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Daddi-Moussa-Ider A, Tjhung E, Richter T, Menzel AM. Hydrodynamics of a disk in a thin film of weakly nematic fluid subject to linear friction. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:445101. [PMID: 39029503 DOI: 10.1088/1361-648x/ad65ad] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/19/2024] [Indexed: 07/21/2024]
Abstract
To make progress towards the development of a theory on the motion of inclusions in thin structured films and membranes, we here consider as an initial step a circular disk in a two-dimensional, uniaxially anisotropic fluid layer. We assume overdamped dynamics, incompressibility of the fluid, and global alignment of the axis of anisotropy. Motion within this layer is affected by additional linear friction with the environment, for instance, a supporting substrate. We investigate the induced flows in the fluid when the disk is translated parallel or perpendicular to the direction of anisotropy. Moreover, expressions for corresponding mobilities and resistance coefficients of the disk are derived. Our results are obtained within the framework of a perturbative expansion in the parameters that quantify the anisotropy of the fluid. Good agreement is found for moderate anisotropy when compared to associated results from finite-element simulations. At pronounced anisotropy, the induced flow fields are still predicted qualitatively correctly by the perturbative theory, although quantitative deviations arise. We hope to stimulate with our investigations corresponding experimental analyses, for example, concerning fluid flows in anisotropic thin films on uniaxially rubbed supporting substrates.
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Affiliation(s)
- Abdallah Daddi-Moussa-Ider
- School of Mathematics and Statistics, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Elsen Tjhung
- School of Mathematics and Statistics, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Thomas Richter
- Institut für Analysis und Numerik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Andreas M Menzel
- Institut für Physik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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2
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Schoch RL, Haran G, Brown FLH. Dynamic correlations in lipid bilayer membranes over finite time intervals. J Chem Phys 2023; 158:044112. [PMID: 36725516 DOI: 10.1063/5.0129130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Recent single-molecule measurements [Schoch et al., Proc. Natl. Acad. Sci. U. S. A. 118, e2113202118 (2021)] have observed dynamic lipid-lipid correlations in membranes with submicrometer spatial resolution and submillisecond temporal resolution. While short from an instrumentation standpoint, these length and time scales remain long compared to microscopic molecular motions. Theoretical expressions are derived to infer experimentally measurable correlations from the two-body diffusion matrix appropriate for membrane-bound bodies coupled by hydrodynamic interactions. The temporal (and associated spatial) averaging resulting from finite acquisition times has the effect of washing out correlations as compared to naive predictions (i.e., the bare elements of the diffusion matrix), which would be expected to hold for instantaneous measurements. The theoretical predictions are shown to be in excellent agreement with Brownian dynamics simulations of experimental measurements. Numerical results suggest that the experimental measurement of membrane protein diffusion, in complement to lipid diffusion measurements, might help to resolve the experimental ambiguities encountered for certain black lipid membranes.
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Affiliation(s)
- Rafael L Schoch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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3
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Arricca M, Salvadori A, Bonanno C, Serpelloni M. Modeling Receptor Motility along Advecting Lipid Membranes. MEMBRANES 2022; 12:membranes12070652. [PMID: 35877855 PMCID: PMC9317916 DOI: 10.3390/membranes12070652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022]
Abstract
This work aims to overview multiphysics mechanobiological computational models for receptor dynamics along advecting cell membranes. Continuum and statistical models of receptor motility are the two main modeling methodologies identified in reviewing the state of the art. Within the former modeling class, a further subdivision based on different biological purposes and processes of proteins’ motion is recognized; cell adhesion, cell contractility, endocytosis, and receptor relocations on advecting membranes are the most relevant biological processes identified in which receptor motility is pivotal. Numerical and/or experimental methods and approaches are highlighted in the exposure of the reviewed works provided by the literature, pertinent to the topic of the present manuscript. With a main focus on the continuum models of receptor motility, we discuss appropriate multiphyisics laws to model the mass flux of receptor proteins in the reproduction of receptor relocation and recruitment along cell membranes to describe receptor–ligand chemical interactions, and the cell’s structural response. The mass flux of receptor modeling is further supported by a discussion on the methodology utilized to evaluate the protein diffusion coefficient developed over the years.
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Affiliation(s)
- Matteo Arricca
- The Mechanobiology Research Center, University of Brescia (UNIBS), 25123 Brescia, Italy; (M.A.); (C.B.); (M.S.)
- Department of Mechanical and Industrial Engineering, Università degli Studi di Brescia, via Branze 38, 25123 Brescia, Italy
| | - Alberto Salvadori
- The Mechanobiology Research Center, University of Brescia (UNIBS), 25123 Brescia, Italy; (M.A.); (C.B.); (M.S.)
- Department of Mechanical and Industrial Engineering, Università degli Studi di Brescia, via Branze 38, 25123 Brescia, Italy
- Correspondence:
| | - Claudia Bonanno
- The Mechanobiology Research Center, University of Brescia (UNIBS), 25123 Brescia, Italy; (M.A.); (C.B.); (M.S.)
- Department of Civil, Environmental, Architectural Engineering and Mathematics, Università degli Studi di Brescia, via Branze 43, 25123 Brescia, Italy
| | - Mattia Serpelloni
- The Mechanobiology Research Center, University of Brescia (UNIBS), 25123 Brescia, Italy; (M.A.); (C.B.); (M.S.)
