1
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Kompella VPS, Romano MC, Stansfield I, Mancera RL. What determines sub-diffusive behavior in crowded protein solutions? Biophys J 2024; 123:134-146. [PMID: 38073154 PMCID: PMC10808025 DOI: 10.1016/j.bpj.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
The aqueous environment inside cells is densely packed. A typical cell has a macromolecular concentration in the range 90-450 g/L, with 5%-40% of its volume being occupied by macromolecules, resulting in what is known as macromolecular crowding. The space available for the free diffusion of metabolites and other macromolecules is thus greatly reduced, leading to so-called excluded volume effects. The slow diffusion of macromolecules under crowded conditions has been explained using transient complex formation. However, sub-diffusion noted in earlier works is not well characterized, particularly the role played by transient complex formation and excluded volume effects. We have used Brownian dynamics simulations to characterize the diffusion of chymotrypsin inhibitor 2 in protein solutions of bovine serum albumin and lysozyme at concentrations ranging from 50 to 300 g/L. The predicted changes in diffusion coefficient as a function of crowder concentration are consistent with NMR experiments. The sub-diffusive behavior observed in the sub-microsecond timescale can be explained in terms of a so-called cage effect, arising from rattling motion in a local molecular cage as a consequence of excluded volume effects. By selectively manipulating the nature of interactions between protein molecules, we determined that excluded volume effects induce sub-diffusive dynamics at sub-microsecond timescales. These findings may help to explain the diffusion-mediated effects of protein crowding on cellular processes.
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Affiliation(s)
- Vijay Phanindra Srikanth Kompella
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia; Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Maria Carmen Romano
- Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom; Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia.
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2
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Weisgerber AW, Otruba Z, Knowles MK. Syntaxin clusters and cholesterol affect the mobility of Syntaxin1a. Biophys J 2024:S0006-3495(24)00028-6. [PMID: 38221759 DOI: 10.1016/j.bpj.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/02/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024] Open
Abstract
Syntaxin1a (Syx1a) is essential for stimulated exocytosis in neuroendocrine cells. The vesicle docking process involves the formation of nanoscale Syx1a domains on the plasma membrane and the Syx1a clusters disintegrate during the fusion process. Syx1a nanodomains are static yet Syx1a molecules dynamically enter and leave the domains; the process by which these clusters maintain this balance is unclear. In this work, the dynamics of the Syx1a molecules is elucidated relative to the cluster position through a labeling strategy that allows both the bulk position of the Syx clusters to be visualized concurrent with the trajectories of single Syx1a molecules on the surface of PC12 cells. Single Syx1a molecules were tracked in time relative to cluster positions to decipher how Syx1a moves within a cluster and when clusters are not present. Syx1a is mobile on the plasma membrane, more mobile at the center of clusters, and less mobile near the edges of clusters; this depends on the presence of the N-terminal Habc domain and cholesterol, which are essential for proper exocytosis. Simulations of the dynamics observed at clusters support a model where clusters are maintained by a large cage (r = 100 nm) within which Syx1a remains highly mobile within the cluster (r = 50 nm). The depletion of cholesterol dramatically reduces the mobility of Syx1a within clusters and less so over the rest of the plasma membrane. This suggests that fluidity of Syx1a supramolecular clusters is needed for function.
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Affiliation(s)
- Alan W Weisgerber
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Zdeněk Otruba
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Michelle K Knowles
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado.
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3
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Tantiwong C, Dunster JL, Cavill R, Tomlinson MG, Wierling C, Heemskerk JWM, Gibbins JM. An agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts. Sci Rep 2023; 13:3906. [PMID: 36890261 PMCID: PMC9994409 DOI: 10.1038/s41598-023-30884-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
Receptor diffusion plays an essential role in cellular signalling via the plasma membrane microenvironment and receptor interactions, but the regulation is not well understood. To aid in understanding of the key determinants of receptor diffusion and signalling, we developed agent-based models (ABMs) to explore the extent of dimerisation of the platelet- and megakaryocyte-specific receptor for collagen glycoprotein VI (GPVI). This approach assessed the importance of glycolipid enriched raft-like domains within the plasma membrane that lower receptor diffusivity. Our model simulations demonstrated that GPVI dimers preferentially concentrate in confined domains and, if diffusivity within domains is decreased relative to outside of domains, dimerisation rates are increased. While an increased amount of confined domains resulted in further dimerisation, merging of domains, which may occur upon membrane rearrangements, was without effect. Modelling of the proportion of the cell membrane which constitutes lipid rafts indicated that dimerisation levels could not be explained by these alone. Crowding of receptors by other membrane proteins was also an important determinant of GPVI dimerisation. Together, these results demonstrate the value of ABM approaches in exploring the interactions on a cell surface, guiding the experimentation for new therapeutic avenues.
