1
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Sil D, Osmanbasic E, Mandal SC, Acharya A, Dutta C. Variable Non-Gaussian Transport of Nanoplastic on Supported Lipid Bilayers in Saline Conditions. J Phys Chem Lett 2024; 15:5428-5435. [PMID: 38743920 PMCID: PMC11129298 DOI: 10.1021/acs.jpclett.4c00806] [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: 03/15/2024] [Revised: 04/23/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Nanoplastic-lipid interaction is vital to understanding the nanoscale mechanism of plastic adsorption and aggregation on a lipid membrane surface. However, a single-particle mechanistic picture of the nanoplastic transport process on a lipid surface remains unclear. Here, we report a salt-dependent non-Gaussian transport mechanism of polystyrene particles on a supported 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer surface. Particle stickiness on the POPC surface increases with salt concentration, where the particles stay longer at the surface and diffuse to shorter distances. Additionally, a non-Gaussian diffusion state dominates the transport process at high salt concentrations. Our current study provides insight into the transport mechanism of polystyrene (PS) particles on supported lipid membranes, which is essential to understanding fundamental questions regarding the adsorption mechanisms of nanoplastics on lipid surfaces.
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Affiliation(s)
- Diyali Sil
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United
States
| | - Edin Osmanbasic
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United
States
| | - Sasthi Charan Mandal
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United
States
| | - Atanu Acharya
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United
States
- BioInspired
Syracuse, Syracuse University, Syracuse, New York 13244, United
States
| | - Chayan Dutta
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United
States
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2
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Santos DS, De Nicola A, dos Santos VF, Milano G, Soares TA. Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism. J Phys Chem B 2023; 127:6694-6702. [PMID: 37467380 PMCID: PMC10405212 DOI: 10.1021/acs.jpcb.3c02848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed vesiculation mechanism by simulating the resulting lipid-A vesicle at the atom level. The spatial confinement imposed by the vesicle geometry on the conformation and packing of lipid-A induces significant heterogeneity of physical properties in the inner and outer leaflets. It also induces tighter molecular packing and lower acyl chain order compared to the lamellar arrangement. Around 5% of water molecules passively permeates the vesicle membrane inward and outward. The permeation is facilitated by interactions with water molecules that are transported across the membrane by a network of electrostatic interactions with the hydrogen bond donors/acceptors in the N-acetylglucosamine ring and upper region of the acyl chains of lipid-A. The permeation process takes place at low rates but still at higher frequencies than observed for the lamellar arrangement of lipid-A. These findings not only substantiate the proposed lipid-A vesiculation mechanism but also reveal the complex structural dynamics of an important nonlamellar arrangement of lipid-A.
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Affiliation(s)
- Denys
E. S. Santos
- Departmento
de Química Fundamental, Universidade
Federal de Pernambuco, Recife 50740-560, Brazil
| | - Antonio De Nicola
- Scuola
Superiore Meridionale, Largo S. Marcellino 10, Napoli 80138, Italy
- Graduate
School of Organic Materials Science, Yamagata
University, Yonezawa 992-8510, Yamagata, Japan
| | - Vinicius F. dos Santos
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
| | - Giuseppe Milano
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, Napoli 80125, Italy
| | - Thereza A. Soares
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, Norway
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3
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Lequieu J. Combining particle and field-theoretic polymer models with multi-representation simulations. J Chem Phys 2023; 158:244902. [PMID: 37377157 DOI: 10.1063/5.0153104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Particle-based and field-theoretic simulations are both widely used methods to predict the properties of polymeric materials. In general, the advantages of each method are complementary. Field-theoretic simulations are preferred for polymers with high molecular weights and can provide direct access to chemical potentials and free energies, which makes them the method-of-choice for calculating phase diagrams. The trade-off is that field-theoretic simulations sacrifice the molecular details present in particle-based simulations, such as the configurations of individual molecules and their dynamics. In this work, we describe a new approach to conduct "multi-representation" simulations that efficiently map between particle-based and field-theoretic simulations. Our approach involves the construction of formally equivalent particle-based and field-based models, which are then simulated subject to the constraint that their spatial density profiles are equal. This constraint provides the ability to directly link particle-based and field-based simulations and enables calculations that can switch between one representation to the other. By switching between particle/field representations during a simulation, we demonstrate that our approach can leverage many of the advantages of each representation while avoiding their respective limitations. Although our method is illustrated in the context of complex sphere phases in linear diblock copolymers, we anticipate that it will be useful whenever free energies, rapid equilibration, molecular configurations, and dynamic information are all simultaneously desired.