- Department of Mechanical and Industrial Engineering, Università degli Studi di Brescia, via Branze 38, 25123 Brescia, Italy
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4
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Kubyshkin V, Grage SL, Ulrich AS, Budisa N. Bilayer thickness determines the alignment of model polyproline helices in lipid membranes. Phys Chem Chem Phys 2019; 21:22396-22408. [PMID: 31577299 DOI: 10.1039/c9cp02996f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our understanding of protein folds relies fundamentally on the set of secondary structures found in the proteomes. Yet, there also exist intriguing structures and motifs that are underrepresented in natural biopolymeric systems. One example is the polyproline II helix, which is usually considered to have a polar character and therefore does not form membrane spanning sections of membrane proteins. In our work, we have introduced specially designed polyproline II helices into the hydrophobic membrane milieu and used 19F NMR to monitor the helix alignment in oriented lipid bilayers. Our results show that these artificial hydrophobic peptides can adopt several different alignment states. If the helix is shorter than the thickness of the hydrophobic core of the membrane, it is submerged into the bilayer with its long axis parallel to the membrane plane. The polyproline helix adopts a transmembrane alignment when its length exceeds the bilayer thickness. If the peptide length roughly matches the lipid thickness, a coexistence of both states is observed. We thus show that the lipid thickness plays a determining role in the occurrence of a transmembrane polyproline II helix. We also found that the adaptation of polyproline II helices to hydrophobic mismatch is in some notable aspects different from α-helices. Finally, our results prove that the polyproline II helix is a competent structure for the construction of transmembrane peptide segments, despite the fact that no such motif has ever been reported in natural systems.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany and Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg MB R3T 2N2, Canada.
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, Karlsruhe 76021, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, Karlsruhe 76021, Germany and Institute of Organic Chemistry, KIT, Fritz-Haber-Weg 6, Karlsruhe 76131, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany and Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg MB R3T 2N2, Canada.
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5
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Block S. Brownian Motion at Lipid Membranes: A Comparison of Hydrodynamic Models Describing and Experiments Quantifying Diffusion within Lipid Bilayers. Biomolecules 2018; 8:biom8020030. [PMID: 29789471 PMCID: PMC6023006 DOI: 10.3390/biom8020030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/07/2018] [Accepted: 05/16/2018] [Indexed: 12/29/2022] Open
Abstract
The capability of lipid bilayers to exhibit fluid-phase behavior is a fascinating property, which enables, for example, membrane-associated components, such as lipids (domains) and transmembrane proteins, to diffuse within the membrane. These diffusion processes are of paramount importance for cells, as they are for example involved in cell signaling processes or the recycling of membrane components, but also for recently developed analytical approaches, which use differences in the mobility for certain analytical purposes, such as in-membrane purification of membrane proteins or the analysis of multivalent interactions. Here, models describing the Brownian motion of membrane inclusions (lipids, peptides, proteins, and complexes thereof) in model bilayers (giant unilamellar vesicles, black lipid membranes, supported lipid bilayers) are summarized and model predictions are compared with the available experimental data, thereby allowing for evaluating the validity of the introduced models. It will be shown that models describing the diffusion in freestanding (Saffman-Delbrück and Hughes-Pailthorpe-White model) and supported bilayers (the Evans-Sackmann model) are well supported by experiments, though only few experimental studies have been published so far for the latter case, calling for additional tests to reach the same level of experimental confirmation that is currently available for the case of freestanding bilayers.
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Affiliation(s)
- Stephan Block
- Department of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany.
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6
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Senac C, Urbach W, Kurtisovski E, Hünenberger PH, Horta BAC, Taulier N, Fuchs PFJ. Simulating Bilayers of Nonionic Surfactants with the GROMOS-Compatible 2016H66 Force Field. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10225-10238. [PMID: 28832154 DOI: 10.1021/acs.langmuir.7b01348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Polyoxyethylene glycol alkyl ether amphiphiles (CiEj) are important nonionic surfactants, often used for biophysical and membrane protein studies. In this work, we extensively test the GROMOS-compatible 2016H66 force field in molecular dynamics simulations involving the lamellar phase of a series of CiEj surfactants, namely C12E2, C12E3, C12E4, C12E5, and C14E4. The simulations reproduce qualitatively well the monitored structural properties and their experimental trends along the surfactant series, although some discrepancies remain, in particular in terms of the area per surfactant, the equilibrium phase of C12E5, and the order parameters of C12E3, C12E4, and C12E5. The polar head of the CiEj surfactants is highly hydrated, almost like a single polyethyleneoxide (PEO) molecule at full hydration, resulting in very compact conformations. Within the bilayer, all CiEj surfactants flip-flop spontaneously within tens of nanoseconds. Water-permeation is facilitated, and the bending rigidity is 4 to 5 times lower than that of typical phospholipid bilayers. In line with another recent theoretical study, the simulations show that the lamellar phase of CiEj contains large hydrophilic pores. These pores should be abundant in order to reproduce the comparatively low NMR order parameters. We show that their contour length is directly correlated to the order parameters, and we estimate that they should occupy approximately 7-10% of the total membrane area. Due to their highly dynamic nature (rapid flip-flops, high water permeability, observed pore formation), CiEj surfactant bilayers are found to represent surprisingly challenging systems in terms of modeling. Given this difficulty, the results presented here show that the 2016H66 parameters, optimized independently considering pure-liquid as well as polar and nonpolar solvation properties of small organic molecules, represent a good starting point for simulating these systems.
