1
|
Burrows SA, Shon JW, Peychev B, Slavchov RI, Smoukov SK. Phase transitions of fluorotelomer alcohols at the water|alkane interface studied via molecular dynamics simulation. SOFT MATTER 2024; 20:2243-2257. [PMID: 38351894 DOI: 10.1039/d3sm01444d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Fluorosurfactants are long-lasting environmental pollutants that accumulate at interfaces ranging from aerosol droplet surfaces to cell membranes. Modeling of adsorption-based removal technologies for fluorosurfactants requires accurate simulation methods which can predict their adsorption isotherm and monolayer structure. Fluorotelomer alcohols with one or two methylene groups adjacent to the alcohol (7 : 1 FTOH and 6 : 2 FTOH, respectively) are investigated using the OPLS-AA force field at the water|hexane interface, varying the interfacial area per surfactant. The acquired interfacial pressure isotherms and monolayer phase behavior are compared with previous experimental results. The results are consistent with the experimental data inasmuch as, at realistic adsorption densities, only 7 : 1 FTOH shows a phase transition between liquid-expanded (LE) and 2D crystalline phases. Structures of the LE and crystalline phases are in good agreement with the sticky disc and Langmuir defective crystal models, respectively, used previously to interpret experimental data. Interfacial pressure of the LE phase agrees well with experiment, and sticky disc interaction parameters indicate no 2D LE-gas transition is present for either molecule. Conformation analysis reveals 7 : 1 FTOH favors conformers where the OH dipole is perpendicular to the molecular backbone, such that the crystalline phase is stabilized when these dipoles align.
Collapse
Affiliation(s)
- Stephen A Burrows
- Centre for Sustainable Engineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Jang Won Shon
- Centre for Sustainable Engineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Boyan Peychev
- Centre for Sustainable Engineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Radomir I Slavchov
- Centre for Sustainable Engineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Stoyan K Smoukov
- Centre for Sustainable Engineering, School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| |
Collapse
|
2
|
Karal MAS, Billah MM, Ahmed M, Ahamed MK. A review on the measurement of the bending rigidity of lipid membranes. SOFT MATTER 2023; 19:8285-8304. [PMID: 37873600 DOI: 10.1039/d3sm00882g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
This review provides an overview of the latest developments in both experimental and simulation techniques used to assess the bending rigidity of lipid membranes. It places special emphasis on experimental methods that utilize model vesicles to manipulate lipid compositions and other experimental parameters to determine the bending rigidity of the membrane. It also describes two commonly used simulation methods for estimating bending rigidity. The impact of various factors on membrane bending rigidity is summarized, including cholesterol, lipids, salt concentration, surface charge, membrane phase state, peptides, proteins, and polyethylene glycol. These factors are shown to influence the bending rigidity, contributing to a better understanding of the biophysical properties of membranes and their role in biological processes. Furthermore, the review discusses future directions and potential advancements in this research field, highlighting areas where further investigation is required.
Collapse
Affiliation(s)
- Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh.
| | - Md Masum Billah
- Department of Physics, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Marzuk Ahmed
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Md Kabir Ahamed
- Radiation, Transport and Waste Safety Division, Bangladesh Atomic Energy Regulatory Authority, Agargaon, Dhaka 1207, Bangladesh
| |
Collapse
|
3
|
Kwon S, Pantelopulos GA, Straub JE. Efficient calculation of the free energy for protein partitioning using restraining potentials. Biophys J 2023; 122:1914-1925. [PMID: 35962549 PMCID: PMC10257010 DOI: 10.1016/j.bpj.2022.07.031] [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: 05/31/2022] [Revised: 07/14/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
An approach for the efficient simulation of phase-separated lipid bilayers, for use in the calculation of equilibrium free energies of partitioning between lipid domains, is proposed. The methodology exploits restraint potentials and rectangular aspect ratios that enforce lipid phase separation, allowing for the simulation of smaller systems that approximately reproduce bulk behavior. The utility of this approach is demonstrated through the calculation of potentials of mean force for the translation of a transmembrane protein between lipid domains. The impact of the imposed restraints on lipid tail ordering and lipid packing are explored, providing insight into how restraints can best be employed to compute accurate free-energy surfaces. This approach should be useful in the accurate calculation of equilibrium partition coefficients for transmembrane protein partitioning in heterogeneous membranes, providing insight into the thermodynamic driving forces that control this fundamental biophysical phenomenon.