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Affiliation(s)
- Joshua Lequieu
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
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4
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Ledum M, Sen S, Bore SL, Cascella M. On the equivalence of the hybrid particle-field and Gaussian core models. J Chem Phys 2023; 158:2890484. [PMID: 37184022 DOI: 10.1063/5.0145142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Hybrid particle-field molecular dynamics is a molecular simulation strategy, wherein particles couple to a density field instead of through ordinary pair potentials. Traditionally considered a mean-field theory, a momentum and energy-conserving hybrid particle-field formalism has recently been introduced, which was demonstrated to approach the Gaussian Core model potential in the grid-converged limit. Here, we expand on and generalize the correspondence between the Hamiltonian hybrid particle-field method and particle-particle pair potentials. Using the spectral procedure suggested by Bore and Cascella, we establish compatibility to any local soft pair potential in the limit of infinitesimal grid spacing. Furthermore, we document how the mean-field regime often observed in hybrid particle-field simulations is due to the systems under consideration, and not an inherent property of the model. Considering the Gaussian filter form, in particular, we demonstrate the ability of the Hamiltonian hybrid particle-field model to recover all structural and dynamical properties of the Gaussian Core model, including solid phases, a first-order phase transition, and anomalous transport properties. We quantify the impact of the grid spacing on the correspondence, as well as the effect of the particle-field filtering length scale on the emergent particle-particle correlations.
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Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Samiran Sen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
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5
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Sen S, Ledum M, Bore SL, Cascella M. Soft Matter under Pressure: Pushing Particle–Field Molecular Dynamics to the Isobaric Ensemble. J Chem Inf Model 2023; 63:2207-2217. [PMID: 36976890 PMCID: PMC10091448 DOI: 10.1021/acs.jcim.3c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Hamiltonian hybrid particle-field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer.
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6
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Wu Z, Müller-Plathe F. Slip-Spring Hybrid Particle-Field Molecular Dynamics for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example. J Chem Theory Comput 2022; 18:3814-3828. [PMID: 35617016 DOI: 10.1021/acs.jctc.2c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The topology of chains significantly modifies the dynamical properties of polymer melts. Here, we extend a recently developed efficient simulation method, namely the slip-spring hybrid particle-field (SS-hPF) model, to study the structural and dynamical properties of branched polymer melts over large spatial-temporal scales. In the coarse-grained SS-hPF simulation of polymers, the bonded potentials are derived by iterative Boltzmann inversion from the underlying fine-grained model. The nonbonded potentials are computed from a density functional field instead of pairwise interactions used in standard molecular dynamics simulations, which increases the computational efficiency by a factor of 10-20. The entangled dynamics is lost due to the soft-core nature of density functional field interactions. It is recovered by a multichain slip-spring model that is rigorously parametrized from existing experimental or simulation data. To quantitatively predict the relaxation and diffusion of branched polymers, which are dominated by arm retraction rather than chain reptation, the slip-spring algorithm is augmented to improve the polymer dynamics near the branch point. Multiple dynamical observables, e.g., diffusion coefficients, arm relaxations, and tube survival probabilities, are characterized in an example coarse-grained model of symmetric and asymmetric star-shaped polystyrene melts. Consistent dynamical behaviors are identified and compared with theoretical predictions. With a single rescaling factor, the prediction of diffusion coefficients agrees well with the available experimental measurements. In this work, an efficient approach is provided to build chemistry-specific coarse-grained models for predicting the dynamics of branched polymers.
