1
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Hossein A, Beaven AH, Sapp K, Sodt AJ. Softening in Two-Component Lipid Mixtures by Spontaneous Curvature Variance. J Phys Chem B 2024; 128:6317-6326. [PMID: 38889363 DOI: 10.1021/acs.jpcb.3c08117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The bending modulus of a lipid bilayer quantifies its mechanical resistance to curvature. It is typically understood in terms of thickness; e.g., thicker bilayers are usually stiffer. Here, we describe an additional and powerful molecular determinant of stiffness─the variance in the distribution of curvature sensitivity of lipids and lipid conformations. Zwitterionic choline and ethanolamine headgroups of glycerophospholipids dynamically explore inter- and intraspecies interactions, leading to transient clustering. We demonstrate that these clusters couple strongly to negative curvature, exciting undulatory membrane modes and reducing the apparent bending modulus. Three force fields (Martini 2, Martini 3, and all-atom CHARMM C36) each show the effect to a different extent, with the coarse-grained Martini models showing the most clustering and thus the most softening. The theory is a guide to understanding the stiffness of biological membranes with their complex composition, as well as how choices of force field parameterization are translated into mechanical stiffness.
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Affiliation(s)
- Amirali Hossein
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
| | - Andrew H Beaven
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, Bethesda, Maryland 20892, United States
| | - Kayla Sapp
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
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2
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Gudyka J, Ceja-Vega J, Krmic M, Porteus R, Lee S. The Role of Lipid Intrinsic Curvature in the Droplet Interface Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:11428-11435. [PMID: 38764431 PMCID: PMC11155247 DOI: 10.1021/acs.langmuir.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
Model bilayers are constructed from lipids having different intrinsic curvatures using the droplet interface bilayer (DIB) method, and their static physicochemical properties are determined. Geometrical and tensiometric measurements are used to derive the free energy of formation (ΔF) of a two-droplet DIB relative to a pair of isolated aqueous droplets, each decorated with a phospholipid monolayer. The lipid molecules employed have different headgroup sizes but identical hydrophobic tail structure, and each is characterized by an intrinsic curvature value (c0) that increases in absolute value with decreasing size of headgroup. Mixtures of lipids at different ratios were also investigated. The role of curvature stress on the values of ΔF of the respective lipid bilayers in these model membranes is discussed and is illuminated by the observation of a decrement in ΔF that scales as a near linear function of c02. Overall, the results reveal an association that should prove useful in studies of ion channels and other membrane proteins embedded in model droplet bilayer systems that will impact the understanding of protein function in cellular membranes composed of lipids of high and low curvature.
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Affiliation(s)
- Jamie Gudyka
- Department of Chemistry and
Biochemistry, Iona University, New Rochelle, New York 10801, United States
| | - Jasmin Ceja-Vega
- Department of Chemistry and
Biochemistry, Iona University, New Rochelle, New York 10801, United States
| | - Michael Krmic
- Department of Chemistry and
Biochemistry, Iona University, New Rochelle, New York 10801, United States
| | - Riley Porteus
- Department of Chemistry and
Biochemistry, Iona University, New Rochelle, New York 10801, United States
| | - Sunghee Lee
- Department of Chemistry and
Biochemistry, Iona University, New Rochelle, New York 10801, United States
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3
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Hossein A, Sapp K, Sodt A. Computing the influence of lipids and lipid complexes on membrane mechanics. Methods Enzymol 2024; 701:515-540. [PMID: 39025581 DOI: 10.1016/bs.mie.2024.04.002] [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
Methodology for extracting the spontaneous curvature, bending modulus, and neutral surface of a lipid bilayer is described. The "SPEX" method is a robust technique for computing the bilayer bending modulus while allowing for resolution of the spontaneous curvature of specific interacting lipids and complexes, and the dependence of spontaneous curvature on wavelength. The method is described referring to the publicly available MembraneAnalysis.jl software package.
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Affiliation(s)
- Amirali Hossein
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, Intramural Research Program, National Institutes of Health
| | - Kayla Sapp
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, Intramural Research Program, National Institutes of Health
| | - Alexander Sodt
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, Intramural Research Program, National Institutes of Health.
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4
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Ozturk TN, König M, Carpenter TS, Pedersen KB, Wassenaar TA, Ingólfsson HI, Marrink SJ. Building complex membranes with Martini 3. Methods Enzymol 2024; 701:237-285. [PMID: 39025573 DOI: 10.1016/bs.mie.2024.03.010] [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
The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.
