1
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Tang Y, Zhang Y, Zhang D, Liu Y, Nussinov R, Zheng J. Exploring pathological link between antimicrobial and amyloid peptides. Chem Soc Rev 2024; 53:8713-8763. [PMID: 39041297 DOI: 10.1039/d3cs00878a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
| | - Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Dong Zhang
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
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2
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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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3
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Roterman I, Stapor K, Konieczny L. Transmembrane proteins-Different anchoring systems. Proteins 2024; 92:593-609. [PMID: 38062872 DOI: 10.1002/prot.26646] [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: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/17/2023] [Indexed: 04/13/2024]
Abstract
Transmembrane proteins are active in amphipathic environments. To stabilize the protein in such surrounding the exposure of hydrophobic residues on the protein surface is required. Transmembrane proteins are responsible for the transport of various molecules. Therefore, they often represent structures in the form of channels. This analysis focused on the stability and local flexibility of transmembrane proteins, particularly those related to their biological activity. Different forms of anchorage were identified using the fuzzy oil-drop model (FOD) and its modified form, FOD-M. The mainly helical as well as β-barrel structural forms are compared with respect to the mechanism of stabilization in the cell membrane. The different anchoring system was found to stabilize protein molecules with possible local fluctuation.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Krakow, Poland
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Krakow, Poland
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4
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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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5
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Bossa GV, May S. Bragg-Williams Theory for Particles with a Size-Modulating Internal Degree of Freedom. Molecules 2023; 28:5060. [PMID: 37446721 DOI: 10.3390/molecules28135060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The field of soft matter teems with molecules and aggregates of molecules that have internal size-modulating degrees of freedom. Proteins, peptides, microgels, polymers, micelles, and even some colloids can exist in multiple-often just two dominating-states with different effective sizes, where size can refer to the volume or to the cross-sectional area for particles residing on surfaces. The size-dependence of their accessible states renders the behavior of these particles pressure-sensitive. The Bragg-Williams model is among the most simple mean-field methods to translate the presence of inter-particle interactions into an approximate phase diagram. Here, we extend the Bragg-Williams model to account for the presence of particles that are immersed in a solvent and exist in two distinct states, one occupying a smaller and the other one a larger size. The basis of the extension is a lattice-sublattice approximation that we use to host the two size-differing states. Our model includes particle-solvent interactions that act as an effective surface tension between particles and solvent and are ignorant of the state in which the particles reside. We analyze how the energetic preference of the particles for one or the other state affects the phase diagrams. The possibility of a single phase-two phases-single phase sequence of phase transitions as a function of increasing temperature is demonstrated.
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Affiliation(s)
- Guilherme Volpe Bossa
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Sylvio May
- Department of Physics, North Dakota State University, Fargo, ND 58108-6050, USA
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6
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Yong X, Du K. Effects of Shape on Interaction Dynamics of Tetrahedral Nanoplastics and the Cell Membrane. J Phys Chem B 2023; 127:1652-1663. [PMID: 36763902 DOI: 10.1021/acs.jpcb.2c07460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Cellular uptake of nanoplastics is instrumental in their environmental accumulation and transfer to humans through the food chain. Despite extensive studies using spherical plastic nanoparticles, the influence of the morphological characteristics of environmentally released nanoplastics is understudied. Using dissipative particle dynamics simulations, we modeled the interactions between a cell membrane and hydrophobic nanotetrahedra, which feature high shape anisotropy and large surface curvature seen for environmental nanoplastics. We observe robust uptake of nanotetrahedra with sharp vertices and edges by the lipid membrane. Two local energy minimum configurations of nanotetrahedra embedded in the membrane bilayer were identified for particles of large sizes. Further analysis of particle dynamics within the membrane shows that the two interaction states exhibit distinct translational and rotational dynamics in the directions normal and parallel to the plane of the membrane. The membrane confinement significantly arrests the out-of-plane motion, resulting in caged translation and subdiffusive rotation. While the in-plane diffusion remains Brownian, we find that the translational and rotational modes decouple from each other as the particle size increases. The rotational diffusion decreases by a greater extent compared to the translational diffusion, deviating from the continuum theory predictions. These results provide fundamental insights into the shape effect on the nanoparticle dynamics in crowded lipid membranes.
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Affiliation(s)
- Xin Yong
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902, United States
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
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7
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Tran BM, Linnik DS, Punter CM, Śmigiel WM, Mantovanelli L, Iyer A, O’Byrne C, Abee T, Johansson J, Poolman B. Super-resolving microscopy reveals the localizations and movement dynamics of stressosome proteins in Listeria monocytogenes. Commun Biol 2023; 6:51. [PMID: 36641529 PMCID: PMC9840623 DOI: 10.1038/s42003-023-04423-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
The human pathogen Listeria monocytogenes can cope with severe environmental challenges, for which the high molecular weight stressosome complex acts as the sensing hub in a complicated signal transduction pathway. Here, we show the dynamics and functional roles of the stressosome protein RsbR1 and its paralogue, the blue-light receptor RsbL, using photo-activated localization microscopy combined with single-particle tracking and single-molecule displacement mapping and supported by physiological studies. In live cells, RsbR1 is present in multiple states: in protomers with RsbS, large clusters of stressosome complexes, and in connection with the plasma membrane via Prli42. RsbL diffuses freely in the cytoplasm but forms clusters upon exposure to light. The clustering of RsbL is independent of the presence of Prli42. Our work provides a comprehensive view of the spatial organization and intracellular dynamics of the stressosome proteins in L. monocytogenes, which paves the way towards uncovering the stress-sensing mechanism of this signal transduction pathway.
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Affiliation(s)
- Buu Minh Tran
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Dmitrii Sergeevich Linnik
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Christiaan Michiel Punter
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Wojciech Mikołaj Śmigiel
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Luca Mantovanelli
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Aditya Iyer
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Conor O’Byrne
- Microbiology, School of Biological & Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Laboratory of Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jörgen Johansson
- grid.12650.300000 0001 1034 3451Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Bert Poolman
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
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8
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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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9
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Santo KP, Neimark AV. Dissipative particle dynamics simulations in colloid and Interface science: a review. Adv Colloid Interface Sci 2021; 298:102545. [PMID: 34757286 DOI: 10.1016/j.cis.2021.102545] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022]
Abstract
Dissipative particle dynamics (DPD) is one of the most efficient mesoscale coarse-grained methodologies for modeling soft matter systems. Here, we comprehensively review the progress in theoretical formulations, parametrization strategies, and applications of DPD over the last two decades. DPD bridges the gap between the microscopic atomistic and macroscopic continuum length and time scales. Numerous efforts have been performed to improve the computational efficiency and to develop advanced versions and modifications of the original DPD framework. The progress in the parametrization techniques that can reproduce the engineering properties of experimental systems attracted a lot of interest from the industrial community longing to use DPD to characterize, help design and optimize the practical products. While there are still areas for improvements, DPD has been efficiently applied to numerous colloidal and interfacial phenomena involving phase separations, self-assembly, and transport in polymeric, surfactant, nanoparticle, and biomolecules systems.
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Affiliation(s)
- Kolattukudy P Santo
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Alexander V Neimark
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.