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Affiliation(s)
- Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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7
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Zoni V, Campomanes P, Vanni S. Investigating the structural properties of hydrophobic solvent-rich lipid bilayers. SOFT MATTER 2021; 17:5329-5335. [PMID: 33969832 PMCID: PMC8170560 DOI: 10.1039/d0sm02270e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
In vitro reconstitutions of lipid membranes have proven to be an indispensable tool to rationalize their molecular complexity and to understand their role in countless cellular processes. However, amongst the various techniques used to reconstitute lipid bilayers in vitro, several approaches are not solvent-free, but rather contain residual hydrophobic solvents in between the two bilayer leaflets, generally as a consequence of the procedure used to generate the bilayer. To what extent the presence of these hydrophobic solvents modifies bilayer properties with respect to native, solvent-free, conditions remains an open question that has important implications for the appropriate interpretation of numerous experimental observations. Here, we thorouhgly characterize hydrophobic solvent-rich lipid bilayers using atomistic molecular dynamics simulations. Our data indicate that while the presence of hydrophobic solvents at high concentrations, such as hexadecane, has a significant effect on membrane thickness, their effects on surface properties, membrane order and lateral stress are quite moderate. Our results corroborate the validity of in vitro approaches as model systems for the investigations of biological membranes but raise a few cautionary aspects that must be considered when investigating specific membrane properties.
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Affiliation(s)
- Valeria Zoni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
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8
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Schlick T, Portillo-Ledesma S. Biomolecular modeling thrives in the age of technology. NATURE COMPUTATIONAL SCIENCE 2021; 1:321-331. [PMID: 34423314 PMCID: PMC8378674 DOI: 10.1038/s43588-021-00060-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
Abstract
The biomolecular modeling field has flourished since its early days in the 1970s due to the rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase in size and timespan of biomolecular simulations has outpaced Moore's law. Here, we discuss the role of knowledge-based versus physics-based methods and hardware versus software advances in propelling the field forward. This rapid adaptation and outreach suggests a bright future for modeling, where theory, experimentation and simulation define three pillars needed to address future scientific and biomedical challenges.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
- New York University–East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China
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9
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Srinivasan S, Zoni V, Vanni S. Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein–membrane interactions. Faraday Discuss 2021; 232:131-148. [DOI: 10.1039/d0fd00058b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we investigate the ability of the MARTINI CG force field, specifically the 3 open-beta version, to reproduce known experimental observations regarding the membrane binding behavior of 12 peripheral membrane proteins and peptides.
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Affiliation(s)
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland
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10
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Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers. Molecules 2020; 25:molecules25215120. [PMID: 33158044 PMCID: PMC7663769 DOI: 10.3390/molecules25215120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling the prediction of experimental observables for a variety of chemical systems and processes and majorly impacting the study of biological membranes. However, the chemical diversity of complex lipids beyond phospholipids brings new challenges to well-established protocols used in MD simulations of soft matter and requires continuous assessment to ensure simulation reproducibility and minimize unphysical behavior. Lipopolysaccharides (LPS) are highly charged glycolipids whose aggregation in a lamellar arrangement requires the binding of numerous cations to oppositely charged groups deep inside the membrane. The delicate balance between the fully hydrated carbohydrate region and the smaller hydrophobic core makes LPS membranes very sensitive to the choice of equilibration protocol. In this work, we show that the protocol successfully used to equilibrate phospholipid bilayers when applied to complex lipopolysaccharide membranes occasionally leads to a small expansion of the simulation box very early in the equilibration phase. Although the use of a barostat algorithm controls the system dimension and particle distances according to the target pressure, fluctuation in the fleeting pressure occasionally enables a few water molecules to trickle into the hydrophobic region of the membrane, with spurious solvent buildup. We show that this effect stems from the initial steps of NPT equilibration, where initial pressure can be fairly high. This can be solved with the use of a stepwise-thermalization NVT/NPT protocol, as demonstrated for atomistic MD simulations of LPS/DPPE and lipid-A membranes in the presence of different salts using an extension of the GROMOS forcefield within the GROMACS software. This equilibration protocol should be standard procedure for the generation of consistent structural ensembles of charged glycolipids starting from atomic coordinates not previously pre-equilibrated. Although different ways to deal with this issue can be envisioned, we investigated one alternative that could be readily available in major MD engines with general users in mind.
