1
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Patil SS, Sanghrajka K, Sriram M, Chakraborty A, Majumdar S, Bhaskar BR, Das D. Synaptobrevin2 monomers and dimers differentially engage to regulate the functional trans-SNARE assembly. Life Sci Alliance 2024; 7:e202402568. [PMID: 38238088 PMCID: PMC10796598 DOI: 10.26508/lsa.202402568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
The precise cell-to-cell communication relies on SNARE-catalyzed membrane fusion. Among ∼70 copies of synaptobrevin2 (syb2) in synaptic vesicles, only ∼3 copies are sufficient to facilitate the fusion process at the presynaptic terminal. It is unclear what dictates the number of SNARE complexes that constitute the fusion pore assembly. The structure-function relation of these dynamic pores is also unknown. Here, we demonstrate that syb2 monomers and dimers differentially engage in regulating the trans-SNARE assembly during membrane fusion. The differential recruitment of two syb2 structures at the membrane fusion site has consequences in regulating individual nascent fusion pore properties. We have identified a few syb2 transmembrane domain residues that control monomer/dimer conversion. Overall, our study indicates that syb2 monomers and dimers are differentially recruited at the release sites for regulating membrane fusion events.
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Affiliation(s)
- Swapnali S Patil
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Kinjal Sanghrajka
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Malavika Sriram
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Aritra Chakraborty
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sougata Majumdar
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Bhavya R Bhaskar
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Debasis Das
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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2
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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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3
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Shafieenezhad A, Mitra S, Wassall SR, Tristram-Nagle S, Nagle JF, Petrache HI. Location of dopamine in lipid bilayers and its relevance to neuromodulator function. Biophys J 2023; 122:1118-1129. [PMID: 36804668 PMCID: PMC10111280 DOI: 10.1016/j.bpj.2023.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/18/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Dopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.
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Affiliation(s)
- Azam Shafieenezhad
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Saheli Mitra
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Stephen R Wassall
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | | | - John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Horia I Petrache
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana.
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4
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Yan C, Jiang J, Yang Y, Geng X, Dong W. The function of VAMP2 in mediating membrane fusion: An overview. Front Mol Neurosci 2022; 15:948160. [PMID: 36618823 PMCID: PMC9816800 DOI: 10.3389/fnmol.2022.948160] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Vesicle-associated membrane protein 2 (VAMP2, also known as synaptobrevin-2), encoded by VAMP2 in humans, is a key component of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex. VAMP2 combined with syntaxin-1A (SYX-1A) and synaptosome-associated protein 25 (SNAP-25) produces a force that induces the formation of fusion pores, thereby mediating the fusion of synaptic vesicles and the release of neurotransmitters. VAMP2 is largely unstructured in the absence of interaction partners. Upon interaction with other SNAREs, the structure of VAMP2 stabilizes, resulting in the formation of four structural domains. In this review, we highlight the current knowledge of the roles of the VAMP2 domains and the interaction between VAMP2 and various fusion-related proteins in the presynaptic cytoplasm during the fusion process. Our summary will contribute to a better understanding of the roles of the VAMP2 protein in membrane fusion.
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Affiliation(s)
- Chong Yan
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China
| | - Jie Jiang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China
| | - Yuan Yang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China
| | - Xiaoqi Geng
- Department of Neurosurgery, Neurosurgical Clinical Research Center of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, China,*Correspondence: Xiaoqi Geng,
| | - Wei Dong
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China,Wei Dong,
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5
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Cail RC, Drubin DG. Membrane curvature as a signal to ensure robustness of diverse cellular processes. Trends Cell Biol 2022; 33:427-441. [PMID: 36244874 DOI: 10.1016/j.tcb.2022.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/05/2022]
Abstract
An increasing corpus of research has demonstrated that membrane shape, generated either by the external environment of the cell or by intrinsic mechanisms such as cytokinesis and vesicle or organelle formation, is an important parameter in the control of diverse cellular processes. In this review we discuss recent findings that demonstrate how membrane curvature (from nanometer to micron length-scales) alters protein function. We describe an expanding toolkit for experimentally modulating membrane curvature to reveal effects on protein function, and discuss how membrane curvature - far from being a passive consequence of the physical environment and the internal protein activity of a cell - is an important signal that controls protein affinity and enzymatic activity to ensure robust forward progression of key processes within the cell.