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Affiliation(s)
- Chukiat Tantiwong
- School of Biological Sciences, University of Reading, Reading, UK.,Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands
| | - Joanne L Dunster
- School of Biological Sciences, University of Reading, Reading, UK
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | | | | | - Johan W M Heemskerk
- Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands.,Synapse Research Institute, Maastricht, The Netherlands
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4
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Tepperman A, Zheng DJ, Taka MA, Vrieze A, Le Lam A, Heit B. Customizable live-cell imaging chambers for multimodal and multiplex fluorescence microscopy. Biochem Cell Biol 2020; 98:612-623. [PMID: 32339465 DOI: 10.1139/bcb-2020-0064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Using multiple imaging modalities while performing independent experiments in parallel can greatly enhance the throughput of microscopy-based research, but requires the provision of appropriate experimental conditions in a format that meets the optical requirements of the microscope. Although customized imaging chambers can meet these challenges, the difficulty of manufacturing custom chambers and the relatively high cost and design inflexibility of commercial chambers has limited the adoption of this approach. Herein, we demonstrate the use of 3D printing to produce inexpensive, customized, live-cell imaging chambers that are compatible with a range of imaging modalities, including super-resolution microscopy. In this approach, biocompatible plastics are used to print imaging chambers designed to meet the specific needs of an experiment, followed by adhesion of the printed chamber to a glass coverslip, producing a chamber that is impermeant to liquids and that supports the growth and imaging of cells over multiple days. This approach can also be used to produce moulds for casting microfluidic devices made of polydimethylsiloxane. The utility of these chambers is demonstrated using designs for multiplex microscopy, imaging under shear, chemotaxis, and general cellular imaging. Together, this approach represents an inexpensive yet highly customizable approach for producing imaging chambers that are compatible with modern microscopy techniques.
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Affiliation(s)
- Adam Tepperman
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - David Jiao Zheng
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Maria Abou Taka
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Angela Vrieze
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Austin Le Lam
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.,Robarts Research Institute, London, Ontario, Canada
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5
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Crawford M, Liu N, Mahdipour E, Barr K, Heit B, Dagnino L. Integrin-linked kinase regulates melanosome trafficking and melanin transfer in melanocytes. Mol Biol Cell 2020; 31:768-781. [PMID: 32049584 PMCID: PMC7185957 DOI: 10.1091/mbc.e19-09-0510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Melanosomes are melanin-containing organelles that provide pigmentation and protection from solar UV radiation to the skin. In melanocytes, melanosomes mature and traffic to dendritic tips, where they are transferred to adjacent epidermal keratinocytes through pathways that involve microtubule networks and the actin cytoskeleton. However, the role of scaffold proteins in these processes is poorly understood. Integrin-linked kinase (ILK) is a scaffold protein that regulates microtubule stability and F-actin dynamics. Here we show that ILK is necessary for normal trafficking of melanosomes along microtubule tracks. In the absence of ILK, immature melanosomes are not retained in perinuclear regions, and mature melanosome trafficking along microtubule tracks is impaired. These deficits can be attenuated by microtubule stabilization. Microtubules are also necessary for the formation of dendrites in melanocytes, and Ilk inactivation reduces melanocyte dendricity. Activation of glycogen synthase kinase-3 (GSK-3) interferes with microtubule assembly. Significantly, inhibition of GSK-3 activity or exogenous expression of the GSK-3 substrate collapsin response mediator protein 2 (CRMP2) in ILK-deficient melanocytes restored dendricity. ILK is also required for normal melanin transfer, and GSK-3 inhibition in melanocytes partially restored melanin transfer to neighboring keratinocytes. Thus, our work shows that ILK is a central modulator of melanosome movements in primary epidermal melanocytes and identifies ILK and GSK-3 as important modulators of melanin transfer to keratinocytes, a key process for epidermal UV photoprotection.