Collapse
Affiliation(s)
- Seulki Kwon
- Department of Chemistry, Boston University, Boston, Massachusetts
| | - George A Pantelopulos
- Department of Chemistry, Boston University, Boston, Massachusetts; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts.
| |
Collapse
|
4
|
Scheidegger L, Stricker L, Beltramo PJ, Vermant J. Domain Size Regulation in Phospholipid Model Membranes Using Oil Molecules and Hybrid Lipids. J Phys Chem B 2022; 126:5842-5854. [PMID: 35895895 PMCID: PMC9377339 DOI: 10.1021/acs.jpcb.2c02862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of domains in multicomponent lipid mixtures has been suggested to play a role in moderating signal transduction in cells. Understanding how domain size may be regulated by both hybrid lipid molecules and impurities is important for understanding real biological processes; at the same time, developing model systems where domain size can be regulated is crucial to enable systematic studies of domain formation kinetics and thermodynamics. Here, we perform a model study of the effects of oil molecules, which swell the bilayer, and line-active hybrid phospholipids using a thermally induced liquid-solid phase separation in planar, free-standing lipid bilayers consisting of DOPC and DPPC (1,2-dioleoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, respectively). The experiments show that the kinetics of domain growth are significantly affected by the type and molecular structure of the oil (squalene, hexadecane, or decane), with the main contributing factors being the degree of swelling of the bilayer and the changes in line tension induced by the different oils, with smaller domains resulting from systems with smaller values of the line tension. POPC (1-palmitoyl-sn-2-oleoyl-glycero-3-phosphocholine), on the other hand, acts as a line-active hybrid lipid, reducing the domain size when added in small amounts and slowing down domain coarsening. Finally, we show that despite the regulation of domain size by both methods, the phase transition temperature is influenced by the presence of oil molecules but not significantly by the presence of hybrid lipids. Overall, our results show how to regulate domain size in binary membrane model systems, over a wide range of length scales, by incorporating oil molecules and hybrid lipids.
Collapse
Affiliation(s)
- Laura Scheidegger
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Laura Stricker
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Peter J Beltramo
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jan Vermant
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| |
Collapse
|
5
|
Fábián B, Thallmair S, Hummer G. Small ionic radii limit time step in Martini 3 molecular dynamics simulations. J Chem Phys 2022; 157:034101. [DOI: 10.1063/5.0095523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Among other improvements, the Martini~3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the representation of Na+ and Cl- ions as ``tiny' (TQ5) beads limits the accessible time step to 25~fs. By contrast, with Martini~2, time steps of 30-40~fs were possible for lipid bilayer systems without proteins. This limitation is relevant for systems that require long equilibration times. We derive a quantitative kinetic model of time-integration instabilities in molecular dynamics as a function of time step, ion concentration and mass, system size, and simulation time. We demonstrate that ion-water interactions are the main source of instability at physiological conditions, followed closely by ion-ion interactions. We show that increasing the ionic masses makes it possible to use time steps up to 40~fs with minimal impact on static equilibrium properties and on dynamical quantities such as lipid and ion diffusion coefficients. Increasing the size of the bead representing the ions (and thus changing their hydration) also permits longer time steps. For a soluble protein, we find that increasing the mass of tiny beads also on the protein permits simulations with 30-fs time step. The use of larger time steps in Martini~3 results in a more efficient exploration of configuration space. The kinetic model of MD simulation crashes can be used to determine the maximum allowed time step upfront for an efficient use of resources and whenever sampling efficiency is critical.