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Affiliation(s)
- Tugba Nur Ozturk
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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5
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Shurer CR, Levental KR. Membranes get in shape: Biophysics of curving bilayers. Biophys J 2024; 123:273-276. [PMID: 38219739 PMCID: PMC10870166 DOI: 10.1016/j.bpj.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Membrane curvature is ubiquitous and essential in cell biology. Curved membranes have several distinct features, including specific protein and lipid sorting, distinct lipid ordering, and changes in transbilayer stress. Curvature also interplays with membrane tension to generate forces that change membrane shape. This research highlight summarizes recent contributions to this topic published in Biophysical Journal.
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Affiliation(s)
- Carolyn R Shurer
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia.
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6
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Dugić M, Brzobohatá H, Mojr V, Dolejšová T, Lišková P, Do Pham DD, Rejman D, Mikušová G, Fišer R. LEGO-lipophosphonoxins: length of hydrophobic module affects permeabilizing activity in target membranes of different phospholipid composition. RSC Adv 2024; 14:2745-2756. [PMID: 38234873 PMCID: PMC10792433 DOI: 10.1039/d3ra07251g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
In the past few decades, society has faced rapid development and spreading of antimicrobial resistance due to antibiotic misuse and overuse and the immense adaptability of bacteria. Difficulties in obtaining effective antimicrobial molecules from natural sources challenged scientists to develop synthetic molecules with antimicrobial effect. We developed modular molecules named LEGO-Lipophosphonoxins (LEGO-LPPO) capable of inducing cytoplasmic membrane perforation. In this structure-activity relationship study we focused on the role of the LEGO-LPPO hydrophobic module directing the molecule insertion into the cytoplasmic membrane. We selected three LEGO-LPPO molecules named C9, C8 and C7 differing in the length of their hydrophobic chain and consisting of an alkenyl group containing one double bond. The molecule with the long hydrophobic chain (C9) was shown to be the most effective with the lowest MIC and highest perforation rate both in vivo and in vitro. We observed high antimicrobial activity against both G+ and G- bacteria with significant differences in LEGO-LPPOs mechanism of action on these two cell types. We observed a highly cooperative mechanism of LEGO-LPPO action on G- bacteria as well as on liposomes resembling G- bacteria. LEGO-LPPO action on G- bacteria was significantly slower compared to G+ bacteria suggesting the role of the outer membrane in affecting the LEGO-LPPOs perforation rate. This notion was supported by the higher sensitivity of the E. coli strain with a compromised outer membrane. Finally, we noted that the composition of the cytoplasmic membrane affects the activity of LEGO-LPPOs since the presence of phosphatidylethanolamine increases their membrane disrupting activity.
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Affiliation(s)
- Milica Dugić
- Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 128 00 Prague 2 Czech Republic
| | - Hana Brzobohatá
- Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 128 00 Prague 2 Czech Republic
| | - Viktor Mojr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i. Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Tereza Dolejšová
- Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 128 00 Prague 2 Czech Republic
| | - Petra Lišková
- Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 128 00 Prague 2 Czech Republic
| | - Duy Dinh Do Pham
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i. Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i. Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Gabriela Mikušová
- Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 128 00 Prague 2 Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i. Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Radovan Fišer
- Department of Genetics and Microbiology, Faculty of Science, Charles University Viničná 5 128 00 Prague 2 Czech Republic
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7
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Gupta S, Soni J, Kumar A, Mandal T. Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures. J Chem Phys 2023; 159:165102. [PMID: 37873964 DOI: 10.1063/5.0167144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023] Open
Abstract
Structural and mechanical properties of membranes such as thickness, tail order, bending modulus and curvature energetics play crucial role in controlling various cellular functions that depend on the local lipid organization and membrane reshaping. While behavior of these biophysical properties are well understood in single component membranes, very little is known about how do they change in the mixed lipid membranes. Often various properties of the mixed lipid bilayers are assumed to change linearly with the mole fractions of the constituent lipids which, however, is true for "ideal" mixing only. In this study, using molecular dynamics simulations, we show that structural and mechanical properties of binary lipid mixture change nonlinearly with the lipid mole fractions, and the strength of the nonlinearity depends on two factors - spontaneous curvature difference and locally inhomogeneous interactions between the lipid components.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jatin Soni
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Awneesh Kumar
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
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8
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Fiorin G, Forrest LR, Faraldo-Gómez JD. Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening. PNAS NEXUS 2023; 2:pgad269. [PMID: 37637198 PMCID: PMC10456217 DOI: 10.1093/pnasnexus/pgad269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023]
Abstract
All lipid membranes have inherent morphological preferences and resist deformation. Yet adaptations in membrane shape can and do occur at multiple length scales. While this plasticity is crucial for cellular physiology, the factors controlling the morphological energetics of lipid bilayers and the dominant mechanisms of membrane remodeling remain to be fully understood. An ongoing debate regarding the universality of the stiffening effect of cholesterol underscores the challenges facing this field, both experimentally and theoretically, even for simple lipid mixtures. On the computational side, we have argued that enhanced-sampling all-atom molecular dynamics simulations are uniquely suited for the quantification of membrane conformational energetics, as they minimize a priori assumptions and permit analysis of bilayers in deformed states. To showcase this approach, we examine reported inconsistencies between alternative experimental measurements of bending moduli for cholesterol-enriched membranes. Specifically, we analyze lipid bilayers with different chain saturation and compute free-energy landscapes for curvature deformations distributed over areas from ∼5 to ∼60 nm2 . These enhanced simulations, totaling over 100 μs of sampling time, enable us to directly quantify both bending and tilt moduli and to dissect the contributing factors and molecular mechanisms of curvature generation at each length scale. Our results show that the effects of cholesterol on bending rigidity are lipid-specific and suggest that this specificity arises from differences in the torsional dynamics of the acyl chains. In summary, we demonstrate that quantitative relationships can now be established between lipid structure and bending energetics, paving the way for addressing open fundamental questions in cell membrane mechanics.