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Affiliation(s)
- Melissa Crawford
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, University of Western Ontario, London, ON N6G 2C4, Canada
| | - Nancy Liu
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, University of Western Ontario, London, ON N6G 2C4, Canada
| | - Elahe Mahdipour
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, University of Western Ontario, London, ON N6G 2C4, Canada.,Department of Medical Biotechnology and Nanotechnology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kevin Barr
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, University of Western Ontario, London, ON N6G 2C4, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology and Robarts Research Institute, University of Western Ontario, London, ON N6G 2C4, Canada
| | - Lina Dagnino
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, University of Western Ontario, London, ON N6G 2C4, Canada.,Department of Oncology, University of Western Ontario, London, ON N6G 2C4, Canada
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6
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Lenzini S, Bargi R, Chung G, Shin JW. Matrix mechanics and water permeation regulate extracellular vesicle transport. NATURE NANOTECHNOLOGY 2020; 15:217-223. [PMID: 32066904 PMCID: PMC7075670 DOI: 10.1038/s41565-020-0636-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/09/2020] [Indexed: 05/25/2023]
Abstract
Cells release extracellular vesicles (EVs) to communicate over long distances, which requires EVs to traverse the extracellular matrix (ECM). However, given that the size of EVs is usually larger than the mesh size of the ECM, it is not clear how they can travel through the dense ECM. Here we show that, in contrast to synthetic nanoparticles, EVs readily transport through nanoporous ECM. Using engineered hydrogels, we demonstrate that the mechanical properties of the matrix regulate anomalous EV transport under confinement. Matrix stress relaxation allows EVs to overcome the confinement, and a higher crosslinking density facilitates a fluctuating transport motion through the polymer mesh, which leads to free diffusion and fast transport. Furthermore, water permeation through aquaporin-1 mediates the EV deformability, which further supports EV transport in hydrogels and a decellularized matrix. Our results provide evidence for the nature of EV transport within confined environments and demonstrate an unexpected dependence on matrix mechanics and water permeation.
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Affiliation(s)
- Stephen Lenzini
- Department of Pharmacology and Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Raymond Bargi
- Department of Pharmacology and Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Gina Chung
- Department of Pharmacology and Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Jae-Won Shin
- Department of Pharmacology and Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
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7
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Abstract
Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this is far from the truth. Here we shed light on the complexity and importance of diffusion in bacteria, illustrating the similarities and differences of diffusive behaviors of molecules within different compartments of bacterial cells. We first describe common methodologies used to probe diffusion and the associated models and analyses. We then discuss distinct diffusive behaviors of molecules within different bacterial cellular compartments, highlighting the influence of metabolism, size, crowding, charge, binding, and more. We also explicitly discuss where further research and a united understanding of what dictates diffusive behaviors across the different compartments of the cell are required, pointing out new research avenues to pursue.
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Affiliation(s)
- Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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8
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Basak S, Sengupta S, Chattopadhyay K. Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells. Biophys Rev 2019; 11:851-872. [PMID: 31444739 PMCID: PMC6957588 DOI: 10.1007/s12551-019-00580-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 01/24/2023] Open
Abstract
In order to maintain cellular function, biomolecules like protein, DNA, and RNAs have to diffuse to the target spaces within the cell. Changes in the cytosolic microenvironment or in the nucleus during the fulfillment of these cellular processes affect their mobility, folding, and stability thereby impacting the transient or stable interactions with their adjacent neighbors in the organized and dynamic cellular interior. Using classical Brownian motion to elucidate the diffusion behavior of these biomolecules is hard considering their complex nature. The understanding of biomolecular diffusion inside cells still remains elusive due to the lack of a proper model that can be extrapolated to these cases. In this review, we have comprehensively addressed the progresses in this field, laying emphasis on the different aspects of anomalous diffusion in the different biochemical reactions in cell interior. These experiment-based models help to explain the diffusion behavior of biomolecules in the cytosolic and nuclear microenvironment. Moreover, since understanding of biochemical reactions within living cellular system is our main focus, we coupled the experimental observations with the concept of sub-diffusion from in vitro to in vivo condition. We believe that the pairing between the understanding of complex behavior and structure-function paradigm of biological molecules would take us forward by one step in order to solve the puzzle around diseases caused by cellular dysfunction.