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Affiliation(s)
- Caroline Senac
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale , F-75006 Paris, France
| | - Wladimir Urbach
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale , F-75006 Paris, France
- Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University; Université Paris Diderot, Sorbonne Paris-Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS , 24 rue Lhomond, 75005 Paris, France
| | - Erol Kurtisovski
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale , F-75006 Paris, France
- Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University; Université Paris Diderot, Sorbonne Paris-Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS , 24 rue Lhomond, 75005 Paris, France
| | | | - Bruno A C Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-909, Brazil
| | - Nicolas Taulier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale , F-75006 Paris, France
| | - Patrick F J Fuchs
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot , Sorbonne Paris Cité, F-75205 Paris, France
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7
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Piantanida L, Bolt HL, Rozatian N, Cobb SL, Voïtchovsky K. Ions Modulate Stress-Induced Nanotexture in Supported Fluid Lipid Bilayers. Biophys J 2017; 113:426-439. [PMID: 28746853 PMCID: PMC5529180 DOI: 10.1016/j.bpj.2017.05.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022] Open
Abstract
Most plasma membranes comprise a large number of different molecules including lipids and proteins. In the standard fluid mosaic model, the membrane function is effected by proteins whereas lipids are largely passive and serve solely in the membrane cohesion. Here we show, using supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers in different saline solutions, that ions can locally induce ordering of the lipid molecules within the otherwise fluid bilayer when the latter is supported. This nanoordering exhibits a characteristic length scale of ∼20 nm, and manifests itself clearly when mechanical stress is applied to the membrane. Atomic force microscopy (AFM) measurements in aqueous solutions containing NaCl, KCl, CaCl2, and Tris buffer show that the magnitude of the effect is strongly ion-specific, with Ca2+ and Tris, respectively, promoting and reducing stress-induced nanotexturing of the membrane. The AFM results are complemented by fluorescence recovery after photobleaching experiments, which reveal an inverse correlation between the tendency for molecular nanoordering and the diffusion coefficient within the bilayer. Control AFM experiments on other lipids and at different temperatures support the hypothesis that the nanotexturing is induced by reversible, localized gel-like solidification of the membrane. These results suggest that supported fluid phospholipid bilayers are not homogenous at the nanoscale, but specific ions are able to locally alter molecular organization and mobility, and spatially modulate the membrane’s properties on a length scale of ∼20 nm. To illustrate this point, AFM was used to follow the adsorption of the membrane-penetrating antimicrobial peptide Temporin L in different solutions. The results confirm that the peptides do not absorb randomly, but follow the ion-induced spatial modulation of the membrane. Our results suggest that ionic effects have a significant impact for passively modulating the local properties of biological membranes, when in contact with a support such as the cytoskeleton.
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Affiliation(s)
- Luca Piantanida
- Department of Physics, Durham University, Durham, United Kingdom
| | - Hannah L Bolt
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Neshat Rozatian
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Steven L Cobb
- Department of Chemistry, Durham University, Durham, United Kingdom
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8
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Fried ES, Li YM, Gilchrist ML. Phase Composition Control in Microsphere-Supported Biomembrane Systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3028-3039. [PMID: 28198634 PMCID: PMC5568755 DOI: 10.1021/acs.langmuir.6b04150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The popularization of studies in membrane protein lipid phase coexistence has prompted the development of new techniques to construct and study biomimetic systems with cholesterol-rich lipid microdomains. Here, microsphere-supported biomembranes with integrated α-helical peptides, referred to as proteolipobeads (PLBs), were used to model peptide/protein partitioning within DOPC/DPPC/cholesterol phase-separated membranes. Due to the appearance of compositional heterogeneity and impurities in the formation of model PLB assemblies, fluorescence-activated cell sorting (FACS) was used to characterize and sort PLB populations on the basis of disordered phase (Ld) content. In addition, spectral imaging was used to assess the partitioning of FITC-labeled α-helical peptide between fluorescently labeled Ld phase and unlabeled ordered phase (Lo) phase lipid microdomains. The apparent peptide partition coefficient, Kp,app, was measured to be 0.89 ± 0.06, indicating a slight preference of the peptide for the Lo phase. A biomimetic motif of the Lo phase concentration enhancement of the biotinyl-peptide ligand display in proteolipobeads was also observed. Finally, peptide mobility was measured by FRAP separately in each lipid phase, yielding diffusivities of 0.036 ± 0.005 and 0.014 ± 0.003 μm2/s in the Ld and Lo phases, respectively.
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Affiliation(s)
- Eric S. Fried
- Department of Chemical Engineering, The City College of the City University of New York, 140th Street and Convent Avenue, New York, NY 10031
| | - Yue-Ming Li
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
- Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - M. Lane Gilchrist
- Department of Chemical Engineering, The City College of the City University of New York, 140th Street and Convent Avenue, New York, NY 10031
- Department of Biomedical Engineering, The City College of the City University of New York, 140th Street and Convent Avenue, New York, NY 10031
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9
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Clinton RW, Mears JA. Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro. J Vis Exp 2017. [PMID: 28117823 DOI: 10.3791/54971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating these studies, reincorporation of detergent-solubilized membrane proteins into liposomes is a stochastic process where protein topology is impossible to enforce. This paper offers an alternative method to these challenging techniques that utilizes a liposome-based scaffold. Protein solubility is enhanced by deletion of the transmembrane domain, and these amino acids are replaced with a tethering moiety, such as a His-tag. This tether interacts with an anchoring group (Ni2+ coordinated by nitrilotriacetic acid (NTA(Ni2+)) for His-tagged proteins), which enforces a uniform protein topology at the surface of the liposome. An example is presented wherein the interaction between Dynamin-related protein 1 (Drp1) with an integral membrane protein, Mitochondrial Fission Factor (Mff), was investigated using this scaffold liposome method. In this work, we have demonstrated the ability of Mff to efficiently recruit soluble Drp1 to the surface of liposomes, which stimulated its GTPase activity. Moreover, Drp1 was able to tubulate the Mff-decorated lipid template in the presence of specific lipids. This example demonstrates the effectiveness of scaffold liposomes using structural and functional assays and highlights the role of Mff in regulating Drp1 activity.
