1
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Schneider F, Cespedes PF, Karedla N, Dustin ML, Fritzsche M. Quantifying biomolecular organisation in membranes with brightness-transit statistics. Nat Commun 2024; 15:7082. [PMID: 39152104 PMCID: PMC11329664 DOI: 10.1038/s41467-024-51435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024] Open
Abstract
Cells crucially rely on the interactions of biomolecules at their plasma membrane to maintain homeostasis. Yet, a methodology to systematically quantify biomolecular organisation, measuring diffusion dynamics and oligomerisation, represents an unmet need. Here, we introduce the brightness-transit statistics (BTS) method based on fluorescence fluctuation spectroscopy and combine information from brightness and transit times to elucidate biomolecular diffusion and oligomerisation in both cell-free in vitro and in vitro systems incorporating living cells. We validate our approach in silico with computer simulations and experimentally using oligomerisation of EGFP tethered to supported lipid bilayers. We apply our pipeline to study the oligomerisation of CD40 ectodomain in vitro and endogenous CD40 on primary B cells. While we find a potential for CD40 to oligomerize in a concentration or ligand depended manner, we do not observe mobile oligomers on B cells. The BTS method combines sensitive analysis, quantification, and intuitive visualisation of dynamic biomolecular organisation.
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Affiliation(s)
- Falk Schneider
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom.
- Translational Imaging Center, University of Southern California, Los Angeles, California, 90089, United States of America.
| | - Pablo F Cespedes
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Narain Karedla
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom
| | - Michael L Dustin
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Marco Fritzsche
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom.
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom.
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2
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Prikhodko IV, Guria GT. The method for assessing the specificity of developing CAR therapies. BIOPHYSICAL REPORTS 2024; 4:100172. [PMID: 39025235 PMCID: PMC11344002 DOI: 10.1016/j.bpr.2024.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
The effectiveness of antitumor chimeric antigen receptor (CAR) therapy mainly dealt with an elevated sensitivity of CAR cells to target cells. However, CAR therapies are associated with nonspecific side effects: on-target off-tumor toxicity. Sensitivity and specificity of CAR cells are the most important properties of the recognition process of target cells among other cells. Current developments are mainly concentrated on exploring molecular biology methods for designing CAR cells with the highest sensitivity, while the problem of the CAR cell specificity is rarely considered. For the assessment of CAR cell specificity, we suggest that, in addition to an elevated level of CAR-antigen affinity, the ability of CARs for clustering should be taken into account. We assume that the CAR cell cytotoxicity is determined by CAR clustering. The latter is treated within the framework of nucleation theory. The master equation for the probability of CAR cell cytotoxicity is derived. The size of a critical CAR cluster is found to be one of two most essential parameters. The conditions for necessary sensitivity and sufficient specificity are explored. Relevant parametric diagrams are derived. Possible applications of the method for assessing the specificity of developing CAR therapies are discussed.
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Affiliation(s)
- Ivan V Prikhodko
- Laboratory for Mathematical Modelling of Biological Processes, National Medical Research Center for Hematology, Moscow, Russia
| | - Georgy Th Guria
- Laboratory for Mathematical Modelling of Biological Processes, National Medical Research Center for Hematology, Moscow, Russia; Chair of the Living Systems Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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3
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Nordahl L, Akkuratov EE, Heimgärtner J, Schach K, Meineke B, Elsässer S, Wennmalm S, Brismar H. Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS. Biochim Biophys Acta Gen Subj 2024; 1868:130619. [PMID: 38643888 DOI: 10.1016/j.bbagen.2024.130619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
The sodium potassium pump, Na,K-ATPase (NKA), is an integral plasma membrane protein, expressed in all eukaryotic cells. It is responsible for maintaining the transmembrane Na+ gradient and is the major determinant of the membrane potential. Self-interaction and oligomerization of NKA in cell membranes has been proposed and discussed but is still an open question. Here, we have used a combination of FRET and Fluorescence Correlation Spectroscopy, FRET-FCS, to analyze NKA in the plasma membrane of living cells. Click chemistry was used to conjugate the fluorescent labels Alexa 488 and Alexa 647 to non-canonical amino acids introduced in the NKA α1 and β1 subunits. We demonstrate that FRET-FCS can detect an order of magnitude lower concentration of green-red labeled protein pairs in a single-labeled red and green background than what is possible with cross-correlation (FCCS). We show that a significant fraction of NKA is expressed as a dimer in the plasma membrane. We also introduce a method to estimate not only the number of single and double labeled NKA, but the number of unlabeled, endogenous NKA and estimate the density of endogenous NKA at the plasma membrane to 1400 ± 800 enzymes/μm2.
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Affiliation(s)
- Linnea Nordahl
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | - Evgeny E Akkuratov
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Katja Schach
- Graduate Training Centre of Neuroscience, University of Tübingen, Otfried-Müller-Str. 27, 72076 Tübingen, Germany
| | - Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Simon Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Stefan Wennmalm
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
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4
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Pérez-Mitta G, Sezgin Y, Wang W, MacKinnon R. Freestanding bilayer microscope for single-molecule imaging of membrane proteins. SCIENCE ADVANCES 2024; 10:eado4722. [PMID: 38905330 PMCID: PMC11192074 DOI: 10.1126/sciadv.ado4722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Integral membrane proteins (IMPs) constitute a large fraction of organismal proteomes, playing fundamental roles in physiology and disease. Despite their importance, the mechanisms underlying dynamic features of IMPs, such as anomalous diffusion, protein-protein interactions, and protein clustering, remain largely unknown due to the high complexity of cell membrane environments. Available methods for in vitro studies are insufficient to study IMP dynamics systematically. This publication introduces the freestanding bilayer microscope (FBM), which combines the advantages of freestanding bilayers with single-particle tracking. The FBM, based on planar lipid bilayers, enables the study of IMP dynamics with single-molecule resolution and unconstrained diffusion. This paper benchmarks the FBM against total internal reflection fluorescence imaging on supported bilayers and is used here to estimate ion channel open probability and to examine the diffusion behavior of an ion channel in phase-separated bilayers. The FBM emerges as a powerful tool to examine membrane protein/lipid organization and dynamics to understand cell membrane processes.
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Affiliation(s)
- Gonzalo Pérez-Mitta
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Yeliz Sezgin
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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5
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Liu TT, Huang SH, Chao L. Rapid Enrichment of a Native Multipass Transmembrane Protein via Cell Membrane Electrophoresis through Buffer pH and Ionic Strength Adjustment. J Am Chem Soc 2024; 146:11634-11647. [PMID: 38628144 PMCID: PMC11066866 DOI: 10.1021/jacs.3c13579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Supported membrane electrophoresis is a promising technique for collecting membrane proteins in native bilayer environments. However, the slow mobility of typical transmembrane proteins has impeded the technique's advancement. Here, we successfully applied cell membrane electrophoresis to rapidly enrich a 12-transmembrane helix protein, glucose transporter 1 with antibodies (GLUT1 complex), by tuning the buffer pH and ionic strength. The identified conditions allowed the separation of the GLUT1 complex and a lipid probe, Fast-DiO, within a native-like environment in a few minutes. A force model was developed to account for distinct electric and drag forces acting on the transmembrane and aqueous-exposed portion of a transmembrane protein as well as the electroosmotic force. This model not only elucidates the impact of size and charge properties of transmembrane proteins but also highlights the influence of pH and ionic strength on the driving forces and, consequently, electrophoretic mobility. Model predictions align well with experimentally measured electrophoretic mobilities of the GLUT1 complex and Fast-DiO at various pH and ionic strengths as well as with several lipid probes, lipid-anchored proteins, and reconstituted membrane proteins from previous studies. Force analyses revealed the substantial membrane drag of the GLUT1 complex, significantly slowing down electrophoretic mobility. Besides, the counterbalance of similar magnitudes of electroosmotic and electric forces results in a small net driving force and, consequently, reduced mobility under typical neutral pH conditions. Our results further highlight how the size and charge properties of transmembrane proteins influence the suitable range of operating conditions for effective movement, providing potential applications for concentrating and isolating membrane proteins within this platform.
