1
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Sheikh S, Lonetti B, Touche I, Mohammadi A, Li Z, Abbas M. Brownian motion of soft particles near a fluctuating lipid bilayer. J Chem Phys 2023; 159:244903. [PMID: 38149741 DOI: 10.1063/5.0182499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/12/2023] [Indexed: 12/28/2023] Open
Abstract
The dynamics of a soft particle suspended in a viscous fluid can be changed by the presence of an elastic boundary. Understanding the mechanisms and dynamics of soft-soft surface interactions can provide valuable insights into many important research fields, including biomedical engineering, soft robotics development, and materials science. This work investigates the anomalous transport properties of a soft nanoparticle near a visco-elastic interface, where the particle consists of a polymer assembly in the form of a micelle and the interface is represented by a lipid bilayer membrane. Mesoscopic simulations using a dissipative particle dynamics model are performed to examine the impact of micelle's proximity to the membrane on its Brownian motion. Two different sizes are considered, which correspond to ≈10-20nm in physical units. The wavelengths typically seen by the largest micelle fall within the range of wavenumbers where the Helfrich model captures fairly well the bilayer mechanical properties. Several independent simulations allowed us to compute the micelle trajectories during an observation time smaller than the diffusive time scale (whose order of magnitude is similar to the membrane relaxation time of the largest wavelengths), this time scale being hardly accessible by experiments. From the probability density function of the micelle normal position with respect to the membrane, it is observed that the position remains close to the starting position during ≈0.05τd (where τd corresponds to the diffusion time), which allowed us to compare the negative excess of mean-square displacement (MSD) to existing theories. In that time range, the MSD exhibits different behaviors along parallel and perpendicular directions. When the micelle is sufficiently close to the bilayer (its initial distance from the bilayer equals approximately twice its gyration radius), the micelle motion becomes quickly subdiffusive in the normal direction. Moreover, the temporal evolution of the micelle MSD excess in the perpendicular direction follows that of a nanoparticle near an elastic membrane. However, in the parallel direction, the MSD excess is rather similar to that of a nanoparticle near a liquid interface.
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Affiliation(s)
- S Sheikh
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - B Lonetti
- IMRCP, UMR5623 CNRS, Université de Toulouse, Toulouse, France
- FR FERMAT, Université de Toulouse, CNRS, INPT, INSA, UPS, Toulouse, France
| | - I Touche
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - A Mohammadi
- Department of Mechanical Engineering, Clemson University, Clemson, South Carolina 29634, USA
| | - Z Li
- Department of Mechanical Engineering, Clemson University, Clemson, South Carolina 29634, USA
| | - M Abbas
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
- FR FERMAT, Université de Toulouse, CNRS, INPT, INSA, UPS, Toulouse, France
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2
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Yong X, Du K. Effects of Shape on Interaction Dynamics of Tetrahedral Nanoplastics and the Cell Membrane. J Phys Chem B 2023; 127:1652-1663. [PMID: 36763902 DOI: 10.1021/acs.jpcb.2c07460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Cellular uptake of nanoplastics is instrumental in their environmental accumulation and transfer to humans through the food chain. Despite extensive studies using spherical plastic nanoparticles, the influence of the morphological characteristics of environmentally released nanoplastics is understudied. Using dissipative particle dynamics simulations, we modeled the interactions between a cell membrane and hydrophobic nanotetrahedra, which feature high shape anisotropy and large surface curvature seen for environmental nanoplastics. We observe robust uptake of nanotetrahedra with sharp vertices and edges by the lipid membrane. Two local energy minimum configurations of nanotetrahedra embedded in the membrane bilayer were identified for particles of large sizes. Further analysis of particle dynamics within the membrane shows that the two interaction states exhibit distinct translational and rotational dynamics in the directions normal and parallel to the plane of the membrane. The membrane confinement significantly arrests the out-of-plane motion, resulting in caged translation and subdiffusive rotation. While the in-plane diffusion remains Brownian, we find that the translational and rotational modes decouple from each other as the particle size increases. The rotational diffusion decreases by a greater extent compared to the translational diffusion, deviating from the continuum theory predictions. These results provide fundamental insights into the shape effect on the nanoparticle dynamics in crowded lipid membranes.