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Affiliation(s)
- Giacomo Fiorin
- National Institute for Neurological Disorders and Stroke, Bethesda, MD 20892, USA
- National Heart, Lung and Blood Institute, Bethesda, MD 20894, USA
| | - Lucy R Forrest
- National Institute for Neurological Disorders and Stroke, Bethesda, MD 20892, USA
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9
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Beaven AH, Sapp K, Sodt AJ. Simulated dynamic cholesterol redistribution favors membrane fusion pore constriction. Biophys J 2023; 122:2162-2175. [PMID: 36588341 PMCID: PMC10257089 DOI: 10.1016/j.bpj.2022.12.024] [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: 02/08/2022] [Revised: 06/17/2022] [Accepted: 12/16/2022] [Indexed: 01/01/2023] Open
Abstract
Endo- and exocytosis proceed through a highly strained membrane fusion pore topology regardless of the aiding protein machinery. The membrane's lipid components bias fusion pores toward expansion or closure, modifying the necessary work done by proteins. Cholesterol, a key component of plasma membranes, promotes both inverted lipid phases with concave leaflets (i.e., negative total curvature, which thins the leaflet) and flat bilayer phases with thick, ordered hydrophobic interiors. We demonstrate by theory and simulation that both leaflets of nascent catenoidal fusion pores have negative total curvature. Furthermore, the hydrophobic core of bilayers with strong negative Gaussian curvature is thinned. Therefore, it is an open question whether cholesterol will be enriched in these regions because of the negative total curvature or depleted because of the membrane thinning. Here, we compare all-atom molecular dynamics simulations (built using a procedure to create specific fusion pore geometries) and theory to understand the underlying reasons for lipid redistribution on fusion pores. Our all-atom molecular dynamics simulations resolve this question by showing that cholesterol is strongly excluded from the thinned neck of fusion and fission pores, revealing that thickness (and/or lipid order) influences cholesterol distributions more than curvature. The results imply that cholesterol exclusion can drive fusion pore closure by creating a small, cholesterol-depleted zone in the neck. This model agrees with literature evidence that membrane reshaping is connected to cholesterol-dependent lateral phase separation.
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Affiliation(s)
- Andrew H Beaven
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland
| | - Kayla Sapp
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alexander J Sodt
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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10
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Angerer N, Piller P, Semeraro EF, Keller S, Pabst G. Interaction of detergent with complex mimics of bacterial membranes. Biophys Chem 2023; 296:107002. [PMID: 36921495 DOI: 10.1016/j.bpc.2023.107002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
Detergents are valuable tools to extract membrane proteins for biophysical, biochemical, and structural scrutiny. The detergent-driven solubilization of bilayers made from a single lipid species is commonly described in terms of pseudo-phase diagrams and a three-stage model accounting for three ranges comprising (i) intact vesicles, (ii) vesicle/micelle co-existence, or (iii) mixed micelles. Moreover, the pseudo-phase boundaries thus determined can often be quantitatively rationalized in terms of the molecular shapes of the lipid and the detergent used. Yet, it has remained unclear to what extent this approach can be applied to multi-component lipid membranes that more closely mimic the compositional complexity of cellular membranes. Here, we studied how lipid mixtures composed of palmitoyl oleoyl phosphatidylethanolamine (POPE), palmitoyl oleoyl phosphatidylglycerol (POPG), and tetraoleoyl cardiolipin (TOCL) are solubilized by the commonly used zwitterionic detergent lauryldimethylamine N-oxide using isothermal titration calorimetry. While phase diagrams of the diverse lipid mixtures showed the typical ranges of the three-stage model, we found that POPG-rich POPE/POPG bilayers are more difficult to solubilize than POPG-poor POPE/POPG bilayers. In turn, POPE/POPG/TOCL bilayers became increasingly resistant to detergent with increasing TOCL content. Since POPG is nearly cylindrically shaped and TOCL adopts inverted cone-like shapes under current buffer conditions, our solubilization data do not align with shape-based arguments. Instead, additional electrostatic interactions between lipids and detergents lead to non-additive mixing behavior affecting the resilience of complex lipid bilayers against solubilization.