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Affiliation(s)
- Tzu-Tzu Liu
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Sin-Han Huang
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Ling Chao
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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6
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Rentsch J, Bandstra S, Sezen B, Sigrist P, Bottanelli F, Schmerl B, Shoichet S, Noé F, Sadeghi M, Ewers H. Sub-membrane actin rings compartmentalize the plasma membrane. J Cell Biol 2024; 223:e202310138. [PMID: 38252080 PMCID: PMC10807028 DOI: 10.1083/jcb.202310138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The compartmentalization of the plasma membrane (PM) is a fundamental feature of cells. The diffusivity of membrane proteins is significantly lower in biological than in artificial membranes. This is likely due to actin filaments, but assays to prove a direct dependence remain elusive. We recently showed that periodic actin rings in the neuronal axon initial segment (AIS) confine membrane protein motion between them. Still, the local enrichment of ion channels offers an alternative explanation. Here we show, using computational modeling, that in contrast to actin rings, ion channels in the AIS cannot mediate confinement. Furthermore, we show, employing a combinatorial approach of single particle tracking and super-resolution microscopy, that actin rings are close to the PM and that they confine membrane proteins in several neuronal cell types. Finally, we show that actin disruption leads to loss of compartmentalization. Taken together, we here develop a system for the investigation of membrane compartmentalization and show that actin rings compartmentalize the PM.
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Affiliation(s)
- Jakob Rentsch
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Selle Bandstra
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Batuhan Sezen
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Philipp Sigrist
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Francesca Bottanelli
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Bettina Schmerl
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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7
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Vögele M, Köfinger J, Hummer G. Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS APPLIED BIO MATERIALS 2024; 7:528-534. [PMID: 36070609 PMCID: PMC10880049 DOI: 10.1021/acsabm.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable filter. Supported dense-packed 2D-crystals of single-walled carbon nanotube (CNT) porins with ∼1 nm wide pores could, in principle, meet these challenges. However, such CNT membranes cannot currently be synthesized at high pore density. Here, we use computer simulations to explore lipid-mediated self-assembly as a route toward densely packed CNT membranes, motivated by the analogy to membrane-protein 2D crystallization. In large-scale coarse-grained molecular dynamics (MD) simulations, we find that CNTs in lipid membranes readily self-assemble into large clusters. Lipids trapped between the CNTs lubricate CNT repacking upon collisions of diffusing clusters, thereby facilitating the formation of large ordered structures. Cluster diffusion follows the Saffman-Delbrück law and its generalization by Hughes, Pailthorpe, and White. On longer time scales, we expect the formation of close-packed CNT structures by depletion of the intervening shared annular lipid shell, depending on the relative strength of CNT-CNT and CNT-lipid interactions. Our simulations identify CNT length, diameter, and end functionalization as major factors for the self-assembly of CNT membranes.
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Affiliation(s)
- Martin Vögele
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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8
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Wu YL, Lee K, Diloknawarit B, Odom TW. Ligand Separation on Nanoconstructs Affects Targeting Selectivity to Protein Dimers on Cell Membranes. NANO LETTERS 2024; 24:519-524. [PMID: 38126338 PMCID: PMC11252445 DOI: 10.1021/acs.nanolett.3c04641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This work demonstrates that targeting ligand density on nanoparticles can affect interactions between the nanoconstructs and cell membrane receptors. We discovered that when the separation between covalently grafted DNA aptamers on gold nanostars was comparable to the distance between binding sites on a receptor dimer (matched density; MD), nanoconstructs exhibited a higher selectivity for binding to the dimeric form of the protein. Single-particle dynamics of MD nanoconstructs showed slower rotational rates and larger translational footprints on cancer cells expressing more dimeric forms of receptors (dimer+) compared with cells having more monomeric forms (dimer-). In contrast, nanoconstructs with either increased (nonmatched density; NDlow) or decreased ligand spacing (NDhigh) had minimal changes in dynamics on either dimer+ or dimer- cells. Real-time, single-particle analyses can reveal the importance of nanoconstruct ligand density for the selective targeting of membrane receptors in live cells.
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Affiliation(s)
- Yuhao Leo Wu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kwahun Lee
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Bundit Diloknawarit
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Teri W Odom
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
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9
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Liu P, Beltramo PJ. Effects of crowding on the diffusivity of membrane adhered particles. SOFT MATTER 2023; 19:7708-7716. [PMID: 37791427 DOI: 10.1039/d3sm01269g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation of complexes, cell-cell signaling, and membrane trafficking. These diffusive processes are complicated by how concentrated, or "crowded", the inclusions are, which can occupy between 30-50% of the area fraction of the membrane. In this work, we elucidate the effects of increasing concentration of model membrane inclusions in a free-standing artificial cell membrane on inclusion diffusivity and the apparent viscosity of the membrane. By multiple particle tracking of fluorescent microparticles covalently tethered to the bilayer, we show the transition from expected Brownian dynamics, which accurately measure the membrane viscosity, to subdiffusive behavior with decreased diffusion coefficient as the particle area fraction increases from 1% to around 30%, approaching physiological levels of crowding. At high crowding, the onset of non-Gaussian behavior is observed. Using hydrodynamic models relating the 2D diffusion coefficient to the viscosity of a membrane, we determine the apparent viscosity of the bilayer from the particle diffusivity and show an increase in the apparent membrane viscosity with increasing particle area fraction. However, the scaling of this increase is in contrast with the behavior of monolayer inclusion diffusion and bulk suspension rheology. These results demonstrate that physiological levels of model membrane crowding nontrivially alter the dynamics and apparent viscosity of the system, which has implications for understanding membrane protein interactions and particle-membrane transport processes.
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Affiliation(s)
- Paige Liu
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Peter J Beltramo
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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10
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de Caestecker C, Macara IG. A Size Filter Regulates Apical Protein Sorting. RESEARCH SQUARE 2023:rs.3.rs-3210598. [PMID: 37577471 PMCID: PMC10418535 DOI: 10.21203/rs.3.rs-3210598/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Despite decades of research, apical sorting of epithelial membrane proteins remains incompletely understood. We noted that apical cytoplasmic domains are smaller than those of basolateral proteins; however, the reason for this discrepancy is unknown. We investigated whether a size barrier at the trans-Golgi network (TGN) might hinder apical sorting of proteins with large cytoplasmic tails. We focused on Crb3 and Ace2 as representative apical proteins with short cytoplasmic tails. By incorporating a streptavidin-binding peptide, these proteins can be trapped in the endoplasmic reticulum (ER) until addition of biotin, which triggers synchronous release to the Golgi and subsequent transport to the apical cortex. Strikingly, departure from the Golgi could be significantly delayed simply by increasing cytoplasmic bulk. Moreover, large and small Crb3 segregated into spatially distinct Golgi regions as detected by super resolution imaging. Biologically, Crb3 forms a complex through its cytoplasmic tail with the Pals1 protein, which could also delay departure, but although associated at the ER and Golgi, we found that Pals1 disassociates prior to Crb3 departure. Notably, a non-dissociable mutant Pals1 hampers the exit of Crb3. We conclude that an unexpected mechanism involving a size filter at the TGN facilitates apical sorting of proteins with small cytoplasmic domains and that timely release of Pals1, to reduce cytoplasmic domain size, is essential for the normal kinetics of Crb3 sorting.
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Affiliation(s)
- Christian de Caestecker
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine; Nashville TN 37205, U.S
| | - Ian G. Macara
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine; Nashville TN 37205, U.S
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11
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Henning P, Köster T, Haack F, Burrage K, Uhrmacher AM. Implications of different membrane compartmentalization models in particle-based in silico studies. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221177. [PMID: 37416823 PMCID: PMC10320350 DOI: 10.1098/rsos.221177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Studying membrane dynamics is important to understand the cellular response to environmental stimuli. A decisive spatial characteristic of the plasma membrane is its compartmental structure created by the actin-based membrane-skeleton (fences) and anchored transmembrane proteins (pickets). Particle-based reaction-diffusion simulation of the membrane offers a suitable temporal and spatial resolution to analyse its spatially heterogeneous and stochastic dynamics. Fences have been modelled via hop probabilities, potentials or explicit picket fences. Our study analyses the different approaches' constraints and their impact on simulation results and performance. Each of the methods comes with its own constraints; the picket fences require small timesteps, potential fences might induce a bias in diffusion in crowded systems, and probabilistic fences, in addition to carefully scaling the probability with the timesteps, induce higher computational costs for each propagation step.