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Affiliation(s)
- Ryan W Clinton
- Department of Pharmacology, Center for Mitochondrial Diseases, The Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine
| | - Jason A Mears
- Department of Pharmacology, Center for Mitochondrial Diseases, The Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine;
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10
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Adrien V, Rayan G, Reffay M, Porcar L, Maldonado A, Ducruix A, Urbach W, Taulier N. Characterization of a Biomimetic Mesophase Composed of Nonionic Surfactants and an Aqueous Solvent. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10268-10275. [PMID: 27618561 DOI: 10.1021/acs.langmuir.6b02744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We have investigated the physical and biomimetic properties of a sponge (L3) phase composed of pentaethylene glycol monododecyl ether (C12E5), a nonionic surfactant, an aqueous solvent, and a cosurfactant. The following cosurfactants, commonly used for solubilizing membrane proteins, were incorporated: n-octyl-β-d-glucopyranoside (β-OG), n-dodecyl-β-d-maltopyranoside (DDM), 4-cyclohexyl-1-butyl-β-d-maltoside (CYMAL-4), and 5-cyclohexyl-1-pentyl-β-d-maltoside (CYMAL-5). Partial phase diagrams of these systems were created. The L3 phase was characterized using crossed polarizers, diffusion of a fluorescent probe by fluorescence recovery after pattern photobleaching (FRAPP), and freeze fracture electron microscopy (FFEM). By varying the hydration of the phase, we were able to tune the distance between adjacent bilayers. The characteristic distance (db) of the phase was obtained from small angle scattering (SAXS/SANS) as well as from FFEM, which yielded complementary db values. These db values were neither affected by the nature of the cosurfactant nor by the addition of membrane proteins. These findings illustrate that a biomimetic surfactant sponge phase can be created in the presence of several common membrane protein-solubilizing detergents, thus making it a versatile medium for membrane protein studies.
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Affiliation(s)
- V Adrien
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
- Univ Paris Descartes, Sorbonne Paris Cité. Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Paris, France
| | - G Rayan
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - M Reffay
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - L Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - A Maldonado
- Departamento de Física, Universidad de Sonora , Apdo Postal 1626, 83000 Hermosillo, Sonora Mexico
| | - A Ducruix
- Univ Paris Descartes, Sorbonne Paris Cité. Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Paris, France
| | - W Urbach
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75006, Paris, France
| | - N Taulier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75006, Paris, France
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11
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Abstract
The investigation of pH-dependent membrane-associated folding has both fundamental interest and practical applications for targeting of acidic tumors and specific delivery of therapeutic molecules across membrane of cancer cells. We and others investigated molecular mechanism and medical uses of class of water soluble membrane peptides, pH (Low) Insertion Peptides (pHLIP® peptides). Here we employed optical spectroscopy methods to study interactions of the truncated pHLIP® peptide (Short pHLIP®) with lipid bilayer of membrane. Tryptophan fluorescence, CD and OCD data indicate on pH-triggered formation of transmembrane helical structure. Dual quenching and FRET assays demonstrated that Short pHLIP® peptide spans lipid bilayer of membrane similar to Long pHLIP® peptides. Truncated pHLIP® peptides with multiple charged and protonatable residues in their sequences potentially can make these peptides to be less hydrophobic compared to Long pHLIP® peptides, and might have utility in tumor imaging, and potentially, in pH-regulated cytoplasmic delivery of moderately hydrophobic drugs. Protonation of single Asp triggers pH-dependent insertion into membrane. Truncated pHLIP® peptide adopts TM helical orientation at low pH. Truncated pHLIP® peptide spans lipid bilayer similar to full-length long peptide. Potential applications in cytoplasmic delivery of small hydrophobic molecules.