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Affiliation(s)
- Xin Yong
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902, United States
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
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3
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Sun L, Wang S, Tian F, Zhu H, Dai L. Organizations of melittin peptides after spontaneous penetration into cell membranes. Biophys J 2022; 121:4368-4381. [PMID: 36199252 PMCID: PMC9703044 DOI: 10.1016/j.bpj.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
The antimicrobial peptide, melittin, is a potential next-generation antibiotic because melittin can spontaneously form pores in bacterial cell membranes and cause cytoplasm leakage. However, the organizations of melittin peptides in cell membranes remain elusive, which impedes the understanding of the poration mechanism. In this work, we use coarse-grained and all-atom molecular dynamics (MD) simulations to investigate the organizations of melittin peptides during and after spontaneous penetration into DPPC/POPG lipid bilayers. We find that the peptides in lipid bilayers adopt either a transmembrane conformation or a U-shaped conformation, which are referred to as T- and U-peptides, respectively. Several U-peptides and/or T-peptides aggregate to form stable pores. We analyze a T-pore consisting of four T-peptides and a U-pore consisting of three U-peptides and one T-peptide. In both pores, peptides are organized in a manner such that polar residues face inward and hydrophobic residues face outward, which stabilizes the pores and produces water channels. Compared with the U-pore, the T-pore has lower energy, larger pore diameter, and higher permeability. However, the T-pore occurs less frequently than the U-pore in our simulations, probably because the formation of the T-pore is kinetically slower than the U-pore. The stability and permeability of both pores are confirmed by 300 ns all-atom MD simulations. The peptide organizations obtained in this work should deepen the understanding of the stability, poration mechanism, and permeability of melittin, and facilitate the optimization of melittin to enhance the antibacterial ability.
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Affiliation(s)
- Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China.
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4
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Blovský T, Šindelka K, Limpouchová Z, Procházka K. Changes in Ion Concentrations upon the Binding of Short Polyelectrolytes on Phospholipid Bilayers: Computer Study Addressing Interesting Physiological Consequences. Polymers (Basel) 2022; 14:polym14173634. [PMID: 36080710 PMCID: PMC9459791 DOI: 10.3390/polym14173634] [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: 07/27/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
This computer study was inspired by the experimental observation of Y. Qian et al. published in ACS Applied Materials and Interfaces, 2018 that the short positively charged β-peptide chains and their oligomeric analogues efficiently suppress severe medical problems caused by antimicrobial drug-resistant bacteria despite them not penetrating the bacterial membrane. Our coarse-grained molecular dynamics (dissipative particle dynamics) simulations confirm the tentative explanation of the authors of the experimental study that the potent antimicrobial activity is a result of the entropically driven release of divalent ions (mainly magnesium ions essential for the proper biological function of bacteria) into bulk solution upon the electrostatic binding of β-peptides to the bacterial membrane. The study shows that in solutions containing cations Na+, Ca2+ and Mg2+, and anions Cl−, the divalent cations preferentially concentrate close to the membrane and neutralize the negative charge. Upon the addition of positively charged oligomer chains (models of β-peptides and their analogues), the oligomers electrostatically bind to the membrane replacing divalent ions, which are released into bulk solvent. Our simulations indicate that the entropy of small ions (which controls the behavior of synthetic polyelectrolyte solutions) plays an important role in this and also in other similar biologically important systems.