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Affiliation(s)
- Philipp Henning
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Till Köster
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Fiete Haack
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- Visiting Professor, Department of Computer Science, University of Oxford, Oxford, UK
| | - Adelinde M. Uhrmacher
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
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12
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Álvarez Z, Ortega JA, Sato K, Sasselli IR, Kolberg-Edelbrock AN, Qiu R, Marshall KA, Nguyen TP, Smith CS, Quinlan KA, Papakis V, Syrgiannis Z, Sather NA, Musumeci C, Engel E, Stupp SI, Kiskinis E. Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons. Cell Stem Cell 2023; 30:219-238.e14. [PMID: 36638801 PMCID: PMC9898161 DOI: 10.1016/j.stem.2022.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/04/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023]
Abstract
Human induced pluripotent stem cell (hiPSC) technologies offer a unique resource for modeling neurological diseases. However, iPSC models are fraught with technical limitations including abnormal aggregation and inefficient maturation of differentiated neurons. These problems are in part due to the absence of synergistic cues of the native extracellular matrix (ECM). We report on the use of three artificial ECMs based on peptide amphiphile (PA) supramolecular nanofibers. All nanofibers display the laminin-derived IKVAV signal on their surface but differ in the nature of their non-bioactive domains. We find that nanofibers with greater intensity of internal supramolecular motion have enhanced bioactivity toward hiPSC-derived motor and cortical neurons. Proteomic, biochemical, and functional assays reveal that highly mobile PA scaffolds caused enhanced β1-integrin pathway activation, reduced aggregation, increased arborization, and matured electrophysiological activity of neurons. Our work highlights the importance of designing biomimetic ECMs to study the development, function, and dysfunction of human neurons.
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Affiliation(s)
- Zaida Álvarez
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Medicine, Northwestern University, Chicago, IL 60611, USA; Biomaterials for Regenerative Therapies, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain
| | - J Alberto Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Kohei Sato
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Ivan R Sasselli
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA; Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
| | - Alexandra N Kolberg-Edelbrock
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Ruomeng Qiu
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Kelly A Marshall
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Thao Phuong Nguyen
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Cara S Smith
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Katharina A Quinlan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zois Syrgiannis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Nicholas A Sather
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA
| | - Chiara Musumeci
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Elisabeth Engel
- Biomaterials for Regenerative Therapies, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA; Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA; Department of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Evangelos Kiskinis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, IL 60611, USA; The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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13
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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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14
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Fullstone G. Rapid Particle-Based Simulations of Cellular Signalling with the FLAME-Accelerated Signalling Tool (FaST) and GPUs. Methods Mol Biol 2023; 2634:191-212. [PMID: 37074580 DOI: 10.1007/978-1-0716-3008-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Cellular signalling is a vital process in living organisms for coordinating highly diverse responses to various stimuli. Particle-based modelling excels in its ability to model complex features of cellular signalling pathways including stochasticity, spatial effects, and heterogeneity, thus improving our understanding of critical decision processes in biology. Yet, particle-based modelling is computationally prohibitive to implement. We recently developed FaST (FLAME-accelerated signalling tool), a software tool that harnesses the power of high-performance computation to reduce the computational burden of particle-based modelling. In particular, employing the unique massively parallel architecture of graphic processing units (GPUs) provided extreme speed ups of simulations by >650-fold. In this chapter, we provide a step-by-step walkthrough of how to use FaST to create GPU-accelerated simulations of a simple cellular signalling network. We further explore how the flexibility of FaST can be used to implement entirely customized simulations while still including the intrinsic speed up advantages of GPU-based parallelization.
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Affiliation(s)
- Gavin Fullstone
- Institute for Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.
- Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany.
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15
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Bellotti AA, Murphy JG, O’Leary TS, Hoffman DA. Transport between im/mobile fractions shapes the speed and profile of cargo distribution in neurons. BIOPHYSICAL REPORTS 2022; 2:100082. [PMID: 36425667 PMCID: PMC9680811 DOI: 10.1016/j.bpr.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Neuronal function requires continuous distribution of ion channels and other proteins throughout large cell morphologies. Protein distribution is complicated by immobilization of freely diffusing subunits such as on lipid rafts or in postsynaptic densities. Here, we infer rates of immobilization for the voltage-gated potassium channel Kv4.2. Fluorescence recovery after photobleaching quantifies protein diffusion kinetics, typically reported as a recovery rate and mobile fraction. We show that, implicit in the fluorescence recovery, are rates of particle transfer between mobile and immobile fractions (im/mobilization). We performed photobleaching of fluorescein-tagged ion channel Kv4.2-sGFP2 in over 450 dendrites of rat hippocampal cells. Using mass-action models, we infer rates of Kv4.2-sGFP2 im/mobilization. Using a realistic neuron morphology, we show how these rates shape the speed and profile of subunit distribution. The experimental protocol and model inference introduced here is widely applicable to other cargo and experimental systems.
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Affiliation(s)
- Adriano A. Bellotti
- Department of Engineering, University of Cambridge, Cambridge, UK
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Jonathan G. Murphy
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | | | - Dax A. Hoffman
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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16
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Abstract
The sensitivity of the αβ T cell receptor (TCR) is enhanced by the coreceptors CD4 and CD8αβ, which are expressed primarily by cells of the helper and cytotoxic T cell lineages, respectively. The coreceptors bind to major histocompatibility complex (MHC) molecules and associate intracellularly with the Src-family kinase Lck, which catalyzes TCR phosphorylation during receptor triggering. Although coreceptor/kinase occupancy was initially believed to be high, a recent study suggested that most coreceptors exist in an Lck-free state, and that this low occupancy helps to effect TCR antigen discrimination. Here, using the same method, we found instead that the CD4/Lck interaction was stoichiometric (~100%) and that the CD8αβ/Lck interaction was substantial (~60%). We confirmed our findings in live cells using fluorescence cross-correlation spectroscopy (FCCS) to measure coreceptor/Lck codiffusion in situ. After introducing structurally guided mutations into the intracellular domain of CD4, we used FCCS to also show that stoichiometric coupling to Lck required an amphipathic α-helix present in CD4 but not CD8α. In double-positive cells expressing equal numbers of both coreceptors, but limiting amounts of kinase, CD4 outcompeted CD8αβ for Lck. In T cells, TCR signaling induced CD4/Lck oligomerization but did not affect the high levels of CD4/Lck occupancy. These findings help settle the question of kinase occupancy and suggest that the binding advantages that CD4 has over CD8 could be important when Lck levels are limiting.
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17
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Gurdap CO, Wedemann L, Sych T, Sezgin E. Influence of the extracellular domain size on the dynamic behavior of membrane proteins. Biophys J 2022; 121:3826-3836. [PMID: 36110044 PMCID: PMC9674980 DOI: 10.1016/j.bpj.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/15/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
The dynamic behavior of plasma membrane proteins mediates various cellular processes such as cellular motility, communication, and signaling. It is widely accepted that the dynamics of the membrane proteins is determined either by the interactions of the transmembrane domain with the surrounding lipids or by the interactions of the intracellular domain with cytosolic components such as cortical actin. Although initiation of different cellular signaling events at the plasma membrane has been attributed to the extracellular domain (ECD) properties recently, the impact of ECDs on the dynamic behavior of membrane proteins is rather unexplored. Here, we investigate how ECD properties influence protein dynamics in the lipid bilayer by reconstituting ECDs of different sizes or glycosylation in model membrane systems and analyzing ECD-driven protein sorting in lipid domains as well as protein mobility. Our data show that increasing the ECD mass or glycosylation leads to a decrease in ordered domain partitioning and diffusivity. Our data reconcile different mechanisms proposed for the initiation of cellular signaling by linking the ECD size of membrane proteins with their localization and diffusion dynamics in the plasma membrane.
