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Sokolov Y, Diamant H. Permeability of immobile rings of membrane inclusions to in-plane flow. J Chem Phys 2019; 150:154901. [DOI: 10.1063/1.5086865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Yulia Sokolov
- Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Haim Diamant
- Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
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2
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Damioli V, Salvadori A, Beretta GP, Ravelli C, Mitola S. Multi-physics interactions drive VEGFR2 relocation on endothelial cells. Sci Rep 2017; 7:16700. [PMID: 29196628 PMCID: PMC5711959 DOI: 10.1038/s41598-017-16786-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 11/04/2017] [Indexed: 12/31/2022] Open
Abstract
Vascular Endothelial Growth Factor Receptor-2 (VEGFR2) is a pro-angiogenic receptor, expressed on endothelial cells (ECs). Although biochemical pathways that follow the VEGFR2 activation are well established, knowledge about the dynamics of receptors on the plasma membrane remains limited. Ligand stimulation induces the polarization of ECs and the relocation of VEGFR2, either in cell protrusions or in the basal aspect in cells plated on ligand-enriched extracellular matrix (ECM). We develop a mathematical model in order to simulate the relocation of VEGFR2 on the cell membrane during the mechanical adhesion of cells onto a ligand-enriched substrate. Co-designing the in vitro experiments with the simulations allows identifying three phases of the receptor dynamics, which are controlled respectively by the high chemical reaction rate, by the mechanical deformation rate, and by the diffusion of free receptors on the membrane. The identification of the laws that regulate receptor polarization opens new perspectives toward developing innovative anti-angiogenic strategies through the modulation of EC activation.
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Affiliation(s)
- Valentina Damioli
- Università degli Studi di Brescia, DIMI Department of Mechanical and Industrial Engineering, Brescia, 25123, Italy
| | - Alberto Salvadori
- Università degli Studi di Brescia, DICATAM, Department of Civil, Environmental, Architectural Engineering and Mathematics, Brescia, 25123, Italy.,Laboratory for Preventive and Personalized Medicine (MPP Lab), Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Gian Paolo Beretta
- Università degli Studi di Brescia, DIMI Department of Mechanical and Industrial Engineering, Brescia, 25123, Italy
| | - Cosetta Ravelli
- Università degli Studi di Brescia, DMMT, Department of Molecular and Translational Medicine, Brescia, 25123, Italy. .,Laboratory for Preventive and Personalized Medicine (MPP Lab), Università degli Studi di Brescia, Brescia, 25123, Italy.
| | - Stefania Mitola
- Università degli Studi di Brescia, DMMT, Department of Molecular and Translational Medicine, Brescia, 25123, Italy. .,Laboratory for Preventive and Personalized Medicine (MPP Lab), Università degli Studi di Brescia, Brescia, 25123, Italy.
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3
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Deshpande SA, Pawar AB, Dighe A, Athale CA, Sengupta D. Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association–diffusion models. Phys Biol 2017; 14:036002. [DOI: 10.1088/1478-3975/aa6b68] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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4
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Koldsø H, Reddy T, Fowler PW, Duncan AL, Sansom MSP. Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane. J Phys Chem B 2016; 120:8873-81. [PMID: 27483109 DOI: 10.1021/acs.jpcb.6b05846] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The cytoskeleton underlying cell membranes may influence the dynamic organization of proteins and lipids within the bilayer by immobilizing certain transmembrane (TM) proteins and forming corrals within the membrane. Here, we present coarse-grained resolution simulations of a biologically realistic membrane model of asymmetrically organized lipids and TM proteins. We determine the effects of a model of cytoskeletal immobilization of selected membrane proteins using long time scale coarse-grained molecular dynamics simulations. By introducing compartments with varying degrees of restraints within the membrane models, we are able to reveal how compartmentalization caused by cytoskeletal immobilization leads to reduced and anomalous diffusional mobility of both proteins and lipids. This in turn results in a reduced rate of protein dimerization within the membrane and of hopping of membrane proteins between compartments. These simulations provide a molecular realization of hierarchical models often invoked to explain single-molecule imaging studies of membrane proteins.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, OX1 3QU Oxford, United Kingdom
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5
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Chen J, Xie ZR, Wu Y. Elucidating the general principles of cell adhesion with a coarse-grained simulation model. MOLECULAR BIOSYSTEMS 2016; 12:205-18. [DOI: 10.1039/c5mb00612k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained simulation of interplay between cell adhesion and cell signaling.