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Affiliation(s)
- Sujit Basak
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
| | - Sombuddha Sengupta
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
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9
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Goiko M, de Bruyn JR, Heit B. Membrane Diffusion Occurs by Continuous-Time Random Walk Sustained by Vesicular Trafficking. Biophys J 2019; 114:2887-2899. [PMID: 29925025 DOI: 10.1016/j.bpj.2018.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/06/2018] [Accepted: 04/16/2018] [Indexed: 10/28/2022] Open
Abstract
Diffusion in cellular membranes is regulated by processes that occur over a range of spatial and temporal scales. These processes include membrane fluidity, interprotein and interlipid interactions, interactions with membrane microdomains, interactions with the underlying cytoskeleton, and cellular processes that result in net membrane movement. The complex, non-Brownian diffusion that results from these processes has been difficult to characterize, and moreover, the impact of factors such as membrane recycling on membrane diffusion remains largely unexplored. We have used a careful statistical analysis of single-particle tracking data of the single-pass plasma membrane protein CD93 to show that the diffusion of this protein is well described by a continuous-time random walk in parallel with an aging process mediated by membrane corrals. The overall result is an evolution in the diffusion of CD93: proteins initially diffuse freely on the cell surface but over time become increasingly trapped within diffusion-limiting membrane corrals. Stable populations of freely diffusing and corralled CD93 are maintained by an endocytic/exocytic process in which corralled CD93 is selectively endocytosed, whereas freely diffusing CD93 is replenished by exocytosis of newly synthesized and recycled CD93. This trafficking not only maintained CD93 diffusivity but also maintained the heterogeneous distribution of CD93 in the plasma membrane. These results provide insight into the nature of the biological and biophysical processes that can lead to significantly non-Brownian diffusion of membrane proteins and demonstrate that ongoing membrane recycling is critical to maintaining steady-state diffusion and distribution of proteins in the plasma membrane.
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Affiliation(s)
- Maria Goiko
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada; Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - John R de Bruyn
- Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada; Centre for Human Immunology, The University of Western Ontario, London, Ontario, Canada.
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10
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Chein M, Perlson E, Roichman Y. Flow Arrest in the Plasma Membrane. Biophys J 2019; 117:810-816. [PMID: 31326106 DOI: 10.1016/j.bpj.2019.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 07/01/2019] [Indexed: 10/26/2022] Open
Abstract
The arrangement of receptors in the plasma membrane strongly affects the ability of a cell to sense its environment both in terms of sensitivity and in terms of spatial resolution. The spatial and temporal arrangement of the receptors is affected in turn by the mechanical properties and the structure of the cell membrane. Here, we focus on characterizing the flow of the membrane in response to the motion of a protein embedded in it. We do so by measuring the correlated diffusion of extracellularly tagged transmembrane neurotrophin receptors TrkB and p75 on transfected neuronal cells. In accord with previous reports, we find that the motion of single receptors exhibits transient confinement to submicron domains. We confirm predictions based on hydrodynamics of fluid membranes, finding long-range correlations in the motion of the receptors in the plasma membrane. However, we discover that these correlations do not persist for long ranges, as predicted, but decay exponentially, with a typical decay length on the scale of the average confining domain size.
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Affiliation(s)
- Michael Chein
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - Yael Roichman
- School of Chemistry, School of Physics & Astronomy, and the Tel Aviv Center for Light Matter Interaction, Tel Aviv University, Tel Aviv, Israel.