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Affiliation(s)
- Cenk Onur Gurdap
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Linda Wedemann
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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18
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Hetero-pentamerization determines mobility and conductance of Glycine receptor α3 splice variants. Cell Mol Life Sci 2022; 79:540. [PMID: 36197517 PMCID: PMC9534812 DOI: 10.1007/s00018-022-04506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/05/2022]
Abstract
Glycine receptors (GlyRs) are ligand-gated pentameric chloride channels in the central nervous system. GlyR-α3 is a possible target for chronic pain treatment and temporal lobe epilepsy. Alternative splicing into K or L variants determines the subcellular fate and function of GlyR-α3, yet it remains to be shown whether its different splice variants can functionally co-assemble, and what the properties of such heteropentamers would be. Here, we subjected GlyR-α3 to a combined fluorescence microscopy and electrophysiology analysis. We employ masked Pearson’s and dual-color spatiotemporal correlation analysis to prove that GlyR-α3 splice variants heteropentamerize, adopting the mobility of the K variant. Fluorescence-based single-subunit counting experiments revealed a variable and concentration ratio dependent hetero-stoichiometry. Via cell-attached single-channel electrophysiology we show that heteropentamers exhibit currents in between those of K and L variants. Our data are compatible with a model where α3 heteropentamerization fine-tunes mobility and activity of GlyR-α3 channels, which is important to understand and tackle α3 related diseases.
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19
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Wierenga H, Wolde PRT. Energetic constraints on filament-mediated cell polarization. Phys Rev E 2022; 105:064406. [PMID: 35854527 DOI: 10.1103/physreve.105.064406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on the membrane and create a high-density spot of membrane-bound proteins. Yet, the thermodynamic constraints on filament-based cell polarization remain unknown. We show by mathematical modeling that cell polarization requires detailed balance to be broken, and we quantify the free-energy cost of maintaining a polarized state of the cell. Our study reveals that detailed balance cannot only be broken via the active transport of proteins along filaments but also via a chemical modification cycle, allowing detailed balance to be broken by the shuttling of proteins between the filament, membrane, and cytosol. Our model thus shows that cell polarization can be established via two distinct driving mechanisms, one based on active transport and one based on nonequilibrium binding. Furthermore, the model predicts that the driven binding process dissipates orders of magnitude less free energy than the transport-based process to create the same membrane spot. Active transport along filaments may be sufficient to create a polarized distribution of membrane-bound proteins, but an additional chemical modification cycle of the proteins themselves is more efficient and less sensitive to the physical exclusion of proteins on the transporting filaments, providing insight in the design principles of the Pom1/Tea1/Tea4 system in fission yeast and the Cdc42 system in budding yeast.
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20
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Fournier JB. Field-mediated interactions of passive and conformation-active particles: multibody and retardation effects. SOFT MATTER 2022; 18:2634-2645. [PMID: 35302131 DOI: 10.1039/d1sm01823j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Particles in soft matter interact through the deformation field they create, as in the "cheerios" effect or the curvature-mediated interactions of membrane proteins. Using a simple model for field-mediated interactions between passive particles, or active particles that switch conformation randomly or synchronously, we derive generic results concerning multibody interactions, activity driven patterns, and retardation effects.
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Affiliation(s)
- Jean-Baptiste Fournier
- Université Paris Cité, CNRS, Laboratoire Matière et Systèmes Complexes (MSC), F-75013 Paris, France.
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21
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Morzy D, Bastings M. Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes. Angew Chem Int Ed Engl 2022; 61:e202114167. [PMID: 34982497 PMCID: PMC9303963 DOI: 10.1002/anie.202114167] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Indexed: 01/16/2023]
Abstract
Numerous key biological processes rely on the concept of multivalency, where ligands achieve stable binding only upon engaging multiple receptors. These processes, like viral entry or immune synapse formation, occur on the diffusive cellular membrane. One crucial, yet underexplored aspect of multivalent binding is the mobility of coupled receptors. Here, we discuss the consequences of mobility in multivalent processes from four perspectives: (I) The facilitation of receptor recruitment by the multivalent ligand due to their diffusivity prior to binding. (II) The effects of receptor preassembly, which allows their local accumulation. (III) The consequences of changes in mobility upon the formation of receptor/ligand complex. (IV) The changes in the diffusivity of lipid environment surrounding engaged receptors. We demonstrate how understanding mobility is essential for fully unravelling the principles of multivalent membrane processes, leading to further development in studies on receptor interactions, and guide the design of new generations of multivalent ligands.
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Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale de Lausanne, Route Cantonale, 1015, Lausanne, Switzerland
| | - Maartje Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale de Lausanne, Route Cantonale, 1015, Lausanne, Switzerland
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22
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Morzy D, Bastings M. Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory Institute of Materials School of Engineering École Polytechnique Fédérale de Lausanne Route Cantonale 1015 Lausanne Switzerland
| | - Maartje Bastings
- Programmable Biomaterials Laboratory Institute of Materials School of Engineering École Polytechnique Fédérale de Lausanne Route Cantonale 1015 Lausanne Switzerland
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23
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Chen J, Zhao Y, Wan Y, Zhu L, Li B, Wu J, Li L, Huang Y, Li Y, Long X, Deng S. Electrochemiluminescent Ion-Channeling Framework for Membrane Binding and Transmembrane Activity Assays. Anal Chem 2022; 94:2154-2162. [PMID: 35041791 DOI: 10.1021/acs.analchem.1c04593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent upgrades in the electrochemiluminescence (ECL) technique showcased its brilliant knack in probing microscopic biointerfacial events, many of which were actually underlain by the ionotropic membrane processes, yet not being ostensive. Here, by modeling an artificial lipoid-supported porin ensemble, we explore and establish the ECL potency in profiling ion-channel activities. A lipophilic hollowed construct dubbed ZnPC was made out of the dynamic covalent chemistry, and its unique geometry was characterized that configured stoichiometric ECL-emissive units in a cubic stance; while the aliphatic vertices of ZnPC helped it safely snorkel and steadily irradiate in a biofilm fusion. After expounding basic ECL properties, the brightness was traced out in response to halogen contents that was lit up by F-/Cl- but down by Br-/I-. The overall pattern fitted the Langmuir isotherm, from which the membrane-binding strengths of the four were analyzed, compared, and collaterally examined in impedimetrics. On the other hand, one could derive anionic transmembrane kinetics from the time-dependent ECL statistics that pinpointed the ECL signaling via the nanocage-directed mass-transfer pathway. More data mining unveiled an ECL-featured Hofmeister series and the thermodynamic governing force behind all scenes. Finally, combining with halide-selective fluorometry, the synthetic conduit was identified as an ECL symporter. In short, this work develops a novel ECL model for the evaluation of life-mimicking membrane permeation. It might intrigue the outreach of ECL applications in the measurement of diverse surface-confined transient scenarios, e.g., in vitro gated ion or molecule trafficking, which used to be handled by nanopore and electrofluorochromic assays.
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24
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Abstract
Dynamic processes on membrane surfaces are essential for biological function. Traditionally, quantitative measurements of lipid/protein motion have been interpreted in the framework of membrane hydrodynamics. However, some recent single-molecule tracking studies have proven difficult to interpret via hydrodynamic arguments. Does this suggest a failure of hydrodynamic theory or simply highlight the dangers in attempting to extend hydrodynamic arguments down to molecular scales? Intermolecular correlations are superior to single-molecule observations for studying hydrodynamics due to the longer length scales involved. The current work reports dynamic pair correlations of lipids in model membranes. Submicron distance-dependent correlations are well resolved, and complementary numerical calculations indicate that hydrodynamic theory can predict membrane dynamics over distances of tens of nanometers and longer. Lipid membranes are complex quasi–two-dimensional fluids, whose importance in biology and unique physical/materials properties have made them a major target for biophysical research. Recent single-molecule tracking experiments in membranes have caused some controversy, calling the venerable Saffman–Delbrück model into question and suggesting that, perhaps, current understanding of membrane hydrodynamics is imperfect. However, single-molecule tracking is not well suited to resolving the details of hydrodynamic flows; observations involving correlations between multiple molecules are superior for this purpose. Here dual-color molecular tracking with submillisecond time resolution and submicron spatial resolution is employed to reveal correlations in the Brownian motion of pairs of fluorescently labeled lipids in membranes. These correlations extend hundreds of nanometers in freely floating bilayers (black lipid membranes) but are severely suppressed in supported lipid bilayers. The measurements are consistent with hydrodynamic predictions based on an extended Saffman–Delbrück theory that explicitly accounts for the two-leaflet bilayer structure of lipid membranes.