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Affiliation(s)
- Jiawen Chen
- Department of Systems and Computational Biology
- Albert Einstein College of Medicine of Yeshiva University
- Bronx
- USA
| | - Zhong-Ru Xie
- Department of Systems and Computational Biology
- Albert Einstein College of Medicine of Yeshiva University
- Bronx
- USA
| | - Yinghao Wu
- Department of Systems and Computational Biology
- Albert Einstein College of Medicine of Yeshiva University
- Bronx
- USA
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McKenna JF, Tolmie AF, Runions J. Across the great divide: the plant cell surface continuum. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:132-140. [PMID: 25460078 DOI: 10.1016/j.pbi.2014.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/21/2014] [Accepted: 11/01/2014] [Indexed: 06/04/2023]
Abstract
The plant cell wall, plasma membrane and cytoskeleton exist as a cell surface continuum. This interconnection of organelles forms the interface between the plant cell and the external environment and is important for detecting the presence of a diverse range of stimuli. A plethora of plasma membrane microdomains with putative roles in membrane localized enzymatic or signalling processes have been described. While regulation of cell wall composition is defined by proteins within the plasma membrane, the cell wall has been shown to have an anchoring role on plasma membrane proteins which affects their lateral mobility. This interplay between plasma membrane and cell wall components is necessary for plasma membrane microdomain function. Actin and microtubule cytoskeletons are also involved in maintenance and function of the cell surface continuum. Investigation of the interactions between organellar components of this mechanism are important if we are to understand how cells respond to external signals.
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Affiliation(s)
- Joseph F McKenna
- Plant Cell Biology, Oxford Brookes University, Department of Biological & Medical Sciences, Gipsy Lane, Oxford OX3 0BP, UK
| | - A Frances Tolmie
- Plant Cell Biology, Oxford Brookes University, Department of Biological & Medical Sciences, Gipsy Lane, Oxford OX3 0BP, UK
| | - John Runions
- Plant Cell Biology, Oxford Brookes University, Department of Biological & Medical Sciences, Gipsy Lane, Oxford OX3 0BP, UK.
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7
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Mainali D, Smith EA. Select cytoplasmic and membrane proteins increase the percentage of immobile integrins but do not affect the average diffusion coefficient of mobile integrins. Anal Bioanal Chem 2013; 405:8561-8. [DOI: 10.1007/s00216-013-7279-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 12/25/2022]
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8
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Sukharev S, Sachs F. Molecular force transduction by ion channels: diversity and unifying principles. J Cell Sci 2012; 125:3075-83. [PMID: 22797911 DOI: 10.1242/jcs.092353] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cells perceive force through a variety of molecular sensors, of which the mechanosensitive ion channels are the most efficient and act the fastest. These channels apparently evolved to prevent osmotic lysis of the cell as a result of metabolite accumulation and/or external changes in osmolarity. From this simple beginning, nature developed specific mechanosensitive enzymes that allow us to hear, maintain balance, feel touch and regulate many systemic variables, such as blood pressure. For a channel to be mechanosensitive it needs to respond to mechanical stresses by changing its shape between the closed and open states. In that way, forces within the lipid bilayer or within a protein link can do work on the channel and stabilize its state. Ion channels have the highest turnover rates of all enzymes, and they can act as both sensors and effectors, providing the necessary fluxes to relieve osmotic pressure, shift the membrane potential or initiate chemical signaling. In this Commentary, we focus on the common mechanisms by which mechanical forces and the local environment can regulate membrane protein structure, and more specifically, mechanosensitive ion channels.
