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Tyoe O, Zhang K, Diao J. Molecular Dynamics Simulation for Membrane Fusion. Methods Mol Biol 2025; 2887:53-68. [PMID: 39806145 PMCID: PMC11808403 DOI: 10.1007/978-1-0716-4314-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Abstract
The soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein complex drives membrane fusion, and this process is further aided by accessory proteins, including complexin and α-synuclein. To understand the molecular mechanism underlying membrane fusion, we introduce an all-atom molecular dynamics (MD) simulation method. This method is used to understand and predict the conformations of protein and lipids, membrane geometry, and their interaction at femtosecond precision, by describing complex chemical systems with atomic models. Simulation results reveal information on distinct membrane fusion stages, including docking, hemifusion, and kiss-and-run fusion. Here, we introduce the simulation workflow, consisting of pre-MD construction, pre-MD setup in GROMACS, MD in GROMACS, and analysis.
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Affiliation(s)
- Owen Tyoe
- Department of Physics, University of Cincinnati College of Arts and Sciences, Cincinnati, OH, USA
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kai Zhang
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Jiajie Diao
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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2
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Veretenenko II, Trofimov YA, Krylov NA, Efremov RG. Nanoscale lipid domains determine the dynamic molecular portraits of mixed DOPC/DOPS bilayers in a fluid phase: A computational insight. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184376. [PMID: 39111381 DOI: 10.1016/j.bbamem.2024.184376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Lateral heterogeneity, or mosaicity, is a fundamental property inherent to cell membranes that is crucial for their functioning. While microscopic inhomogeneities (e.g. rafts) are easily detected experimentally, lipid domains with nanoscale dimensions (nanoclusters of nanodomains, NDs) resist reliable characterization by instrumental methods. In such a case, important insight can be gained via computer modeling. Here, NDs composed of lipid's head groups in the mixed zwitterionic dioleoylphosphatidylcholine (DOPC) and negatively charged dioleoylphosphatidylserine (DOPS) bilayers were studied by molecular dynamics. A new algorithm has been developed to identify NDs. Unlike most similar methods, it implicitly considers the heterogeneous distribution of lipid head atomic density and does not require subjectively chosen parameters. In DOPS-rich membranes, lipids form more compact and stable NDs due to strong interlipid interactions. In DOPC-rich systems, NDs arise due to the "packing" effect of weakly bound lipid heads. The clustering picture is related to the physical properties of the bilayer surface: DOPS-rich systems show more pronounced surface heterogeneity of hydrophilic/hydrophobic regions compared to DOPC-rich ones. The results obtained are important for the effective quantitative characterization of the "dynamic molecular portrait" of a membrane surface - its "fingerprint" characterizing dynamical distribution of its physicochemical properties.
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Affiliation(s)
- Irina I Veretenenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region 141701, Russia.
| | - Yury A Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Nikolay A Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region 141701, Russia; National Research University Higher School of Economics, Moscow 101000, Russia.
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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
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Kinjal Sanghrajka
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Malavika Sriram
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Aritra Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sougata Majumdar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Bhavya R Bhaskar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Debasis Das
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Khvotchev M, Soloviev M. SNARE Modulators and SNARE Mimetic Peptides. Biomolecules 2022; 12:biom12121779. [PMID: 36551207 PMCID: PMC9776023 DOI: 10.3390/biom12121779] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) proteins play a central role in most forms of intracellular membrane trafficking, a key process that allows for membrane and biocargo shuffling between multiple compartments within the cell and extracellular environment. The structural organization of SNARE proteins is relatively simple, with several intrinsically disordered and folded elements (e.g., SNARE motif, N-terminal domain, transmembrane region) that interact with other SNAREs, SNARE-regulating proteins and biological membranes. In this review, we discuss recent advances in the development of functional peptides that can modify SNARE-binding interfaces and modulate SNARE function. The ability of the relatively short SNARE motif to assemble spontaneously into stable coiled coil tetrahelical bundles has inspired the development of reduced SNARE-mimetic systems that use peptides for biological membrane fusion and for making large supramolecular protein complexes. We evaluate two such systems, based on peptide-nucleic acids (PNAs) and coiled coil peptides. We also review how the self-assembly of SNARE motifs can be exploited to drive on-demand assembly of complex re-engineered polypeptides.