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11
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Schäfer K, Kolli HB, Killingmoe Christensen M, Bore SL, Diezemann G, Gauss J, Milano G, Lund R, Cascella M. Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles. Angew Chem Int Ed Engl 2020; 59:18591-18598. [PMID: 32543728 PMCID: PMC7589243 DOI: 10.1002/anie.202004522] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/29/2020] [Indexed: 12/16/2022]
Abstract
The shape and size of self-assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long-range interactions. Combining small-angle X-ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabilization of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.
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Affiliation(s)
- Ken Schäfer
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Hima Bindu Kolli
- Department of Physics and AstronomyThe University of SheffieldWestern BankSheffieldS10 2TNUK
| | - Mikkel Killingmoe Christensen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Gregor Diezemann
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Jürgen Gauss
- Department ChemieJohannes Gutenberg-Universität MainzDuesbergweg 10–1455128MainzGermany
| | - Giuseppe Milano
- Department of Organic Materials ScienceYamagata University4-3-16 JonanYonezawaYamagata-ken992-8510Japan
| | - Reidar Lund
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular SciencesUniversity of OsloPO-Box 1033 Blindern0315OsloNorway
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12
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Bore SL, Cascella M. Hamiltonian and alias-free hybrid particle–field molecular dynamics. J Chem Phys 2020; 153:094106. [DOI: 10.1063/5.0020733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern 0315, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern 0315, Oslo, Norway
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13
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Schäfer K, Kolli HB, Killingmoe Christensen M, Bore SL, Diezemann G, Gauss J, Milano G, Lund R, Cascella M. Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ken Schäfer
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Hima Bindu Kolli
- Department of Physics and Astronomy The University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Mikkel Killingmoe Christensen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Gregor Diezemann
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Jürgen Gauss
- Department Chemie Johannes Gutenberg-Universität Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Giuseppe Milano
- Department of Organic Materials Science Yamagata University 4-3-16 Jonan Yonezawa Yamagata-ken 992-8510 Japan
| | - Reidar Lund
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo PO-Box 1033 Blindern 0315 Oslo Norway
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14
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Carrer M, Škrbić T, Bore SL, Milano G, Cascella M, Giacometti A. Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents? J Phys Chem B 2020; 124:6448-6458. [PMID: 32618191 PMCID: PMC8009519 DOI: 10.1021/acs.jpcb.0c04842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
We investigate the
self-assembly process of a surfactant with inverted
polarity in water and cyclohexane using both all-atom and coarse-grained
hybrid particle-field molecular dynamics simulations. Unlike conventional
surfactants, the molecule under study, proposed in a recent experiment,
is formed by a rigid and compact hydrophobic adamantane moiety, and
a long and floppy triethylene glycol tail. In water, we report the
formation of stable inverted micelles with the adamantane heads grouping
together into a hydrophobic core and the tails forming hydrogen bonds
with water. By contrast, microsecond simulations do not provide evidence
of stable micelle formation in cyclohexane. Validating the computational
results by comparison with experimental diffusion constant and small-angle
X-ray scattering intensity, we show that at laboratory thermodynamic
conditions the mixture resides in the supercritical region of the
phase diagram, where aggregated and free surfactant states coexist
in solution. Our simulations also provide indications as to how to
escape this region to produce thermodynamically stable micellar aggregates.
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Affiliation(s)
- Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, United States.,Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia,Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, 992-8510 Yamagata-ken, Japan.,Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia,Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.,European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro, Calle Crosera, 30123 Venice, Italy
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15
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Ledum M, Løland Bore S, Cascella M. Automated determination of hybrid particle-field parameters by machine learning. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1785571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
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16
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Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nat Commun 2020; 11:2951. [PMID: 32528158 PMCID: PMC7289815 DOI: 10.1038/s41467-020-16424-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit molecular modelling of biologically relevant membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Coarse-grained solvent-free membrane models offer efficient sampling but sacrifice realistic kinetics, thereby limiting the ability to predict pathways and mechanisms of membrane processes. Here, we present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics. This framework facilitates efficient simulation of large biomembrane systems with large timesteps, while achieving realistic equilibrium and non-equilibrium kinetics. It helps to bridge between the nanometer/nanosecond spatiotemporal resolutions of coarse-grained models and biologically relevant time- and lengthscales. As a demonstration, we investigate fluctuations of red blood cells, with varying cytoplasmic viscosities, in 150-milliseconds-long trajectories, and compare kinetic properties against single-cell experimental observations.