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10
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Celebi AT, Jamali SH, Bardow A, Vlugt TJH, Moultos OA. Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1810685] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alper T. Celebi
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Seyed Hossein Jamali
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - André Bardow
- Energy & Process Systems Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Zürich, Switzerland
| | - Thijs J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
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11
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Kinoshita M, Kyo T, Matsumori N. Assembly formation of minor dihydrosphingomyelin in sphingomyelin-rich ordered membrane domains. Sci Rep 2020; 10:11794. [PMID: 32678223 PMCID: PMC7366691 DOI: 10.1038/s41598-020-68688-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/18/2020] [Indexed: 11/22/2022] Open
Abstract
The lipidome of mammalian cells not only contain sphingomyelin (SM) but also, as a minor component, dihydrosphongomyelin (DHSM), in which the double bond at C4–C5 in the sphingosine base is reduced to a single-bond linkage. It has been indicated that DHSM forms ordered domains more effectively than SM due to its greater potential to induce intermolecular hydrogen bonds. However, direct information on partition and dynamic behaviors of DHSM in raft-like liquid-ordered (Lo) and non-raft-like liquid-disordered (Ld) phase-segregated membranes has been lacking. In the present study, we prepared fluorescent derivatives of DHSM and compared their behaviors to those of fluorescent SM and phosphatidylcholine (PC) derivatives. Fluorescence microscopy showed that DHSM is more preferentially localized to the Lo domains in the Lo/Ld phase-segregated giant unilamellar vesicles than SM and PC. Most importantly, diffusion coefficient measurements indicated that DHSM molecules form DHSM-condensed assembly inside the SM-rich Lo domain of the SM/dioleoylphosphatidylcholine/cholesterol system even when DHSM accounts for 1–3.3 mol% of total lipids. Such heterogeneous distribution of DHSM in the SM-rich Lo domains was further confirmed by inter-lipid FRET experiments. This study provides new insights into the biological functions and significance of minor component DHSM in lipid rafts.
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Affiliation(s)
- Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Takumi Kyo
- Department of Chemistry, Graduate School of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan.
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12
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Xu Z, Gao L, Chen P, Yan LT. Diffusive transport of nanoscale objects through cell membranes: a computational perspective. SOFT MATTER 2020; 16:3869-3881. [PMID: 32236197 DOI: 10.1039/c9sm02338k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diffusion is an essential and fundamental means of transport of substances on cell membranes, and the dynamics of biomembranes plays a crucial role in the regulation of numerous cellular processes. The understanding of the complex mechanisms and the nature of particle diffusion have a bearing on establishing guidelines for the design of efficient transport materials and unique therapeutic approaches. Herein, this review article highlights the most recent advances in investigating diffusion dynamics of nanoscale objects on biological membranes, focusing on the approaches of tailored computer simulations and theoretical analysis. Due to the presence of the complicated and heterogeneous environment on native cell membranes, the diffusive transport behaviors of nanoparticles exhibit unique and variable characteristics. The general aspects and basic theories of normal diffusion and anomalous diffusion have been introduced. In addition, the influence of a series of external and internal factors on the diffusion behaviors is discussed, including particle size, membrane curvature, particle-membrane interactions or particle-inclusion, and the crowding degree of membranes. Finally, we seek to identify open problems in the existing experimental, simulation, and theoretical research studies, and to propose challenges for future development.
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Affiliation(s)
- Ziyang Xu
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Lijuan Gao
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Pengyu Chen
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Li-Tang Yan
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China.
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13
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Onoa B, Fukuda S, Iwai M, Bustamante C, Niyogi KK. Atomic Force Microscopy Visualizes Mobility of Photosynthetic Proteins in Grana Thylakoid Membranes. Biophys J 2020; 118:1876-1886. [PMID: 32224302 PMCID: PMC7175462 DOI: 10.1016/j.bpj.2020.02.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/10/2020] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Thylakoid membranes in chloroplasts contain photosynthetic protein complexes that convert light energy into chemical energy. Photosynthetic protein complexes are considered to undergo structural reorganization to maintain the efficiency of photochemical reactions. A detailed description of the mobility of photosynthetic complexes in real time is necessary to understand how macromolecular organization of the membrane is altered by environmental fluctuations. Here, we used high-speed atomic force microscopy to visualize and characterize the in situ mobility of individual protein complexes in grana thylakoid membranes isolated from Spinacia oleracea. Our observations reveal that these membranes can harbor complexes with at least two distinctive classes of mobility. A large fraction of grana membranes contained proteins with quasistatic mobility exhibiting molecular displacements smaller than 10 nm2. In the remaining fraction, the protein mobility is variable with molecular displacements of up to 100 nm2. This visualization at high spatiotemporal resolution enabled us to estimate an average diffusion coefficient of ∼1 nm2 s-1. Interestingly, both confined and Brownian diffusion models could describe the protein mobility of the second group of membranes. We also provide the first direct evidence, to our knowledge, of rotational diffusion of photosynthetic complexes. The rotational diffusion of photosynthetic complexes could be an adaptive response to the high protein density in the membrane to guarantee the efficiency of electron transfer reactions. This characterization of the mobility of individual photosynthetic complexes in grana membranes establishes a foundation that could be adapted to study the dynamics of the complexes inside intact and photosynthetically functional thylakoid membranes to be able to understand its structural responses to diverse environmental fluctuations.
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Affiliation(s)
- Bibiana Onoa
- Howard Hughes Medical Institute, University of California, Berkeley, California.
| | - Shingo Fukuda
- Howard Hughes Medical Institute, University of California, Berkeley, California
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Department of Plant and Microbial Biology, University of California, Berkeley, California
| | - Carlos Bustamante
- Howard Hughes Medical Institute, University of California, Berkeley, California; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, California; Department of Molecular and Cell Biology, University of California, Berkeley, California; Department of Physics, University of California, Berkeley, California; Kavli Energy NanoScience Institute, Lawrence Berkeley National Laboratory, University of California, Berkeley, California
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, California; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Department of Plant and Microbial Biology, University of California, Berkeley, California.
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14
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Javanainen M, Ollila OHS, Martinez-Seara H. Rotational Diffusion of Membrane Proteins in Crowded Membranes. J Phys Chem B 2020; 124:2994-3001. [PMID: 32188248 DOI: 10.1021/acs.jpcb.0c00884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Membrane proteins travel along cellular membranes and reorient themselves to form functional oligomers and protein-lipid complexes. Following the Saffman-Delbrück model, protein radius sets the rate of this diffusive motion. However, it is unclear how this model, derived for ideal and dilute membranes, performs under crowded conditions of cellular membranes. Here, we study the rotational motion of membrane proteins using molecular dynamics simulations of coarse-grained membranes and 2-dimensional Lennard-Jones fluids with varying levels of crowding. We find that the Saffman-Delbrück model captures the size-dependency of rotational diffusion under dilute conditions where protein-protein interactions are negligible, whereas stronger scaling laws arise under crowding. Together with our recent work on lateral diffusion, our results reshape the description of protein dynamics in native membrane environments: The translational and rotational motions of proteins with small transmembrane domains are rapid, whereas larger proteins or protein complexes display substantially slower dynamics.
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Affiliation(s)
- Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.,Computational Physics Laboratory, Tampere University, Tampere 33720, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic
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15
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Liu X, Tian F, Yue T, Zhang X, Zhong C. Radial aggregation of proteins prevails over axial aggregation on membrane tubes. NANOSCALE 2020; 12:3029-3037. [PMID: 31967160 DOI: 10.1039/c9nr09303f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tubular membrane structures are abundant in living cells and participate in various cell activities with the help of specific proteins. This complicated protein-membrane interaction raises a largely unclear question of how cells create, maintain and eliminate membrane nanotubes with a variety of proteins involved. To simplify the question and to give a common mechanism, we simply model membrane proteins as various solid nanoparticles (NPs) of different shapes, instead of considering the detailed structure of different proteins. With this minimal model of membrane proteins, we use molecular simulations to study the common features for protein self-assembly on membrane tubes. Both molecular simulations and energy analysis reveal that on tubular membrane surfaces, the radial aggregation structure of spherical NPs prevails over axial aggregation. We demonstrate that anisotropic deformation of membrane tubes by NP adhesion leads to a direction-dependent (effective) inter-NP attraction, which controls the direction of NP assembly. Moreover, this radial aggregation morphology seems to be independent of the shape of NPs, except for NPs with a length comparable to the tube diameter. This observation indicates that proteins with strong adhesion to a membrane tube tend to form ring-like aggregates, and this finding offers an insight into how proteins play their roles in generating, maintaining and breaking tubular membrane structures.