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Affiliation(s)
- Nadine Angerer
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Paulina Piller
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Enrico F Semeraro
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Sandro Keller
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Georg Pabst
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, Graz 8010, Austria; BioTechMed Graz, Graz, Austria; Field of Excellence BioHealth - University of Graz, Graz, Austria.
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11
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Sapp K, Aleksanyan M, Kerr K, Dimova R, Sodt A. Kinetic relaxation of giant vesicles validates diffusional softening in a binary lipid mixture. Phys Rev E 2023; 107:054403. [PMID: 37329029 PMCID: PMC10548837 DOI: 10.1103/physreve.107.054403] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
The stiffness of biological membranes determines the work required by cellular machinery to form and dismantle vesicles and other lipidic shapes. Model membrane stiffness can be determined from the equilibrium distribution of giant unilamellar vesicle surface undulations observable by phase contrast microscopy. With two or more components, lateral fluctuations of composition will couple to surface undulations depending on the curvature sensitivity of the constituent lipids. The result is a broader distribution of undulations whose complete relaxation is partially determined by lipid diffusion. In this work, kinetic analysis of the undulations of giant unilamellar vesicles made of phosphatidylcholine-phosphatidylethanolamine mixtures validates the molecular mechanism by which the membrane is made 25% softer than a single-component one. The mechanism is relevant to biological membranes, which have diverse and curvature-sensitive lipids.
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Affiliation(s)
- Kayla Sapp
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Mina Aleksanyan
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kaitlyn Kerr
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Alexander Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, 20892 Maryland, USA
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12
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Du Y, Zhang S, Cheng D, Liu Y, Sun M, Zhao Q, Cui M, Zhao X. The full model of micropipette aspiration of cells: A mesoscopic simulation. Acta Biomater 2023; 157:297-309. [PMID: 36543279 DOI: 10.1016/j.actbio.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Studies on the interaction between cells and micromanipulation tools are necessary to optimize the procedures and improve the developmental potential of cells. The molecular dynamics simulation is not possible for such a large-scale simulation, and the spring-damped viscoelastic models and the constitutive equations of the continuum are usually adopted to model the cells as a whole without consideration of the different properties presented by the heterogeneous subcellular components. In this study, we utilized coarse-grained modeling to develop a subcellular model of suspension cell dynamics and a model of a holding micropipette for the fixation of a suspension cell, and designed a large-scale, accurate mesoscopic simulation environment for specific cell micromanipulation. We established a triangular mesh cell membrane and a uniformly distributed, non-intersecting cytoskeleton network and added polymerization/depolymerization processes to connect the cytoskeleton chains with the membrane and cross-linking proteins. In the cell aspiration model, we adopted the profile of the reversed Poiseuille flow to calibrate the viscosity of the fluid and set the bounce-back condition and the appropriate solid-fluid force coefficient to realize non-slip flow at the boundary. The rheological properties of the cells during micropipette aspiration were further analyzed in the simulation by varying parameters such as the inner diameter of the micropipette, negative pressure, and maximum bond length. The model well reproduced the experimentally observed cell deformation phenomenon at low and high pressures. The dynamic response of the cell elongation observed from the simulation was consistent with that obtained from the analysis of the experimental data collected from a custom-designed micromanipulation system. STATEMENT OF SIGNIFICANCE: In this study, we extended the coarse-grained modeling of cells by developing a relatively large-scale micromanipulation environment consisting of a subcellular cell dynamics model and a fluid flow model for cell aspiration. We simulated cytoskeleton filaments that were uniformly distributed in space via applying Harmonic energy to model cytoskeleton with a high level of fidelity. The shortcoming of the soft repulsion in the solid-fluid interaction in the current simulation technique was solved by implementing the bounce-back boundary and the condition that the total force imposed by the wall particles on the fluid particles was equal to the pressure of the fluid. This work paved the way for understanding the mechanical properties of cells and improving the biological efficacy of micromanipulation.
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Affiliation(s)
- Yue Du
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China; Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, China
| | - Shuai Zhang
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China; Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, China
| | - Dai Cheng
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China
| | - Yaowei Liu
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China; Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, China
| | - Mingzhu Sun
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China; Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, China
| | - Qili Zhao
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China; Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, China
| | - Maosheng Cui
- Institute of Animal Science and Veterinary of Tianjin, Tianjin, China
| | - Xin Zhao
- Institute of Robotics and Automatic Information System, College of Artificial Intelligence, Nankai University, China; Tianjin Key Laboratory of Intelligent Robotics, Nankai University, China; Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, China.
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