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17
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Bore SL, Kolli HB, De Nicola A, Byshkin M, Kawakatsu T, Milano G, Cascella M. Hybrid particle-field molecular dynamics under constant pressure. J Chem Phys 2020; 152:184908. [PMID: 32414244 DOI: 10.1063/5.0007445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hybrid particle-field methods are computationally efficient approaches for modeling soft matter systems. So far, applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field interactions to represent systems coupled to constant external pressure. First, we show that the commonly used particle-field energy functional can be modified to model and parameterize the isotropic contributions to the pressure tensor without interfering with the microscopic forces on the particles. Second, we employ a square gradient particle-field interaction term to model non-isotropic contributions to the pressure tensor, such as in surface tension phenomena. This formulation is implemented within the hybrid particle-field molecular dynamics approach and is tested on a series of model systems. Simulations of a homogeneous water box demonstrate that it is possible to parameterize the equation of state to reproduce any target density for a given external pressure. Moreover, the same parameterization is transferable to systems of similar coarse-grained mapping resolution. Finally, we evaluate the feasibility of the proposed approach on coarse-grained models of phospholipids, finding that the term between water and the lipid hydrocarbon tails is alone sufficient to reproduce the experimental area per lipid in constant-pressure simulations and to produce a qualitatively correct lateral pressure profile.
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Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Hima Bindu Kolli
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Antonio De Nicola
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata-ken 992-8510, Japan
| | - Maksym Byshkin
- Institute of Computational Science, Università Della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
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18
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Jiang K, Liu X, He H, Wang J, Zhang S. Insight into the formation and permeability of ionic liquid unilamellar vesicles by molecular dynamics simulation. SOFT MATTER 2020; 16:2605-2610. [PMID: 32096807 DOI: 10.1039/c9sm02339a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Unilamellar vesicles in solution could open up new horizons for reaction and material delivery, but the formation mechanism especially for the permeability of the small molecule through the vesicle membrane is still unknown. In this study, the formation and permeability of the unilamellar vesicles formed by the ionic liquid 1-dodecyl-3-methylimidazolium salicylate ([C12mim][Sal]) have been investigated by molecular dynamics simulation. Starting from a random distribution of ionic liquids, the entire process of vesicle formation could be observed on a nanosecond time scale, during which planar and cup-like structures are formed at the intermediate stage. Energy analysis reveals that the electrostatic interactions between cations and anions play a dominant role in forming and stabilizing the vesicle. Radial density distribution functions indicate that the final stable vesicle is a spherical bilayer structure. Besides, it was found that the structure of vesicles is maintained with the increase of temperature, while the water molecules in the vesicles could be completely exchanged quickly. These results suggest that vesicles may be beneficial for the enrichment or release of molecules.
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Affiliation(s)
- Kun Jiang
- School of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, Shandong, China.
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19
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Dannenhoffer-Lafage T, Voth GA. Reactive Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2020; 16:2541-2549. [DOI: 10.1021/acs.jctc.9b01140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas Dannenhoffer-Lafage
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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20
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Aggregation of Lipid A Variants: A Hybrid Particle-Field Model. Biochim Biophys Acta Gen Subj 2020; 1865:129570. [PMID: 32105775 DOI: 10.1016/j.bbagen.2020.129570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/23/2022]
Abstract
Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e., the type of counter-ions, through electrostatic interactions. In this paper, we report on a coarse-grained model of chemical variants of Lipid A based on the hybrid particle-field/molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayers for two different hexa- and tetra-acylated structures. Comparing particle density profiles along bilayer cross-sections, we find good agreement between the hPF-MD model and reference all-atom simulation for both chemical variants of Lipid A. hPF-MD models of constituted bilayers composed by hexa-acylated Lipid A in water are stable within the simulation time. We further validate our model by verifying that the phase behavior of Lipid A/counterion/water mixtures is correctly reproduced. In particular, hPF-MD simulations predict the correct self-assembly of different lamellar and micellar phases from an initially random distribution of Lipid A molecules with counterions in water. Finally, it is possible to observe the spontaneous formation and stability of Lipid A vesicles by fusion of micellar aggregates.