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6
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Zhang Y, Ma L, Bao H. Energetics, kinetics, and pathways of SNARE assembly in membrane fusion. Crit Rev Biochem Mol Biol 2022; 57:443-460. [PMID: 36151854 PMCID: PMC9588726 DOI: 10.1080/10409238.2022.2121804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fusion of transmitter-containing vesicles with plasma membranes at the synaptic and neuromuscular junctions mediates neurotransmission and muscle contractions, respectively, thereby underlying all thoughts and actions. The fusion process is driven by the coupled folding and assembly of three synaptic SNARE proteins--syntaxin-1 and SNAP-25 on the target plasma membrane (t-SNAREs) and VAMP2 on the vesicular membrane (v-SNARE) into a four-helix bundle. Their assembly is chaperoned by Munc18-1 and many other proteins to achieve the speed and accuracy required for neurotransmission. However, the physiological pathway of SNARE assembly and its coupling to membrane fusion remains unclear. Here, we review recent progress in understanding SNARE assembly and membrane fusion, with a focus on results obtained by single-molecule manipulation approaches and electric recordings of single fusion pores. We describe two pathways of synaptic SNARE assembly, their associated intermediates, energetics, and kinetics. Assembly of the three SNAREs in vitro begins with the formation of a t-SNARE binary complex, on which VAMP2 folds in a stepwise zipper-like fashion. Munc18-1 significantly alters the SNARE assembly pathway: syntaxin-1 and VAMP2 first bind on the surface of Munc18-1 to form a template complex, with which SNAP-25 associates to conclude SNARE assembly and displace Munc18-1. During membrane fusion, multiple trans-SNARE complexes cooperate to open a dynamic fusion pore in a manner dependent upon their copy number and zippering states. Together, these results demonstrate that stepwise and cooperative SNARE assembly drive stagewise membrane fusion.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA;,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA;,Conatct: and
| | - Lu Ma
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA;,Present address: Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida, 33458,Conatct: and
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7
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Di Bartolo AL, Tomes CN, Mayorga LS, Masone D. Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains. J Chem Theory Comput 2022; 18:4544-4554. [PMID: 35759758 DOI: 10.1021/acs.jctc.2c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fusion pore controls the release of exocytotic vesicle contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore (membrane fusion, nucleation, and expansion) that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve toward full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Claudia N Tomes
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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8
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Chen N, He Y, Zang M, Zhang Y, Lu H, Zhao Q, Wang S, Gao Y. Approaches and materials for endocytosis-independent intracellular delivery of proteins. Biomaterials 2022; 286:121567. [DOI: 10.1016/j.biomaterials.2022.121567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
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9
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Poojari CS, Scherer KC, Hub JS. Free energies of membrane stalk formation from a lipidomics perspective. Nat Commun 2021; 12:6594. [PMID: 34782611 PMCID: PMC8593120 DOI: 10.1038/s41467-021-26924-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/18/2021] [Indexed: 11/21/2022] Open
Abstract
Many biological membranes are asymmetric and exhibit complex lipid composition, comprising hundreds of distinct chemical species. Identifying the biological function and advantage of this complexity is a central goal of membrane biology. Here, we study how membrane complexity controls the energetics of the first steps of membrane fusions, that is, the formation of a stalk. We first present a computationally efficient method for simulating thermodynamically reversible pathways of stalk formation at coarse-grained resolution. The method reveals that the inner leaflet of a typical plasma membrane is far more fusogenic than the outer leaflet, which is likely an adaptation to evolutionary pressure. To rationalize these findings by the distinct lipid compositions, we computed ~200 free energies of stalk formation in membranes with different lipid head groups, tail lengths, tail unsaturations, and sterol content. In summary, the simulations reveal a drastic influence of the lipid composition on stalk formation and a comprehensive fusogenicity map of many biologically relevant lipid classes. Fusion of cellular membranes begins with the formation of a stalk. Here, the authors develop a computationally efficient method for coarse-grained simulations of stalk formation and apply this approach to comprehensively analyse how stalk formation is influenced by the membrane lipid composition.