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Affiliation(s)
- Dhammika Weerakkody
- Department of Physics, University of Rhode Island, Kingston, RI 02881, United States
| | - Oleg A Andreev
- Department of Physics, University of Rhode Island, Kingston, RI 02881, United States
| | - Yana K Reshetnyak
- Department of Physics, University of Rhode Island, Kingston, RI 02881, United States
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12
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Camley BA, Lerner MG, Pastor RW, Brown FLH. Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes. J Chem Phys 2016; 143:243113. [PMID: 26723598 DOI: 10.1063/1.4932980] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Saffman-Delbrück hydrodynamic model for lipid-bilayer membranes is modified to account for the periodic boundary conditions commonly imposed in molecular simulations. Predicted lateral diffusion coefficients for membrane-embedded solid bodies are sensitive to box shape and converge slowly to the limit of infinite box size, raising serious doubts for the prospects of using detailed simulations to accurately predict membrane-protein diffusivities and related transport properties. Estimates for the relative error associated with periodic boundary artifacts are 50% and higher for fully atomistic models in currently feasible simulation boxes. MARTINI simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
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Affiliation(s)
- Brian A Camley
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, California 92093, USA
| | - Michael G Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana 47374, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, California 93106, USA
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13
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FRAP to Characterize Molecular Diffusion and Interaction in Various Membrane Environments. PLoS One 2016; 11:e0158457. [PMID: 27387979 PMCID: PMC4936743 DOI: 10.1371/journal.pone.0158457] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/16/2016] [Indexed: 11/19/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) is a standard method used to study the dynamics of lipids and proteins in artificial and cellular membrane systems. The advent of confocal microscopy two decades ago has made quantitative FRAP easily available to most laboratories. Usually, a single bleaching pattern/area is used and the corresponding recovery time is assumed to directly provide a diffusion coefficient, although this is only true in the case of unrestricted Brownian motion. Here, we propose some general guidelines to perform FRAP experiments under a confocal microscope with different bleaching patterns and area, allowing the experimentalist to establish whether the molecules undergo Brownian motion (free diffusion) or whether they have restricted or directed movements. Using in silico simulations of FRAP measurements, we further indicate the data acquisition criteria that have to be verified in order to obtain accurate values for the diffusion coefficient and to be able to distinguish between different diffusive species. Using this approach, we compare the behavior of lipids in three different membrane platforms (supported lipid bilayers, giant liposomes and sponge phases), and we demonstrate that FRAP measurements are consistent with results obtained using other techniques such as Fluorescence Correlation Spectroscopy (FCS) or Single Particle Tracking (SPT). Finally, we apply this method to show that the presence of the synaptic protein Munc18-1 inhibits the interaction between the synaptic vesicle SNARE protein, VAMP2, and its partner from the plasma membrane, Syn1A.
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Rayan G, Adrien V, Reffay M, Picard M, Ducruix A, Schmutz M, Urbach W, Taulier N. Surfactant bilayers maintain transmembrane protein activity. Biophys J 2015; 107:1129-1135. [PMID: 25185548 DOI: 10.1016/j.bpj.2014.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 06/21/2014] [Accepted: 07/07/2014] [Indexed: 11/26/2022] Open
Abstract
In vitro studies of membrane proteins are of interest only if their structure and function are significantly preserved. One approach is to insert them into the lipid bilayers of highly viscous cubic phases rendering the insertion and manipulation of proteins difficult. Less viscous lipid sponge phases are sometimes used, but their relatively narrow domain of existence can be easily disrupted by protein insertion. We present here a sponge phase consisting of nonionic surfactant bilayers. Its extended domain of existence and its low viscosity allow easy insertion and manipulation of membrane proteins. We show for the first time, to our knowledge, that transmembrane proteins, such as bacteriorhodopsin, sarcoplasmic reticulum Ca(2+)ATPase (SERCA1a), and its associated enzymes, are fully active in a surfactant phase.
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Affiliation(s)
- Gamal Rayan
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France
| | - Vladimir Adrien
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France; Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Myriam Reffay
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Arnaud Ducruix
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Marc Schmutz
- Institut Charles Sadron - UPR 022 - CNRS - Unistra, Strasbourg, France
| | - Wladimir Urbach
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France; Sorbonnes Université Univ Paris 6, UMR 7371, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France; CNRS, UMR 7371, Laboratoire d'Imagerie Biomédicale, Paris, France; INSERM, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France
| | - Nicolas Taulier
- Sorbonnes Université Univ Paris 6, UMR 7371, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France; CNRS, UMR 7371, Laboratoire d'Imagerie Biomédicale, Paris, France; INSERM, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France.
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15
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Noruzifar E, Camley BA, Brown FLH. Calculating hydrodynamic interactions for membrane-embedded objects. J Chem Phys 2015; 141:124711. [PMID: 25273465 DOI: 10.1063/1.4896180] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recently introduced numerical scheme for calculating self-diffusion coefficients of solid objects embedded in lipid bilayer membranes is extended to enable calculation of hydrodynamic interactions between multiple objects. The method is used to validate recent analytical predictions by Oppenheimer and Diamant [Biophys. J. 96, 3041 2009] related to the coupled diffusion of membrane embedded proteins and is shown to converge to known near-field lubrication results as objects closely approach one another; however, the present methodology also applies outside of the limiting regimes where analytical results are available. Multiple different examples involving pairs of disk-like objects with various constraints imposed on their relative motions demonstrate the importance of hydrodynamic interactions in the dynamics of proteins and lipid domains on membrane surfaces. It is demonstrated that the relative change in self-diffusion of a membrane embedded object upon perturbation by a similar proximal solid object displays a maximum for object sizes comparable to the Saffman-Delbrück length of the membrane.
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Affiliation(s)
- Ehsan Noruzifar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106-9510, USA
| | - Brian A Camley
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106-9510, USA
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16
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Astafyeva K, Urbach W, Garroum N, Taulier N, Thiam AR. Stability of C(12)E(j) Bilayers Probed with Adhesive Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6791-6796. [PMID: 26035626 DOI: 10.1021/acs.langmuir.5b00749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The stability of model surfactant bilayers from the poly(ethylene glycol) mono-n-dodecyl ether (C12Ej) family was probed. The surfactant bilayers were formed by the adhesion of emulsion droplets. We generated C12Ej bilayers by forming water-in-oil (w/o) emulsions with saline water droplets, covered by the surfactant, in a silicone and octane oil mixture. Using microfluidics, we studied the stability of those bilayers. C12E1 allowed only short-lived bilayers whereas C12E2 bilayers were stable over a wide range of oil mixtures. At high C12E2 concentration, a two-phase region was displayed in the phase diagram: bilayers formed by the adhesion of two water droplets and Janus-like particles consisting of adhering aqueous and amphiphilic droplets. C12E8 and C12E25 did not mediate bilayer formation and caused phase inversion leading to o/w emulsion. With intermediate C12E4 and C12E5 surfactants, both w/o and o/w emulsions were unstable. We provided the titration of the C12E2 bilayer with C12E4 and C12E5 to study and predict their stability behavior.
