MD supercomputers, the importance of appropriate LPS and ions parameterization to obtain reliable results, and the complementary views that MD and wet-lab experiments provide. Thereby, this work, which covers the last five years of research, apart from outlining the phenomena and strategies that are being explored, evidences the valuable insights that are gained by MD, which may be useful to advance antibiotic design, and what the prospects of this in silico method could be in LPS research.
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Affiliation(s)
- Cristina González-Fernández
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Eugenio Bringas
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Inmaculada Ortiz
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
- Corresponding author.
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20
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Maglia de Souza R, Karttunen M, Ribeiro MCC. Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline. J Chem Inf Model 2021; 61:5938-5947. [PMID: 34797679 DOI: 10.1021/acs.jcim.1c01181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular, for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019 is the first general, transferable, and polarizable force field for MD simulations of different types of DESs. The original formulation contains, however, some problems that appear in simulations of ethaline and may also have a broader impact. First, the originally proposed atomic diameter parameters are unbalanced, resulting in too weak interactions between the chlorides and the hydroxyl groups of the ethylene glycol molecules. This, in turn, causes an artificial phase separation in long simulations. Second, there is an overpolarization of chlorides due to strong induced dipoles that give rise to the presence of peaks and antipeaks at very low q-vector values (2.4 nm-1) in the partial components of the structure factors. In physical terms, this is equivalent to overestimated spatial nanoscale heterogeneity. To correct these problems, we adjusted the chloride-hydroxyl radial distribution functions against ab initio data and then extended the use of the Tang-Toennis damping function for the chlorides' induced dipoles. These adjustments correct the problems without losing the robustness of the CL&Pol force field. The results were also compared with the nonpolarizable version, the CL&P force field. We expect that the corrections will facilitate reliable use of the CL&Pol force field for other types of DESs.
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Affiliation(s)
- Rafael Maglia de Souza
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo 05508-070, Brazil
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg 199004, Russia
| | - Mauro Carlos Costa Ribeiro
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo 05508-070, Brazil
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21
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Bakulin I, Kondratyuk N, Lankin A, Norman G. Properties of aqueous 1,4-dioxane solution via molecular dynamics. J Chem Phys 2021; 155:154501. [PMID: 34686058 DOI: 10.1063/5.0059337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polyethers are promising compounds for the creation of electrochemical energy storage systems. The molecular dynamics method can facilitate the search of compounds that have the most potential. However, the application of this method requires verification of the force fields. We perform molecular dynamics calculations of the physical properties of the aqueous 1,4-dioxane solution (density, enthalpy of mixing, and viscosity) and compare them to the available experimental data. In addition, we confirm the idea that the solution structure depends on the dioxane molar fraction, proposed in the experiment of Takamuku et al. [J. Mol. Liq. 83(1-3), 163-177 (1999)]. The hydrogen bonds between dioxane and water are analyzed. The correlation between the excess viscosity and enthalpy of mixing is demonstrated.
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Affiliation(s)
- I Bakulin
- Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudnyi, Russia
| | - N Kondratyuk
- Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudnyi, Russia
| | - A Lankin
- Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudnyi, Russia
| | - G Norman
- Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudnyi, Russia
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22
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Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021; 17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - Tuǧba N Öztürk
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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23
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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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24
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Development of coarse-grained force field to investigate sodium-ion transport mechanisms in cyanoborate-based ionic liquid. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Tolmachev D, Mamistvalov G, Lukasheva N, Larin S, Karttunen M. Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes. Polymers (Basel) 2021; 13:polym13111789. [PMID: 34071693 PMCID: PMC8199235 DOI: 10.3390/polym13111789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022] Open
Abstract
We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side-chain rotation, enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side-chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main-chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.
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Affiliation(s)
- Dmitry Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 Petersburg, Russia; (N.L.); (S.L.)
- Correspondence: (D.T.); (M.K.)
| | - George Mamistvalov
- Faculty of Physics, St. Petersburg State University, Petrodvorets, 198504 Petersburg, Russia;
| | - Natalia Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 Petersburg, Russia; (N.L.); (S.L.)
| | - Sergey Larin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 Petersburg, Russia; (N.L.); (S.L.)
- Faculty of Physics, St. Petersburg State University, Petrodvorets, 198504 Petersburg, Russia;
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 Petersburg, Russia; (N.L.); (S.L.)
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Applied Mathematics, 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
- Correspondence: (D.T.); (M.K.)
