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Fábián B, Javanainen M. Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch. J Phys Chem Lett 2024; 15:5344-5349. [PMID: 38738950 PMCID: PMC11129306 DOI: 10.1021/acs.jpclett.4c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Hydrophobic mismatch between a lipid membrane and embedded transmembrane peptides or proteins plays a role in their lateral localization and function. Earlier studies have resolved numerous mechanisms through which the peptides and membrane proteins adapt to mismatch, yet the energetics of lateral sorting due to hydrophobic mismatch have remained elusive due to the lack of suitable computational or experimental protocols. Here, we pioneer a molecular dynamics simulation approach to study the sorting of peptides along a membrane thickness gradient. Peptides of different lengths tilt and diffuse along the membrane to eliminate mismatch with a rate directly proportional to the magnitude of mismatch. We extract the 2-dimensional free energy profiles as a function of local thickness and peptide orientation, revealing the relative contributions of sorting and tilting, and suggesting their thermally accessible regimes. Our approach can readily be applied to study other membrane systems of biological interest where hydrophobic mismatch, or membrane thickness in general, plays a role.
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Affiliation(s)
- Balázs Fábián
- Department
of Theoretical Biophysics, MPI Biophysics, DE-60438 Frankfurt
am Main, Germany
| | - Matti Javanainen
- Institute
of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
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2
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van Hilten N, Methorst J, Verwei N, Risselada HJ. Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders. SCIENCE ADVANCES 2023; 9:eade8839. [PMID: 36930719 PMCID: PMC10022891 DOI: 10.1126/sciadv.ade8839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Proteins can specifically bind to curved membranes through curvature-induced hydrophobic lipid packing defects. The chemical diversity among such curvature "sensors" challenges our understanding of how they differ from general membrane "binders" that bind without curvature selectivity. Here, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations (Evo-MD) to resolve the peptide sequences that optimally recognize the curvature of lipid membranes. We subsequently demonstrate how a synergy between Evo-MD and a neural network (NN) can enhance the identification and discovery of curvature sensing peptides and proteins. To this aim, we benchmark a physics-trained NN model against experimental data and show that we can correctly identify known sensors and binders. We illustrate that sensing and binding are phenomena that lie on the same thermodynamic continuum, with only subtle but explainable differences in membrane binding free energy, consistent with the serendipitous discovery of sensors.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Jeroen Methorst
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Nino Verwei
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
- Department of Physics, Technical University Dortmund, Otto-Hahn-Strasse 4, Dortmund, 44227, Germany
- Institute of Theoretical Physics, Georg-August-University Göttingen, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany
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3
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Tiwari A, Pradhan S, Sannigrahi A, Mahakud AK, Jha S, Chattopadhyay K, Biswas M, Saleem M. “Interplay of lipid-head group and packing defects in driving Amyloid-beta mediated myelin-like model membrane deformation”. J Biol Chem 2023; 299:104653. [PMID: 36990217 PMCID: PMC10148160 DOI: 10.1016/j.jbc.2023.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Accumulating evidence suggests that amyloid plaque associated myelin lipid loss as a result of elevated amyloid burden might also contribute to Alzheimer's disease. The amyloid fibrils though closely associated with lipids under physiological conditions, however, the progression of membrane remodeling events leading to lipid-fibril assembly remains unknown. Here we first reconstitute the interaction of Aβ-40 with myelin-like model membrane and show that the binding of Aβ-40 induces extensive tubulation. To look into the mechanism of membrane tubulation we chose a set of membrane conditions varying in lipid packing density and net charge that allows us to dissect the contribution of lipid specificity of Aβ-40 binding, aggregation kinetics, and subsequent changes in membrane parameters such as fluidity, diffusion, and compressibility modulus. We show that the binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin-like model membrane during the early phase of amyloid aggregation. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the model membrane followed by extensive lipid membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40 - myelin-like model membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril-mediated load generation results in the consequent association of lipids with growing amyloid fibrils.
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4
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Angelotti T. Exploring the eukaryotic Yip and REEP/Yop superfamily of membrane-shaping adapter proteins (MSAPs): A cacophony or harmony of structure and function? Front Mol Biosci 2022; 9:912848. [PMID: 36060263 PMCID: PMC9437294 DOI: 10.3389/fmolb.2022.912848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Polytopic cargo proteins are synthesized and exported along the secretory pathway from the endoplasmic reticulum (ER), through the Golgi apparatus, with eventual insertion into the plasma membrane (PM). While searching for proteins that could enhance cell surface expression of olfactory receptors, a new family of proteins termed “receptor expression-enhancing proteins” or REEPs were identified. These membrane-shaping hairpin proteins serve as adapters, interacting with intracellular transport machinery, to regulate cargo protein trafficking. However, REEPs belong to a larger family of proteins, the Yip (Ypt-interacting protein) family, conserved in yeast and higher eukaryotes. To date, eighteen mammalian Yip family members, divided into four subfamilies (Yipf, REEP, Yif, and PRAF), have been identified. Yeast research has revealed many intriguing aspects of yeast Yip function, functions that have not completely been explored with mammalian Yip family members. This review and analysis will clarify the different Yip family nomenclature that have encumbered prior comparisons between yeast, plants, and eukaryotic family members, to provide a more complete understanding of their interacting proteins, membrane topology, organelle localization, and role as regulators of cargo trafficking and localization. In addition, the biological role of membrane shaping and sensing hairpin and amphipathic helical domains of various Yip proteins and their potential cellular functions will be described. Lastly, this review will discuss the concept of Yip proteins as members of a larger superfamily of membrane-shaping adapter proteins (MSAPs), proteins that both shape membranes via membrane-sensing and hairpin insertion, and well as act as adapters for protein-protein interactions. MSAPs are defined by their localization to specific membranes, ability to alter membrane structure, interactions with other proteins via specific domains, and specific interactions/effects on cargo proteins.