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Affiliation(s)
- Ksenia Astafyeva
- †Laboratoire de Physique Statistique, Ecole Normale Supérieure, Sorbonne Universités, UPMC Université, and Université Paris Diderot, CNRS, 24 rue Lhomond, F-75005 Paris, France
| | - Wladimir Urbach
- †Laboratoire de Physique Statistique, Ecole Normale Supérieure, Sorbonne Universités, UPMC Université, and Université Paris Diderot, CNRS, 24 rue Lhomond, F-75005 Paris, France
- ‡Université René Descartes, Paris, France
| | - Nabil Garroum
- †Laboratoire de Physique Statistique, Ecole Normale Supérieure, Sorbonne Universités, UPMC Université, and Université Paris Diderot, CNRS, 24 rue Lhomond, F-75005 Paris, France
| | - Nicolas Taulier
- §Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire d'Imagerie Biomédicale, INSERM, F-75006 Paris, France
| | - Abdou R Thiam
- †Laboratoire de Physique Statistique, Ecole Normale Supérieure, Sorbonne Universités, UPMC Université, and Université Paris Diderot, CNRS, 24 rue Lhomond, F-75005 Paris, France
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17
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The proapoptotic protein tBid forms both superficially bound and membrane-inserted oligomers. Biophys J 2014; 106:2085-95. [PMID: 24853737 DOI: 10.1016/j.bpj.2014.03.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 03/13/2014] [Accepted: 03/31/2014] [Indexed: 11/22/2022] Open
Abstract
Bid is a proapopotic activator protein of the Bcl-2 family that plays a pivotal role in controlling mitochondrial outer membrane permeabilization during apoptosis. Here, we characterized the interaction of fluorescently labeled truncated Bid (tBid) with a mitochondria-like supported lipid bilayer at the single-molecule level. The proteins observed at the membrane exhibited a very wide range of mobility. Confocal images of the membrane displayed both diffraction-limited Gaussian spots and horizontal streaks, corresponding to immobile and mobile tBid species, respectively. We observed 1), fast-diffusing proteins corresponding to a loosely, probably electrostatically bound state; 2), slowly diffusing proteins, likely corresponding to a superficially inserted state; and 3), fully immobilized proteins, suggesting a fully inserted state. The stoichiometry of these proteins was determined by normalizing their fluorescence intensity by the brightness of a tBid monomer, measured separately using fluorescence fluctuation techniques. Strikingly, the immobile species were found to be mainly tetramers and higher, whereas the mobile species had on average a significantly lower stoichiometry. Taken together, these results show that as soluble Bid progresses toward a membrane-inserted state, it undergoes an oligomerization process similar to that observed for Bax.
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18
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Schuberth C, Wedlich-Söldner R. Building a patchwork - The yeast plasma membrane as model to study lateral domain formation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:767-74. [PMID: 25541280 DOI: 10.1016/j.bbamcr.2014.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 12/01/2014] [Accepted: 12/14/2014] [Indexed: 01/03/2023]
Abstract
The plasma membrane (PM) has to fulfill a wide range of biological functions including selective uptake of substances, signal transduction and modulation of cell polarity and cell shape. To allow efficient regulation of these processes many resident proteins and lipids of the PM are laterally segregated into different functional domains. A particularly striking example of lateral segregation has been described for the budding yeast PM, where integral membrane proteins as well as lipids exhibit very slow translational mobility and form a patchwork of many overlapping micron-sized domains. Here we discuss the molecular and physical mechanisms contributing to the formation of a multi-domain membrane and review our current understanding of yeast PM organization. Many of the fundamental principles underlying membrane self-assembly and organization identified in yeast are expected to equally hold true in other organisms, even for the more transient and elusive organization of the PM in mammalian cells. This article is part of a Special Issue entitled: Nanoscale membrane organisation and signalling.
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Affiliation(s)
- Christian Schuberth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany; Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Roland Wedlich-Söldner
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany; Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany.
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19
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Saxton MJ. Wanted: scalable tracers for diffusion measurements. J Phys Chem B 2014; 118:12805-17. [PMID: 25319586 PMCID: PMC4234437 DOI: 10.1021/jp5059885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/03/2014] [Indexed: 12/02/2022]
Abstract
Scalable tracers are potentially a useful tool to examine diffusion mechanisms and to predict diffusion coefficients, particularly for hindered diffusion in complex, heterogeneous, or crowded systems. Scalable tracers are defined as a series of tracers varying in size but with the same shape, structure, surface chemistry, deformability, and diffusion mechanism. Both chemical homology and constant dynamics are required. In particular, branching must not vary with size, and there must be no transition between ordinary diffusion and reptation. Measurements using scalable tracers yield the mean diffusion coefficient as a function of size alone; measurements using nonscalable tracers yield the variation due to differences in the other properties. Candidate scalable tracers are discussed for two-dimensional (2D) diffusion in membranes and three-dimensional diffusion in aqueous solutions. Correlations to predict the mean diffusion coefficient of globular biomolecules from molecular mass are reviewed briefly. Specific suggestions for the 3D case include the use of synthetic dendrimers or random hyperbranched polymers instead of dextran and the use of core-shell quantum dots. Another useful tool would be a series of scalable tracers varying in deformability alone, prepared by varying the density of crosslinking in a polymer to make say "reinforced Ficoll" or "reinforced hyperbranched polyglycerol."