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25
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Berselli G, Gimenez A, O’Connor A, Keyes TE. Robust Photoelectric Biomolecular Switch at a Microcavity-Supported Lipid Bilayer. ACS APPLIED MATERIALS & INTERFACES 2021; 13:29158-29169. [PMID: 34121400 PMCID: PMC8289237 DOI: 10.1021/acsami.1c06798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/01/2021] [Indexed: 05/08/2023]
Abstract
Biomolecular devices based on photo-responsive proteins have been widely proposed for medical, electrical, and energy storage and production applications. Also, bacteriorhodopsin (bR) has been extensively applied in such prospective devices as a robust photo addressable proton pump. As it is a membrane protein, in principle, it should function most efficiently when reconstituted into a fully fluid lipid bilayer, but in many model membranes, lateral fluidity of the membrane and protein is sacrificed for electrochemical addressability because of the need for an electroactive surface. Here, we reported a biomolecular photoactive device based on light-activated proton pump, bR, reconstituted into highly fluidic microcavity-supported lipid bilayers (MSLBs) on functionalized gold and polydimethylsiloxane cavity array substrates. The integrity of reconstituted bR at the MSLBs along with the lipid bilayer formation was evaluated by fluorescence lifetime correlation spectroscopy, yielding a protein lateral diffusion coefficient that was dependent on the bR concentration and consistent with the Saffman-Delbrück model. The photoelectrical properties of bR-MSLBs were evaluated from the photocurrent signal generated by bR under continuous and transient light illumination. The optimal conditions for a self-sustaining photoelectrical switch were determined in terms of protein concentration, pH, and light switch frequency of activation. Overall, a significant increase in the transient current was observed for lipid bilayers containing approximately 0.3 mol % bR with a measured photo-current of 250 nA/cm2. These results demonstrate that the platforms provide an appropriate lipid environment to support the proton pump, enabling its efficient operation. The bR-reconstituted MSLB model serves both as a platform to study the protein in a highly addressable biomimetic environment and as a demonstration of reconstitution of seven-helix receptors into MSLBs, opening the prospect of reconstitution of related membrane proteins including G-protein-coupled receptors on these versatile biomimetic substrates.
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Affiliation(s)
- Guilherme
B. Berselli
- School of Chemical Sciences, National
Centre for Sensor Research, Dublin City
University, Dublin D09 FW22, Ireland
| | - Aurélien
V. Gimenez
- School of Chemical Sciences, National
Centre for Sensor Research, Dublin City
University, Dublin D09 FW22, Ireland
| | - Alexandra O’Connor
- School of Chemical Sciences, National
Centre for Sensor Research, Dublin City
University, Dublin D09 FW22, Ireland
| | - Tia E. Keyes
- School of Chemical Sciences, National
Centre for Sensor Research, Dublin City
University, Dublin D09 FW22, Ireland
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26
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Yamamoto E, Akimoto T, Mitsutake A, Metzler R. Universal Relation between Instantaneous Diffusivity and Radius of Gyration of Proteins in Aqueous Solution. PHYSICAL REVIEW LETTERS 2021; 126:128101. [PMID: 33834804 DOI: 10.1103/physrevlett.126.128101] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Protein conformational fluctuations are highly complex and exhibit long-term correlations. Here, molecular dynamics simulations of small proteins demonstrate that these conformational fluctuations directly affect the protein's instantaneous diffusivity D_{I}. We find that the radius of gyration R_{g} of the proteins exhibits 1/f fluctuations that are synchronous with the fluctuations of D_{I}. Our analysis demonstrates the validity of the local Stokes-Einstein-type relation D_{I}∝1/(R_{g}+R_{0}), where R_{0}∼0.3 nm is assumed to be a hydration layer around the protein. From the analysis of different protein types with both strong and weak conformational fluctuations, the validity of the Stokes-Einstein-type relation appears to be a general property.
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Affiliation(s)
- Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Ayori Mitsutake
- Department of Physics, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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27
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Schneider F, Sych T, Eggeling C, Sezgin E. Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins. iScience 2021; 24:101891. [PMID: 33364580 PMCID: PMC7753935 DOI: 10.1016/j.isci.2020.101891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022] Open
Abstract
Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena Center of Soft Matters, Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
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28
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Efficient Lipid Bilayer Formation by Dipping Lipid-Loaded Microperforated Sheet in Aqueous Solution. MICROMACHINES 2021; 12:mi12010053. [PMID: 33466555 PMCID: PMC7824848 DOI: 10.3390/mi12010053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
This paper describes a method for a bilayer lipid membrane (BLM) formation using a perforated sheet along with an open chamber. Microscopic observation of the formed membrane showed a typical droplet interface bilayer. We proved that the formed membrane was a BLM based on electrical measurements of the membrane protein α-hemolysin, which produces nanopores in BLMs. Unlike the conventional approach for BLM formation based on the droplet contact method, this method provides aqueous surfaces with no organic solvent coating layer. Hence, this method is suitable for producing BLMs that facilitate the direct addition of chemicals into the aqueous phase.
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29
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Witkowska A, Spindler S, Mahmoodabadi RG, Sandoghdar V, Jahn R. Differential Diffusional Properties in Loose and Tight Docking Prior to Membrane Fusion. Biophys J 2020; 119:2431-2439. [PMID: 33189687 PMCID: PMC7822739 DOI: 10.1016/j.bpj.2020.10.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022] Open
Abstract
Fusion of biological membranes, although mediated by divergent proteins, is believed to follow a common pathway. It proceeds through distinct steps, including docking, merger of proximal leaflets (stalk formation), and formation of a fusion pore. However, the structure of these intermediates is difficult to study because of their short lifetime. Previously, we observed a loosely and tightly docked state preceding leaflet merger using arresting point mutations in SNARE proteins, but the nature of these states remained elusive. Here, we used interferometric scattering (iSCAT) microscopy to monitor diffusion of single vesicles across the surface of giant unilamellar vesicles (GUVs). We observed that the diffusion coefficients of arrested vesicles decreased during progression through the intermediate states. Modeling allowed for predicting the number of tethering SNARE complexes upon loose docking and the size of the interacting membrane patches upon tight docking. These results shed new light on the nature of membrane-membrane interactions immediately before fusion.
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Affiliation(s)
- Agata Witkowska
- Laboratory of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Susann Spindler
- Max Planck Institute for the Science of Light, Erlangen, Germany; Department of Physics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Reza Gholami Mahmoodabadi
- Max Planck Institute for the Science of Light, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany; Department of Physics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany; Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; University of Göttingen, Göttingen, Germany.
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30
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S Mogre S, Brown AI, Koslover EF. Getting around the cell: physical transport in the intracellular world. Phys Biol 2020; 17:061003. [PMID: 32663814 DOI: 10.1088/1478-3975/aba5e5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.
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Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California, San Diego, San Diego, California 92093, United States of America
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31
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Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W. Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex. SCIENCE ADVANCES 2020; 6:6/41/eabb9605. [PMID: 33028525 PMCID: PMC7541076 DOI: 10.1126/sciadv.abb9605] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/17/2020] [Indexed: 05/15/2023]
Abstract
Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo-electron microscopy (cryo-EM) structure of yeast Vo proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of Vo that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free Vo that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.
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Affiliation(s)
- Soung-Hun Roh
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Mrinal Shekhar
- Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Grigore Pintilie
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Laboratoire International Associé CNRS-UIUC, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| | - Abhishek Singharoy
- Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85801, USA.
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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32
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Grebnev G, Cvitkovic M, Fritz C, Cai G, Smith AS, Kost B. Quantitative Structural Organization of Bulk Apical Membrane Traffic in Pollen Tubes. PLANT PHYSIOLOGY 2020; 183:1559-1585. [PMID: 32482906 PMCID: PMC7401101 DOI: 10.1104/pp.20.00380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/15/2020] [Indexed: 05/13/2023]
Abstract
Pollen tube tip growth depends on balancing secretion of cell wall material with endocytic recycling of excess material incorporated into the plasma membrane (PM). The classical model of tip growth, which predicts bulk secretion, occurs apically, and is compensated by subapical endocytosis, has been challenged in recent years. Many signaling proteins and lipids with important functions in the regulation of membrane traffic underlying tip growth associate with distinct regions of the pollen tube PM, and understanding the mechanisms responsible for the targeting of these regulatory factors to specific PM domains requires quantitative information concerning the sites of bulk secretion and endocytosis. Here, we quantitatively characterized the spatial organization of membrane traffic during tip growth by analyzing steady-state distributions and dynamics of FM4-64-labeled lipids and YFP-tagged transmembrane (TM) proteins in tobacco (Nicotiana tabacum) pollen tubes growing normally or treated with Brefeldin A to block secretion. We established that (1) secretion delivers TM proteins and recycled membrane lipids to the same apical PM domain, and (2) FM4-64-labeled lipids, but not the analyzed TM proteins, undergo endocytic recycling within a clearly defined subapical region. We mathematically modeled the steady-state PM distributions of all analyzed markers to better understand differences between them and to support the experimental data. Finally, we mapped subapical F-actin fringe and trans-Golgi network positioning relative to sites of bulk secretion and endocytosis to further characterize functions of these structures in apical membrane traffic. Our results support and further define the classical model of apical membrane traffic at the tip of elongating pollen tubes.