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Affiliation(s)
- Xuejuan Liu
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, PR China. and Technical Innovation Center for Utilization of Edible and Medicinal Fungi in Hebei Province, Edible and Medicinal Fungi Research and Development Center of Hebei Universities, College of Life Science, Lang Fang Normal University, Langfang 065000, PR China
| | - Falin Tian
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Chongli Zhong
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, PR China. and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing 100029, PR China
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16
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Abstract
The endoplasmic reticulum (ER) is the site for folding and maturation of secreted and membrane proteins. When the ER protein-folding machinery is overwhelmed, misfolded proteins trigger ER stress, which is frequently linked to human diseases, including cancer and neurodegeneration. Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident sensor that assembles into large clusters of previously unknown organization upon its activation by unfolded peptides. We demonstrate that IRE1 clusters are topologically complex dynamic structures that remain contiguous with the ER membrane throughout their lifetime. The majority of clustered IRE1 molecules are diffusionally trapped inside the clusters until IRE1 signaling attenuates, at which point they are released back into the ER through a pathway that is functionally distinct from cluster assembly. The endoplasmic reticulum (ER) membrane-resident stress sensor inositol-requiring enzyme 1 (IRE1) governs the most evolutionarily conserved branch of the unfolded protein response. Upon sensing an accumulation of unfolded proteins in the ER lumen, IRE1 activates its cytoplasmic kinase and ribonuclease domains to transduce the signal. IRE1 activity correlates with its assembly into large clusters, yet the biophysical characteristics of IRE1 clusters remain poorly characterized. We combined superresolution microscopy, single-particle tracking, fluorescence recovery, and photoconversion to examine IRE1 clustering quantitatively in living human and mouse cells. Our results revealed that: 1) In contrast to qualitative impressions gleaned from microscopic images, IRE1 clusters comprise only a small fraction (∼5%) of the total IRE1 in the cell; 2) IRE1 clusters have complex topologies that display features of higher-order organization; 3) IRE1 clusters contain a diffusionally constrained core, indicating that they are not phase-separated liquid condensates; 4) IRE1 molecules in clusters remain diffusionally accessible to the free pool of IRE1 molecules in the general ER network; 5) when IRE1 clusters disappear at later time points of ER stress as IRE1 signaling attenuates, their constituent molecules are released back into the ER network and not degraded; 6) IRE1 cluster assembly and disassembly are mechanistically distinct; and 7) IRE1 clusters’ mobility is nearly independent of cluster size. Taken together, these insights define the clusters as dynamic assemblies with unique properties. The analysis tools developed for this study will be widely applicable to investigations of clustering behaviors in other signaling proteins.
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17
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Moreno-Pescador G, Florentsen CD, Østbye H, Sønder SL, Boye TL, Veje EL, Sonne AK, Semsey S, Nylandsted J, Daniels R, Bendix PM. Curvature- and Phase-Induced Protein Sorting Quantified in Transfected Cell-Derived Giant Vesicles. ACS NANO 2019; 13:6689-6701. [PMID: 31199124 DOI: 10.1021/acsnano.9b01052] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Eukaryotic cells possess a dynamic network of membranes that vary in lipid composition. To perform numerous biological functions, cells modulate their shape and the lateral organization of proteins associated with membranes. The modulation is generally facilitated by physical cues that recruit proteins to specific regions of the membrane. Analyzing these cues is difficult due to the complexity of the membrane conformations that exist in cells. Here, we examine how different types of membrane proteins respond to changes in curvature and to lipid phases found in the plasma membrane. By using giant plasma membrane vesicles derived from transfected cells, the proteins were positioned in the correct orientation and the analysis was performed in plasma membranes with a biological composition. Nanoscale membrane curvatures were generated by extracting nanotubes from these vesicles with an optical trap. The viral membrane protein neuraminidase was not sensitive to curvature, but it did exhibit strong partitioning (coefficient of K = 0.16) disordered membrane regions. In contrast, the membrane repair protein annexin 5 showed a preference for nanotubes with a density up to 10-15 times higher than that on the more flat vesicle membrane. The investigation of nanoscale effects in isolated plasma membranes provides a quantitative platform for studying peripheral and integral membrane proteins in their natural environment.
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Affiliation(s)
| | | | - Henrik Østbye
- Department of Biochemistry and Biophysics , Stockholm University , 10691 Stockholm , Sweden
| | - Stine L Sønder
- Membrane Integrity Group, Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease , Danish Cancer Society Research Center , Strandboulevarden 49 , DK-2100 Copenhagen , Denmark
| | - Theresa L Boye
- Membrane Integrity Group, Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease , Danish Cancer Society Research Center , Strandboulevarden 49 , DK-2100 Copenhagen , Denmark
| | - Emilie L Veje
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Alexander K Sonne
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Szabolcs Semsey
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Jesper Nylandsted
- Membrane Integrity Group, Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease , Danish Cancer Society Research Center , Strandboulevarden 49 , DK-2100 Copenhagen , Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences , University of Copenhagen , DK-2200 Copenhagen N , Denmark
| | - Robert Daniels
- Department of Biochemistry and Biophysics , Stockholm University , 10691 Stockholm , Sweden
| | - Poul Martin Bendix
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
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18
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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: 184] [Impact Index Per Article: 36.8] [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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19
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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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20
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Yue T, Zhou H, Sun H, Li S, Zhang X, Cao D, Yi X, Yan B. Why are nanoparticles trapped at cell junctions when the cell density is high? NANOSCALE 2019; 11:6602-6609. [PMID: 30896700 DOI: 10.1039/c9nr01024f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Research on nanoparticle (NP)-cell interactions has been extensively carried out in dilute cell cultures, where NPs are heavily internalized by cells. However, it is not known whether the findings from cell culture studies are still true in tissues where cells are tightly packed. Here, we show experimentally and theoretically that when cells are tightly packed, cellular uptake is strongly hindered. When simultaneously encountering two adjacent cells as is often the case in tissues, adhesion, bending and protrusion of at least two membranes from these cells generate complicated energy contributions that cause trapping of NPs at cell junctions with impeded uptake.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
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21
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Nakamura K, Omori T, Ishikawa T. Shear-Induced Migration of a Transmembrane Protein within a Vesicle. Biophys J 2019; 116:1483-1494. [PMID: 30979554 DOI: 10.1016/j.bpj.2019.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/13/2019] [Accepted: 03/21/2019] [Indexed: 11/19/2022] Open
Abstract
Biomembranes feature phospholipid bilayers and serve as the interface between cells or organelles and the extracellular and/or cellular environment. Lipids can move freely throughout the membrane; the lipid bilayer behaves like a fluid. Such fluidity is important in terms of the actions of membrane transport proteins, which often mediate biological functions; membrane protein motion has attracted a great deal of attention. Because the proteins are small, diffusion phenomena are often in play, but flow-induced transport has rarely been addressed. Here, we used a dissipative particle dynamics approach to investigate flow-induced membrane protein transport. We analyzed the drift of a membrane protein located within a vesicle. Under the influence of shear flow, the protein gradually migrated toward the vorticity axis via a random walk, and the probability of retention around the axis was high. To understand the mechanism of protein migration, we varied both shear strength and protein size. Protein migration was induced by the balance between the drag and thermodynamic diffusion forces and could be represented by the Péclet number. These results improve our understanding of flow-induced membrane protein transport.
