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Li L, Gao J, Milewski Ł, Hu J, Różycki B. Lattice-based mesoscale simulations and mean-field theory of cell membrane adhesion. Methods Enzymol 2024; 701:425-455. [PMID: 39025578 DOI: 10.1016/bs.mie.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Adhesion of cell membranes involves multi-scale phenomena, ranging from specific molecular binding at Angstrom scale all the way up to membrane deformations and phase separation at micrometer scale. Consequently, theory and simulations of cell membrane adhesion require multi-scale modeling and suitable approximations that capture the essential physics of these phenomena. Here, we present a mesoscale model for membrane adhesion which we have employed in a series of our recent studies. This model quantifies, in particular, how nanoscale lipid clusters physically affect and respond to the intercellular receptor-ligand binding that mediates membrane adhesion. The goal of this Chapter is to present all details and subtleties of the mean-field theory and Monte Carlo simulations of this mesoscale model, which can be used to further explore physical phenomena related to cell membrane adhesion.
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Affiliation(s)
- Long Li
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China; State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jie Gao
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Łukasz Milewski
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China.
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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Li L, Gui C, Hu J, Różycki B. Membrane-Mediated Cooperative Interactions of CD47 and SIRP α. MEMBRANES 2023; 13:871. [PMID: 37999357 PMCID: PMC10673186 DOI: 10.3390/membranes13110871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
The specific binding of the ubiquitous 'marker of self' protein CD47 to the SIRPα protein anchored in the macrophage plasma membrane results in the inhibition of the engulfment of 'self' cells by macrophages and thus constitutes a key checkpoint of our innate immune system. Consequently, the CD47-SIRPα protein complex has been recognized as a potential therapeutic target in cancer and inflammation. Here, we introduce a lattice-based mesoscale model for the biomimetic system studied recently in fluorescence microscopy experiments where GFP-tagged CD47 proteins on giant plasma membrane vesicles bind to SIRPα proteins immobilized on a surface. Computer simulations of the lattice-based mesoscale model allow us to study the biomimetic system on multiple length scales, ranging from single nanometers to several micrometers and simultaneously keep track of single CD47-SIRPα binding and unbinding events. Our simulations not only reproduce data from the fluorescence microscopy experiments but also are consistent with results of several other experiments, which validates our numerical approach. In addition, our simulations yield quantitative predictions on the magnitude and range of effective, membrane-mediated attraction between CD47-SIRPα complexes. Such detailed information on CD47-SIRPα interactions cannot be obtained currently from experiments alone. Our simulation results thus extend the present understanding of cooperative effects in CD47-SIRPα interactions and may have an influence on the advancement of new cancer treatments.
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Affiliation(s)
- Long Li
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China; (L.L.); (C.G.); (J.H.)
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Chen Gui
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China; (L.L.); (C.G.); (J.H.)
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China; (L.L.); (C.G.); (J.H.)
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland
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Mioduszewski Ł, Różycki B, Cieplak M. Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins. J Chem Theory Comput 2020; 16:4726-4733. [PMID: 32436706 PMCID: PMC7588027 DOI: 10.1021/acs.jctc.0c00338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a new coarse-grained Cα-based protein model with a nonradial multibody pseudo-improper-dihedral potential that is transferable, time-independent, and suitable for molecular dynamics. It captures the nature of backbone and side-chain interactions between amino acid residues by adapting a simple improper dihedral term for a one-bead-per-residue model. It is parameterized for intrinsically disordered proteins and applicable to simulations of such proteins and their assemblies on millisecond time scales.