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5
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van Hilten N, Stroh KS, Risselada HJ. Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36. J Chem Theory Comput 2022; 18:4503-4514. [PMID: 35709386 PMCID: PMC9281404 DOI: 10.1021/acs.jctc.2c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sensing can be defined as the difference in mechanical work required to stretch a membrane with and without a peptide bound to the surface. We also demonstrate that a peptide's ability to concurrently induce excess leaflet area (tension) and elastic softening─a property we call the "characteristic area of sensing" (CHAOS)─and lipid packing sensing behavior are in fact two sides of the same coin. In essence, defect sensing displays a peptide's propensity to generate tension. The here-proposed mechanical pathway is equally accurate yet, computationally, about 40 times less costly than the commonly used alchemical pathway (thermodynamic integration), allowing for more feasible free energy calculations in atomistic simulations. This enabled us to directly compare the Martini 2 and 3 coarse-grained and the CHARMM36 atomistic force fields in terms of relative binding free energies for six representative peptides including the curvature sensor ALPS and two antiviral amphipathic helices (AH). We observed that Martini 3 qualitatively reproduces experimental trends while producing substantially lower (relative) binding free energies and shallower membrane insertion depths compared to atomistic simulations. In contrast, Martini 2 tends to overestimate (relative) binding free energies. Finally, we offer a glimpse into how our end-state-based free energy method can enable the inverse design of optimal lipid packing defect sensing peptides when used in conjunction with our recently developed evolutionary molecular dynamics (Evo-MD) method. We argue that these optimized defect sensors─aside from their biomedical and biophysical relevance─can provide valuable targets for the development of lipid force fields.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Kai Steffen Stroh
- Department of Physics, Technical University Dortmund, Dortmund 44221, Germany.,Institute for Theoretical Physics, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands.,Department of Physics, Technical University Dortmund, Dortmund 44221, Germany.,Institute for Theoretical Physics, Georg-August-University Göttingen, Göttingen 37077, Germany
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6
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Tumor protein D54 binds intracellular nanovesicles via an extended amphipathic region. J Biol Chem 2022; 298:102136. [PMID: 35714773 PMCID: PMC9270247 DOI: 10.1016/j.jbc.2022.102136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Tumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical (e.g. COPI and COPII) transport vesicles. Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by four amphipathic helices (AH1-4), which could fold upon binding to lipid membranes. Limited proteolysis, circular dichroism (CD) spectroscopy, tryptophan fluorescence, and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe showed that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. Furthermore, site-directed mutagenesis indicated that AH2 and AH3 have a predominant role in TPD54 binding to membranes both in cells and using model liposomes. We found that AH3 has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Accordingly, we observed that binding of TPD54 to liposomes is very sensitive to membrane curvature and lipid unsaturation. We conclude that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.
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7
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Cino EA, Tieleman DP. Curvature-based sorting of eight lipid types in asymmetric buckled plasma membrane models. Biophys J 2022; 121:2060-2068. [PMID: 35524412 DOI: 10.1016/j.bpj.2022.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 05/02/2022] [Indexed: 11/02/2022] Open
Abstract
Curvature is a fundamental property of biological membranes and has essential roles in cellular function. Bending of membranes can be induced by their lipid and protein compositions, as well as peripheral proteins, such as those that make up the cytoskeleton. An important aspect of membrane function is the grouping of lipid species into microdomains, or rafts, which serve as platforms for specific biochemical processes. The fluid mosaic model of membranes has evolved to recognize the importance of curvature and leaflet asymmetry, and there are efforts towards evaluating their functional roles. This work investigates the effect of curvature on the sorting of lipids in buckled asymmetric bilayers containing eight lipid types, approximating an average mammalian plasma membrane, through coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field. The simulations reveal that i) leaflet compositional asymmetry can induce curvature asymmetry, ii) lipids are sorted by curvature to different extents, and iii) curvature-based partitioning trends show moderate to strong correlations with lipid molecular volumes and head to tail bead ratios, respectively. The findings provide unique insights into the role of curvature in membrane organization, and the curvature-based sorting trends should be useful references for later investigations, and potentially interpreting the functional roles of specific lipids.