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Affiliation(s)
- Koyo Nakamura
- Department of Finemechanics, Tohoku University, Sendai, Miyagi, Japan
| | - Toshihiro Omori
- Department of Finemechanics, Tohoku University, Sendai, Miyagi, Japan.
| | - Takuji Ishikawa
- Department of Finemechanics, Tohoku University, Sendai, Miyagi, Japan
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22
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Shi X, Tian F. Multiscale Modeling and Simulation of Nano‐Carriers Delivery through Biological Barriers—A Review. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800105] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xinghua Shi
- CAS Key Laboratory for Nanosystem and Hierarchy FabricationCAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyChinese Academy of Sciences Beijing 100190 China
- School of Nanoscience and TechnologyUniversity of Chinese Academy of Sciences NO.19A Yuquan Road Beijing 100049 China
| | - Falin Tian
- CAS Key Laboratory for Nanosystem and Hierarchy FabricationCAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyChinese Academy of Sciences Beijing 100190 China
- School of Nanoscience and TechnologyUniversity of Chinese Academy of Sciences NO.19A Yuquan Road Beijing 100049 China
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23
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Woodward X, Stimpson EE, Kelly CV. Single-lipid tracking on nanoscale membrane buds: The effects of curvature on lipid diffusion and sorting. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2064-2075. [PMID: 29856992 DOI: 10.1016/j.bbamem.2018.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/30/2018] [Accepted: 05/19/2018] [Indexed: 01/25/2023]
Abstract
Nanoscale membrane curvature in cells is critical for endocytosis/exocytosis and membrane trafficking. However, the biophysical ramifications of nanoscale membrane curvature on the behavior of lipids remain poorly understood. Here, we created an experimental model system of membrane curvature at a physiologically-relevant scale and obtained nanoscopic information on single-lipid distributions and dynamics. Supported lipid bilayers were created over 50 and 70 nm radius nanoparticles to create membrane buds. Single-molecule localization microscopy was performed with diverse mixtures of fluorescent and non-fluorescent lipids. Variations in lipid acyl tales length, saturation, head-group, and fluorescent labeling strategy were tested while maintaining a single fluid lipid phase throughout the membrane. Monte Carlo simulations were used to fit our experimental results and quantify the effects of curvature on the lipid diffusion and sorting. Whereas varying the composition of the non-fluorescent lipids yielded minimal changes to the curvature effects, the labeling strategy of the fluorescent lipids yielded highly varying effects of curvature. Most conditions yield single-population Brownian diffusion throughout the membrane; however, curvature-induced lipid sorting, slowing, and aggregation were observed in some conditions. Head-group labeled lipids such as DPPE-Texas Red and POPE-Rhodamine diffused >2.4× slower on the curved vs. the planar membranes; tail-labeled lipids such as NBD-PPC, TopFluor-PPC, and TopFluor-PIP2, as well as DiIC12 and DiIC18 displayed no significant changes in diffusion due to the membrane curvature. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Eric E Stimpson
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States.
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24
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Zeno WF, Ogunyankin MO, Longo ML. Scaling relationships for translational diffusion constants applied to membrane domain dissolution and growth. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1994-2003. [PMID: 29501605 DOI: 10.1016/j.bbamem.2018.02.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 01/10/2023]
Abstract
We compare the way that relationships for diffusion constants scale with the size of diffusing membrane domains and the geometry of their environments. Then, we review our experimental work on the dynamics of dissolution/growth of membrane domains in crowding induced mixing, phase separation, and Ostwald ripening in a highly confined environment. Overall, the scaling relationships applied to diffusion constants obtained by fits to our dynamic data indicate that dissolution and growth is influenced by the diffusion of clusters or small domains of lipids, in addition to kinetic processes and geometrical constraints.
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Affiliation(s)
- Wade F Zeno
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States
| | - Maria O Ogunyankin
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States
| | - Marjorie L Longo
- Department of Chemical Engineering, University of California Davis, Davis, CA 95616, United States.
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25
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Chelladurai R, Debnath K, Jana NR, Basu JK. Nanoscale Heterogeneities Drive Enhanced Binding and Anomalous Diffusion of Nanoparticles in Model Biomembranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1691-1699. [PMID: 29320202 DOI: 10.1021/acs.langmuir.7b04003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Interaction of functional nanoparticles with cells and model biomembranes has been widely studied to evaluate the effectiveness of the particles as potential drug delivery vehicles and bioimaging labels as well as in understanding nanoparticle cytotoxicity effects. Charged nanoparticles, in particular, with tunable surface charge have been found to be effective in targeting cellular membranes as well as the subcellular matrix. However, a microscopic understanding of the underlying physical principles that govern nanoparticle binding, uptake, or diffusion on cells is lacking. Here, we report the first experimental studies of nanoparticle diffusion on model biomembranes and correlate this to the existence of nanoscale dynamics and structural heterogeneities using super-resolution stimulated emission depletion (STED) microscopy. Using confocal and STED microscopy coupled with fluorescence correlation spectroscopy (FCS), we provide novel insight on why these nanoparticles show enhanced binding on two-component lipid bilayers as compared to single-component membranes and how binding and diffusion is correlated to subdiffraction nanoscale dynamics and structure. The enhanced binding is also dictated, in part, by the presence of structural and dynamic heterogeneity, as revealed by STED-FCS studies, which could potentially be used to understand enhanced nanoparticle binding in raft-like domains in cell membranes. In addition, we also observe a clear correlation between the enhanced nanoparticle diffusion on membranes and the extent of membrane penetration by the nanoparticles. Our results not only have a significant impact on our understanding of nanoparticle binding and uptake as well as diffusion in cell and biomembranes, but have very strong implications for uptake mechanisms and diffusion of other biomolecules, like proteins on cell membranes and their connections to functional membrane nanoscale platform.
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Affiliation(s)
- Roobala Chelladurai
- Department of Physics, Indian Institute of Science , Bangalore 560012, India
| | - Koushik Debnath
- Centre for Advanced Materials, Indian Association for the Cultivation of Sciences , Kolkata 700032, India
| | - Nikhil R Jana
- Centre for Advanced Materials, Indian Association for the Cultivation of Sciences , Kolkata 700032, India
| | - Jaydeep Kumar Basu
- Department of Physics, Indian Institute of Science , Bangalore 560012, India
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26
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Javanainen M, Martinez-Seara H, Metzler R, Vattulainen I. Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J Phys Chem Lett 2017; 8:4308-4313. [PMID: 28823153 DOI: 10.1021/acs.jpclett.7b01758] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbrück (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D ∝ ln(1/R). However, instead of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes-like dependence D ∝ 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different from protein-poor conditions and plays a significant role in formation of functional multiprotein complexes.
