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Cornet J, Coulonges N, Pezeshkian W, Penissat-Mahaut M, Desgrez-Dautet H, Marrink SJ, Destainville N, Chavent M, Manghi M. There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. SOFT MATTER 2024; 20:4998-5013. [PMID: 38884641 DOI: 10.1039/d4sm00089g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.
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Affiliation(s)
- Julie Cornet
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
| | - Nelly Coulonges
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Maël Penissat-Mahaut
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
| | - Hermes Desgrez-Dautet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, 31400, Toulouse, France.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, France.
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Mukhopadhyay U, Mandal T, Chakraborty M, Sinha B. The Plasma Membrane and Mechanoregulation in Cells. ACS OMEGA 2024; 9:21780-21797. [PMID: 38799362 PMCID: PMC11112598 DOI: 10.1021/acsomega.4c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Cells inhabit a mechanical microenvironment that they continuously sense and adapt to. The plasma membrane (PM), serving as the boundary of the cell, plays a pivotal role in this process of adaptation. In this Review, we begin by examining well-studied processes where mechanoregulation proves significant. Specifically, we highlight examples from the immune system and stem cells, besides discussing processes involving fibroblasts and other cell types. Subsequently, we discuss the common molecular players that facilitate the sensing of the mechanical signal and transform it into a chemical response covering integrins YAP/TAZ and Piezo. We then review how this understanding of molecular elements is leveraged in drug discovery and tissue engineering alongside a discussion of the methodologies used to measure mechanical properties. Focusing on the processes of endocytosis, we discuss how cells may respond to altered membrane mechanics using endo- and exocytosis. Through the process of depleting/adding the membrane area, these could also impact membrane mechanics. We compare pathways from studies illustrating the involvement of endocytosis in mechanoregulation, including clathrin-mediated endocytosis (CME) and the CLIC/GEEC (CG) pathway as central examples. Lastly, we review studies on cell-cell fusion during myogenesis, the mechanical integrity of muscle fibers, and the reported and anticipated roles of various molecular players and processes like endocytosis, thereby emphasizing the significance of mechanoregulation at the PM.
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Affiliation(s)
- Upasana Mukhopadhyay
- Department of Biological
Sciences, Indian Institute of Science Education
and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Tithi Mandal
- Department of Biological
Sciences, Indian Institute of Science Education
and Research Kolkata, Mohanpur, West Bengal 741246, India
| | | | - Bidisha Sinha
- Department of Biological
Sciences, Indian Institute of Science Education
and Research Kolkata, Mohanpur, West Bengal 741246, India
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Pinigin KV. Determination of Elastic Parameters of Lipid Membranes with Molecular Dynamics: A Review of Approaches and Theoretical Aspects. MEMBRANES 2022; 12:membranes12111149. [PMID: 36422141 PMCID: PMC9692374 DOI: 10.3390/membranes12111149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 05/12/2023]
Abstract
Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and fission, membrane-mediated interaction between membrane inclusions, lipid-protein interaction, formation of pores, etc. In all of these cases, elastic parameters of lipid membranes are important for the description of membrane deformations, as these parameters determine energy barriers and characteristic times of membrane-involved phenomena. Since the development of molecular dynamics (MD), a variety of in silico methods have been proposed for the determination of elastic parameters of simulated lipid membranes. These MD methods allow for the consideration of details unattainable in experimental techniques and represent a distinct scientific field, which is rapidly developing. This work provides a review of these MD approaches with a focus on theoretical aspects. Two main challenges are identified: (i) the ambiguity in the transition from the continuum description of elastic theories to the discrete representation of MD simulations, and (ii) the determination of intrinsic elastic parameters of lipid mixtures, which is complicated due to the composition-curvature coupling effect.
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Affiliation(s)
- Konstantin V Pinigin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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Durand M. Frame tension governs the thermal fluctuations of a fluid membrane: new evidence. SOFT MATTER 2022; 18:3891-3901. [PMID: 35535647 DOI: 10.1039/d1sm01765a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Two different tensions can be defined for a fluid membrane: the internal tension, γ, conjugated to the real membrane area in the Hamiltonian, and the frame tension, τ, conjugated to the projected (or frame) area. According to the standard statistical description of a membrane, the fluctuation spectrum is governed by γ. However, using rotational invariance arguments, several studies argued that the fluctuation spectrum must be governed by the frame tension τ instead. These studies disagree on the origin of the result obtained with the standard description yet: either a miscounting of configurations, quantified with the integration measure, or the use of a quadratic approximation of the Helfrich Hamiltonian. Analyzing the simplest case of a one-dimensional membrane, for which the arc length offers a natural parametrization, we give a new proof that the fluctuations are driven by τ, and show that the origin of the issue with the standard description is a miscounting of membrane configurations. The origin itself of this miscounting depends on the thermodynamic ensemble in which calculations are made.