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Affiliation(s)
- Sergei Sukharev
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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9
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Looyenga BD, Mackeigan JP. Characterization of differential protein tethering at the plasma membrane in response to epidermal growth factor signaling. J Proteome Res 2012; 11:3101-11. [PMID: 22559174 DOI: 10.1021/pr201077d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Physical tethering of membrane proteins to the cortical actin cytoskeleton provides functional organization to the plasma membrane and contributes to diverse cellular processes including cell signaling, vesicular trafficking, endocytosis, and migration. For these processes to occur, membrane protein tethering must be dynamically regulated in response to environmental cues. In this study, we describe a novel biochemical scheme for isolating the complement of plasma membrane proteins that are physically tethered to the actin cytoskeleton. We utilized this method in combination with tandem liquid chromatography/mass spectrometry (LC-MS/MS) to demonstrate that cytoskeletal tethering of membrane proteins is acutely regulated by epidermal growth factor (EGF) in normal human kidney (HK2) cells. Our results indicate that several proteins known to be involved in EGF signaling, as well as other proteins not traditionally associated with this pathway, are tethered to the cytoskeleton in dynamic fashion. Further analysis of one hit from our proteomic survey, the receptor phosphotyrosine phosphatase PTPRS, revealed a correlation between cytoskeletal tethering and endosomal trafficking in response to EGF. This finding parallels previous indications that PTPRS is involved in the desensitization of EGFR and provides a potential mechanism to coordinate localization of these two membrane proteins in the same compartment upon EGFR activation.
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Affiliation(s)
- Brendan D Looyenga
- Laboratory of Systems Biology, Van Andel Research Institute , Grand Rapids, Michigan 49503, United States
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10
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Wallace R. Neural membrane signaling platforms. Int J Mol Sci 2010; 11:2421-42. [PMID: 20640161 PMCID: PMC2904925 DOI: 10.3390/ijms11062421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 06/03/2010] [Accepted: 06/09/2010] [Indexed: 11/16/2022] Open
Abstract
Throughout much of the history of biology, the cell membrane was functionally defined as a semi-permeable barrier separating aqueous compartments, and an anchoring site for proteins. Little attention was devoted to its possible regulatory role in intracellular molecular processes and neuron electrical signaling. This article reviews the history of membrane studies and the current state of the art. Emphasis is placed on natural and artificial membrane studies of electric field effects on molecular organization, especially as these may relate to impulse propagation in neurons. Implications of these studies for new designs in artificial intelligence are briefly examined.
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Affiliation(s)
- Ron Wallace
- Department of Anthropology, University of Central Florida, Box 25000, Orlando, FL, 32816, USA; E-Mail: ; Tel.: +1-407-823-2227
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11
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Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. BMC Bioinformatics 2010; 11:218. [PMID: 20429923 PMCID: PMC2868014 DOI: 10.1186/1471-2105-11-218] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Accepted: 04/29/2010] [Indexed: 11/12/2022] Open
Abstract
Background An adaptive coarse-grained (kinetic) Monte Carlo (ACGMC) simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimerization dynamics of epidermal growth factor receptor (EGFR) in the presence of plasma membrane heterogeneity and specifically receptor clustering. We perform simulations representing EGFR cluster dissipation in heterogeneous plasma membranes consisting of higher density clusters of receptors surrounded by low population areas using the ACGMC method. We further investigate the effect of key parameters on the cluster lifetime. Results Coarse-graining of dimerization, rather than of diffusion, may lead to computational error. It is shown that the ACGMC method is an effective technique to minimize error in diffusion-reaction processes and is superior to the microscopic kinetic Monte Carlo simulation in terms of computational cost while retaining accuracy. The low computational cost enables sensitivity analysis calculations. Sensitivity analysis indicates that it may be possible to retain clusters of receptors over the time scale of minutes under suitable conditions and the cluster lifetime may depend on both receptor density and cluster size. Conclusions The ACGMC method is an ideal platform to resolve large length and time scales in heterogeneous biological systems well beyond the plasma membrane and the EGFR system studied here. Our results demonstrate that cluster size must be considered in conjunction with receptor density, as they synergistically affect EGFR cluster lifetime. Further, the cluster lifetime being of the order of several seconds suggests that any mechanisms responsible for EGFR aggregation must operate on shorter timescales (at most a fraction of a second), to overcome dissipation and produce stable clusters observed experimentally.