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Affiliation(s)
- Matti Javanainen
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- Department of Physics, University of Helsinki , 00014 Helsinki, Finland
| | - Hector Martinez-Seara
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , 166 10 Prague, Czech Republic
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- Department of Physics, University of Helsinki , 00014 Helsinki, Finland
- MEMPHYS - Centre for Biomembrane Physics, University of Southern Denmark , 5230 Odense, Denmark
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27
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Abstract
In the plasma membrane of eukaryotic cells, proteins and lipids are organized in clusters, the latter ones often called lipid domains or "lipid rafts." Recent findings highlight the dynamic nature of such domains and the key role of membrane geometry and spatial boundaries. In this study, we used porous substrates with different pore radii to address precisely the extent of the geometric constraint, permitting us to modulate and investigate the size and mobility of lipid domains in phase-separated continuous pore-spanning membranes (PSMs). Fluorescence video microscopy revealed two types of liquid-ordered (lo) domains in the freestanding parts of the PSMs: (i) immobile domains that were attached to the pore rims and (ii) mobile, round-shaped lo domains within the center of the PSMs. Analysis of the diffusion of the mobile lo domains by video microscopy and particle tracking showed that the domains' mobility is slowed down by orders of magnitude compared with the unrestricted case. We attribute the reduced mobility to the geometric confinement of the PSM, because the drag force is increased substantially due to hydrodynamic effects generated by the presence of these boundaries. Our system can serve as an experimental test bed for diffusion of 2D objects in confined geometry. The impact of hydrodynamics on the mobility of enclosed lipid domains can have great implications for the formation and lateral transport of signaling platforms.
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28
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Measuring the Viscosity of the Escherichia coli Plasma Membrane Using Molecular Rotors. Biophys J 2017; 111:1528-1540. [PMID: 27705775 PMCID: PMC5052448 DOI: 10.1016/j.bpj.2016.08.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 11/20/2022] Open
Abstract
The viscosity is a highly important parameter within the cell membrane, affecting the diffusion of small molecules and, hence, controlling the rates of intracellular reactions. There is significant interest in the direct, quantitative assessment of membrane viscosity. Here we report the use of fluorescence lifetime imaging microscopy of the molecular rotor BODIPY C10 in the membranes of live Escherichia coli bacteria to permit direct quantification of the viscosity. Using this approach, we investigated the viscosity in live E. coli cells, spheroplasts, and liposomes made from E. coli membrane extracts. For live cells and spheroplasts, the viscosity was measured at both room temperature (23°C) and the E. coli growth temperature (37°C), while the membrane extract liposomes were studied over a range of measurement temperatures (5–40°C). At 37°C, we recorded a membrane viscosity in live E. coli cells of 950 cP, which is considerably higher than that previously observed in other live cell membranes (e.g., eukaryotic cells, membranes of Bacillus vegetative cells). Interestingly, this indicates that E. coli cells exhibit a high degree of lipid ordering within their liquid-phase plasma membranes.
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29
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Danial JSH, Cronin B, Mallik C, Wallace MI. On demand modulation of lipid composition in an individual bilayer. SOFT MATTER 2017; 13:1788-1793. [PMID: 28165095 DOI: 10.1039/c6sm01774f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Changes in local lipid composition are thought to play a key role in regulating many complex cellular processes. By studying lipid organization in artificial lipid bilayers the physical principles underlying these process can be studied in detail. However, such in vitro measurements are often hindered by heterogeneities in the lipid composition of individual bilayers prepared by current bulk methods. Here, the lipid composition of an individual droplet interface bilayer is varied by lipid titration into the bilayer from the oil phase in a microfluidic device. Control of lipid composition allows the reversible switching between single- and two-phase regions and sampling of specific lipid compositions in an individual bilayer. This method enables controlled modulation of composition-sensitive processes in a single lipid membrane.
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Affiliation(s)
- John S H Danial
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Bríd Cronin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Chandini Mallik
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
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30
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Chen P, Huang Z, Liang J, Cui T, Zhang X, Miao B, Yan LT. Diffusion and Directionality of Charged Nanoparticles on Lipid Bilayer Membrane. ACS NANO 2016; 10:11541-11547. [PMID: 27936576 DOI: 10.1021/acsnano.6b07563] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Diffusion dynamics of charged nanoparticles on the lipid membrane is of essential importance to cellular functioning. Yet a fundamental insight into electrostatics-mediated diffusion dynamics of charged nanoparticles on the membrane is lacking and remains to be an urgent issue. Here we present the computational investigation to uncover the pivotal role of electrostatics in the diffusion dynamics of charged nanoparticles on the lipid membrane. Our results demonstrate diffusive behaviors and directional transport of a charged nanoparticle, significantly depending on the sign and spatial distribution of charges on its surface. In contrast to the Fickian diffusion of neutral nanoparticles, randomly charged nanoparticles undergo superdiffusive transport with directionality. However, the dynamics of uniformly charged nanoparticles favors Fickian diffusion that is significantly enhanced. Such observations can be explained in term of electrostatics-induced surface reconstruction and fluctuation of lipid membrane. We finally present an analytical model connecting surface reconstruction and local deformation of the membrane. Our findings bear wide implications for the understanding and control of the transport of charged nanoparticles on the cell membrane.
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Affiliation(s)
- Pengyu Chen
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Zihan Huang
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Junshi Liang
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Tianqi Cui
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Xinghua Zhang
- School of Science, Beijing Jiaotong University , Beijing 100044, China
| | - Bing Miao
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Li-Tang Yan
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
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31
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Abstract
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular scale can exhibit complex transient density fluctuations. Here the lateral heterogeneity of lipid dynamics is explored in free standing lipid monolayers. As the temperature is lowered the probes exhibit increasingly broad and heterogeneous rotational correlation. This increase in heterogeneity appears to exhibit a critical onset, similar to those observed for glass forming fluids. We explore heterogeneous relaxation in in a single constituent lipid monolayer of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine by measuring the rotational diffusion of a fluorescent probe (1-palmitoyl-2-[1]-sn-glycero-3-phosphocholine), which is embedded in the lipid monolayer at low labeling density. Dynamic distributions are measured using wide-field time-resolved fluorescence anisotropy. The observed relaxation exhibits a narrow, liquid-like distribution at high temperatures (τ ∼ 2.4 ns), consistent with previous experimental measures (Dadashvand et al 2014 Struct. Dyn. 1 054701, Loura and Ramalho 2007 Biochim. Biophys. Acta 1768 467-478). However, as the temperature is quenched, the distribution broadens, and we observe the appearance of a long relaxation population (τ ∼ 16.5 ns). This supports the heterogeneity observed for lipids at high packing densities, and demonstrates that the nanoscale diffusion and reorganization in lipid structures can be significantly complex, even in the simplest amorphous architectures. Dynamical heterogeneity of this form can have a significant impact on the organization, permeability and energetics of lipid membrane structures.
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Affiliation(s)
- Neda Dadashvand
- Department of Physics, Wesleyan University, Middletown, CT 06457, USA
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32
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Klaus CJS, Raghunathan K, DiBenedetto E, Kenworthy AK. Analysis of diffusion in curved surfaces and its application to tubular membranes. Mol Biol Cell 2016; 27:3937-3946. [PMID: 27733625 PMCID: PMC5170615 DOI: 10.1091/mbc.e16-06-0445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/08/2016] [Accepted: 10/04/2016] [Indexed: 11/11/2022] Open
Abstract
Diffusion of particles in curved surfaces is inherently complex compared with diffusion in a flat membrane, owing to the nonplanarity of the surface. The consequence of such nonplanar geometry on diffusion is poorly understood but is highly relevant in the case of cell membranes, which often adopt complex geometries. To address this question, we developed a new finite element approach to model diffusion on curved membrane surfaces based on solutions to Fick's law of diffusion and used this to study the effects of geometry on the entry of surface-bound particles into tubules by diffusion. We show that variations in tubule radius and length can distinctly alter diffusion gradients in tubules over biologically relevant timescales. In addition, we show that tubular structures tend to retain concentration gradients for a longer time compared with a comparable flat surface. These findings indicate that sorting of particles along the surfaces of tubules can arise simply as a geometric consequence of the curvature without any specific contribution from the membrane environment. Our studies provide a framework for modeling diffusion in curved surfaces and suggest that biological regulation can emerge purely from membrane geometry.