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Affiliation(s)
- Chetan S Poojari
- Saarland University, Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Katharina C Scherer
- Saarland University, Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Jochen S Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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10
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Dabral D, van den Bogaart G. The Roles of Phospholipase A 2 in Phagocytes. Front Cell Dev Biol 2021; 9:673502. [PMID: 34179001 PMCID: PMC8222813 DOI: 10.3389/fcell.2021.673502] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Phagocytic cells, such as macrophages, neutrophils, and dendritic cells, ingest particles larger than about 0.5 μM and thereby clear microbial pathogens and malignant cells from the body. These phagocytic cargoes are proteolytically degraded within the lumen of phagosomes, and peptides derived from them are presented on Major Histocompatibility Complexes (MHC) for the activation of T cells. Mammalian PLA2 isozymes belong to a large family of enzymes that cleave phospholipids at the second position of the glycerol backbone, releasing a free fatty acid and a lysolipid moiety. In human macrophages, at least 15 different PLA2 forms are expressed, and expression of many of these is dependent on pathogenic stimulation. Intriguing questions are why so many PLA2 forms are expressed in macrophages, and what are the functional consequences of their altered gene expression after encountering pathogenic stimuli. In this review, we discuss the evidence of the differential roles of different forms of PLA2 in phagocytic immune cells. These roles include: lipid signaling for immune cell activation, initial phagocytic particle uptake, microbial action for the killing and degradation of ingested microbes, and the repair of membranes induced by oxygen radicals. We also discuss the roles of PLA2 in the subsequent digestion of ingested phagocytic cargoes for antigen presentation to T cells.
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Affiliation(s)
- Deepti Dabral
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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11
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Abstract
SNARE proteins and Sec1/Munc18 (SM) proteins constitute the core molecular engine that drives nearly all intracellular membrane fusion and exocytosis. While SNAREs are known to couple their folding and assembly to membrane fusion, the physiological pathways of SNARE assembly and the mechanistic roles of SM proteins have long been enigmatic. Here, we review recent advances in understanding the SNARE-SM fusion machinery with an emphasis on biochemical and biophysical studies of proteins that mediate synaptic vesicle fusion. We begin by discussing the energetics, pathways, and kinetics of SNARE folding and assembly in vitro. Then, we describe diverse interactions between SM and SNARE proteins and their potential impact on SNARE assembly in vivo. Recent work provides strong support for the idea that SM proteins function as chaperones, their essential role being to enable fast, accurate SNARE assembly. Finally, we review the evidence that SM proteins collaborate with other SNARE chaperones, especially Munc13-1, and briefly discuss some roles of SNARE and SM protein deficiencies in human disease.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA;
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12
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Kandy SK, Janmey PA, Radhakrishnan R. Membrane signalosome: where biophysics meets systems biology. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 25:34-41. [PMID: 33997528 PMCID: PMC8117111 DOI: 10.1016/j.coisb.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We opine on the recent advances in experiments and modeling of modular signaling complexes assembled on mammalian cell membranes (membrane signalosomes) in the context of several applications including intracellular trafficking, cell migration, and immune response. Characterizing the individual components of the membrane assemblies at the nanoscale, ranging from protein-lipid and protein-protein interactions, to membrane morphology, and the energetics of emergent assemblies at the subcellular to cellular scales pose significant challenges. Overcoming these challenges through the iterative coupling of multiscale modeling and experiment can be transformative in terms of addressing the gaps between structural biology and super-resolution microscopy, as it holds the key to the discovery of fundamental mechanisms behind the emergence of function in the membrane signalosome.
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Affiliation(s)
- Sreeja K Kandy
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
| | - Paul A Janmey
- Department of Physiology, University of Pennsylvania, Philadelphia, PA
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
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13
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Hub JS. Joint Reaction Coordinate for Computing the Free-Energy Landscape of Pore Nucleation and Pore Expansion in Lipid Membranes. J Chem Theory Comput 2021; 17:1229-1239. [PMID: 33427469 DOI: 10.1021/acs.jctc.0c01134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Topological transitions of membranes, such as pore formation or membrane fusion, play key roles in biology, biotechnology, and in medical applications. Calculating the related free-energy landscapes has been complicated by the fact that such processes involve a sequence of transitions along highly distinct directions in conformational space, making it difficult to define good reaction coordinates (RCs) for the overall process. In this study, a new RC capable of driving both pore nucleation and pore expansion in lipid membranes is presented. The potential of mean force (PMF) along the RC computed with molecular dynamics simulations provides a comprehensive view on the free-energy landscape of pore formation, including a barrier for pore nucleation; the size, free energy, and metastability of the open pore; and the energetic cost for further pore expansion against the line tension of the pore rim. The RC is illustrated by quantifying the effects of (i) simulation system size and (ii) the addition of dimethyl sulfoxide on the free-energy landscape of pore formation. PMF calculations along the RC provide mechanistic and energetic understanding of pore formation, hence they will be useful to rationalize the effects of membrane-active peptides, electric fields, and membrane composition on transmembrane pores.
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Affiliation(s)
- Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken D-66123, Germany
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