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21
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Zoni V, Nieto V, Endter LJ, Risselada HJ, Monticelli L, Vanni S. To Bud or Not to Bud: A Perspective on Molecular Simulations of Lipid Droplet Budding. Front Mol Biosci 2019; 6:124. [PMID: 31799255 PMCID: PMC6863888 DOI: 10.3389/fmolb.2019.00124] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
- Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Vincent Nieto
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universitè de Lyon, Lyon, France
| | - Laura J Endter
- Department of Theoretical Physics, Georg-August University Göttingen, Göttingen, Germany
| | - Herre J Risselada
- Department of Theoretical Physics, Georg-August University Göttingen, Göttingen, Germany
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universitè de Lyon, Lyon, France
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Valbonne, France
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22
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Santos DES, Pontes FJS, Lins RD, Coutinho K, Soares TA. SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. J Chem Inf Model 2019; 60:473-484. [DOI: 10.1021/acs.jcim.9b00569] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Denys E. S. Santos
- Departmento Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil
| | - Frederico J. S. Pontes
- Departmento Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil
| | - Roberto D. Lins
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, 50740-465 Cidade Universitária, Recife, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo, Brazil
| | - Thereza A. Soares
- Departmento Química Fundamental, Universidade Federal de Pernambuco, 50740-560 Cidade Universitária, Recife, Brazil
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23
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Bore SL, Kolli HB, Kawakatsu T, Milano G, Cascella M. Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics. J Chem Theory Comput 2019; 15:2033-2041. [DOI: 10.1021/acs.jctc.8b01201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Hima Bindu Kolli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan ,Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
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24
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Pfeiffer T, De Nicola A, Montis C, Carlà F, van der Vegt NFA, Berti D, Milano G. Nanoparticles at Biomimetic Interfaces: Combined Experimental and Simulation Study on Charged Gold Nanoparticles/Lipid Bilayer Interfaces. J Phys Chem Lett 2019; 10:129-137. [PMID: 30563321 DOI: 10.1021/acs.jpclett.8b03399] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The poor understanding of the interaction of nanomaterials with biologically relevant interfaces is recognized as one of the major issues currently limiting the development of nanomedicine. The central purpose of this study is to compare experimental (confocal microscopy, fluorescence correlation spectroscopy, X-ray reflectivity) and computational (molecular dynamics simulations) results to thoroughly describe the interaction of cationic gold nanoparticles (AuNPs) with mixed zwitterionic/anionic lipid membranes. The adhesion of AuNPs to the lipid membrane is investigated on different length scales from a structural and dynamical point of view; with this approach, a series of complex phenomena, spanning from lipid extraction, localized membrane disruption, lateral phase separation, and slaved diffusion, are characterized and interpreted from a molecular level to macroscopic observations.
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Affiliation(s)
- Tobias Pfeiffer
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie , Technische Universität Darmstadt , Alarich-Weiss-Straße 10 , Darmstadt 64289 , Germany
| | - Antonio De Nicola
- Department of Organic Materials Science , Yamagata University , 4-3-16 Jonan Yonezawa , Yamagata-ken 992-8510 , Japan
| | - Costanza Montis
- Department of Chemistry "Ugo Schiff" and CSGI , University of Florence , via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy
| | - Francesco Carlà
- European Synchrotron Radiation Facility , CS 40220 , Grenoble Cedex 9, France
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie , Technische Universität Darmstadt , Alarich-Weiss-Straße 10 , Darmstadt 64289 , Germany
| | - Debora Berti
- Department of Chemistry "Ugo Schiff" and CSGI , University of Florence , via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy
| | - Giuseppe Milano
- Department of Organic Materials Science , Yamagata University , 4-3-16 Jonan Yonezawa , Yamagata-ken 992-8510 , Japan
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25
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Munaò G, Pizzirusso A, Kalogirou A, De Nicola A, Kawakatsu T, Müller-Plathe F, Milano G. Molecular structure and multi-body potential of mean force in silica-polystyrene nanocomposites. NANOSCALE 2018; 10:21656-21670. [PMID: 30256374 DOI: 10.1039/c8nr05135f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano, et al., J. Chem. Phys., 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles (NPs) in a melt. Specifically, we consider Silica NPs bare or grafted with Polystyrene chains, aiming to shed light on the interactions among free and grafted chains affecting the dispersion of NPs in the nanocomposite. The proposed hybrid models show good performances in catching the local structure of the chains, and in particular their density profiles, documenting the existence of the "wet-brush-to-dry-brush" transition. By using these models, the PMF between pairs of ungrafted and grafted NPs in Polystyrene matrix are calculated. Moreover, we estimate the three-particle contribution to the total PMF and its role in regulating the phase separation on the nanometer scale. In particular, the multi-particle contribution to the PMF is able to give an explanation of the complex experimental morphologies observed at low grafting densities. More in general, we propose this approach and the models utilized here for a molecular understanding of specific systems and the impact of the chemical nature of the systems on the composite final properties.