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Affiliation(s)
- Mikhail Khvotchev
- Department of Biochemistry, Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (M.K.); (M.S.)
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- Correspondence: (M.K.); (M.S.)
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5
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Smuggle tau through a secret(ory) pathway. Biochem J 2021; 478:2921-2925. [PMID: 34319403 DOI: 10.1042/bcj20210324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022]
Abstract
Secretion of misfolded tau, a microtubule-binding protein enriched in nerve cells, is linked to the progression of tau pathology. However, the molecular mechanisms underlying tau secretion are poorly understood. Recent work by Lee et al. [Biochemical J. (2021) 478: 1471-1484] demonstrated that the transmembrane domains of syntaxin6 and syntaxin8 could be exploited for tau release, setting a stage for testing a novel hypothesis that has profound implications in tauopathies (e.g. Alzheimer's disease, FTDP-17, and CBD/PSP) and other related neurodegenerative diseases. The present commentary highlights the importance and limitations of the study, and discusses opportunities and directions for future investigations.
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Dynamic "Molecular Portraits" of Biomembranes Drawn by Their Lateral Nanoscale Inhomogeneities. Int J Mol Sci 2021; 22:ijms22126250. [PMID: 34200697 PMCID: PMC8230387 DOI: 10.3390/ijms22126250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/22/2023] Open
Abstract
To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called "dynamic molecular portrait". The latter reflects a combination of time-dependent surface distributions of various physicochemical properties, inherent in both model lipid bilayers and natural multi-component cell membranes. One of the most important features of biomembranes is their mosaicity, which is expressed in the constant presence of lateral inhomogeneities, the sizes and lifetimes of which vary in a wide range-from 1 to 103 nm and from 0.1 ns to milliseconds. In addition to the relatively well-studied macroscopic domains (so-called "rafts"), the analysis of micro- and nanoclusters (or domains) that form an instantaneous picture of the distribution of structural, dynamic, hydrophobic, electrical, etc., properties at the membrane-water interface is attracting increasing interest. This is because such nanodomains (NDs) have been proven to be crucial for the proper membrane functioning in cells. Therefore, an understanding with atomistic details the phenomena associated with NDs is required. The present mini-review describes the recent results of experimental and in silico studies of spontaneously formed NDs in lipid membranes. The main attention is paid to the methods of ND detection, characterization of their spatiotemporal parameters, the elucidation of the molecular mechanisms of their formation. Biological role of NDs in cell membranes is briefly discussed. Understanding such effects creates the basis for rational design of new prospective drugs, therapeutic approaches, and artificial membrane materials with specified properties.
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Pezeshkian W, Marrink SJ. Simulating realistic membrane shapes. Curr Opin Cell Biol 2021; 71:103-111. [PMID: 33721706 DOI: 10.1016/j.ceb.2021.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. These two central features of biomembranes have been the subject of numerous simulation studies, using a diverse range of computational techniques. Currently, the field is able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Here we highlight recent advances in this topic, identify current bottlenecks, and sketch possible ways ahead.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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Rebiai R, Givogri MI, Gowrishankar S, Cologna SM, Alford ST, Bongarzone ER. Synaptic Function and Dysfunction in Lysosomal Storage Diseases. Front Cell Neurosci 2021; 15:619777. [PMID: 33746713 PMCID: PMC7978225 DOI: 10.3389/fncel.2021.619777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
Lysosomal storage diseases (LSDs) with neurological involvement are inherited genetic diseases of the metabolism characterized by lysosomal dysfunction and the accumulation of undegraded substrates altering glial and neuronal function. Often, patients with neurological manifestations present with damage to the gray and white matter and irreversible neuronal decline. The use of animal models of LSDs has greatly facilitated studying and identifying potential mechanisms of neuronal dysfunction, including alterations in availability and function of synaptic proteins, modifications of membrane structure, deficits in docking, exocytosis, recycling of synaptic vesicles, and inflammation-mediated remodeling of synapses. Although some extrapolations from findings in adult-onset conditions such as Alzheimer's disease or Parkinson's disease have been reported, the pathogenetic mechanisms underpinning cognitive deficits in LSDs are still largely unclear. Without being fully inclusive, the goal of this mini-review is to present a discussion on possible mechanisms leading to synaptic dysfunction in LSDs.