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12
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Bressloff PC, Earnshaw BA. A dynamic corral model of receptor trafficking at a synapse. Biophys J 2009; 96:1786-802. [PMID: 19254538 DOI: 10.1016/j.bpj.2008.12.3889] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 12/01/2008] [Indexed: 11/29/2022] Open
Abstract
The postsynaptic density (PSD) is a cytoskeletal specialization within the postsynaptic membrane of a neuron that helps to concentrate and organize neurotransmitter receptors at a chemical synapse. The total number of receptors within the PSD, which is a major factor in determining the physiological strength or weight of a synapse, fluctuates due to the surface diffusion of receptors into and out of the PSD, and the interactions of receptors with scaffolding proteins and cytoskeletal elements within the PSD. In this article, we present a stochastic model of protein receptor trafficking at the PSD that takes into account these various processes. The PSD is treated as a stochastically gated corral, which contributes a source of extrinsic or environmental noise that supplements the intrinsic noise arising from small receptor numbers. Using a combination of stochastic analysis and Monte Carlo simulations, we determine the time-dependent variation in the mean and variance of synaptic receptor numbers for a variety of initial conditions that simulate fluorescence recovery after photobleaching experiments, and indicate how such data might be used to infer certain properties of the PSD.
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Affiliation(s)
- Paul C Bressloff
- Department of Mathematics, University of Utah, Salt Lake City, Utah, USA.
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13
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Auth T, Gov NS. Diffusion in a fluid membrane with a flexible cortical cytoskeleton. Biophys J 2009; 96:818-30. [PMID: 19186123 DOI: 10.1016/j.bpj.2008.10.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/15/2008] [Indexed: 10/21/2022] Open
Abstract
We calculate the influence of a flexible network of long-chain proteins, which is anchored to a fluid membrane, on protein diffusion in this membrane. This is a model for the cortical cytoskeleton and the lipid bilayer of the red blood cell, which we apply to predict the influence of the cytoskeleton on the diffusion coefficient of a mobile band 3 protein. Using the pressure field that the cytoskeleton exerts on the membrane, from the steric repulsion between the diffusing protein and the cytoskeletal filaments, we define a potential landscape for the diffusion within the bilayer. We study the changes to the diffusion coefficient on removal of one type of anchor proteins, e.g., in several hemolytic anemias, as well as for isotropic and anisotropic stretching of the cytoskeleton. We predict an overall increase of the diffusion for a smaller number of anchor proteins and increased diffusion for anisotropic stretching in the direction of the stretch, because of the decrease in the spatial frequency as well as in the height of the potential barriers.
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Affiliation(s)
- Thorsten Auth
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot, Israel; Institute for Solid State Research, Research Centre Jülich, Jülich, Germany.
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14
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Affiliation(s)
- Frank L.H. Brown
- Department of Chemistry and Biochemistry and Department of Physics, University of California, Santa Barbara, California 93106;
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15
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Bates IR, Wiseman PW, Hanrahan JW. Investigating membrane protein dynamics in living cells. Biochem Cell Biol 2007; 84:825-31. [PMID: 17215870 DOI: 10.1139/o06-189] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Live cell imaging is a powerful tool for understanding the function and regulation of membrane proteins. In this review, we briefly discuss 4 fluorescence-microscopy-based techniques for studying the transport dynamics of membrane proteins: fluorescence-correlation spectroscopy, image-correlation spectroscopy, fluorescence recovery after photobleaching, and single-particle and (or) molecule tracking. The advantages and limitations of each approach are illustrated using recent studies of an ion channel and cell adhesion molecules.
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Affiliation(s)
- Ian R Bates
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montréal, QC H3G 1Y6, Canada.