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Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, 132, I-84084, Fisciano, SA, Italy.
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26
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Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. J Membr Biol 2018; 251:609-631. [PMID: 30350011 PMCID: PMC6244758 DOI: 10.1007/s00232-018-0050-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences and Centre of Excellence "Biomaterials Chemistry", Linnæus University, Kalmar, Sweden.
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, UK
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mikkel Christensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark.,Sino-Danish Center for Education and Research, Beijing, China
| | - João T S Coimbra
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Simona Concilio
- Department of Industrial Engineering, University of Salerno, Fisciano, SA, Italy
| | - Csaba Daday
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | | | - Konstantina Karathanou
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | | | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Antara Mazumdar
- GBB Institute, University of Groningen, Groningen, The Netherlands
| | - Richard Naftalin
- Physiology and Vascular Biology Departments, King's College London School of Medicine, London, UK
| | - Mónica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires, Argentina
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Peter Quinn
- Biochemistry Department, King's College London, London, UK
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
| | - Lucia Sessa
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down Bath, BA2 7AY, UK.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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27
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Kolli HB, de Nicola A, Bore SL, Schäfer K, Diezemann G, Gauss J, Kawakatsu T, Lu ZY, Zhu YL, Milano G, Cascella M. Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment. J Chem Theory Comput 2018; 14:4928-4937. [DOI: 10.1021/acs.jctc.8b00466] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hima Bindu Kolli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033, Blindern, 0315 Oslo, Norway
| | - Antonio de Nicola
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan Yonezawa, Yamagata-ken 992-8510, Japan
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033, Blindern, 0315 Oslo, Norway
| | - Ken Schäfer
- Institut für
Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für
Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für
Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - You-Liang Zhu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033, Blindern, 0315 Oslo, Norway
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28
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Molecular dynamics simulations of lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2094-2107. [PMID: 29729280 DOI: 10.1016/j.bbamem.2018.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 01/02/2023]
Abstract
A lipid nanodisc is a discoidal lipid bilayer stabilized by proteins, peptides, or polymers on its edge. Nanodiscs have two important connections to structural biology. The first is associated with high-density lipoprotein (HDL), a particle with a variety of functionalities including lipid transport. Nascent HDL (nHDL) is a nanodisc stabilized by Apolipoprotein A-I (APOA1). Determining the structure of APOA1 and its mimetic peptides in nanodiscs is crucial to understanding pathologies related to HDL maturation and designing effective therapies. Secondly, nanodiscs offer non-detergent membrane-mimicking environments and greatly facilitate structural studies of membrane proteins. Although seemingly similar, natural and synthetic nanodiscs are different in that nHDL is heterogeneous in size, due to APOA1 elasticity, and gradually matures to become spherical. Synthetic nanodiscs, in contrast, should be homogenous, stable, and size-tunable. This report reviews previous molecular dynamics (MD) simulation studies of nanodiscs and illustrates convergence and accuracy issues using results from new multi-microsecond atomistic MD simulations. These new simulations reveal that APOA1 helices take 10-20 μs to rearrange on the nanodisc, while peptides take 2 μs to migrate from the disc surfaces to the edge. These systems can also become kinetically trapped depending on the initial conditions. For example, APOA1 was trapped in a biologically irrelevant conformation for the duration of a 10 μs trajectory; the peptides were similarly trapped for 5 μs. It therefore remains essential to validate MD simulations of these systems with experiments due to convergence and accuracy issues. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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29