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Affiliation(s)
- Łukasz Mioduszewski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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Zhao ZL, Liu ZY, Du J, Xu GK, Feng XQ. A Dynamic Biochemomechanical Model of Geometry-Confined Cell Spreading. Biophys J 2017; 112:2377-2386. [PMID: 28591610 DOI: 10.1016/j.bpj.2017.04.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/11/2017] [Accepted: 04/13/2017] [Indexed: 01/09/2023] Open
Abstract
Cell spreading is involved in many physiological and pathological processes. The spreading behavior of a cell significantly depends on its microenvironment, but the biochemomechanical mechanisms of geometry-confined cell spreading remain unclear. A dynamic model is here established to investigate the spreading of cells confined in a finite region with different geometries, e.g., rectangle, ellipse, triangle, and L-shape. This model incorporates both biophysical and biochemical mechanisms, including actin polymerization, integrin-mediated binding, plasma viscoelasticity, and the elasticity of membranes and microtubules. We simulate the dynamic configurational evolution of a cell under different geometric microenvironments, including the angular distribution of microtubule forces and the deformation of the nucleus. The results indicate that the positioning of the cell-division plane is affected by its boundary confinement: a cell divides in a plane perpendicular to its minimal principal axis of inertia of area. In addition, the effects of such physical factors as the adhesive bond density, membrane tension, and microtubule number are examined on the cell spreading dynamics. The theoretical predictions show a good agreement with relevant experimental results. This work sheds light on the geometry-confined spreading dynamics of cells and holds potential applications in regulating cell division and designing cell-based sensors.
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Affiliation(s)
- Zi-Long Zhao
- AML, Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, Tsinghua University, Beijing, China; Center for Nano and Micro Mechanics, Tsinghua University, Beijing, China
| | - Zong-Yuan Liu
- AML, Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, Tsinghua University, Beijing, China; Center for Nano and Micro Mechanics, Tsinghua University, Beijing, China
| | - Jing Du
- AML, Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, Tsinghua University, Beijing, China
| | - Guang-Kui Xu
- International Center for Applied Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi'an Jiaotong University, Xi'an, China
| | - Xi-Qiao Feng
- AML, Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, Tsinghua University, Beijing, China; Center for Nano and Micro Mechanics, Tsinghua University, Beijing, China.
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Mallory SA, Valeriani C, Cacciuto A. Anomalous dynamics of an elastic membrane in an active fluid. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012314. [PMID: 26274169 DOI: 10.1103/physreve.92.012314] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 06/04/2023]
Abstract
Using numerical simulations, we characterized the behavior of an elastic membrane immersed in an active fluid. Our findings reveal a nontrivial folding and re-expansion of the membrane that is controlled by the interplay of its resistance to bending and the self-propulsion strength of the active components in solution. We show how flexible membranes tend to collapse into multifolded states, whereas stiff membranes fluctuate between an extended configuration and a singly folded state. This study provides a simple example of how to exploit the random motion of active particles to perform mechanical work at the microscale.
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Affiliation(s)
- S A Mallory
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - C Valeriani
- Departamento de Fisica Aplicada I, Facultad de Ciencias Fisica, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - A Cacciuto
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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Nucleation and growth of integrin adhesions. Biophys J 2009; 96:3555-72. [PMID: 19413961 DOI: 10.1016/j.bpj.2009.02.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 01/28/2009] [Accepted: 02/02/2009] [Indexed: 01/09/2023] Open
Abstract
We present a model that provides a mechanistic understanding of the processes that govern the formation of the earliest integrin adhesions ex novo from an approximately planar plasma membrane. Using an analytic analysis of the free energy of a dynamically deformable membrane containing freely diffusing receptors molecules and long repeller molecules that inhibit integrins from binding with ligands on the extracellular matrix, we predict that a coalescence of polymerizing actin filaments can deform the membrane toward the extracellular matrix and facilitate integrin binding. Monte Carlo simulations of this system show that thermally induced membrane fluctuations can either zip-up and increase the radius of a nucleated adhesion or unzip and shrink an adhesion, but the fluctuations cannot bend the ventral membrane to nucleate an adhesion. To distinguish this integrin adhesion from more mature adhesions, we refer to this early adhesion as a nouveau adhesion.
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El Alaoui Faris MD, Lacoste D, Pécréaux J, Joanny JF, Prost J, Bassereau P. Membrane tension lowering induced by protein activity. PHYSICAL REVIEW LETTERS 2009; 102:038102. [PMID: 19257398 DOI: 10.1103/physrevlett.102.038102] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Indexed: 05/27/2023]
Abstract
Using videomicroscopy we present measurements of the fluctuation spectrum of giant vesicles containing bacteriorhodopsin pumps. When the pumps are activated, we observe a significant increase of the fluctuations in the low wave vector region, which we interpret as due to a lowering of the effective tension of the membrane.