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Affiliation(s)
- Tomáš Blovský
- The Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Karel Šindelka
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, v.v.i., Rozvojová 135/1, Suchdol, 165 02 Prague 6, Czech Republic
| | - Zuzana Limpouchová
- The Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Karel Procházka
- The Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
- Correspondence:
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5
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Zhou T, Wu Z, Das S, Eslami H, Müller-Plathe F. How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative Particle Dynamics Simulation Study. J Chem Theory Comput 2022; 18:2597-2615. [PMID: 35286098 PMCID: PMC8938819 DOI: 10.1021/acs.jctc.1c01120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Indexed: 01/03/2023]
Abstract
We have developed dissipative particle dynamics models for pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and dimyristoylphosphatidylcholine (DMPC) as well as their binary and ternary mixed membranes, as coronavirus model membranes. The stabilities of pure and mixed membranes, surrounded by aqueous solutions containing up to 70 mol % ethanol (alcoholic disinfectants), have been investigated at room temperature. We found that aqueous solutions containing 5-10 mol % ethanol already have a significant weakening effect on the pure and mixed membranes. The magnitude of the effect depends on the membrane composition and the ethanol concentration. Ethanol permeabilizes the membrane, causing its lateral swelling and thickness shrinking and reducing the orientational order of the hydrocarbon tail of the bilayer. The free energy barrier for the permeation of ethanol in the bilayers is considerably reduced by the ethanol uptake. The rupture-critical ethanol concentrations causing the membrane failure are 20.7, 27.5, and 31.7 mol % in the aqueous phase surrounding pure DMPC, DOPC, and DPPC membranes, respectively. Characterizing the failure of lipid membranes by a machine-learning neural network framework, we found that all mixed binary and/or ternary membranes disrupt when immersed in an aqueous solution containing a rupture-critical ethanol concentration, ranging from 20.7 to 31.7 mol %, depending on the composition of the membrane; the DPPC-rich membranes are more intact, while the DMPC-rich membranes are least intact. Due to the tight packing of long, saturated hydrocarbon tails in DPPC, increasing the DPPC content of the mixed membrane increases its stability against the disinfectant. At high DPPC concentrations, where the DOPC and DMPC molecules are confined between the DPPC lipids, the ordered hydrocarbon tails of DPPC also induce order in the DOPC and DMPC molecules and, hence, stabilize the membrane more. Our simulations on pure and mixed membranes of a diversity of compositions reveal that a maximum ethanol concentration of 32 mol % (55 wt %) in the alcohol-based disinfectants is enough to disintegrate any membrane composed of these three lipids.
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Affiliation(s)
- Tianhang Zhou
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Shubhadip Das
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Hossein Eslami
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
- College of Sciences, Persian Gulf
University, Boushehr 75168, Iran
| | - 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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6
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Feng YH, Chen BZ, Fei WM, Cui Y, Zhang CY, Guo XD. Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review. AIChE J 2021. [DOI: 10.1002/aic.17507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yun Hao Feng
- Beijing Laboratory of Biomedical Materials College of Materials Science and Engineering, Beijing University of Chemical Technology Beijing China
| | - Bo Zhi Chen
- Beijing Laboratory of Biomedical Materials College of Materials Science and Engineering, Beijing University of Chemical Technology Beijing China
| | - Wen Min Fei
- Department of Dermatology China‐Japan Friendship Hospital Beijing China
- Graduate School Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Yong Cui
- Department of Dermatology China‐Japan Friendship Hospital Beijing China
- Graduate School Peking Union Medical College and Chinese Academy of Medical Sciences Beijing China
| | - Can Yang Zhang
- Biopharmaceutical and Health Engineering Division Tsinghua Shenzhen International Graduate School Shenzhen China
| | - Xin Dong Guo
- Beijing Laboratory of Biomedical Materials College of Materials Science and Engineering, Beijing University of Chemical Technology Beijing China
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7
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Song J, Wan M, Yang Y, Gao L, Fang W. Development of accurate coarse-grained force fields for weakly polar groups by an indirect parameterization strategy. Phys Chem Chem Phys 2021; 23:6763-6774. [PMID: 33720253 DOI: 10.1039/d1cp00032b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coarse-grained (CG) molecular dynamics simulations are widely used to predict morphological structures and interpret mechanisms of mesoscopic behavior between the scope of traditional experiments and all-atom simulations. However, most current CG force fields (FFs) are not precise enough, especially for polar molecules or functional groups. A main obstacle in developing accurate CG FFs for polar molecules is the freezing problem met at room temperature. In this work, we introduce an indirect parametrization strategy for weakly polar groups by considering their short-chain homologs to avoid freezing. Here, a polar group containing three to four heavy atoms is mapped into one CG bead that is connected to one alkyl bead composed of three or four carbons. The CG beads interact via 4-parameter nonbonded Morse potentials and harmonic bonded potentials. An efficient meta-multilinear interpolation parameterization algorithm, as recently developed by us, is used to rigorously optimize the force parameters. Satisfactory accuracy is witnessed in terms of the density, heat of vaporization, surface tension, and solvation free energy of the homologs of twelve polar molecules, all deviating from the experiment by less than 5%. The transferability of the current FF is indicated by the predicted density, heat of vaporization, and end-to-end distance distributions of fatty acid methyl esters composed of multiple functional groups parameterized in this work.
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Affiliation(s)
- Junjie Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing 100875, China.