Collapse
Affiliation(s)
- Balázs Fábián
- Max Planck Institute of BiophysicsDepartment of Theoretical Biophysics, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Germany
| |
Collapse
|
6
|
Lee H. Vitamin E acetate as linactant in the pathophysiology of EVALI. Med Hypotheses 2020; 144:110182. [PMID: 33254504 PMCID: PMC7422838 DOI: 10.1016/j.mehy.2020.110182] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/25/2020] [Accepted: 08/11/2020] [Indexed: 11/11/2022]
Abstract
The recent identification of Vitamin E acetate as one of the causal agents for the e-cigarette, or vaping, product use associated lung injury (EVALI) is a major milestone. In membrane biophysics, Vitamin E is a linactant and a potent modulator of lateral phase separation that effectively reduces the line tension at the two-dimensional phase boundaries and thereby exponentially increases the surface viscosity of the pulmonary surfactant. Disrupted dynamics of respiratory compression-expansion cycling may result in an extensive hypoxemia, leading to an acute respiratory distress entailing the formation of intraalveolar lipid-laden macrophages. Supplementation of pulmonary surfactants which retain moderate level of cholesterol and controlled hypothermia for patients are recommended when the hypothesis that the line-active property of the vitamin derivative drives the pathogenesis of EVALI holds.
Collapse
Affiliation(s)
- Hanjun Lee
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| |
Collapse
|
7
|
Zheng X, Gallot G. Dynamics of Cell Membrane Permeabilization by Saponins Using Terahertz Attenuated Total Reflection. Biophys J 2020; 119:749-755. [PMID: 32735777 DOI: 10.1016/j.bpj.2020.05.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 11/30/2022] Open
Abstract
Understanding the relevant parameters of the formation of pores during permeabilization is very challenging for medical applications. Several components are involved: the arrival of the permeabilizing molecules to the membrane, the efficiency of formation of the pores and their specific dynamics, and the flux of molecules through the plasma membrane. Using attenuated total reflection in the terahertz domain, we studied the dynamics of Madine-Darby canine kidney cells after permeabilization by saponin molecules. We developed an analytical model taking into account saponin molecule diffusion, cell geometry, cytosol molecule diffusion, and pore dynamics. We also studied the effect of possible pore overlapping on the cell membrane, introducing a dimensionless quantity that is the ratio between overlapping and diffusive effects. Pores are found to be static within 1 h after their creation, hinting that the diffusion of the saponin molecules to the membrane is the limiting factor in our experiments.
Collapse
Affiliation(s)
- Xiujun Zheng
- LOB, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Guilhem Gallot
- LOB, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France.
| |
Collapse
|
8
|
Iyer SS, Negi A, Srivastava A. Interpretation of Phase Boundary Fluctuation Spectra in Biological Membranes with Nanoscale Organization. J Chem Theory Comput 2020; 16:2736-2750. [DOI: 10.1021/acs.jctc.9b00929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sahithya S. Iyer
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Archit Negi
- Department of Physics, Indian Institute of Technology, Bombay, Mumbai 400076, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
9
|
Noh SY, Nash A, Notman R. The aggregation of striped nanoparticles in mixed phospholipid bilayers. NANOSCALE 2020; 12:4868-4881. [PMID: 31916561 DOI: 10.1039/c9nr07106g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The unique and adjustable properties of nanoparticles present enormous opportunities for their use as targeted drug delivery vectors. For example, nanoparticles functionalized with key surface ligands have been shown to pass through phospholipid bilayers without causing localised disruption. However, the further effects nanoparticles have on multi-component phospholipid bilayers remain unclear. We use coarse-grained computational models to investigate the structural properties of mixed phospholipid bilayers in the presence of ligand-functionalized nanoparticles. Model bilayers are composed of DPPC, DUPC, DFPC and cholesterol, and the nanoparticles are striped with a hydrophobic-ligand band and charged-ligand spherical caps. Our results show that nanoparticles aggregate near unsaturated phospholipid regions, phospholipid bilayer phase-separation is promoted in the presence of nanoparticles, and the heterogeneous components of a phospholipid bilayer play a significant role in the lateral organization of nanoparticles. This study highlights the need for considering the complexity of realistic phospholipid bilayers when optimising ligand functionalized nanoparticles for efficient drug delivery vectors.