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Affiliation(s)
- M D El Alaoui Faris
- Institut Curie, Centre de Recherche; CNRS, UMR 168; Université Pierre et Marie Curie, Paris, F-75248 France
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Popova H, Milchev A. Adsorption of self-avoiding tethered membranes: A Monte Carlo simulation study. J Chem Phys 2008; 129:215103. [DOI: 10.1063/1.3028055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Auth T, Safran SA, Gov NS. Fluctuations of coupled fluid and solid membranes with application to red blood cells. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:051910. [PMID: 18233690 DOI: 10.1103/physreve.76.051910] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 08/01/2007] [Indexed: 05/21/2023]
Abstract
The fluctuation spectra and the intermembrane interaction of two membranes at a fixed average distance are investigated. Each membrane can either be a fluid or a solid membrane, and in isolation, its fluctuations are described by a bare or a wave-vector-dependent bending modulus, respectively. The membranes interact via their excluded-volume interaction; the average distance is maintained by an external, homogeneous pressure. For strong coupling, the fluctuations can be described by a single, effective membrane that combines the elastic properties. For weak coupling, the fluctuations of the individual, noninteracting membranes are recovered. The case of a composite membrane consisting of one fluid and one solid membrane can serve as a microscopic model for the plasma membrane and cytoskeleton of the red blood cell. We find that, despite the complex microstructure of bilayers and cytoskeletons in a real cell, the fluctuations with wavelengths lambda greater, similar 400 nm are well described by the fluctuations of a single, polymerized membrane (provided that there are no inhomogeneities of the microstructure). The model is applied to the fluctuation data of discocytes ("normal" red blood cells), a stomatocyte, and an echinocyte. The elastic parameters of the membrane and an effective temperature that quantifies active, metabolically driven fluctuations are extracted from the experiments.
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Affiliation(s)
- Thorsten Auth
- Weizmann Institute of Science, Department of Materials and Interfaces, P.O. Box 26, Rehovot 76100, Israel
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Abstract
Formation of protrusions and protein segregation on the membrane is of a great importance for the functioning of the living cell. This is most evident in recent experiments that show the effects of the mechanical properties of the surrounding substrate on cell morphology. We propose a mechanism for the formation of membrane protrusions and protein phase separation, which may lay behind this effect. In our model, the fluid cell membrane has a mobile but constant population of proteins with a convex spontaneous curvature. Our basic assumption is that these membrane proteins represent small adhesion complexes, and also include proteins that activate actin polymerization. Such a continuum model couples the membrane and protein dynamics, including cell-substrate adhesion and protrusive actin force. Linear stability analysis shows that sufficiently strong adhesion energy and actin polymerization force can bring about phase separation of the membrane protein and the appearance of protrusions. Specifically, this occurs when the spontaneous curvature and aggregation potential alone (passive system) do not cause phase separation. Finite-size patterns may appear in the regime where the spontaneous curvature energy is a strong factor. Different instability characteristics are calculated for the various regimes, and are compared to various types of observed protrusions and phase separations, both in living cells and in artificial model systems. A number of testable predictions are proposed.
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Affiliation(s)
- Alex Veksler
- Department of Chemical Physics, The Weizmann Institute of Science, Rehovot, Israel.
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Rózycki B, Weikl TR, Lipowsky R. Stochastic resonance for adhesion of membranes with active stickers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2007; 22:97-106. [PMID: 17318287 DOI: 10.1140/epje/i2006-10075-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Indexed: 05/14/2023]
Abstract
The behavior of two membranes that interact by active adhesion molecules or stickers is studied theoretically using mean-field theory and Monte Carlo simulations. The stickers are anchored in one of the membranes and undergo conformational transitions between on and off states. In their on states, the stickers can bind to ligands that are anchored in the other membrane. The transitions between the on and off states arise from the coupling of the stickers to some active, energy-releasing process, which keeps the system out of equilibrium. As one varies the transition rates of this active process, the membrane separation undergoes a stochastic resonance: this separation is maximal at intermediate rates of the sticker transitions and considerably smaller both at high and at low transition rates. This implies that the effective, fluctuation-induced repulsion between the membranes contains a rate-dependent contribution that arises from the switching of the active stickers.
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Affiliation(s)
- B Rózycki
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany.
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