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Affiliation(s)
- Gleb Grebnev
- Cell Biology, Department of Biology, Friedrich-Alexander-University Erlangen Nuremberg, 91058 Erlangen, Germany
| | - Mislav Cvitkovic
- PULS Group, Department of Physics, Friedrich-Alexander-University Erlangen Nuremberg, 91058 Erlangen, Germany
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Carolin Fritz
- Cell Biology, Department of Biology, Friedrich-Alexander-University Erlangen Nuremberg, 91058 Erlangen, Germany
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Ana-Suncana Smith
- PULS Group, Department of Physics, Friedrich-Alexander-University Erlangen Nuremberg, 91058 Erlangen, Germany
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Benedikt Kost
- Cell Biology, Department of Biology, Friedrich-Alexander-University Erlangen Nuremberg, 91058 Erlangen, Germany
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33
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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34
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Ghosh A, Enderlein J, Butkevich E. Dimerization of Human Drebrin-like Protein Governs Its Biological Activity. Biochemistry 2020; 59:1553-1558. [PMID: 32282191 DOI: 10.1021/acs.biochem.9b01095] [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
Drebrin-like protein (DBNL) is a multidomain F-actin-binding protein, which also interacts with other molecules within different intracellular pathways. Here, we present quantitative measurements on the size and conformation of human DBNL. Using dual-focus fluorescence correlation spectroscopy, we determined the hydrodynamic radius of the DBNL monomer. Native gel electrophoresis and dual-color fluorescence cross-correlation spectroscopy show that both endogenous DBNL and recombinant DBNL exist as dimers under physiological conditions. We demonstrate that C-terminal truncations of DBNL downstream of the coiled-coil domain result in its oligomerization at nanomolar concentrations. In contrast, the ADF-H domain alone is a monomer, which displays a concentration-dependent self-assembly. In vivo FLIM-FRET imaging shows that the presence of only actin-binding domains is not sufficient for DBNL to localize properly at the actin filament inside the cell. In summary, our work provides detailed insight into the structure-function relationship of human drebrin-like protein.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Eugenia Butkevich
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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35
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Fullstone G, Guttà C, Beyer A, Rehm M. The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling. NPJ Syst Biol Appl 2020; 6:10. [PMID: 32313030 PMCID: PMC7170865 DOI: 10.1038/s41540-020-0128-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/17/2020] [Indexed: 11/18/2022] Open
Abstract
Agent-based modelling is particularly adept at modelling complex features of cell signalling pathways, where heterogeneity, stochastic and spatial effects are important, thus increasing our understanding of decision processes in biology in such scenarios. However, agent-based modelling often is computationally prohibitive to implement. Parallel computing, either on central processing units (CPUs) or graphical processing units (GPUs), can provide a means to improve computational feasibility of agent-based applications but generally requires specialist coding knowledge and extensive optimisation. In this paper, we address these challenges through the development and implementation of the FLAME-accelerated signalling tool (FaST), a software that permits easy creation and parallelisation of agent-based models of cell signalling, on CPUs or GPUs. FaST incorporates validated new agent-based methods, for accurate modelling of reaction kinetics and, as proof of concept, successfully converted an ordinary differential equation (ODE) model of apoptosis execution into an agent-based model. We finally parallelised this model through FaST on CPUs and GPUs resulting in an increase in performance of 5.8× (16 CPUs) and 53.9×, respectively. The FaST takes advantage of the communicating X-machine approach used by FLAME and FLAME GPU to allow easy alteration or addition of functionality to parallel applications, but still includes inherent parallelisation optimisation. The FaST, therefore, represents a new and innovative tool to easily create and parallelise bespoke, robust, agent-based models of cell signalling.
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Affiliation(s)
- Gavin Fullstone
- Institute for Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany. .,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Nobelstrasse 15, 70569, Stuttgart, Germany.
| | - Cristiano Guttà
- Institute for Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Amatus Beyer
- Institute for Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Markus Rehm
- Institute for Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany. .,Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, Nobelstrasse 15, 70569, Stuttgart, Germany.
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36
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Camley BA, Brown FLH. Motion of objects embedded in lipid bilayer membranes: Advection and effective viscosity. J Chem Phys 2019; 151:124104. [PMID: 31575184 DOI: 10.1063/1.5121418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An interfacial regularized Stokeslet scheme is presented to predict the motion of solid bodies (e.g., proteins or gel-phase domains) embedded within flowing lipid bilayer membranes. The approach provides a numerical route to calculate velocities and angular velocities in complex flow fields that are not amenable to simple Faxén-like approximations. Additionally, when applied to shearing motions, the calculations yield predictions for the effective surface viscosity of dilute rigid-body-laden membranes. In the case of cylindrical proteins, effective viscosity calculations are compared to two prior analytical predictions from the literature. Effective viscosity predictions for a dilute suspension of rod-shaped objects in the membrane are also presented.
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Affiliation(s)
- Brian A Camley
- Departments of Physics & Astronomy and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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37
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Electromigration of cell surface macromolecules in DC electric fields during cell polarization and galvanotaxis. J Theor Biol 2019; 478:58-73. [DOI: 10.1016/j.jtbi.2019.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 12/14/2022]
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38
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Chein M, Perlson E, Roichman Y. Flow Arrest in the Plasma Membrane. Biophys J 2019; 117:810-816. [PMID: 31326106 DOI: 10.1016/j.bpj.2019.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 07/01/2019] [Indexed: 10/26/2022] Open
Abstract
The arrangement of receptors in the plasma membrane strongly affects the ability of a cell to sense its environment both in terms of sensitivity and in terms of spatial resolution. The spatial and temporal arrangement of the receptors is affected in turn by the mechanical properties and the structure of the cell membrane. Here, we focus on characterizing the flow of the membrane in response to the motion of a protein embedded in it. We do so by measuring the correlated diffusion of extracellularly tagged transmembrane neurotrophin receptors TrkB and p75 on transfected neuronal cells. In accord with previous reports, we find that the motion of single receptors exhibits transient confinement to submicron domains. We confirm predictions based on hydrodynamics of fluid membranes, finding long-range correlations in the motion of the receptors in the plasma membrane. However, we discover that these correlations do not persist for long ranges, as predicted, but decay exponentially, with a typical decay length on the scale of the average confining domain size.
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Affiliation(s)
- Michael Chein
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - Yael Roichman
- School of Chemistry, School of Physics & Astronomy, and the Tel Aviv Center for Light Matter Interaction, Tel Aviv University, Tel Aviv, Israel.
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39
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Wilson BA, Ramanathan A, Lopez CF. Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Simulations. Biophys J 2019; 117:429-444. [PMID: 31349988 PMCID: PMC6697365 DOI: 10.1016/j.bpj.2019.06.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 01/30/2023] Open
Abstract
Cardiolipin is an anionic lipid found in the mitochondrial membranes of eukaryotes ranging from unicellular microorganisms to metazoans. This unique lipid contributes to various mitochondrial functions, including metabolism, mitochondrial membrane fusion and/or fission dynamics, and apoptosis. However, differences in cardiolipin content between the two mitochondrial membranes, as well as dynamic fluctuations in cardiolipin content in response to stimuli and cellular signaling events, raise questions about how cardiolipin concentration affects mitochondrial membrane structure and dynamics. Although cardiolipin’s structural and dynamic roles have been extensively studied in binary mixtures with other phospholipids, the biophysical properties of cardiolipin in higher number lipid mixtures are still not well resolved. Here, we used molecular dynamics simulations to investigate the cardiolipin-dependent properties of ternary lipid bilayer systems that mimic the major components of mitochondrial membranes. We found that changes to cardiolipin concentration only resulted in minor changes to bilayer structural features but that the lipid diffusion was significantly affected by those alterations. We also found that cardiolipin position along the bilayer surfaces correlated to negative curvature deflections, consistent with the induction of negative curvature stress in the membrane monolayers. This work contributes to a foundational understanding of the role of cardiolipin in altering the properties in ternary lipid mixtures composed of the major mitochondrial phospholipids, providing much-needed insights to help understand how cardiolipin concentration modulates the biophysical properties of mitochondrial membranes.