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11
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Barbera S, Nardi F, Elia I, Realini G, Lugano R, Santucci A, Tosi GM, Dimberg A, Galvagni F, Orlandini M. The small GTPase Rab5c is a key regulator of trafficking of the CD93/Multimerin-2/β1 integrin complex in endothelial cell adhesion and migration. Cell Commun Signal 2019; 17:55. [PMID: 31138217 PMCID: PMC6537425 DOI: 10.1186/s12964-019-0375-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023] Open
Abstract
Background In the endothelium, the single-pass membrane protein CD93, through its interaction with the extracellular matrix protein Multimerin-2, activates signaling pathways that are critical for vascular development and angiogenesis. Trafficking of adhesion molecules through endosomal compartments modulates their signaling output. However, the mechanistic basis coordinating CD93 recycling and its implications for endothelial cell (EC) function remain elusive. Methods Human umbilical vein ECs (HUVECs) and human dermal blood ECs (HDBEC) were used in this study. Fluorescence confocal microscopy was employed to follow CD93 retrieval, recycling, and protein colocalization in spreading cells. To better define CD93 trafficking, drug treatments and transfected chimeric wild type and mutant CD93 proteins were used. The scratch assay was used to evaluate cell migration. Gene silencing strategies, flow citometry, and quantification of migratory capability were used to determine the role of Rab5c during CD93 recycling to the cell surface. Results Here, we identify the recycling pathway of CD93 following EC adhesion and migration. We show that the cytoplasmic domain of CD93, by its interaction with Moesin and F-actin, is instrumental for CD93 retrieval in adhering and migrating cells and that aberrant endosomal trafficking of CD93 prevents its localization at the leading edge of migration. Moreover, the small GTPase Rab5c turns out to be a key component of the molecular machinery that is able to drive CD93 recycling to the EC surface. Finally, in the Rab5c endosomal compartment CD93 forms a complex with Multimerin-2 and active β1 integrin, which is recycled back to the basolaterally-polarized cell surface by clathrin-independent endocytosis. Conclusions Our findings, focusing on the pro-angiogenic receptor CD93, unveil the mechanisms of its polarized trafficking during EC adhesion and migration, opening novel therapeutic opportunities for angiogenic diseases. Electronic supplementary material The online version of this article (10.1186/s12964-019-0375-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefano Barbera
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy
| | - Federica Nardi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy
| | - Ines Elia
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy
| | - Giulia Realini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy
| | - Roberta Lugano
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy
| | - Gian Marco Tosi
- Department of Medicine, Surgery and Neuroscience, Ophthalmology Unit, University of Siena, Policlinico "Le Scotte", Viale Bracci, 53100, Siena, Italy
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy.
| | - Maurizio Orlandini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100, Siena, Italy.
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12
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Lucena D, Mauri M, Schmidt F, Eckhardt B, Graumann PL. Microdomain formation is a general property of bacterial membrane proteins and induces heterogeneity of diffusion patterns. BMC Biol 2018; 16:97. [PMID: 30173665 PMCID: PMC6120080 DOI: 10.1186/s12915-018-0561-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 11/22/2022] Open
Abstract
Background Proteins within the cytoplasmic membrane display distinct localization patterns and arrangements. While multiple models exist describing the dynamics of membrane proteins, to date, there have been few systematic studies, particularly in bacteria, to evaluate how protein size, number of transmembrane domains, and temperature affect their diffusion, and if conserved localization patterns exist. Results We have used fluorescence microscopy, single-molecule tracking (SMT), and computer-aided visualization methods to obtain a better understanding of the three-dimensional organization of bacterial membrane proteins, using the model bacterium Bacillus subtilis. First, we carried out a systematic study of the localization of over 200 B. subtilis membrane proteins, tagged with monomeric mVenus-YFP at their original gene locus. Their subcellular localization could be discriminated in polar, septal, patchy, and punctate patterns. Almost 20% of membrane proteins specifically localized to the cell poles, and a vast majority of all proteins localized in distinct structures, which we term microdomains. Dynamics were analyzed for selected membrane proteins, using SMT. Diffusion coefficients of the analyzed transmembrane proteins did not correlate with protein molecular weight, but correlated inversely with the number of transmembrane helices, i.e., transmembrane radius. We observed that temperature can strongly influence diffusion on the membrane, in that upon growth temperature upshift, diffusion coefficients of membrane proteins increased and still correlated inversely to the number of transmembrane domains, following the Saffman–Delbrück relation. Conclusions The vast majority of membrane proteins localized to distinct multimeric assemblies. Diffusion of membrane proteins can be suitably described by discriminating diffusion coefficients into two protein populations, one mobile and one immobile, the latter likely constituting microdomains. Our results show there is high heterogeneity and yet structural order in the cell membrane, and provide a roadmap for our understanding of membrane organization in prokaryotes. Electronic supplementary material The online version of this article (10.1186/s12915-018-0561-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniella Lucena
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Marco Mauri
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,INRIA Grenoble - Rhône-Alpes, Montbonnot, France
| | - Felix Schmidt
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Fachbereich Physik, Philipps-Universität Marburg, Marburg, Germany
| | - Bruno Eckhardt
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Fachbereich Physik, Philipps-Universität Marburg, Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany.