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16
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Fowlkes JD, Hullander ED, Fletcher BL, Retterer ST, Melechko AV, Hensley DK, Simpson ML, Doktycz MJ. Molecular transport in a crowded volume created from vertically aligned carbon nanofibres: a fluorescence recovery after photobleaching study. NANOTECHNOLOGY 2006; 17:5659-68. [PMID: 21727339 DOI: 10.1088/0957-4484/17/22/021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Rapid and selective molecular exchange across a barrier is essential for emulating the properties of biological membranes. Vertically-aligned carbon nanofibre (VACNF) forests have shown great promise as membrane mimics, owing to their mechanical stability, their ease of integration with microfabrication technologies and the ability to tailor their morphology and surface properties. However, quantifying transport through synthetic membranes having micro- and nanoscale features is challenging. Here, fluorescence recovery after photobleaching (FRAP) is coupled with finite difference and Monte Carlo simulations to quantify diffusive transport in microfluidic structures containing VACNF forests. Anomalous subdiffusion was observed for FITC (hydrodynamic radius of 0.54 nm) diffusion through both VACNFs and SiO(2)-coated VACNFS (oxVACNFs). Anomalous subdiffusion can be attributed to multiple FITC-nanofibre interactions for the case of diffusion through the VACNF forest. Volume crowding was identified as the cause of anomalous subdiffusion in the oxVACNF forest. In both cases the diffusion mode changes to a time-independent, Fickian mode of transport that can be defined by a crossover length (R(CR)). By identifying the space-and time-dependent transport characteristics of the VACNF forest, the dimensional features of membranes can be tailored to achieve predictable molecular exchange.
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Affiliation(s)
- J D Fowlkes
- Molecular-Scale Engineering and Nanoscale Technologies Research Group, Condensed Matter Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6006, USA. Materials Science and Engineering Department, The University of Tennessee, Knoxville, TN 37996-2200, USA. Biological and Nanoscale Systems Group, Life Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6123, USA
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17
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Wallace R. Neural membrane microdomains as computational systems: Toward molecular modeling in the study of neural disease. Biosystems 2006; 87:20-30. [PMID: 16650927 DOI: 10.1016/j.biosystems.2006.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 12/02/2005] [Accepted: 02/28/2006] [Indexed: 11/23/2022]
Abstract
Several studies indicate that the lipid biological membrane contains discrete regions known as rafts or microdomains. These structures range in size from approximately 50 to 70nm to nearly a mum and play important roles in cell signaling. In the neuron, computational models suggest that transiently polarized microdomain ethenes may regulate ion-channel dynamics and control impulse propagation. Thus the microdomain is nominated as the fundamental unit of nervous system signaling. Based on this model, the article proposes a first-approximation design for a supported-membrane device which would mimic microdomain properties. The basic architecture would consist of an electrically addressable biotemplated nanowire crossing an artificial membrane corralled in a vertical carbon nanofiber barrier. Advantages and disadvantages of model components are discussed at length. It is proposed that artificial devices of this type would be medically useful in simulating membrane states correlated with neural disease. This possibility is examined with reference to the A-current potassium channel, implicated in epilepsy.
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Affiliation(s)
- Ron Wallace
- Department of Sociology and Anthropology, University of Central Florida, Box 25000, Orlando, FL 32816, USA.
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18
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Brannigan G, Lin LCL, Brown FLH. Implicit solvent simulation models for biomembranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 35:104-24. [PMID: 16187129 DOI: 10.1007/s00249-005-0013-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 08/03/2005] [Accepted: 08/12/2005] [Indexed: 11/25/2022]
Abstract
Fully atomic simulation strategies are infeasible for the study of many processes of interest to membrane biology, biophysics and biochemistry. We review various coarse-grained simulation methodologies with special emphasis on methods and models that do not require the explicit simulation of water. Examples from our own research demonstrate that such models have potential for simulating a variety of biologically relevant phenomena at the membrane surface.
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Affiliation(s)
- Grace Brannigan
- Department of Physics and Astronomy, University of California, Santa Barbara, CA 93106-9530, USA
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19
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Lin LCL, Brown FLH. Dynamic simulations of membranes with cytoskeletal interactions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:011910. [PMID: 16090004 DOI: 10.1103/physreve.72.011910] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Indexed: 05/03/2023]
Abstract
We describe a simulation algorithm for the dynamics of elastic membrane sheets over long length and time scales. Our model includes implicit hydrodynamic coupling between membrane and surrounding solvent and allows for arbitrary external forces acting on the membrane surface. In particular, the methodology is well suited to studying membranes in interaction with cytoskeletal filaments. We present results for the thermal undulations of a lipid bilayer attached to a regular network of spectrin filaments as a model for the red blood cell membrane. The dynamic fluctuations of the bilayer over the spectrin network are quantified and used to predict the macroscopic diffusion constant of band 3 on the surface of the red blood cell. We find that thermal undulations likely play a role in the mobility of band 3 in the plane of the erythrocyte membrane.