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Jaschonek S, Cascella M, Gauss J, Diezemann G, Milano G. Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers. Biochem Biophys Res Commun 2018; 498:327-333. [PMID: 29101041 DOI: 10.1016/j.bbrc.2017.10.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/29/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
The capability of coarse-grained models based on the MARTINI mapping to reproduce the gel-liquid phase transition in saturated and unsaturated model lipids was investigated. We found that the model is able to reproduce a lower critical temperature for 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with respect to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Nonetheless, the appearance of a gel phase for DOPC is strictly dependent on the intramolecular parameters chosen to model its molecular structure. In particular, we show that the bending angle at the coarse-grained bead corresponding to the unsaturated carbon-carbon bond acts as an order parameter determining the temperature of the phase transition. Structural analysis of the molecular dynamics simulations runs evidences that in the gel phase, the packing of the lipophilic tails of DOPC assume a different conformation than in the liquid phase. In the latter phase, the DOPC geometry resembles that of the relaxed free molecule. DPPC:DOPC mixtures show a single phase transition temperature, indicating that the observation of a phase separation between the two lipids requires the simulation of systems with sizes much larger than the ones used here.
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Affiliation(s)
- Stefan Jaschonek
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Postboks 1033 Blindern, N-0315 Oslo, Norway.
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany.
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Italy.
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30
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Bore SL, Milano G, Cascella M. Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains. J Chem Theory Comput 2018; 14:1120-1130. [DOI: 10.1021/acs.jctc.7b01160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
| | - Giuseppe Milano
- Department
of Organic Materials Science, University of Yamagata, 4-3-16 Jonan
Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
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31
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Santos DES, Pol-Fachin L, Lins RD, Soares TA. Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes. J Chem Inf Model 2017; 57:2181-2193. [DOI: 10.1021/acs.jcim.7b00271] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Denys E. S. Santos
- Department
of Fundamental Chemistry, Federal University of Pernambuco, 50740-560 Recife, Brazil
| | - Laércio Pol-Fachin
- Department
of Fundamental Chemistry, Federal University of Pernambuco, 50740-560 Recife, Brazil
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50740-465 Recife, Brazil
| | - Roberto D. Lins
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50740-465 Recife, Brazil
| | - Thereza A. Soares
- Department
of Fundamental Chemistry, Federal University of Pernambuco, 50740-560 Recife, Brazil
- Department
of Chemistry, Umeå Center for Microbial Research, Umeå University, 90.187 Umeå, Sweden
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Pizzirusso A, De Nicola A, Sevink GJA, Correa A, Cascella M, Kawakatsu T, Rocco M, Zhao Y, Celino M, Milano G. Biomembrane solubilization mechanism by Triton X-100: a computational study of the three stage model. Phys Chem Chem Phys 2017; 19:29780-29794. [DOI: 10.1039/c7cp03871b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The solubilization mechanism of lipid membranes in the presence of Triton X-100 (TX-100) is investigated at molecular resolution using hybrid particle field–self consistence field simulations.
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Affiliation(s)
| | - Antonio De Nicola
- Dipartimento di Chimica e Biologia
- Università di Salerno
- Fisciano
- Italy
| | - G. J. Agur Sevink
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden
- The Netherlands
| | - Andrea Correa
- Department of Chemical Science
- Federico II University of Naples
- 80126 Napoli
- Italy
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences
- University of Oslo
- 0371 Oslo
- Norway
| | | | - Mattia Rocco
- Biopolimeri e Proteomica
- Ospedale Policlinico San Martino
- Genova
- Italy
| | - Ying Zhao
- Institute of Nano-Photonics
- School of Physics and Materials Engineering
- Dalian Minzu University
- Dalian 116600
- China
| | | | - Giuseppe Milano
- Dipartimento di Chimica e Biologia
- Università di Salerno
- Fisciano
- Italy
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