Collapse
Affiliation(s)
- Sang Young Noh
- Department of Chemistry, University of Warwick, Coventry, UK.
| | - Anthony Nash
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Coventry, UK.
| |
Collapse
|
10
|
Träger J, Widder K, Kerth A, Harauz G, Hinderberger D. Effect of Cholesterol and Myelin Basic Protein (MBP) Content on Lipid Monolayers Mimicking the Cytoplasmic Membrane of Myelin. Cells 2020; 9:cells9030529. [PMID: 32106542 PMCID: PMC7140459 DOI: 10.3390/cells9030529] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/16/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Myelin basic protein (MBP) is located in the insulating covers of nerve cells in the brain and spinal cord. By interacting with lipid membranes, it is responsible for compaction of the myelin sheath in the central nervous system, which is weakened in demyelinating diseases. The lipid composition of the myelin leaflet has a high impact on the interaction between the membrane and MBP. Cholesterol is present in the cytoplasmic leaflet with a rather high amount of 44% (mol%). In this study, the focus is on the effect of cholesterol, mainly by varying its content, on the interaction of MBP with a lipid monolayer. Therefore, Langmuir lipid monolayers mimicking the cytoplasmic membrane of myelin and monolayers with variations of cholesterol content between 0% and 100% were measured at the air/water interface with additional imaging by fluorescence microscopy. All experiments were performed with and without bovine MBP to study the dependence of the interaction of the protein with the monolayers on the cholesterol content. The native amount of 44% cholesterol in the monolayer combines optima in the order of the monolayer (presumably correlating to compaction and thermodynamic stability) and protein interaction and shows unique features in comparison to lower or higher cholesterol contents.
Collapse
Affiliation(s)
- Jennica Träger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (J.T.); (K.W.); (A.K.)
- Interdisciplinary Research Center HALOmem at the Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Katharina Widder
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (J.T.); (K.W.); (A.K.)
- Interdisciplinary Research Center HALOmem at the Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Andreas Kerth
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (J.T.); (K.W.); (A.K.)
- Interdisciplinary Research Center HALOmem at the Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - George Harauz
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Dariush Hinderberger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (J.T.); (K.W.); (A.K.)
- Interdisciplinary Research Center HALOmem at the Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
- Correspondence: ; Tel.: +49-345-55-25230
| |
Collapse
|
11
|
Iyer SS, Tripathy M, Srivastava A. Fluid Phase Coexistence in Biological Membrane: Insights from Local Nonaffine Deformation of Lipids. Biophys J 2019; 115:117-128. [PMID: 29972803 DOI: 10.1016/j.bpj.2018.05.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 01/09/2023] Open
Abstract
Lateral heterogeneities in biomembranes play a crucial role in various physiological functions of the cell. Such heterogeneities lead to demixing of lipid constituents and formation of distinct liquid domains in the membrane. We study lateral heterogeneities in terms of topological rearrangements of lipids to identify the liquid-liquid phase coexistence in model membranes. Using ideas from the physics of amorphous systems and glasses, we calculate the degree of nonaffine deformation associated with individual lipids to characterize the liquid-ordered (Lo) and liquid-disordered (Ld) regions in model lipid bilayers. We explore the usage of this method on all-atom and coarse-grained lipid bilayer trajectories. This method is helpful in defining the instantaneous Lo-Ld domain boundaries in complex multicomponent bilayer systems. The characterization is also used to highlight the effect of line-active molecules on the phase boundaries and domain mixing. Overall, we propose a framework to explore the molecular origin of spatial and dynamical heterogeneity in biomembrane systems, which can be exploited not only in computer simulations but also in experiments.