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Affiliation(s)
- Blake A Wilson
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Arvind Ramanathan
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Carlos F Lopez
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University, Nashville, Tennessee.
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40
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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41
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Allard CAH, Opalko HE, Moseley JB. Stable Pom1 clusters form a glucose-modulated concentration gradient that regulates mitotic entry. eLife 2019; 8:e46003. [PMID: 31050341 PMCID: PMC6524964 DOI: 10.7554/elife.46003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
Control of cell size requires molecular size sensors that are coupled to the cell cycle. Rod-shaped fission yeast cells divide at a threshold size partly due to Cdr2 kinase, which forms nodes at the medial cell cortex where it inhibits the Cdk1-inhibitor Wee1. Pom1 kinase phosphorylates and inhibits Cdr2, and forms cortical concentration gradients from cell poles. Pom1 inhibits Cdr2 signaling to Wee1 specifically in small cells, but the time and place of their regulatory interactions were unclear. We show that Pom1 forms stable oligomeric clusters that dynamically sample the cell cortex. Binding frequency is patterned into a concentration gradient by the polarity landmarks Tea1 and Tea4. Pom1 clusters colocalize with Cdr2 nodes, forming a glucose-modulated inhibitory threshold against node activation. Our work reveals how Pom1-Cdr2-Wee1 operates in multiprotein clusters at the cortex to promote mitotic entry at a cell size that can be modified by nutrient availability.
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Affiliation(s)
- Corey A H Allard
- Department of Biochemistry and Cell BiologyThe Geisel School of Medicine at DartmouthHanoverUnited States
| | - Hannah E Opalko
- Department of Biochemistry and Cell BiologyThe Geisel School of Medicine at DartmouthHanoverUnited States
| | - James B Moseley
- Department of Biochemistry and Cell BiologyThe Geisel School of Medicine at DartmouthHanoverUnited States
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42
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Li S, Yan Z, Luo Z, Xu Y, Huang F, Hu G, Zhang X, Yue T. Directional and Rotational Motions of Nanoparticles on Plasma Membranes as Local Probes of Surface Tension Propagation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5333-5341. [PMID: 30908057 DOI: 10.1021/acs.langmuir.9b00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mechanical heterogeneity is ubiquitous in plasma membranes and of essential importance to cellular functioning. As a feedback of mechanical stimuli, local surface tension can be readily changed and immediately propagated through the membrane, influencing structures and dynamics of both inclusions and membrane-associated proteins. Using the nonequilibrium coarse-grained membrane simulation, here we investigate the inter-related processes of tension propagation, lipid diffusion, and transport of nanoparticles (NPs) adhering on the membrane of constant tension gradient, mimicking that of migrating cells or cells under prolonged stimulation. Our results demonstrate that the lipid bilayer membrane can by itself propagate surface tension in defined rates and pathways to reach a dynamic equilibrium state where surface tension is linearly distributed along the gradient maintained by the directional flow-like motion of lipids. Such lipid flow exerts shearing forces to transport adhesive NPs toward the region of a larger surface tension. Under certain conditions, the shearing force can generate nonzero torques driving the rotational motion of NPs, with the direction of the NP rotation determined by the NP-membrane interaction state as functions of both NP property and local membrane surface tension. Such features endow NPs with promising applications ranging from biosensing to targeted drug delivery.
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Affiliation(s)
| | | | | | | | | | - Guoqing Hu
- State Key Laboratory of Nonlinear Mechanics (LNM) , Institute of Mechanics, Chinese Academy of Science , Beijing 100190 , China
- School of Engineering Science , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
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43
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Betaneli V, Mücksch J, Schwille P. Fluorescence Correlation Spectroscopy to Examine Protein-Lipid Interactions in Membranes. Methods Mol Biol 2019; 2003:415-447. [PMID: 31218628 DOI: 10.1007/978-1-4939-9512-7_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a versatile technique to study membrane dynamics and protein-lipid interactions. It can provide information about diffusion coefficients, concentrations, and molecular interactions of proteins and lipids in the membrane. These parameters allow for the determination of protein partitioning into different lipid environments, the identification of lipid domains, and the detection of lipid-protein complexes on the membrane. During the last decades, FCS studies were successfully performed on model membrane systems as also on living cells, to characterize protein-lipid interactions. Recent developments of the method described here improved quantitative measurements on membranes and decreased the number of potential artifacts. The aim of this chapter is to provide the reader with the necessary information and some practical guidelines to perform FCS studies on artificial and cellular membranes.
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Affiliation(s)
- Viktoria Betaneli
- Medical Faculty "Carl Gustav Carus", Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany.
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44
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Olšinová M, Jurkiewicz P, Kishko I, Sýkora J, Sabó J, Hof M, Cwiklik L, Cebecauer M. Roughness of Transmembrane Helices Reduces Lipid Membrane Dynamics. iScience 2018; 10:87-97. [PMID: 30508721 PMCID: PMC6277224 DOI: 10.1016/j.isci.2018.11.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/23/2018] [Accepted: 11/14/2018] [Indexed: 01/23/2023] Open
Abstract
The dynamics of cellular membranes is primarily determined by lipid species forming a bilayer. Proteins are considered mainly as effector molecules of diverse cellular processes. In addition to large assemblies of proteins, which were found to influence properties of fluid membranes, biological membranes are densely populated by small, highly mobile proteins. However, little is known about the effect of such proteins on the dynamics of membranes. Using synthetic peptides, we demonstrate that transmembrane helices interfere with the mobility of membrane components by trapping lipid acyl chains on their rough surfaces. The effect is more pronounced in the presence of cholesterol, which segregates from the rough surface of helical peptides. This may contribute to the formation or stabilization of membrane heterogeneities. Since roughness is a general property of helical transmembrane segments, our results suggest that, independent of their size or cytoskeleton linkage, integral membrane proteins affect local membrane dynamics and organization.
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Affiliation(s)
- Marie Olšinová
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Piotr Jurkiewicz
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Iryna Kishko
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Jan Sýkora
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Ján Sabó
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Martin Hof
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Lukasz Cwiklik
- Department of Theoretical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Marek Cebecauer
- Department of Biophysical Chemistry, J. Heyrovsky Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic.
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45
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Spindler S, Sibold J, Gholami Mahmoodabadi R, Steinem C, Sandoghdar V. High-Speed Microscopy of Diffusion in Pore-Spanning Lipid Membranes. NANO LETTERS 2018; 18:5262-5271. [PMID: 30047737 DOI: 10.1021/acs.nanolett.8b02240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Pore-spanning membranes (PSMs) provide a highly attractive model system for investigating fundamental processes in lipid bilayers. We measure and compare lipid diffusion in the supported and suspended regions of PSMs prepared on a microfabricated porous substrate. Although some properties of the suspended regions in PSMs have been characterized using fluorescence studies, it has not been possible to examine the mobility of membrane components on the supported membrane parts. Here, we resolve this issue by employing interferometric scattering microscopy (iSCAT). We study the location-dependent diffusion of DOPE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) lipids (DOPE) labeled with gold nanoparticles in (1,2-dioleoyl-sn-glycero-3-phosphocholine) (DOPC) bilayers prepared on holey silicon nitride substrates that were either (i) oxygen-plasma-treated or (ii) functionalized with gold and 6-mercapto-1-hexanol. For both substrate treatments, diffusion in regions suspended on pores with diameters of 5 μm is found to be free. In the case of functionalization with gold and 6-mercapto-1-hexanol, similar diffusion coefficients are obtained for both the suspended and the supported regions, whereas for oxygen-plasma-treated surfaces, diffusion is almost 4 times slower in the supported parts of the membranes. We attribute this reduced diffusion on the supported parts in the case of oxygen-plasma-treated surfaces to larger membrane-substrate interactions, which lead to a higher membrane tension in the freestanding membrane parts. Furthermore, we find clear indications for a decrease of the diffusion constant in the freestanding regions away from the pore center. We provide a detailed characterization of the diffusion behavior in these membrane systems and discuss future directions.