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Affiliation(s)
- Lawrence C-L Lin
- Department of Physics, University of California, Santa Barbara, 93106, USA
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20
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Pesen D, Hoh JH. Modes of remodeling in the cortical cytoskeleton of vascular endothelial cells. FEBS Lett 2005; 579:473-6. [PMID: 15642361 DOI: 10.1016/j.febslet.2004.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 12/01/2004] [Accepted: 12/06/2004] [Indexed: 11/30/2022]
Abstract
The cortical cytoskeleton of vascular endothelial cells plays an important role in responding to mechanical stimuli and controlling the distribution of cell surface proteins. Here, we have used atomic force microscopy to visualize the dynamics of cortical cytoskeleton in living bovine pulmonary artery endothelial cells. We demonstrate that the cortical cytoskeleton, organized as a complex polygonal mesh, is highly dynamic and shows two modes of remodeling: intact-boundary-mode where mesh element boundaries remain intact but move at approximately 0.08 microm/min allowing the mesh element to change shape, and altered-boundary-mode where new mesh boundaries form and existing ones disappear.
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Affiliation(s)
- Devrim Pesen
- Department of Physiology, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
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21
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Lin LCL, Brown FLH. Dynamics of pinned membranes with application to protein diffusion on the surface of red blood cells. Biophys J 2004; 86:764-80. [PMID: 14747313 PMCID: PMC1303925 DOI: 10.1016/s0006-3495(04)74153-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Accepted: 10/16/2003] [Indexed: 10/21/2022] Open
Abstract
We present a theoretical treatment and simulation algorithm for the dynamics of Helfrich elastic membrane surfaces in the presence of general harmonic perturbations and hydrodynamic coupling to the surrounding solvent. In the limit of localized and strong interactions, this harmonic model can be used to pin the membrane to intracellular/intercellular structures. We consider the case of pinning to the cytoskeleton and use such a model to estimate the macroscopic diffusion constant for band 3 protein on the surface of human erythrocytes. Comparison to experimental results suggests that thermal undulations of the membrane surface should play a significant role in protein mobility on the red blood cell.
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Affiliation(s)
- Lawrence C-L Lin
- Department of Physics, University of California, Santa Barbara, California 93106-9510, USA
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22
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Barsegov V, Shapir Y, Mukamel S. One-dimensional transport with dynamic disorder. PHYSICAL REVIEW E 2003; 68:011101. [PMID: 12935121 DOI: 10.1103/physreve.68.011101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2003] [Indexed: 11/07/2022]
Abstract
We study the mean quenching time distribution and its moments in a one-dimensional N-site donor-bridge-acceptor system where all sites are coupled to a two-state jump bath for arbitrary disorder and an arbitrary ratio kappa identical with <k>/R of the bath jump rate R and the average hopping rate <k>. When kappaN approximately 1, the quenching time distribution has long power-law tails even when the waiting times are exponentially distributed. These disappear for kappaN<<1 where the hopping rate self-averages on the bath relaxation time scale. In the absence of disorder or for small kappa, the mean quenching time scales linearly with N. Otherwise, we observe a power law, approximately N1+gamma, with a crossover to linear scaling (gamma=0) for large N. Distributions of particle position, its second moment, velocity and diffusion coefficient are computed in the infinite N limit. For times longer than R-1, the dynamic disorder self-averages and the average position, velocity, and diffusion coefficient scale linearly in time.
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Affiliation(s)
- Valeri Barsegov
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
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Brown FLH. Regulation of protein mobility via thermal membrane undulations. Biophys J 2003; 84:842-53. [PMID: 12547768 PMCID: PMC1302664 DOI: 10.1016/s0006-3495(03)74903-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Accepted: 10/16/2002] [Indexed: 11/22/2022] Open
Abstract
The in-plane diffusivelike motion of membrane bound proteins on the surface of cells is considered. We suggest, on the basis of theoretical arguments and simulation, that thermally excited undulations of the lipid bilayer may serve as a mechanism for proteins to hop between adjacent regions on the cell surface separated by barriers composed of internal cellular structure (e.g., the cytoskeleton). We specifically investigate the mobility of band 3 dimer on the surface of red blood cells where the spectrin cytoskeletal meshwork defines a series of "corrals" on the cell surface known to hinder protein motion. Previous models of this system have postulated that the cytoskeleton must deform to allow passage of membrane bound proteins out of these corral regions and have ignored fluctuations of the bilayer. Our model provides a complementary mechanism and we posit that the mobility of real proteins in real cells is likely the result of several mechanisms acting in parallel.