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8
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Ovy SMAI, Obinwa J, Peters AJ. The Effect of Graft Density on the Ordering of Block Copolymer Grafted Nanoparticles. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S M Al Islam Ovy
- College of Engineering & Science, Louisiana Tech University, Ruston, Louisiana 71272, United States of America
| | - Joshua Obinwa
- College of Engineering & Science, Louisiana Tech University, Ruston, Louisiana 71272, United States of America
| | - Andrew J. Peters
- College of Engineering & Science, Louisiana Tech University, Ruston, Louisiana 71272, United States of America
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9
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Feng YH, Zhang XP, Zhao ZQ, Guo XD. Dissipative Particle Dynamics Aided Design of Drug Delivery Systems: A Review. Mol Pharm 2020; 17:1778-1799. [DOI: 10.1021/acs.molpharmaceut.0c00175] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yun Hao Feng
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Xiao Peng Zhang
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Ze Qiang Zhao
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Xin Dong Guo
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
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10
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Wan M, Song J, Li W, Gao L, Fang W. Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm. J Comput Chem 2019; 41:814-829. [DOI: 10.1002/jcc.26131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/07/2019] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mingwei Wan
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
- Institution of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Junjie Song
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
| | - Wenli Li
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
- Institution of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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11
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Vaiwala R, Jadhav S, Thaokar R. Establishing an Electrostatics Paradigm for Membrane Electroporation in the Framework of Dissipative Particle Dynamics. J Chem Theory Comput 2019; 15:5737-5749. [PMID: 31430431 DOI: 10.1021/acs.jctc.9b00573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With an exclusive aim to looking into a mechanism of membrane electroporation on mesoscopic length and time scales, we report the dissipative particle dynamics (DPD) simulation results for systems with and without electrolytes. A polarizable DPD model of water is employed for accurate modeling of long-range electrostatics near the water-lipid interfaces. A great deal of discussion on field induced change in dipole moments of water and lipids together with the special variation of electric field is made in order to understand the dielectrophoretic movement of water, initiating a pore formation via an intrusion through the bilayer core. The presence of salt alters the dipolar arrangement of lipids and water, and thereby it reduces the external field required to create a pore in the membrane. The species fluxes through the pore, distributions for bead density, electrostatic potential, stresses across the membrane, etc. are used to answer some of the key questions pertaining to mechanism of electroporation. The findings are compared with the molecular dynamics simulation results found in the literature, and the comparison successfully establishes an electrostatics paradigm for biomembrane studies using DPD simulations.
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Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai 400 076 , India
| | - Sameer Jadhav
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai 400 076 , India
| | - Rochish Thaokar
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai 400 076 , India
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12
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Pezeshkian W, König M, Marrink SJ, Ipsen JH. A Multi-Scale Approach to Membrane Remodeling Processes. Front Mol Biosci 2019; 6:59. [PMID: 31396522 PMCID: PMC6664084 DOI: 10.3389/fmolb.2019.00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
We present a multi-scale simulation procedure to describe membrane-related biological processes that span over a wide range of length scales. At macroscopic length-scale, a membrane is described as a flexible thin film modeled by a dynamic triangulated surface with its spatial conformations governed by an elastic energy containing only a few model parameters. An implicit protein model allows us to include complex effects of membrane-protein interactions in the macroscopic description. The gist of this multi-scale approach is a scheme to calibrate the implicit protein model using finer scale simulation techniques e.g., all atom and coarse grain molecular dynamics. We previously used this approach and properly described the formation of membrane tubular invaginations upon binding of B-subunit of Shiga toxin. Here, we provide a perspective of our multi-scale approach, summarizing its main features and sketching possible routes for future development.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - John H Ipsen
- Department of Physics, Chemistry and Pharmacy, Center for Biomembrane Physics (MEMPHYS), University of Southern Denmark, Odense, Denmark
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13
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Zavadlav J, Marrink SJ, Praprotnik M. SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 2019; 9:20180075. [PMID: 31065343 PMCID: PMC6501350 DOI: 10.1098/rsfs.2018.0075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive resolution scheme, which concurrently couples atomistic and coarse-grained molecular representations. We showcase the versatility of our multiscale approach on a few applications to biomolecular systems coupling atomistic and supramolecular water models such as the well-established MARTINI and dissipative particle dynamics models and provide an outlook for future work.