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Affiliation(s)
- Rima Rebiai
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, Chicago, IL, United States
| | - Maria I. Givogri
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, Chicago, IL, United States
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, Chicago, IL, United States
| | - Stephania M. Cologna
- Department of Chemistry, College of Liberal Arts and Sciences, The University of Illinois at Chicago, Chicago, IL, United States
| | - Simon T. Alford
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, Chicago, IL, United States
| | - Ernesto R. Bongarzone
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, Chicago, IL, United States
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Membrane dynamics are slowed for Alexa594-labeled membrane proteins due to substrate interactions. BBA ADVANCES 2021; 1:100026. [PMID: 37082018 PMCID: PMC10074974 DOI: 10.1016/j.bbadva.2021.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The addition of fluorescent dyes to proteins, lipids and other biological molecules can affect a range of processes such as mobility, molecular interactions, localization, and, ultimately, function. The dynamics of a protein can be dramatically affected if the label interacts non-specifically with the substrate or with other molecules in the system. To test how dye-substrate interactions affect protein diffusion, fluorescence recovery after photobleaching (FRAP) measurements were designed to explicitly determine the role of the dye on the diffusion of a transmembrane protein, Syntaxin1a, expressed on the cell surface. Syntaxin1a, was tagged with EGFP on the extracellular side and an EGFP nanobody with or without a dye label was attached. FRAP was performed on Syx1a-EGFP and the choice of cell growth substrate affected mobility in the presence of a dye labeled nanobody. This work provides evidence for choosing fibronectin (Fn) over poly-L-lysine (PLL) in FRAP and single molecule tracking measurements when using Alexa594, a common probe for red fluorescent measurements. Alexa594-labeled nanobody but not unlabeled nanobody, dramatically reduced the mobility of Syx1a-EGFP when cells were cultured on PLL. However, when Fn was used, the mobility returned. Mobility measured by single molecule tracking measurements align with the FRAP measurements with Fn coated surfaces being more mobile than PLL.
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Abstract
PURPOSE OF REVIEW The purpose of this brief review is to gain an understanding on the multiple roles that lipids exert on the brain, and to highlight new ideas in the impact of lipid homeostasis in the regulation of synaptic transmission. RECENT FINDINGS Recent data underline the crucial function of lipid homeostasis in maintaining neuronal function and synaptic plasticity. Moreover, new advances in analytical approaches to study lipid classes and species is opening a new door to understand and monitor how alterations in lipid pathways could shed new light into the pathogenesis of neurodegeneration. SUMMARY Lipids are one of the most essential elements of the brain. However, our understanding of the role of lipids within the central nervous system is still largely unknown. Identifying the molecular mechanism (s) by which lipids can regulate neuronal transmission represents the next frontier in neuroscience, and a new challenge in our understanding of the brain and the mechanism(s) behind neurological disorders.