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Affiliation(s)
- Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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24
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Daumas F, Destainville N, Millot C, Lopez A, Dean D, Salomé L. Confined diffusion without fences of a g-protein-coupled receptor as revealed by single particle tracking. Biophys J 2003; 84:356-66. [PMID: 12524289 PMCID: PMC1302617 DOI: 10.1016/s0006-3495(03)74856-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Single particle tracking is a powerful tool for probing the organization and dynamics of the plasma membrane constituents. We used this technique to study the micro -opioid receptor belonging to the large family of the G-protein-coupled receptors involved with other partners in a signal transduction pathway. The specific labeling of the receptor coupled to a T7-tag at its N-terminus, stably expressed in fibroblastic cells, was achieved by colloidal gold coupled to a monoclonal anti T7-tag antibody. The lateral movements of the particles were followed by nanovideomicroscopy at 40 ms time resolution during 2 min with a spatial precision of 15 nm. The receptors were found to have either a slow or directed diffusion mode (10%) or a walking confined diffusion mode (90%) composed of a long-term random diffusion and a short-term confined diffusion, and corresponding to a diffusion confined within a domain that itself diffuses. The results indicate that the confinement is due to an effective harmonic potential generated by long-range attraction between the membrane proteins. A simple model for interacting membrane proteins diffusion is proposed that explains the variations with the domain size of the short-term and long-term diffusion coefficients.
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MESH Headings
- Bacteriophage T7/chemistry
- Cell Line
- Cell Membrane/chemistry
- Cell Membrane/physiology
- Cell Membrane/ultrastructure
- Diffusion
- Fibroblasts/chemistry
- Fibroblasts/physiology
- Fibroblasts/ultrastructure
- GTP-Binding Protein Regulators/chemistry
- GTP-Binding Protein Regulators/physiology
- GTP-Binding Protein Regulators/ultrastructure
- GTP-Binding Proteins/chemistry
- GTP-Binding Proteins/physiology
- GTP-Binding Proteins/ultrastructure
- Gold Colloid/chemistry
- Kidney/chemistry
- Kidney/physiology
- Kidney/ultrastructure
- Microscopy, Video/instrumentation
- Microscopy, Video/methods
- Microspheres
- Models, Biological
- Models, Chemical
- Motion
- Nanotechnology/instrumentation
- Nanotechnology/methods
- Particle Size
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/physiology
- Receptors, Cell Surface/ultrastructure
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/deficiency
- Receptors, Opioid, mu/physiology
- Receptors, Opioid, mu/ultrastructure
- Signal Transduction/physiology
- Staining and Labeling/methods
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Affiliation(s)
- Frédéric Daumas
- Institut de Pharmacologie et Biologie Structurale, CNRS UMR 5089, 205, route de Narbonne, 31077 Toulouse Cedex, France
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Brown FL, Leitner DM, McCammon JA, Wilson KR. Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables. Biophys J 2000; 78:2257-69. [PMID: 10777724 PMCID: PMC1300817 DOI: 10.1016/s0006-3495(00)76772-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We consider the possibility of inferring the nature of cytoskeletal interaction with transmembrane proteins via optical experiments such as single-particle tracking (SPT) and near-field scanning optical microscopy (NSOM). In particular, we demonstrate that it may be possible to differentiate between static and dynamic barriers to diffusion by examining the time-dependent variance and higher moments of protein population inside cytoskeletal "corrals." Simulations modeling Band 3 diffusion on the surface of erythrocytes provide a concrete demonstration that these statistical tools might prove useful in the study of biological systems.
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Affiliation(s)
- F L Brown
- Department of Chemistry, University of California, San Diego, La Jolla, California 92093-0339 USA.
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