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Affiliation(s)
- Julija Zavadlav
- Computational Science and Engineering Laboratory, ETH-Zurich, Clausiusstrasse 33, 8092 Zurich, Switzerland
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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Abstract
The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model’s accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs.
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15
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Vaiwala R, Jadhav S, Thaokar R. Electroporation Using Dissipative Particle Dynamics with a Novel Protocol for Applying Electric Field. J Chem Theory Comput 2019; 15:603-612. [PMID: 30525589 DOI: 10.1021/acs.jctc.8b00911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In molecular dynamics simulations of membrane electroporation, the bilayer is subjected to an electric field E either by direct addition of a force f = qE on the charge-bearing species or by imposing an ion imbalance in the salt solutions on the two sides of the bilayer. The former is believed to mimic electroporation with high fields over nanosecond pulse period, during which the membrane is almost uncharged, especially in the low salt limit. Conversely, the ion imbalance method elucidates a low electric field-induced poration over a longer period of micro- to milliseconds with a fully charged membrane. Both these methods of applying electric field have disadvantages while investigating electroporation using dissipative particle dynamics (DPD) simulations. The method involving direct addition of force fails to address the presence of a nonuniform dielectric background for ions embedded in nonpolarizable DPD water and those found in the core of the bilayer. The ion imbalance method in DPD simulations suffers from its unavoidable use of a wall potential to prevent the movement of ions across the periodic boundaries. To address the above issues, we propose a simple method for imposing a desired transmembrane potential (TMV) by placing oppositely but uniformly charged plates on either side of the bilayer. Our DPD simulations demonstrate that the profiles for bead density, mechanical stress, electrical potential, as well as the transient responses in the dipole moment and species fluxes obtained from the proposed method utilizing charged plates are quite similar to those obtained using the ion imbalance method. The proposed protocol is free from the aforementioned drawbacks of the direct force addition and ion imbalance methods.
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Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai 400 076 , India
| | - Sameer Jadhav
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai 400 076 , India
| | - Rochish Thaokar
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai 400 076 , India
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Zavadlav J, Praprotnik M. Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics. J Chem Phys 2018; 147:114110. [PMID: 28938807 DOI: 10.1063/1.4986916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.
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Affiliation(s)
- Julija Zavadlav
- Chair of Computational Science, ETH Zürich, Clausiusstrasse 33, CH-8092 Zurich, Switzerland
| | - Matej Praprotnik
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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Wan M, Gao L, Fang W. Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme. PLoS One 2018; 13:e0198049. [PMID: 29795682 PMCID: PMC5967728 DOI: 10.1371/journal.pone.0198049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/12/2018] [Indexed: 11/30/2022] Open
Abstract
A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a coarse-grained elementary bead based on functional group. The effective hybrid potential between any pair of beads is composed of a short-range repulsive soft-core potential that directly adopts the form of an explicit-solvent DPD model and a long-range attractive hydrophobic potential. The parameters of the attractive potentials for lipid molecules were obtained by fitting the explicit-solvent DPD simulation of one bead of any type in a water box, then finely tuning it until the bilayer membrane properties obtained in the explicit-solvent model were matched. These parameters were further extended to amino acids according to bead type. The structural and elastic properties of bilayer membranes, free energy profiles for a lipid flip-flop and amino acid analogues translocating across the membrane, and membrane pore formation induced by antimicrobial peptides obtained from this solvent-free DPD force field considerably agreed with the explicit-solvent DPD results. Importantly, the efficiency of this method is guaranteed to accelerate the assembly of vesicles composed of several thousand lipids by up to 50-fold, rendering the experimental liposome dynamics as well as membrane-peptide interactions feasible at accessible computational expense.
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Affiliation(s)
- Mingwei Wan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
- * E-mail:
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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Lu T, Guo H. Phase Behavior of Lipid Bilayers: A Dissipative Particle Dynamics Simulation Study. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Teng Lu
- Beijing National Laboratory for Molecular Sciences; Joint Laboratory of Polymer Sciences and Materials; State Key Laboratory of Polymer Physics and Chemistry; Institute of Chemistry, Chinese Academy of Sciences; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences; Joint Laboratory of Polymer Sciences and Materials; State Key Laboratory of Polymer Physics and Chemistry; Institute of Chemistry, Chinese Academy of Sciences; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
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