Collapse
Affiliation(s)
- Sahithya S Iyer
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India
| | - Madhusmita Tripathy
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka, India.
| |
Collapse
|
12
|
Bandara A, Panahi A, Pantelopulos GA, Nagai T, Straub JE. Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture. J Chem Phys 2019; 150:204702. [PMID: 31153187 DOI: 10.1063/1.5091450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The separation of lipid mixtures into thermodynamically stable phase-separated domains is dependent on lipid composition, temperature, and system size. Using molecular dynamics simulations, the line tension between thermodynamically stable lipid domains formed from ternary mixtures of di-C16:0 PC:di-C18:2 PC:cholesterol at 40:40:20 mol. % ratio was investigated via two theoretical approaches. The line tension was found to be 3.1 ± 0.2 pN by capillary wave theory and 4.7 ± 3.7 pN by pressure tensor anisotropy approaches for coarse-grained models based on the Martini force field. Using an all-atom model of the lipid membrane based on the CHARMM36 force field, the line tension was found to be 3.6 ± 0.9 pN using capillary wave theory and 1.8 ± 2.2 pN using pressure anisotropy approaches. The discrepancy between estimates of the line tension based on capillary wave theory and pressure tensor anisotropy methods is discussed. Inclusion of protein in Martini membrane lipid mixtures was found to reduce the line tension by 25%-35% as calculated by the capillary wave theory approach. To further understand and predict the behavior of proteins in phase-separated membranes, we have formulated an analytical Flory-Huggins model and parameterized it against the simulation results. Taken together these results suggest a general role for proteins in reducing the thermodynamic cost associated with domain formation in lipid mixtures and quantifies the thermodynamic driving force promoting the association of proteins to domain interfaces.
Collapse
Affiliation(s)
- Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Afra Panahi
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - George A Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| |
Collapse
|
13
|
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
Collapse
Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
14
|
Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
Collapse
Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
| |
Collapse
|
15
|
Effects of oxidation on the physicochemical properties of polyunsaturated lipid membranes. J Colloid Interface Sci 2019; 538:404-419. [DOI: 10.1016/j.jcis.2018.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/29/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022]
|
16
|
Lew TTS, Wong MH, Kwak SY, Sinclair R, Koman VB, Strano MS. Rational Design Principles for the Transport and Subcellular Distribution of Nanomaterials into Plant Protoplasts. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802086. [PMID: 30191658 DOI: 10.1002/smll.201802086] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/09/2018] [Indexed: 05/24/2023]
Abstract
The ability to control the subcellular localization of nanoparticles within living plants offers unique advantages for targeted biomolecule delivery and enables important applications in plant bioengineering. However, the mechanism of nanoparticle transport past plant biological membranes is poorly understood. Here, a mechanistic study of nanoparticle cellular uptake into plant protoplasts is presented. An experimentally validated mathematical model of lipid exchange envelope penetration mechanism for protoplasts, which predicts that the subcellular distribution of nanoparticles in plant cells is dictated by the particle size and the magnitude of the zeta potential, is advanced. The mechanism is completely generic, describing nanoparticles ranging from quantum dots, gold and silica nanoparticles, nanoceria, and single-walled carbon nanotubes (SWNTs). In addition, the use of imaging flow cytometry to investigate the influence of protoplasts' morphological characteristics on nanoparticle uptake efficiency is demonstrated. Using DNA-wrapped SWNTs as model nanoparticles, it is found that glycerolipids, the predominant lipids in chloroplast membranes, exhibit stronger lipid-nanoparticle interaction than phospholipids, the major constituent in protoplast membrane. This work can guide the rational design of nanoparticles for targeted delivery into specific compartments within plant cells without the use of chemical or mechanical aid, potentially enabling various plant engineering applications.