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13
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Cholesterol modulates acetylcholine receptor diffusion by tuning confinement sojourns and nanocluster stability. Sci Rep 2018; 8:11974. [PMID: 30097590 PMCID: PMC6086833 DOI: 10.1038/s41598-018-30384-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/20/2018] [Indexed: 11/08/2022] Open
Abstract
Translational motion of neurotransmitter receptors is key for determining receptor number at the synapse and hence, synaptic efficacy. We combine live-cell STORM superresolution microscopy of nicotinic acetylcholine receptor (nAChR) with single-particle tracking, mean-squared displacement (MSD), turning angle, ergodicity, and clustering analyses to characterize the lateral motion of individual molecules and their collective behaviour. nAChR diffusion is highly heterogeneous: subdiffusive, Brownian and, less frequently, superdiffusive. At the single-track level, free walks are transiently interrupted by ms-long confinement sojourns occurring in nanodomains of ~36 nm radius. Cholesterol modulates the time and the area spent in confinement. Turning angle analysis reveals anticorrelated steps with time-lag dependence, in good agreement with the permeable fence model. At the ensemble level, nanocluster assembly occurs in second-long bursts separated by periods of cluster disassembly. Thus, millisecond-long confinement sojourns and second-long reversible nanoclustering with similar cholesterol sensitivities affect all trajectories; the proportion of the two regimes determines the resulting macroscopic motional mode and breadth of heterogeneity in the ensemble population.
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14
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Meldrum OW, Yakubov GE, Bonilla MR, Deshmukh O, McGuckin MA, Gidley MJ. Mucin gel assembly is controlled by a collective action of non-mucin proteins, disulfide bridges, Ca 2+-mediated links, and hydrogen bonding. Sci Rep 2018; 8:5802. [PMID: 29643478 PMCID: PMC5895598 DOI: 10.1038/s41598-018-24223-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/27/2018] [Indexed: 12/24/2022] Open
Abstract
Mucus is characterized by multiple levels of assembly at different length scales which result in a unique set of rheological (flow) and mechanical properties. These physical properties determine its biological function as a highly selective barrier for transport of water and nutrients, while blocking penetration of pathogens and foreign particles. Altered integrity of the mucus layer in the small intestine has been associated with a number of gastrointestinal tract pathologies such as Crohn’s disease and cystic fibrosis. In this work, we uncover an intricate hierarchy of intestinal mucin (Muc2) assembly and show how complex rheological properties emerge from synergistic interactions between mucin glycoproteins, non-mucin proteins, and Ca2+. Using a novel method of mucus purification, we demonstrate the mechanism of assembly of Muc2 oligomers into viscoelastic microscale domains formed via hydrogen bonding and Ca2+-mediated links, which require the joint presence of Ca2+ ions and non-mucin proteins. These microscale domains aggregate to form a heterogeneous yield stress gel-like fluid, the macroscopic rheological properties of which are virtually identical to that of native intestinal mucus. Through proteomic analysis, we short-list potential protein candidates implicated in mucin assembly, thus paving the way for identifying the molecules responsible for the physiologically critical biophysical properties of mucus.
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Affiliation(s)
- Oliver W Meldrum
- ARC Centre of Excellence in Plant Cell Walls, The University of Queensland, St Lucia, 4072, Qld, Australia.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, 4072, Qld, Australia
| | - Gleb E Yakubov
- ARC Centre of Excellence in Plant Cell Walls, The University of Queensland, St Lucia, 4072, Qld, Australia. .,School of Chemical Engineering, The University of Queensland, St Lucia, 4072, Qld, Australia.