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26
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Chang M, Wilson CJ, Karunatilleke NC, Moselhy MH, Karttunen M, Choy WY. Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism. J Chem Theory Comput 2021; 17:3145-3156. [PMID: 33861593 DOI: 10.1021/acs.jctc.0c01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2)-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity, thereby reducing the efficacy of both chemotherapeutics and radiotherapies. Key to this antioxidant pathway is the interaction between Nrf2 and CREB binding protein (CBP), mediated by the Neh4 and Neh5 domains of Nrf2. Disruption of this interaction via small-molecule therapeutics could negate the effects of aberrant Nrf2 upregulation. Due to the disordered nature of these domains, there remains no three-dimensional structure of Neh4 or Neh5, making structure-based drug design a challenge. Here, we performed 48 μs of unbiased molecular dynamics (MD) simulations with the Amber99SB*-ILDNP and CHARMM36m force fields and circular dichroism (CD) spectropolarimetry experiments to elucidate the free-state structures of these domains; no previous data regarding their conformational landscapes exists. There are two main findings: First, we find Neh5 to be markedly more disordered than Neh4, which has nine residues in the middle of the domain showing α-helical propensity, thus pointing to Neh4 and Neh5 having different binding mechanisms. Second, the two force fields show strong differences for the glutamic acid-rich Neh5 peptide but are in reasonable agreement for Neh4, which has no glutamic acid. The CHARMM36m force field agrees more closely with the CD results.
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Affiliation(s)
- Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Carter J Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Nadun Chanaka Karunatilleke
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Mohamed Hesham Moselhy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Computer Science, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
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27
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Espasa-Valdepeñas A, Vega JF, Cruz V, Ramos J, Müller AJ, Martinez-Salazar J. Revisiting Polymer-Particle Interaction in PEO Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3808-3816. [PMID: 33764765 PMCID: PMC9132384 DOI: 10.1021/acs.langmuir.0c02715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/17/2021] [Indexed: 06/12/2023]
Abstract
We have measured the electrophoretic mobility and diffusion coefficient of carboxylate-modified and sulfate-modified polystyrene latex particles in poly(ethylene oxide) aqueous solutions. Carboxylate-modified polystyrene particles have shown a bound polymeric layer as the surface net charge vanishes even at very low poly(ethylene oxide) concentration. The polymeric layer causes a lower electrophoretic mobility and slower Brownian diffusion than that corresponding to the bare particles. We show that the diffusion is the result of a significantly increased effective particle size 2rheff = 30 nm. This bound layer is not present in sulfate-modified polystyrene latex particles. The interaction between the carboxylate-modified particle surface and the macromolecules has been confirmed by means of atomistic computer simulations. The grafted acrylate copolymers, which come from the preparation procedure of the latex particles, confer more hydrophobic surface ready to interact with the polymer. The simulations suggest that the interaction is modulated not only by the nature of the acrylic acid monomer but also by the length of the grafted copolymer. Our results have important implications for particle selection in microrheology experiments.
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Affiliation(s)
- A. Espasa-Valdepeñas
- Biophym,
Departamento de Física Macromolecular, Instituto de Estructura de la Materia (IEM-CSIC) c/Serrano 113 bis, 28006 Madrid, Spain
| | - J. F. Vega
- Biophym,
Departamento de Física Macromolecular, Instituto de Estructura de la Materia (IEM-CSIC) c/Serrano 113 bis, 28006 Madrid, Spain
| | - V. Cruz
- Biophym,
Departamento de Física Macromolecular, Instituto de Estructura de la Materia (IEM-CSIC) c/Serrano 113 bis, 28006 Madrid, Spain
| | - J. Ramos
- Biophym,
Departamento de Física Macromolecular, Instituto de Estructura de la Materia (IEM-CSIC) c/Serrano 113 bis, 28006 Madrid, Spain
| | - A. J. Müller
- POLYMAT
and Department of Polymers and Advanced Materials: Physics, Chemistry
and Technology, Faculty of Chemistry, University
of the Basque Country UPV/EHU, Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation
for Science, 48009, Bilbao, Spain
| | - J. Martinez-Salazar
- Biophym,
Departamento de Física Macromolecular, Instituto de Estructura de la Materia (IEM-CSIC) c/Serrano 113 bis, 28006 Madrid, Spain
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28
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Sterling JD, Jiang W, Botello-Smith WM, Luo YL. Ion Pairing and Dielectric Decrement in Glycosaminoglycan Brushes. J Phys Chem B 2021; 125:2771-2780. [PMID: 33662212 DOI: 10.1021/acs.jpcb.0c11571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cell-surface polysaccharides are essential to many aspects of physiology, serving as a highly conserved evolutionary feature of life and as an important part of the innate immune system in mammals. Here, as simplified biophysical models of these sugar coatings, we present results of molecular dynamics simulations of hyaluronic acid and heparin brushes that show important effects of ion pairing, water dielectric decrease, and coion exclusion. As in prior studies of macromolecular crowding under physiologically relevant salt concentrations, our results show equilibria with electroneutrality attained through screening and pairing of brush anionic charges by monovalent cations at the atomistic detail. Most surprising is the reversal of the Donnan potential obtained from both nonpolarizable and Drude polarizable force fields, in contrast to what would be expected based on electrostatic Boltzmann partitioning alone. Water dielectric decrement within the brush domain is also associated with Born hydration-driven cation exclusion from the brush. We observe that the primary partition energy attracting cations to attain brush electroneutrality is the ion pairing or salt-bridge energy. Potassium and sodium pairings to glycosaminoglycan carboxylates and sulfates show similar abundance of contact-pairing and solvent-separated pairing. We conclude that in these crowded macromolecular brushes, ion-pairing, Born-hydration, and electrostatic potential energies all contribute to attain electroneutrality and should therefore contribute in mean-field models to accurately represent brush electrostatics.