Collapse
Affiliation(s)
- Tedrick Thomas Salim Lew
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Min Hao Wong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Seon-Yeong Kwak
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Rosalie Sinclair
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| |
Collapse
|
17
|
Petty HR. Frontiers of Complex Disease Mechanisms: Membrane Surface Tension May Link Genotype to Phenotype in Glaucoma. Front Cell Dev Biol 2018; 6:32. [PMID: 29682502 PMCID: PMC5897435 DOI: 10.3389/fcell.2018.00032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/13/2018] [Indexed: 12/19/2022] Open
Abstract
Although many monogenic diseases are understood based upon structural changes of gene products, less progress has been made concerning polygenic disease mechanisms. This article presents a new interdisciplinary approach to understand complex diseases, especially their genetic polymorphisms. I focus upon primary open angle glaucoma (POAG). Although elevated intraocular pressure (IOP) and oxidative stress are glaucoma hallmarks, the linkages between these factors and cell death are obscure. Reactive oxygen species (ROS) promote the formation of oxidatively truncated phosphoglycerides (OTP), free fatty acids, lysophosphoglycerides, oxysterols, and other chemical species that promote membrane disruption and decrease membrane surface tension. Several POAG-linked gene polymorphisms identify proteins that manage damaged lipids and/or influence membrane surface tension. POAG-related genes expected to participate in these processes include: ELOVL5, ABCA1, APOE4, GST, CYP46A1, MYOC, and CAV. POAG-related gene products are expected to influence membrane surface tension, strength, and repair. I propose that heightened IOP overcomes retinal ganglion cell (RGC) membrane compressive strength, weakened by damaged lipid accumulation, to form pores. The ensuing structural failure promotes apoptosis and blindness. The linkage between glaucoma genotype and phenotype is mediated by physical events. Force balancing between the IOP and compressive strength regulates pore nucleation; force balancing between pore line tension and membrane surface tension regulates pore growth. Similar events may contribute to traumatic brain injury, Alzheimer's disease, and macular degeneration.
Collapse
Affiliation(s)
- Howard R Petty
- Department of Ophthalmology and Visual Sciences, The University of Michigan Medical School, Ann Arbor, MI, United States
| |
Collapse
|
18
|
Fanani ML, Wilke N. Regulation of phase boundaries and phase-segregated patterns in model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1972-1984. [PMID: 29505769 DOI: 10.1016/j.bbamem.2018.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 12/13/2022]
Abstract
Demixing of components has long been described in model membranes. It is a consequence of non-ideal lateral interactions between membrane components, and it causes the presence of segregated phases, forming patches (domains) of different properties, thus introducing heterogeneity into the membrane. In the present review we first describe the processes through which domains are generated, how they grow, and why they are rounded, striped or fractal-like, as well as why they get distributed forming defined patterns. Next, we focus on the effect of an additive on a lipid mixture, which usually induces shifts in demixing points, thus stabilizing or destabilizing the phase-segregated state. Results found for different model membranes are summarized, detailing the ways in which phase segregation and the generated patterns may be modulated. We focus on which are, from our viewpoint, the most relevant regulating factors affecting the surface texture observed in model membranes. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
Collapse
Affiliation(s)
- María Laura Fanani
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica "Ranwel Caputto", Córdoba, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Natalia Wilke
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica "Ranwel Caputto", Córdoba, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina.
| |
Collapse
|
19
|
Doktorova M, Harries D, Khelashvili G. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys Chem Chem Phys 2018. [PMID: 28627570 DOI: 10.1039/c7cp01921a] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin. By comparing the material properties calculated with the RSF method to those obtained from experimental data and from other computational methodologies, we rigorously demonstrate the validity of our approach and show its robustness. This should allow for future applications of even more complex lipidic assemblies, whose material properties are not tractable by other computational techniques. In addition, we discuss the relationship between different definitions of the tilt modulus appearing in current literature to address some important unresolved discrepancies in the field.
Collapse
Affiliation(s)
- M Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | | | | |
Collapse
|