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Affiliation(s)
- Michael J. Saxton
- Department of Biochemistry
and Molecular Medicine, University of California, One Shields Ave., Davis, California 95616, United States
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20
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Khoshnood A, Jalali MA. Anomalous diffusion of proteins in sheared lipid membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032705. [PMID: 24125292 DOI: 10.1103/physreve.88.032705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 08/08/2013] [Indexed: 06/02/2023]
Abstract
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids, which are generated by hydrophobic mismatch or the transport of lipids by proteins.
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Affiliation(s)
- Atefeh Khoshnood
- Computational Mechanics Laboratory, Department of Mechanical Engineering, Sharif University of Technology, Azadi Avenue, Tehran, Iran and Center of Excellence in Design, Robotics and Automation, Department of Mechanical Engineering, Sharif University of Technology, Azadi Avenue, Tehran, Iran
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21
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Lepzelter D, Zaman M. Subdiffusion of proteins and oligomers on membranes. J Chem Phys 2013; 137:175102. [PMID: 23145748 DOI: 10.1063/1.4764305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Diffusion of proteins on lipid membranes plays a central role in cell signaling processes. From a mathematical perspective, most membrane diffusion processes are explained by the Saffman-Delbrück theory. However, recent studies have suggested a major limitation in the theoretical framework, the lack of complexity in the modeled lipid membrane. Lipid domains (sometimes termed membrane rafts) are known to slow protein diffusion, but there have been no quantitative theoretical examinations of how much diffusion is slowed in a general case. We provide an overall theoretical framework for confined-domain ("corralled") diffusion. Further, there have been multiple apparent contradictions of the basic conclusions of Saffman and Delbrück, each involving cases in which a single protein or an oligomer has multiple transmembrane regions passing through a lipid phase barrier. We present a set of corrections to the Saffman-Delbrück theory to account for these experimental observations. Our corrections are able to provide a quantitative explanation of numerous cellular signaling processes that have been considered beyond the scope of the Saffman-Delbrück theory, and may be extendable to other forms of subdiffusion.
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Affiliation(s)
- David Lepzelter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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22
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NMR methods for measuring lateral diffusion in membranes. Chem Phys Lipids 2013; 166:31-44. [DOI: 10.1016/j.chemphyslip.2012.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 02/07/2023]
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23
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Rossi G, Fuchs PFJ, Barnoud J, Monticelli L. A coarse-grained MARTINI model of polyethylene glycol and of polyoxyethylene alkyl ether surfactants. J Phys Chem B 2012; 116:14353-62. [PMID: 23137188 DOI: 10.1021/jp3095165] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nonionic surfactants are used for the isolation and purification of membrane proteins, as well as for the study of fundamental aspects of protein diffusion in membranes. Here we present a new coarse-grained model of polyethylene glycol (PEG) and of the family of polyoxyethylene alkyl ether (C(i)E(j)) surfactants. The model is compatible with the MARTINI coarse-grained force-field for lipids and proteins. We validate the model by comparing molecular dynamics simulations with experimental data. In particular, we show that the model reproduces the phase behavior of water-surfactant mixtures as a function of water concentration. We also simulate the self-assembly of two ternary mixtures that have been used for the experimental measure of protein diffusion coefficients. The first includes a cosurfactant that affects the curvature of the surfactant bilayers; the second is a mixture of C(i)E(j) surfactants, alkanes and water. In both cases, the results of self-assembly simulations are in agreement with experimental observations and pave the way to the use of the surfactant model in combination with MARTINI peptides and proteins.
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Affiliation(s)
- G Rossi
- INSERM, UMR-S665, Paris, F-75015, France.
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24
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Camley BA, Brown FLH. Contributions to membrane-embedded-protein diffusion beyond hydrodynamic theories. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061921. [PMID: 23005141 DOI: 10.1103/physreve.85.061921] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/25/2012] [Indexed: 06/01/2023]
Abstract
The diffusion coefficients of proteins embedded in a lipid membrane are traditionally described by the hydrodynamic Saffman-Delbrück theory, which predicts a weak dependence of the diffusion coefficient on protein radius, D∼lnR. Recent experiments have observed a stronger dependence, D∼1/R. This has led to speculation that the primary sources of drag on the protein are not hydrodynamic, but originate in coupling to other fields, such as lipid chain stretching or tilt. We discuss a generic model of a protein coupled to a nonconserved scalar order parameter (e.g., chain stretching), and show that earlier results may not be as universal as previously believed. In particular, we note that the drag depends on the way the protein-order parameter coupling is imposed. In this model, D∼1/R can be obtained if the protein is much larger than the order parameter correlation length. However, if we modify the model to include advection of the order parameter, which is a more appropriate assumption for a fluid membrane, we find that the entrainment of the order parameter by the protein's motion significantly changes the scaling of the diffusion coefficient. For parameters appropriate to protein diffusion, the Saffman-Delbrück-like scaling is restored, but with an effective radius for the protein that depends on the order parameter's correlation length. This qualitative difference suggests that hydrodynamic effects cannot be neglected in the computation of drag on a protein interacting with the membrane.