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Affiliation(s)
| | - Krishnan Raghunathan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | | | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232 .,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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33
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Ito H, Higuchi Y, Shimokawa N. Coarse-grained molecular dynamics simulation of binary charged lipid membranes: Phase separation and morphological dynamics. Phys Rev E 2016; 94:042611. [PMID: 27841477 DOI: 10.1103/physreve.94.042611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Indexed: 06/06/2023]
Abstract
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the prior disturbance of the local molecular orientation in the domain.
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Affiliation(s)
- Hiroaki Ito
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Yuji Higuchi
- Institute for Materials Research, Tohoku University, Miyagi 980-8577, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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34
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Hu J, Xu GK, Lipowsky R, Weikl TR. Binding kinetics of membrane-anchored receptors and ligands: Molecular dynamics simulations and theory. J Chem Phys 2016; 143:243137. [PMID: 26723622 DOI: 10.1063/1.4936135] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring of the proteins. In this article, we (i) present detailed data for the binding of membrane-anchored proteins from coarse-grained molecular dynamics simulations and (ii) provide a theory that describes how the binding kinetics depends on the average separation and thermal roughness of the adhering membranes and on the anchoring, lengths, and length variations of the proteins. An important element of our theory is the tilt of bound receptor-ligand complexes and transition-state complexes relative to the membrane normals. This tilt results from an interplay of the anchoring energy and rotational entropy of the complexes and facilitates the formation of receptor-ligand bonds at membrane separations smaller than the preferred separation for binding. In our simulations, we have considered both lipid-anchored and transmembrane receptor and ligand proteins. We find that the binding equilibrium constant and binding on-rate constant of lipid-anchored proteins are considerably smaller than the binding constant and on-rate constant of rigid transmembrane proteins with identical binding domains.
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Affiliation(s)
- Jinglei Hu
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Postdam, Germany
| | - Guang-Kui Xu
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Postdam, Germany
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Postdam, Germany
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Postdam, Germany
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35
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Camley BA, Lerner MG, Pastor RW, Brown FLH. Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes. J Chem Phys 2016; 143:243113. [PMID: 26723598 DOI: 10.1063/1.4932980] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Saffman-Delbrück hydrodynamic model for lipid-bilayer membranes is modified to account for the periodic boundary conditions commonly imposed in molecular simulations. Predicted lateral diffusion coefficients for membrane-embedded solid bodies are sensitive to box shape and converge slowly to the limit of infinite box size, raising serious doubts for the prospects of using detailed simulations to accurately predict membrane-protein diffusivities and related transport properties. Estimates for the relative error associated with periodic boundary artifacts are 50% and higher for fully atomistic models in currently feasible simulation boxes. MARTINI simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
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Affiliation(s)
- Brian A Camley
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, California 92093, USA
| | - Michael G Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana 47374, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, California 93106, USA
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36
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Hartel AJW, Glogger M, Jones NG, Abuillan W, Batram C, Hermann A, Fenz SF, Tanaka M, Engstler M. N-glycosylation enables high lateral mobility of GPI-anchored proteins at a molecular crowding threshold. Nat Commun 2016; 7:12870. [PMID: 27641538 PMCID: PMC5031801 DOI: 10.1038/ncomms12870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/09/2016] [Indexed: 01/17/2023] Open
Abstract
The protein density in biological membranes can be extraordinarily high, but the impact of molecular crowding on the diffusion of membrane proteins has not been studied systematically in a natural system. The diversity of the membrane proteome of most cells may preclude systematic studies. African trypanosomes, however, feature a uniform surface coat that is dominated by a single type of variant surface glycoprotein (VSG). Here we study the density-dependence of the diffusion of different glycosylphosphatidylinositol-anchored VSG-types on living cells and in artificial membranes. Our results suggest that a specific molecular crowding threshold (MCT) limits diffusion and hence affects protein function. Obstacles in the form of heterologous proteins compromise the diffusion coefficient and the MCT. The trypanosome VSG-coat operates very close to its MCT. Importantly, our experiments show that N-linked glycans act as molecular insulators that reduce retarding intermolecular interactions allowing membrane proteins to function correctly even when densely packed.
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Affiliation(s)
- Andreas J. W. Hartel
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Marius Glogger
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Nicola G. Jones
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
| | - Christopher Batram
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Anne Hermann
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Susanne F. Fenz
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
- Institute for Integrated Cell-Material Science (WPI iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Markus Engstler
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
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37
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Weikl TR, Hu J, Xu GK, Lipowsky R. Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory. Cell Adh Migr 2016; 10:576-589. [PMID: 27294442 PMCID: PMC5079412 DOI: 10.1080/19336918.2016.1180487] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022] Open
Abstract
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics of these proteins is affected by the membranes and by the membrane anchoring and molecular properties of the proteins. Simulations and theory both indicate that the binding equilibrium constant [Formula: see text] and the on- and off-rate constants of anchored receptors and ligands in their 2-dimensional (2D) membrane environment strongly depend on the membrane roughness from thermally excited shape fluctuations on nanoscales. Recent theory corroborated by simulations provides a general relation between [Formula: see text] and the binding constant [Formula: see text] of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in 3 dimensions (3D).
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Affiliation(s)
- Thomas R. Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
| | - Jinglei Hu
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
| | - Guang-Kui Xu
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
- International Center for Applied Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi'an Jiaotong University, Xi'an, China
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
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38
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Tian F, Yue T, Dong W, Zhang X. Membrane tube pearling induced by a coupling of osmotic pressure and nanoparticle adhesion. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1161855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Falin Tian
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, China
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, Lyon Cedex, France
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, China
| | - Wei Dong
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, Lyon Cedex, France
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, China
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39
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Guigas G, Weiss M. Effects of protein crowding on membrane systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2441-2450. [PMID: 26724385 DOI: 10.1016/j.bbamem.2015.12.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/19/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromolecules, e.g. proteins, that participate in numerous vital processes. With typical surface densities of 30,000 proteins per μm(2) cellular membranes are indeed crowded places that leave only few nanometers of private space for individual proteins. Here, we review recent advances in our understanding of protein crowding in membrane systems. We first give a brief overview on state-of-the-art approaches in experiment and simulation that are frequently used to study crowded membranes. After that, we review how crowding can affect diffusive transport of proteins and lipids in membrane systems. Next, we discuss lipid and protein sorting in crowded membrane systems, including effects like protein cluster formation, phase segregation, and lipid droplet formation. Subsequently, we highlight recent progress in uncovering crowding-induced conformational changes of membranes, e.g. membrane budding and vesicle formation. Finally, we give a short outlook on potential future developments in the field of crowded membrane systems. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Gernot Guigas
- Experimental Physics I, Universitaetsstr. 30, Bayreuth University, D-95440 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, Universitaetsstr. 30, Bayreuth University, D-95440 Bayreuth, Germany.