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Affiliation(s)
- Marc Durand
- Université Paris Cité, CNRS, UMR 7057, Matière et Systèmes Complexes (MSC), F-75006 Paris, France.
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Membrane Homeostasis: The Role of Actin Cytoskeleton. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-020-00217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Srivastava A, Karmakar S, Debnath A. Quantification of spatio-temporal scales of dynamical heterogeneity of water near lipid membranes above supercooling. SOFT MATTER 2019; 15:9805-9815. [PMID: 31746927 DOI: 10.1039/c9sm01725a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India.
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Bivas I, Tonchev NS. Membrane stretching elasticity and thermal shape fluctuations of nearly spherical lipid vesicles. Phys Rev E 2019; 100:022416. [PMID: 31574724 DOI: 10.1103/physreve.100.022416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 11/07/2022]
Abstract
One of the most widely used methods for determination of the bending elasticity modulus of model lipid membranes is the analysis of the shape fluctuations of nearly spherical lipid vesicles. The theoretical basis of this analysis is given by Milner and Safran [Phys. Rev. A 36, 4371 (1987)0556-279110.1103/PhysRevA.36.4371]. In their theory the stretching effects are not considered. In the present study we generalized their approach including the stretching effects deduced after application of the statistical mechanics to vesicles.
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Affiliation(s)
- Isak Bivas
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko chaussee blvd., Sofia 1784, Bulgaria
| | - Nicholay S Tonchev
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko chaussee blvd., Sofia 1784, Bulgaria
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Schmid F. Physical mechanisms of micro- and nanodomain formation in multicomponent lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:509-528. [PMID: 27823927 DOI: 10.1016/j.bbamem.2016.10.021] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/19/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022]
Abstract
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not involve direct protein-protein interactions. Specifically, it considers (i) equilibrium mechanisms based on lipid-lipid phase separation such as critical cluster formation close to critical points, and multiple domain formation in curved geometries, (ii) equilibrium mechanisms that stabilize two-dimensional microemulsions, such as the effect of linactants and the effect of curvature-composition coupling in bilayers and monolayers, and (iii) non-equilibrium mechanisms induced by the interaction of a biomembrane with the cellular environment, such as membrane recycling and the pinning effects of the cytoplasm. Theoretical predictions are discussed together with simulations and experiments. The presentation is guided by the theory of phase transitions and critical phenomena, and the appendix summarizes the mathematical background in a concise way within the framework of the Ginzburg-Landau theory. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Friederike Schmid
- Institute of Physics, Johannes Gutenberg University, 55099 Mainz, Germany
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Chen R, Subramanyam S, Elcock AH, Spies M, Wold MS. Dynamic binding of replication protein a is required for DNA repair. Nucleic Acids Res 2016; 44:5758-72. [PMID: 27131385 PMCID: PMC4937323 DOI: 10.1093/nar/gkw339] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/15/2016] [Indexed: 12/14/2022] Open
Abstract
Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for replication, repair and recombination. High-affinity ssDNA-binding by RPA depends on two DNA binding domains in the large subunit of RPA. Mutation of the evolutionarily conserved aromatic residues in these two domains results in a separation-of-function phenotype: aromatic residue mutants support DNA replication but are defective in DNA repair. We used biochemical and single-molecule analyses, and Brownian Dynamics simulations to determine the molecular basis of this phenotype. Our studies demonstrated that RPA binds to ssDNA in at least two modes characterized by different dissociation kinetics. We also showed that the aromatic residues contribute to the formation of the longer-lived state, are required for stable binding to short ssDNA regions and are needed for RPA melting of partially duplex DNA structures. We conclude that stable binding and/or the melting of secondary DNA structures by RPA is required for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replication. It is likely that the binding modes are in equilibrium and reflect dynamics in the RPA-DNA complex. This suggests that dynamic binding of RPA to DNA is necessary for different cellular functions.
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Affiliation(s)
- Ran Chen
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Shyamal Subramanyam
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adrian H Elcock
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications. FROM SINGLE MOLECULES TO NANOSCOPICALLY STRUCTURED MATERIALS 2013. [DOI: 10.1007/12_2013_258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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