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Affiliation(s)
- Jorge Montesinos
- Department of Neurology, Columbia University Medical Center, New York, New York, USA
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Neuropathophysiology of Lysosomal Storage Diseases: Synaptic Dysfunction as a Starting Point for Disease Progression. J Clin Med 2020; 9:jcm9030616. [PMID: 32106459 PMCID: PMC7141115 DOI: 10.3390/jcm9030616] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
About two thirds of the patients affected with lysosomal storage diseases (LSD) experience neurological manifestations, such as developmental delay, seizures, or psychiatric problems. In order to develop efficient therapies, it is crucial to understand the neuropathophysiology underlying these symptoms. How exactly lysosomal storage affects biogenesis and function of neurons is still under investigation however recent research highlights a substantial role played by synaptic defects, such as alterations in synaptic spines, synaptic proteins, postsynaptic densities, and synaptic vesicles that might lead to functional impairments in synaptic transmission and neurodegeneration, finally culminating in massive neuronal death and manifestation of cognitive symptoms. Unveiling how the synaptic components are affected in neurological LSD will thus enable a better understanding of the complexity of disease progression as well as identify crucial targets of therapeutic relevance and optimal time windows for targeted intervention.
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Shaaban A, Dhara M, Frisch W, Harb A, Shaib AH, Becherer U, Bruns D, Mohrmann R. The SNAP-25 linker supports fusion intermediates by local lipid interactions. eLife 2019; 8:41720. [PMID: 30883328 PMCID: PMC6422494 DOI: 10.7554/elife.41720] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/05/2019] [Indexed: 12/22/2022] Open
Abstract
SNAP-25 is an essential component of SNARE complexes driving fast Ca2+-dependent exocytosis. Yet, the functional implications of the tandem-like structure of SNAP-25 are unclear. Here, we have investigated the mechanistic role of the acylated “linker” domain that concatenates the two SNARE motifs within SNAP-25. Refuting older concepts of an inert connector, our detailed structure-function analysis in murine chromaffin cells demonstrates that linker motifs play a crucial role in vesicle priming, triggering, and fusion pore expansion. Mechanistically, we identify two synergistic functions of the SNAP-25 linker: First, linker motifs support t-SNARE interactions and accelerate ternary complex assembly. Second, the acylated N-terminal linker segment engages in local lipid interactions that facilitate fusion triggering and pore evolution, putatively establishing a favorable membrane configuration by shielding phospholipid headgroups and affecting curvature. Hence, the linker is a functional part of the fusion complex that promotes secretion by SNARE interactions as well as concerted lipid interplay.
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Affiliation(s)
- Ahmed Shaaban
- ZHMB, Saarland University, Homburg, Germany.,Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Madhurima Dhara
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Walentina Frisch
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Ali Harb
- ZHMB, Saarland University, Homburg, Germany
| | - Ali H Shaib
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Ute Becherer
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Dieter Bruns
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Ralf Mohrmann
- ZHMB, Saarland University, Homburg, Germany.,Institute for Physiology, Otto-von-Guericke University, Magdeburg, Germany.,Center for Behavioral Brain Science, Otto-von-Guericke University, Magdeburg, Germany
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14
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Sharma S, Lindau M. The fusion pore, 60 years after the first cartoon. FEBS Lett 2018; 592:3542-3562. [PMID: 29904915 DOI: 10.1002/1873-3468.13160] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 11/10/2022]
Abstract
Neurotransmitter release occurs in the form of quantal events by fusion of secretory vesicles with the plasma membrane, and begins with the formation of a fusion pore that has a conductance similar to that of a large ion channel or gap junction. In this review, we propose mechanisms of fusion pore formation and discuss their implications for fusion pore structure and function. Accumulating evidence indicates a direct role of soluble N-ethylmaleimide-sensitive-factor attachment receptor proteins in the opening of fusion pores. Fusion pores are likely neither protein channels nor purely lipid, but are of proteolipidic composition. Future perspectives to gain better insight into the molecular structure of fusion pores are discussed.
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Affiliation(s)
- Satyan Sharma
- Laboratory for Nanoscale Cell Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Manfred Lindau
- Laboratory for Nanoscale Cell Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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