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40
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Jouannet S, Saint-Pol J, Fernandez L, Nguyen V, Charrin S, Boucheix C, Brou C, Milhiet PE, Rubinstein E. TspanC8 tetraspanins differentially regulate the cleavage of ADAM10 substrates, Notch activation and ADAM10 membrane compartmentalization. Cell Mol Life Sci 2015; 73:1895-915. [PMID: 26686862 PMCID: PMC4819958 DOI: 10.1007/s00018-015-2111-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/03/2015] [Accepted: 12/03/2015] [Indexed: 01/08/2023]
Abstract
The metalloprotease ADAM10 mediates the shedding of the ectodomain of various cell membrane proteins, including APP, the precursor of the amyloid peptide Aβ, and Notch receptors following ligand binding. ADAM10 associates with the members of an evolutionary conserved subgroup of tetraspanins, referred to as TspanC8, which regulate its exit from the endoplasmic reticulum. Here we show that 4 of these TspanC8 (Tspan5, Tspan14, Tspan15 and Tspan33) which positively regulate ADAM10 surface expression levels differentially impact ADAM10-dependent Notch activation and the cleavage of several ADAM10 substrates, including APP, N-cadherin and CD44. Sucrose gradient fractionation, single molecule tracking and quantitative mass-spectrometry analysis of the repertoire of molecules co-immunoprecipitated with Tspan5, Tspan15 and ADAM10 show that these two tetraspanins differentially regulate ADAM10 membrane compartmentalization. These data represent a unique example where several tetraspanins differentially regulate the function of a common partner protein through a distinct membrane compartmentalization.
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Affiliation(s)
- Stéphanie Jouannet
- Inserm, U935, 94807, Villejuif, France.,Université Paris-Sud, Institut André Lwoff, 94807, Villejuif, France
| | - Julien Saint-Pol
- Inserm, U935, 94807, Villejuif, France.,Université Paris-Sud, Institut André Lwoff, 94807, Villejuif, France
| | - Laurent Fernandez
- Inserm, U1054, 34090, Montpellier, France.,Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier, France
| | - Viet Nguyen
- Université Paris-Sud, Institut André Lwoff, 94807, Villejuif, France
| | - Stéphanie Charrin
- Inserm, U935, 94807, Villejuif, France.,Université Paris-Sud, Institut André Lwoff, 94807, Villejuif, France
| | - Claude Boucheix
- Inserm, U935, 94807, Villejuif, France.,Université Paris-Sud, Institut André Lwoff, 94807, Villejuif, France
| | - Christel Brou
- Institut Pasteur, Laboratoire "Signalisation et Pathogenèse", 75015, Paris, France
| | - Pierre-Emmanuel Milhiet
- Inserm, U1054, 34090, Montpellier, France.,Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier, France
| | - Eric Rubinstein
- Inserm, U935, 94807, Villejuif, France. .,Université Paris-Sud, Institut André Lwoff, 94807, Villejuif, France.
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41
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Smeazzetto S, Tadini-Buoninsegni F, Thiel G, Berti D, Montis C. Phospholamban spontaneously reconstitutes into giant unilamellar vesicles where it generates a cation selective channel. Phys Chem Chem Phys 2015; 18:1629-36. [PMID: 26673394 DOI: 10.1039/c5cp05893g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospholamban (PLN) is a small integral membrane protein, which modulates the activity of the Sarcoplasmic Reticulum Ca(2+)-ATPase (SERCA) of cardiac myocytes. PLN, as a monomer, can directly interact and tune SERCA activity, but the physiological function of the pentameric form is not yet fully understood and still debated. In this work, we reconstituted PLN in Giant Unilamellar Vesicles (GUVs), a simple and reliable experimental model system to monitor the activity of proteins in membranes. By Laser Scanning Confocal Microscopy (LSCM) and Fluorescence Correlation Spectroscopy (FCS) we verified a spontaneous reconstitution of PLN into the phospholipid bilayer. In parallel experiments, we measured with the patch clamp technique canonical ion channel fluctuations, which highlight a preference for Cs(+) over K(+) and do not conduct Ca(2+). The results prove that PLN forms, presumably in its pentameric form, a cation selective ion channel.
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Affiliation(s)
- S Smeazzetto
- Department of Chemistry "Ugo Schiff", University of Florence, Firenze, Italy
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42
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43
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Abstract
Lipid rafts are submicron proteolipid domains thought to be responsible for membrane trafficking and signaling. Their small size and transient nature put an understanding of their dynamics beyond the reach of existing techniques, leading to much contention as to their exact role. Here, we exploit the differences in light scattering from lipid bilayer phases to achieve dynamic imaging of nanoscopic lipid domains without any labels. Using phase-separated droplet interface bilayers we resolve the diffusion of domains as small as 50 nm in radius and observe nanodomain formation, destruction, and dynamic coalescence with a domain lifetime of 220±60 ms. Domain dynamics on this timescale suggests an important role in modulating membrane protein function.
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44
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The molecular size of the extra-membrane domain influences the diffusion of the GPI-anchored VSG on the trypanosome plasma membrane. Sci Rep 2015; 5:10394. [PMID: 26065579 PMCID: PMC5387117 DOI: 10.1038/srep10394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 04/13/2015] [Indexed: 12/14/2022] Open
Abstract
A plethora of proteins undergo random and passive diffusion in biological membranes. While the contribution of the membrane-embedded domain to diffusion is well established, the potential impact of the extra-membrane protein part has been largely neglected. Here, we show that the molecular length influences the diffusion coefficient of GPI-anchored proteins: smaller proteins diffuse faster than larger ones. The distinct diffusion properties of differently sized membrane proteins are biologically relevant. The variant surface glycoprotein (VSG) of African trypanosomes, for example, is sized for an effective diffusion-driven randomization on the cell surface, a process that is essential for parasite virulence. We propose that the molecular sizes of proteins dominating the cell surfaces of other eukaryotic pathogens may also be related to diffusion-limited functions.
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45
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Itel F, Najer A, Palivan CG, Meier W. Dynamics of Membrane Proteins within Synthetic Polymer Membranes with Large Hydrophobic Mismatch. NANO LETTERS 2015; 15:3871-8. [PMID: 26013972 DOI: 10.1021/acs.nanolett.5b00699] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The functioning of biological membrane proteins (MPs) within synthetic block copolymer membranes is an intriguing phenomenon that is believed to offer great potential for applications in life and medical sciences and engineering. The question why biological MPs are able to function in this completely artificial environment is still unresolved by any experimental data. Here, we have analyzed the lateral diffusion properties of different sized MPs within poly(dimethylsiloxane) (PDMS)-containing amphiphilic block copolymer membranes of membrane thicknesses between 9 and 13 nm, which results in a hydrophobic mismatch between the membrane thickness and the size of the proteins of 3.3-7.1 nm (3.5-5 times). We show that the high flexibility of PDMS, which provides membrane fluidities similar to phospholipid bilayers, is the key-factor for MP incorporation.
