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Liu W, Gao T, Li N, Shao S, Liu B. Vesicle fusion and release in neurons under dynamic mechanical equilibrium. iScience 2024; 27:109793. [PMID: 38736547 PMCID: PMC11088343 DOI: 10.1016/j.isci.2024.109793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Vesicular fusion plays a pivotal role in cellular processes, involving stages like vesicle trafficking, fusion pore formation, content release, and membrane integration or separation. This dynamic process is regulated by a complex interplay of protein assemblies, osmotic forces, and membrane tension, which together maintain a mechanical equilibrium within the cell. Changes in cellular mechanics or external pressures prompt adjustments in this equilibrium, highlighting the system's adaptability. This review delves into the synergy between intracellular proteins, structural components, and external forces in facilitating vesicular fusion and release. It also explores how cells respond to mechanical stress, maintaining equilibrium and offering insights into vesicle fusion mechanisms and the development of neurological disorders.
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Affiliation(s)
- Wenhao Liu
- Cancer Hospital of Dalian University of Technology, Shenyang 110042, China
| | - Tianyu Gao
- Cancer Hospital of Dalian University of Technology, Shenyang 110042, China
| | - Na Li
- Cancer Hospital of Dalian University of Technology, Shenyang 110042, China
- Faculty of Medicine, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Shuai Shao
- Cancer Hospital of Dalian University of Technology, Shenyang 110042, China
- Faculty of Medicine, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Bo Liu
- Cancer Hospital of Dalian University of Technology, Shenyang 110042, China
- Faculty of Medicine, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
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Jahn R, Cafiso DC, Tamm LK. Mechanisms of SNARE proteins in membrane fusion. Nat Rev Mol Cell Biol 2024; 25:101-118. [PMID: 37848589 DOI: 10.1038/s41580-023-00668-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2023] [Indexed: 10/19/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of small conserved eukaryotic proteins that mediate membrane fusion between organelles and with the plasma membrane. SNAREs are directly or indirectly anchored to membranes. Prior to fusion, complementary SNAREs assemble between membranes with the aid of accessory proteins that provide a scaffold to initiate SNARE zippering, pulling the membranes together and mediating fusion. Recent advances have enabled the construction of detailed models describing bilayer transitions and energy barriers along the fusion pathway and have elucidated the structures of SNAREs complexed in various states with regulatory proteins. In this Review, we discuss how these advances are yielding an increasingly detailed picture of the SNARE-mediated fusion pathway, leading from first contact between the membranes via metastable non-bilayer intermediates towards the opening and expansion of a fusion pore. We describe how SNARE proteins assemble into complexes, how this assembly is regulated by accessory proteins and how SNARE complexes overcome the free energy barriers that prevent spontaneous membrane fusion.
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Affiliation(s)
- Reinhard Jahn
- Laboratory of Neurobiology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - David C Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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Punia R, Goel G. Free Energy Surface and Molecular Mechanism of Slow Structural Transitions in Lipid Bilayers. J Chem Theory Comput 2023; 19:8245-8257. [PMID: 37947833 DOI: 10.1021/acs.jctc.3c00856] [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: 11/12/2023]
Abstract
Lipid membrane remodeling, crucial for many cellular processes, is governed by the coupling of membrane structure and shape fluctuations. Given the importance of the ∼ nm length scale, details of the transition intermediates for conformational change are not fully captured by a continuum-mechanical description. Slow dynamics and the lack of knowledge of reaction coordinates (RCs) for biasing methods pose a challenge for all-atom (AA) simulations. Here, we map system dynamics on Langevin dynamics in a normal mode space determined from an elastic network model representation for the lipid-water Hamiltonian. AA molecular dynamics (MD) simulations are used to determine model parameters, and Langevin dynamics predictions for bilayer structural, mechanical, and dynamic properties are validated against MD simulations and experiments. Transferability to describe the dynamics of a larger lipid bilayer and a heterogeneous membrane-protein system is assessed. A set of generic RCs for pore formation in two tensionless bilayers is obtained by coupling Langevin dynamics to the underlying energy landscape for membrane deformations. Structure evolution is carried out by AA MD, wherein the generic RCs are used in a path metadynamics or an umbrella sampling simulation to determine the thermodynamics of pore formation and its molecular determinants, such as the role of distinct bilayer motions, lipid solvation, and lipid packing.