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Affiliation(s)
- Brian A Camley
- Department of Physics, University of California, Santa Barbara, California 93106, USA
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25
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Mueller NS, Wedlich-Söldner R, Spira F. From mosaic to patchwork: matching lipids and proteins in membrane organization. Mol Membr Biol 2012; 29:186-96. [PMID: 22594654 DOI: 10.3109/09687688.2012.687461] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Biological membranes encompass and compartmentalize cells and organelles and are a prerequisite to life as we know it. One defining feature of membranes is an astonishing diversity of building blocks. The mechanisms and principles organizing the thousands of proteins and lipids that make up membrane bilayers in cells are still under debate. Many terms and mechanisms have been introduced over the years to account for certain phenomena and aspects of membrane organization and function. Recently, the different viewpoints - focusing on lipids vs. proteins or physical vs. molecular driving forces for membrane organization - are increasingly converging. Here we review the basic properties of biological membranes and the most common theories for lateral segregation of membrane components before discussing an emerging model of a self-organized, multi-domain membrane or 'patchwork membrane'.
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Affiliation(s)
- Nikola S Mueller
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
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26
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Sanderson JM. Resolving the kinetics of lipid, protein and peptide diffusion in membranes. Mol Membr Biol 2012; 29:118-43. [DOI: 10.3109/09687688.2012.678018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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27
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Weiß K, Enderlein J. Lipid Diffusion within Black Lipid Membranes Measured with Dual-Focus Fluorescence Correlation Spectroscopy. Chemphyschem 2012; 13:990-1000. [DOI: 10.1002/cphc.201100680] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 12/15/2011] [Indexed: 11/07/2022]
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28
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Continuum simulations of biomembrane dynamics and the importance of hydrodynamic effects. Q Rev Biophys 2011; 44:391-432. [PMID: 21729348 DOI: 10.1017/s0033583511000047] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Traditional particle-based simulation strategies are impractical for the study of lipid bilayers and biological membranes over the longest length and time scales (microns, seconds and longer) relevant to cellular biology. Continuum-based models developed within the frameworks of elasticity theory, fluid dynamics and statistical mechanics provide a framework for studying membrane biophysics over a range of mesoscopic to macroscopic length and time regimes, but the application of such ideas to simulation studies has occurred only relatively recently. We review some of our efforts in this direction with emphasis on the dynamics in model membrane systems. Several examples are presented that highlight the prominent role of hydrodynamics in membrane dynamics and we argue that careful consideration of fluid dynamics is key to understanding membrane biophysics at the cellular scale.
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29
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Guo L, Smith-Dupont KB, Gai F. Diffusion as a probe of peptide-induced membrane domain formation. Biochemistry 2011; 50:2291-7. [PMID: 21332237 DOI: 10.1021/bi102068j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, we have shown that association with an antimicrobial peptide (AMP) can drastically alter the diffusion behavior of the constituent lipids in model membranes (Biochemistry 49, 4672-4678). In particular, we found that the diffusion time of a tracer fluorescent lipid through a confocal volume measured via fluorescence correlation spectroscopy (FCS) is distributed over a wide range of time scales, indicating the formation of stable and/or transient membrane species that have different mobilities. A simple estimate, however, suggested that the slow diffusing species are too large to be attributed to AMP oligomers or pores that are tightly bound to a small number of lipids. Thus, we tentatively ascribed them to membrane domains and/or clusters that possess distinctively different diffusion properties. In order to further substantiate our previous conjecture, herein we study the diffusion behavior of the membrane-bound peptide molecules using the same AMPs and model membranes. Our results show, in contrast to our previous findings, that the diffusion times of the membrane-bound peptides exhibit a much narrower distribution that is more similar to that of the lipids in peptide-free membranes. Thus, taken together, these results indicate that while AMP molecules prompt domain formation in membranes, they are not tightly associated with the lipid domains thus formed. Instead, they are likely located at the boundary regions separating various domains and acting as mobile fences.
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Affiliation(s)
- Lin Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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30
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Rayan G, Guet JE, Taulier N, Pincet F, Urbach W. Recent applications of fluorescence recovery after photobleaching (FRAP) to membrane bio-macromolecules. SENSORS 2010; 10:5927-48. [PMID: 22219695 PMCID: PMC3247740 DOI: 10.3390/s100605927] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 05/10/2010] [Accepted: 05/28/2010] [Indexed: 01/24/2023]
Abstract
This review examines some recent applications of fluorescence recovery after photobleaching (FRAP) to biopolymers, while mainly focusing on membrane protein studies. Initially, we discuss the lateral diffusion of membrane proteins, as measured by FRAP. Then, we talk about the use of FRAP to probe interactions between membrane proteins by obtaining fundamental information such as geometry and stoichiometry of the interacting complex. Afterwards, we discuss some applications of FRAP at the cellular level as well as the level of organisms. We conclude by comparing diffusion coefficients obtained by FRAP and several other alternative methods.
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Affiliation(s)
- Gamal Rayan
- Laboratoire de Physique Statistique de l'Ecole Normale Supérieure, associe aux Universites Paris 6 et Paris 7, CNRS UMR 8550, 24 rue Lhomond, 75005 Paris, France.
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