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Affiliation(s)
- Susann Spindler
- Max Planck Institute for the Science of Light , Staudtstraße 2 , 91058 Erlangen , Germany
- Department of Physics , Friedrich Alexander University Erlangen-Nuremberg , Staudtstraße 5 , 91058 Erlangen , Germany
| | - Jeremias Sibold
- Institute for Organic and Biomolecular Chemistry , Tammannstraße 2 . 37077 Göttingen , Germany
| | - Reza Gholami Mahmoodabadi
- Max Planck Institute for the Science of Light , Staudtstraße 2 , 91058 Erlangen , Germany
- Department of Physics , Friedrich Alexander University Erlangen-Nuremberg , Staudtstraße 5 , 91058 Erlangen , Germany
| | - Claudia Steinem
- Institute for Organic and Biomolecular Chemistry , Tammannstraße 2 . 37077 Göttingen , Germany
- Max Planck Institute for Dynamics and Self-Organization , Am Faßberg 17 , 37077 Göttingen , Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light , Staudtstraße 2 , 91058 Erlangen , Germany
- Department of Physics , Friedrich Alexander University Erlangen-Nuremberg , Staudtstraße 5 , 91058 Erlangen , Germany
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46
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Gárate F, Pertusa M, Arana Y, Bernal R. Non-invasive Neurite Mechanics in Differentiated PC12 Cells. Front Cell Neurosci 2018; 12:194. [PMID: 30052690 PMCID: PMC6043779 DOI: 10.3389/fncel.2018.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/17/2018] [Indexed: 01/04/2023] Open
Abstract
Thermal Fluctuations Spectroscopy (TFS) in combination with novel optical-based instrumentation was used to study mechanical properties of cell-cultured neurites with a spatial resolution limited only by the light diffraction. The analysis of thermal fluctuations together with a physical model of cellular elasticity allow us to determine relevant mechanical properties of neurite as axial tension σ, flexural rigidity B, plasma membrane tension γ, membrane bending rigidity K, and cytoskeleton to membrane-coupling ρbk, whose values are consistent with previously reported values measured using invasive approaches. The value obtained for the membrane-coupling parameter was used to estimate the average number of coupling elements between the plasma membrane and the cytoskeleton that fell in the range of 30 elements per area of the laser spot used to record the fluctuations. Furthermore, to expand the TFS analysis, we investigate the correlation between F-actin linear density and the mechanical features of PC12 neurites. Using a hybrid instrument that combines TFS and a simple fluorescent technique, our results show that the fluctuations are related with the F-actin concentration. These measurements have an advantage of not requiring the application of an external force, allowing as to directly establish a correlation between changes in the mechanical parameters and cytoskeleton-protein concentrations. The sensibility of our method was also tested by the application of TFS technique to PC12 neurite under Paraformaldehyde and Latrunculin-A effect. These results show a dramatic modification in the fluctuations that are consistent with the reported effect of these drugs, confirming the high sensitivity of this technique. Finally, the thermal fluctuation approach was applied to DRG axons to show that its utility is not limited to studies of PC12 neurites, but it is suitable to measure the general characteristic of various neuron-like cells.
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Affiliation(s)
- Fernanda Gárate
- Cellular Mechanics Laboratory, Physics Department, SMAT-C, University of Santiago, Santiago, Chile.,Biophysics Laboratory, Physics Department, SMAT-C, University of Santiago, Santiago, Chile
| | - María Pertusa
- Department of Biology, Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), University of Santiago de Chile, Santiago, Chile
| | - Yahaira Arana
- Cellular Mechanics Laboratory, Physics Department, SMAT-C, University of Santiago, Santiago, Chile
| | - Roberto Bernal
- Cellular Mechanics Laboratory, Physics Department, SMAT-C, University of Santiago, Santiago, Chile
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47
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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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48
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Sanghavi P, D'Souza A, Rai A, Rai A, Padinhatheeri R, Mallik R. Coin Tossing Explains the Activity of Opposing Microtubule Motors on Phagosomes. Curr Biol 2018; 28:1460-1466.e4. [PMID: 29706510 PMCID: PMC5954897 DOI: 10.1016/j.cub.2018.03.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/03/2018] [Accepted: 03/19/2018] [Indexed: 01/08/2023]
Abstract
How the opposing activity of kinesin and dynein motors generates polarized distribution of organelles inside cells is poorly understood and hotly debated [1, 2]. Possible explanations include stochastic mechanical competition [3, 4], coordinated regulation by motor-associated proteins [5-7], mechanical activation of motors [8], and lipid-induced organization [9]. Here, we address this question by using phagocytosed latex beads to generate early phagosomes (EPs) that move bidirectionally along microtubules (MTs) in an in vitro assay [9]. Dynein/kinesin activity on individual EPs is recorded as real-time force generation of the motors against an optical trap. Activity of one class of motors frequently coincides with, or is rapidly followed by opposite motors. This leads to frequent and rapid reversals of EPs in the trap. Remarkably, the choice between dynein and kinesin can be explained by the tossing of a coin. Opposing motors therefore appear to function stochastically and independently of each other, as also confirmed by observing no effect on kinesin function when dynein is inhibited on the EPs. A simple binomial probability calculation based on the geometry of EP-microtubule contact explains the observed activity of dynein and kinesin on phagosomes. This understanding of intracellular transport in terms of a hypothetical coin, if it holds true for other cargoes, provides a conceptual framework to explain the polarized localization of organelles inside cells.
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Affiliation(s)
- Paulomi Sanghavi
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ashwin D'Souza
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ashim Rai
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Arpan Rai
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ranjith Padinhatheeri
- Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Roop Mallik
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
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49
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Heitkamp T, Grisshammer R, Börsch M. Towards monitoring conformational changes of the GPCR neurotensin receptor 1 by single-molecule FRET. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2018; 10498. [PMID: 30013286 DOI: 10.1117/12.2286787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular side to NTSR1 and induces conformational changes that trigger intracellular signaling processes. Our goal is to monitor the conformational dynamics of single fluorescently labeled NTSR1. For this, we fused the fluorescent protein mNeonGreen to the C terminus of NTSR1, purified the receptor fusion protein from E. coli membranes, and reconstituted NTSR1 into liposomes with E. coli polar lipids. Using single-molecule anisotropy measurements, NTSR1 was found to be monomeric in liposomes, with a small fraction being dimeric and oligomeric, showing homoFRET. Similar results were obtained for NTSR1 in detergent solution. Furthermore, we demonstrated agonist binding to NTSR1 by time-resolved single-molecule Förster resonance energy transfer (smFRET), using neurotensin labeled with the fluorophore ATTO594.
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Affiliation(s)
- Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, Nonnenplan 2 - 4, 07743 Jena, Germany
| | - Reinhard Grisshammer
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20814, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, Nonnenplan 2 - 4, 07743 Jena, Germany
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50
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Elías-Wolff F, Lindén M, Lyubartsev AP, Brandt EG. Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling. J Chem Theory Comput 2018; 14:1643-1655. [PMID: 29350922 DOI: 10.1021/acs.jctc.7b00878] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane-associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch. This buckling approach samples a wide range of curvatures in a single simulation, and anisotropic effects can be extracted from the orientation statistics. We develop an efficient and robust algorithm to extract the motion of the probe along the buckled membrane surface, and evaluate its numerical properties by extensive sampling of three coarse-grained model systems: local lipid density in a curved environment for single-component bilayers, curvature preferences of individual lipids in two-component membranes, and curvature sensing by a homotrimeric transmembrane protein. The method can be used to complement experimental data from curvature partition assays and provides additional insight into mesoscopic theories and molecular mechanisms for curvature sensing.
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Affiliation(s)
- Federico Elías-Wolff
- Department of Biochemistry and Biophysics , Stockholm University , SE-106 91 Stockholm , Sweden.,Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Martin Lindén
- Department of Cell and Molecular Biology , Uppsala University , SE-751 05 Uppsala , Sweden
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Erik G Brandt
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
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