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Affiliation(s)
- Rajat Punia
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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Anosov AA, Smirnova EY, Korepanova EA, Kazamanov VA, Derunets AS. Different effects of two Poloxamers (L61 and F68) on the conductance of bilayer lipid membranes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:14. [PMID: 36920579 DOI: 10.1140/epje/s10189-023-00270-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The integral conductance of planar lipid bilayer membranes in the presence of two Poloxamers (Pluronics) L61 and F68 with the same lengths of hydrophobic poly(propylene oxide) blocks and the different lengths of hydrophilic poly(ethylene oxide) blocks increases with an increase in the concentration of both Pluronics; however, the shape of the conductance-concentration curves is super linear for L61 and sublinear for F68. In the presence of both Pluronics, rare discrete current jumps are observed against the background of continuous current. At high concentrations, the I-V curves of membranes with both L61 and F68 became nonlinear at sufficiently low voltages but differed significantly. At voltages greater than 50 mV, the conductance of membranes with L61 increased sharply and quantized jumps were observed toward higher conductance, which could be interpreted as the appearance of additional pores. On the contrary, the conductance of membranes with F68 decreased and quantized jumps to lower conductance were observed, which could be interpreted as blocking of already existing pores. We attributed the differences in the conductance-concentration and I-V curves of these two Pluronics to their different effects on the dynamics of membrane hydration and, accordingly, on the probability of formation of conducting pores.
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Affiliation(s)
- A A Anosov
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Kotelnikov Institute of Radioengineering and Electronics of RAS, Moscow, Russia
| | - E Yu Smirnova
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - E A Korepanova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - V A Kazamanov
- MIREA-Russian Technological University, Moscow, Russia
| | - A S Derunets
- National Research Center Kurchatov Institute, Moscow, Russia.
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Siegel DP. Bicontinuous inverted cubic phase stabilization as an index of antimicrobial and membrane fusion peptide activity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183815. [PMID: 34748744 DOI: 10.1016/j.bbamem.2021.183815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/06/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Some antimicrobial peptides (AMPs) and membrane fusion-catalyzing peptides (FPs) stabilize bicontinuous inverted cubic (QII) phases. Previous authors proposed a topological rationale: since AMP-induced pores, fusion intermediates, and QII phases all have negative Gaussian curvature (NGC), peptides which produce NGC in one structure also do it in another. This assumes that peptides change the curvature energy of the lipid membranes. Here I test this with a Helfrich curvature energy model. First, experimentally, I show that lipid systems often used to study peptide NGC have NGC without peptides at higher temperatures. To determine the net effect of an AMP on NGC, the equilibrium phase behavior of the host lipids must be determined. Second, the model shows that AMPs must make large changes in the curvature energy to stabilize AMP-induced pores. Peptide-induced changes in elastic constants affect pores and QII phase differently. Changes in spontaneous curvature affect them in opposite ways. The observed correlation between QII phase stabilization and AMP activity doesn't show that AMPs act by lowering pore curvature energy. A different rationale is proposed. In theory, AMPs could simultaneously stabilize QII phase and pores by drastically changing two particular elastic constants. This could be tested by measuring AMP effects on the individual constants. I propose experiments to do that. Unlike AMPs, FPs must make only small changes in the curvature energy to catalyze fusion. It they act in this way, their fusion activity should correlate with their ability to stabilize QII phases.
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Affiliation(s)
- D P Siegel
- Givaudan Inc., 1199 Edison Drive, Cincinnati, OH 45216, United States of America.
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Rocha-Roa C, Orjuela JD, Leidy C, Cossio P, Aponte-Santamaría C. Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Lett 2021; 595:2701-2714. [PMID: 34633077 DOI: 10.1002/1873-3468.14206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's cardiolipin composition to resist such types of perturbations that compromise their membrane stability. Here, we used molecular dynamic simulations to quantify the role of cardiolipin on the formation of pores in simple bacterial-like membrane models composed of phosphatidylglycerol and cardiolipin mixtures. Cardiolipin modified the structure and ordering of the lipid bilayer, making it less susceptible to mechanical changes. Accordingly, the free-energy barrier for the formation of a transmembrane pore and its kinetic instability augmented by increasing the cardiolipin concentration. This is attributed to the unfavorable positioning of cardiolipin near the formed pore, due to its small polar head and bulky hydrophobic body. Overall, our study demonstrates how cardiolipin prevents membrane-pore formation and this constitutes a plausible mechanism used by bacteria to act against stress perturbations and, thereby, gain resistance to antimicrobial agents.
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Affiliation(s)
- Cristian Rocha-Roa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
| | - Juan David Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los Andes, Bogotá, Colombia
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Chad Leidy
- Biophysics Group, Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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Risselada HJ, Grubmüller H. How proteins open fusion pores: insights from molecular simulations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:279-293. [PMID: 33340336 PMCID: PMC8071795 DOI: 10.1007/s00249-020-01484-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Fusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.
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Affiliation(s)
- H. Jelger Risselada
- Department of Theoretical Physics, Georg-August University of Göttingen, Göttingen, Germany
- Leiden University, Leiden Institute of Chemistry (LIC), Leiden, The Netherlands
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Theoretical and Computational Biophysics Department, Göttingen, Germany
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