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Affiliation(s)
- Fabian Itel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Adrian Najer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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46
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Hirschhorn T, di Clemente N, Amsalem AR, Pepinsky RB, Picard JY, Smorodinsky NI, Cate RL, Ehrlich M. Constitutive negative regulation in the processing of the anti-Müllerian hormone receptor II. J Cell Sci 2015; 128:1352-64. [PMID: 25663701 DOI: 10.1242/jcs.160143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The levels and intracellular localization of wild-type transforming growth factor β superfamily (TGFβ-SF) receptors are tightly regulated by endocytic trafficking, shedding and degradation. In contrast, a main regulatory mechanism of mutation-bearing receptors involves their intracellular retention. Anti-Müllerian hormone receptor II (AMHRII, also known as AMHR2) is the type-II receptor for anti-Müllerian hormone (AMH), a TGFβ-SF ligand that mediates Müllerian duct regression in males. Here, we studied AMHRII processing and identified novel mechanisms of its constitutive negative regulation. Immunoblot analysis revealed that a significant portion of AMHRII was missing most of its extracellular domain (ECD) and, although glycosylated, was unfolded and retained in the endoplasmic reticulum. Exogenous expression of AMHRII, but not of type-II TGF-β receptor (TβRII, also known as TGFR2), resulted in its disulfide-bond-mediated homo-oligomerization and intracellular retention, and in a decrease in its AMH-binding capacity. At the plasma membrane, AMHRII differed from TβRII, forming high levels of non-covalent homomeric complexes, which exhibited a clustered distribution and restricted lateral mobility. This study identifies novel mechanisms of negative regulation of a type-II TGFβ-SF receptor through cleavage, intracellular retention and/or promiscuous disulfide-bond mediated homo-oligomerization.
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Affiliation(s)
- Tal Hirschhorn
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel 69978
| | - Nathalie di Clemente
- Université Paris Diderot, Sorbonne Paris Cité, Biologie Fonctionnelle et Adaptative (BFA), F-75013 Paris, France CNRS, UMR 8251, Biologie Fonctionnelle et Adaptative, F-75013 Paris, France INSERM U1133, Physiologie de l'Axe Gonadotrope, F-75013 Paris, France
| | - Ayelet R Amsalem
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - R Blake Pepinsky
- Biogen-Idec, Inc., 14 Cambridge Center, Cambridge, MA 02142, USA
| | - Jean-Yves Picard
- INSERM U1133, Physiologie de l'Axe Gonadotrope, F-75013 Paris, France
| | - Nechama I Smorodinsky
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel 69978
| | - Richard L Cate
- INSERM U1133, Physiologie de l'Axe Gonadotrope, F-75013 Paris, France Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Marcelo Ehrlich
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel 69978
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Guigas G, Weiss M. Membrane protein mobility depends on the length of extra-membrane domains and on the protein concentration. SOFT MATTER 2015; 11:33-37. [PMID: 25407767 DOI: 10.1039/c4sm01846j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Diffusion of membrane proteins is not only determined by the membrane anchor friction but also by the overall concentration of proteins and the length of their extra-membrane domains. We have studied the influence of the latter two cues by mesoscopic simulations. As a result, we have found that the total friction of membrane proteins, γ, increases approximately linearly with the length of the extra-membrane domain, L, whereas a slightly nonlinear dependence on the total protein concentration, ϕ was observed. We provide an educated guess for the functional form of γ(L, ϕ) and the associated diffusion coefficient. This expression not only matches our simulation data but it is also in favorable agreement with previously published experimental data. Our findings indicate that diffusion coefficients of membrane proteins are not solely determined by the friction of membrane anchors but also extra-membrane domains and the crowdedness of the membrane need to be considered to obtain a comprehensive view of protein diffusion on cellular membranes.
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Affiliation(s)
- Gernot Guigas
- Experimental Physics I, University of Bayreuth, 95440 Bayreuth, Germany.
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48
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Wang CY, Hill RJ. Transmembrane protein diffusion in gel-supported dual-leaflet membranes. Biophys J 2014; 107:2296-304. [PMID: 25418298 DOI: 10.1016/j.bpj.2014.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/09/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022] Open
Abstract
Tools to measure transmembrane-protein diffusion in lipid bilayer membranes have advanced in recent decades, providing a need for predictive theoretical models that account for interleaflet leaflet friction on tracer mobility. Here we address the fully three-dimensional flows driven by a (nonprotruding) transmembrane protein embedded in a dual-leaflet membrane that is supported above and below by soft porous supports (e.g., hydrogel or extracellular matrix), each of which has a prescribed permeability and solvent viscosity. For asymmetric configurations, i.e., supports with contrasting permeability, as realized for cells in contact with hydrogel scaffolds or culture media, the diffusion coefficient can reflect interleaflet friction. Reasonable approximations, for sufficiently large tracers on low-permeability supports, are furnished by a recent phenomenological theory from the literature. Interpreting literature data, albeit for hard-supported membranes, provides a theoretical basis for the phenomenological Stokes drag law as well as strengthening assertions that nonhydrodynamic interactions are important in supported bilayer systems, possibly leading to overestimates of the membrane/leaflet viscosity. Our theory provides a theoretical foundation for future experimental studies of tracer diffusion in gel-supported membranes.
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Affiliation(s)
- Chih-Ying Wang
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
| | - Reghan J Hill
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada.
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Saxton MJ. Wanted: scalable tracers for diffusion measurements. J Phys Chem B 2014; 118:12805-17. [PMID: 25319586 PMCID: PMC4234437 DOI: 10.1021/jp5059885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/03/2014] [Indexed: 12/02/2022]
Abstract
Scalable tracers are potentially a useful tool to examine diffusion mechanisms and to predict diffusion coefficients, particularly for hindered diffusion in complex, heterogeneous, or crowded systems. Scalable tracers are defined as a series of tracers varying in size but with the same shape, structure, surface chemistry, deformability, and diffusion mechanism. Both chemical homology and constant dynamics are required. In particular, branching must not vary with size, and there must be no transition between ordinary diffusion and reptation. Measurements using scalable tracers yield the mean diffusion coefficient as a function of size alone; measurements using nonscalable tracers yield the variation due to differences in the other properties. Candidate scalable tracers are discussed for two-dimensional (2D) diffusion in membranes and three-dimensional diffusion in aqueous solutions. Correlations to predict the mean diffusion coefficient of globular biomolecules from molecular mass are reviewed briefly. Specific suggestions for the 3D case include the use of synthetic dendrimers or random hyperbranched polymers instead of dextran and the use of core-shell quantum dots. Another useful tool would be a series of scalable tracers varying in deformability alone, prepared by varying the density of crosslinking in a polymer to make say "reinforced Ficoll" or "reinforced hyperbranched polyglycerol."
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Affiliation(s)
- Michael J. Saxton
- Department of Biochemistry
and Molecular Medicine, University of California, One Shields Ave., Davis, California 95616, United States
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Zhang M, Zhao J, Zheng J. Molecular understanding of a potential functional link between antimicrobial and amyloid peptides. SOFT MATTER 2014; 10:7425-7451. [PMID: 25105988 DOI: 10.1039/c4sm00907j] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antimicrobial and amyloid peptides do not share common sequences, typical secondary structures, or normal biological activity but both the classes of peptides exhibit membrane-disruption ability to induce cell toxicity. Different membrane-disruption mechanisms have been proposed for antimicrobial and amyloid peptides, individually, some of which are not exclusive to either peptide type, implying that certain common principles may govern the folding and functions of different cytolytic peptides and associated membrane disruption mechanisms. Particularly, some antimicrobial and amyloid peptides have been identified to have dual complementary amyloid and antimicrobial properties, suggesting a potential functional link between amyloid and antimicrobial peptides. Given that some similar structural and membrane-disruption characteristics exist between the two classes of peptides, this review summarizes major findings, recent advances, and future challenges related to antimicrobial and amyloid peptides and strives to illustrate the similarities, differences, and relationships in the sequences, structures, and membrane interaction modes between amyloid and antimicrobial peptides, with a special focus on direct interactions of the peptides with the membranes. We hope that this review will stimulate further research at the interface of antimicrobial and amyloid peptides - which has been studied less intensively than either type of peptides - to decipher a possible link between both amyloid pathology and antimicrobial activity, which can guide drug design and peptide engineering to influence peptide-membrane interactions important in human health and diseases.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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