| | - Mauricio R Bonilla
- ARC Centre of Excellence in Plant Cell Walls, The University of Queensland, St Lucia, 4072, Qld, Australia.,School of Chemical Engineering, The University of Queensland, St Lucia, 4072, Qld, Australia
| | - Omkar Deshmukh
- School of Chemical Engineering, The University of Queensland, St Lucia, 4072, Qld, Australia
| | - Michael A McGuckin
- Chronic Disease Biology and Care Program, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Michael J Gidley
- ARC Centre of Excellence in Plant Cell Walls, The University of Queensland, St Lucia, 4072, Qld, Australia.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, 4072, Qld, Australia
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15
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Eckstein J, Holzhütter HG, Berndt N. The importance of membrane microdomains for bile salt-dependent biliary lipid secretion. J Cell Sci 2018; 131:jcs211524. [PMID: 29420298 PMCID: PMC5897720 DOI: 10.1242/jcs.211524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
Alternative models explaining the biliary lipid secretion at the canalicular membrane of hepatocytes exist: successive lipid extraction by preformed bile salt micelles, or budding of membrane fragments with formation of mixed micelles. To test the feasibility of the latter mechanism, we developed a mathematical model that describes the formation of lipid microdomains in the canalicular membrane. Bile salt monomers intercalate into the external hemileaflet of the canalicular membrane, to form a rim to liquid disordered domain patches that then pinch off to form nanometer-scale mixed micelles. Model simulations perfectly recapitulate the measured dependence of bile salt-dependent biliary lipid extraction rates upon modulation of the membrane cholesterol (lack or overexpression of the cholesterol transporter Abcg5-Abcg8) and phosphatidylcholine (lack of Mdr2, also known as Abcb4) content. The model reveals a strong dependence of the biliary secretion rate on the protein density of the membrane. Taken together, the proposed model is consistent with crucial experimental findings in the field and provides a consistent explanation of the central molecular processes involved in bile formation.
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Affiliation(s)
- Johannes Eckstein
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Hermann-Georg Holzhütter
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
| | - Nikolaus Berndt
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany
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16
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Duncan AL, Reddy T, Koldsø H, Hélie J, Fowler PW, Chavent M, Sansom MSP. Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes. Sci Rep 2017; 7:16647. [PMID: 29192147 PMCID: PMC5709381 DOI: 10.1038/s41598-017-16865-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/15/2017] [Indexed: 01/07/2023] Open
Abstract
Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies of an inwardly rectifying potassium (Kir) channel which forms specific interactions with the regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency of protein molecules to cluster has the effect of organizing the membrane into dynamic compartments. At the same time, the diversity of lipids present has a marked effect on the clustering behavior of ion channels. Sub-diffusion of proteins and lipids is observed. Protein crowding alters the sub-diffusive behavior of proteins and lipids such as PIP2 which interact tightly with Kir channels. Protein crowding also affects bilayer properties, such as membrane undulations and bending rigidity, in a PIP2-dependent manner. This interplay between the diffusion and the dynamic organization of Kir channels may have important implications for channel function.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- T-6, MS K710, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- D. E. Shaw Research, 120 W 45th St., New York, NY, 10036, USA
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Semmle, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- IPBS-CNRS, Toulouse, Midi-Pyrénées, France
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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17
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Evans AL, Blackburn JWD, Taruc K, Kipp A, Dirk BS, Hunt NR, Barr SD, Dikeakos JD, Heit B. Antagonistic Coevolution of MER Tyrosine Kinase Expression and Function. Mol Biol Evol 2017; 34:1613-1628. [PMID: 28369510 DOI: 10.1093/molbev/msx102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and Crohn's disease. In addition, certain enveloped viruses utilize TAM receptors for immune evasion and entry into host cells, with several viruses preferentially hijacking MERTK for these purposes. Despite the biological importance of TAM receptors, little is understood of their recent evolution and its impact on their function. Using evolutionary analysis of primate TAM receptor sequences, we identified strong, recent positive selection in MERTK's signal peptide and transmembrane domain that was absent from TYRO3 and AXL. Reconstruction of hominid and primate ancestral MERTK sequences revealed three nonsynonymous single nucleotide polymorphisms in the human MERTK signal peptide, with a G14C mutation resulting in a predicted non-B DNA cruciform motif, producing a significant decrease in MERTK expression with no significant effect on MERTK trafficking or half-life. Reconstruction of MERTK's transmembrane domain identified three amino acid substitutions and four amino acid insertions in humans, which led to significantly higher levels of self-clustering through the creation of a new interaction motif. This clustering counteracted the effect of the signal peptide mutations through enhancing MERTK avidity, whereas the lower MERTK expression led to reduced binding of Ebola virus-like particles. The decreased MERTK expression counterbalanced by increased avidity is consistent with antagonistic coevolution to evade viral hijacking of MERTK.
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Affiliation(s)
- Amanda L Evans
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Jack W D Blackburn
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Kyle Taruc
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Angela Kipp
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Brennan S Dirk
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Nina R Hunt
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Stephen D Barr
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
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