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Affiliation(s)
- James D Sterling
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Dr., Claremont, California 91711, United States
| | - Wenjuan Jiang
- College of Pharmacy, Western University of Health Sciences, 309 E. Second Street, Pomona, California 91766, United States
| | - Wesley M Botello-Smith
- College of Pharmacy, Western University of Health Sciences, 309 E. Second Street, Pomona, California 91766, United States
| | - Yun L Luo
- College of Pharmacy, Western University of Health Sciences, 309 E. Second Street, Pomona, California 91766, United States
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29
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Abstract
Aqueous cosolvent systems (ACoSs) are mixtures of small polar molecules such as amides, alcohols, dimethyl sulfoxide, or ions in water. These liquids have been the focus of fundamental studies due to their complex intermolecular interactions as well as their broad applications in chemistry, medicine, and materials science. ACoSs are fully miscible at the macroscopic level but exhibit nanometer-scale spatial heterogeneity. ACoSs have recently received renewed attention within the chemical physics community as model systems to explore the relationship between intermolecular interactions and microscopic liquid-liquid phase separation. In this perspective, we provide an overview of ACoS spatial segregation, dynamic heterogeneity, and multiscale relaxation dynamics. We describe emerging approaches to characterize liquid microstructure, H-bond networks, and dynamics using modern experimental tools combined with molecular dynamics simulations and network-based analysis techniques.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 19104, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 19104, USA
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30
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Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. J Chem Phys 2021; 153:050901. [PMID: 32770904 DOI: 10.1063/5.0017775] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
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Affiliation(s)
- E Duboué-Dijon
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - M Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Delcroix
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - H Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
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31
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Kolafa J. Pressure in Molecular Simulations with Scaled Charges. 1. Ionic Systems. J Phys Chem B 2020; 124:7379-7390. [PMID: 32790401 DOI: 10.1021/acs.jpcb.0c02641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge scaling, rationalized as MDEC (molecular dynamics in electronic continuum) or ECC (electronic continuum correction), has become a widely used simple approach to how to avoid self-consistent induced dipoles yet approximately take into account the effects of electronic polarizability. It has been assumed that the continuum permittivity does not depend on density; in turn, pressure is calculated by standard formulas. In this work, we elaborate a complementary approximation of density-independent molecular polarizability and derive formulas for pressure corrections within the MDEC framework; real behavior lies between these two extremes. The pressure corrections for test ionic systems are huge and negative, leading to sizable densities in constant-pressure MDEC simulations. A comparison of MDEC results with equivalent polarizable systems gives a good pressure match for a crystal but very low MDEC pressures for ionic liquids. These results witness about the importance of a correct density dependence not only of continuum permittivity in MDEC simulations but also of polarizability in polarizable simulations.
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Affiliation(s)
- Jiří Kolafa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha 6, Czech Republic
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32
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Tolmachev D, Lukasheva N, Mamistvalov G, Karttunen M. Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length. Polymers (Basel) 2020; 12:E1279. [PMID: 32503199 PMCID: PMC7362111 DOI: 10.3390/polym12061279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 11/21/2022] Open
Abstract
Investigation of the effect of CaCl2 salt on conformations of two anionic poly(amino acids) with different side chain lengths, poly-(α-l glutamic acid) (PGA) and poly-(α-l aspartic acid) (PASA), was performed by atomistic molecular dynamics (MD) simulations. The simulations were performed using both unbiased MD and the Hamiltonian replica exchange (HRE) method. The results show that at low CaCl2 concentration adsorption of Ca2+ ions lead to a significant chain size reduction for both PGA and PASA. With the increase in concentration, the chains sizes partially recover due to electrostatic repulsion between the adsorbed Ca2+ ions. Here, the side chain length becomes important. Due to the longer side chain and its ability to distance the charged groups with adsorbed ions from both each other and the backbone, PGA remains longer in the collapsed state as the CaCl2 concentration is increased. The analysis of the distribution of the mineral ions suggests that both poly(amino acids) should induce the formation of mineral with the same structure of the crystal cell.
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Affiliation(s)
- Dmitry Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia;
| | - Natalia Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia;
| | - George Mamistvalov
- Faculty of Physics, St. Petersburg State University, Petrodvorets, 198504 St. Petersburg, Russia;
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia;
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Applied Mathematics, 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
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33
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Machado MR, Pantano S. Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations. J Chem Theory Comput 2020; 16:1367-1372. [PMID: 31999456 DOI: 10.1021/acs.jctc.9b00953] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
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