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Affiliation(s)
- Elio A Cino
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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8
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Chng CP, Cho NJ, Hsia KJ, Huang C. Role of Membrane Stretch in Adsorption of Antiviral Peptides onto Lipid Membranes and Membrane Pore Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13390-13398. [PMID: 34724382 DOI: 10.1021/acs.langmuir.1c02067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many medically important viruses are enveloped viruses, which are surrounded by a structurally conserved, host-derived lipid membrane coating. Agents that target and disrupt this membrane coating could potentially function as broad-spectrum antiviral drugs. The amphipathic α-helical (AH) peptide derived from the N-terminus of the hepatitis C virus NS5A protein is one such candidate and has been demonstrated to be able to selectively rupture lipid vesicles in the size range of viruses (<160 nm diameter). However, the mechanism underlying this membrane curvature selectivity remains elusive. In this study, we have performed molecular dynamics simulations to study the binding of the AH peptide to model membranes that are stretched to resemble the looser lipid headgroup packing present on highly curved outer membranes of nanoscale vesicles. We found that the AH peptide binds more favorably to membranes that are stretched. In addition, a tetrameric placement of peptides across the membrane induced stable pore formation in the stretched membrane. Thus, our results suggest that the AH peptide senses the high curvature of nanoscale vesicles via the enhanced exposure of lipid packing defects induced by membrane area strain.
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Affiliation(s)
- Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 637553, Republic of Singapore
- China-Singapore International Joint Research Institute (CSIJRI), Guangzhou 510000, P. R. China
| | - K Jimmy Hsia
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
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9
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Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells 2021; 10:cells10113124. [PMID: 34831348 PMCID: PMC8624279 DOI: 10.3390/cells10113124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
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10
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Sikdar S, Banerjee M, Vemparala S. Effect of cholesterol on the membrane partitioning dynamics of hepatitis A virus-2B peptide. SOFT MATTER 2021; 17:7963-7977. [PMID: 34378608 DOI: 10.1039/d1sm01019k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding viral peptide detection and partitioning and the subsequent host membrane composition-based response is essential for gaining insights into the viral mechanism. Here, we probe the crucial role of the presence of membrane lipid packing defects, depending on the membrane composition, in allowing the viral peptide belonging to C-terminal Hepatitis A Virus-2B (HAV-2B) to detect, attach and subsequently partition into host cell membrane mimics. Using molecular dynamics simulations, we conclusively show that the hydrophobic residues in the viral peptide detect transiently present lipid packing defects, insert themselves into such defects, form anchor points and facilitate the partitioning of the peptide, thereby inducing membrane disruption. We also show that the presence of cholesterol significantly alters such lipid packing defects, both in size and in number, thus mitigating the partitioning of the membrane active viral peptide into cholesterol-rich membranes. Our results are in excellent agreement with previously published experimental data and further explain the role of lipid defects in understanding such data. These results show differential ways in which the presence and absence of cholesterol can alter the permeability of the host membranes to the membrane active peptide component of HAV-2B virus, via lipid packing defects, and can possibly be a part of the general membrane detection mechanism for viroporins.
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Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
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11
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Nishimura T, Oyama T, Hu HT, Fujioka T, Hanawa-Suetsugu K, Ikeda K, Yamada S, Kawana H, Saigusa D, Ikeda H, Kurata R, Oono-Yakura K, Kitamata M, Kida K, Hikita T, Mizutani K, Yasuhara K, Mimori-Kiyosue Y, Oneyama C, Kurimoto K, Hosokawa Y, Aoki J, Takai Y, Arita M, Suetsugu S. Filopodium-derived vesicles produced by MIM enhance the migration of recipient cells. Dev Cell 2021; 56:842-859.e8. [PMID: 33756122 DOI: 10.1016/j.devcel.2021.02.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 12/31/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are classified as large EVs (l-EVs, or microvesicles) and small EVs (s-EVs, or exosomes). S-EVs are thought to be generated from endosomes through a process that mainly depends on the ESCRT protein complex, including ALG-2 interacting protein X (ALIX). However, the mechanisms of l-EV generation from the plasma membrane have not been identified. Membrane curvatures are generated by the bin-amphiphysin-rvs (BAR) family proteins, among which the inverse BAR (I-BAR) proteins are involved in filopodial protrusions. Here, we show that the I-BAR proteins, including missing in metastasis (MIM), generate l-EVs by scission of filopodia. Interestingly, MIM-containing l-EV production was promoted by in vivo equivalent external forces and by the suppression of ALIX, suggesting an alternative mechanism of vesicle formation to s-EVs. The MIM-dependent l-EVs contained lysophospholipids and proteins, including IRS4 and Rac1, which stimulated the migration of recipient cells through lamellipodia formation. Thus, these filopodia-dependent l-EVs, which we named as filopodia-derived vesicles (FDVs), modify cellular behavior.
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Affiliation(s)
- Tamako Nishimura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Takuya Oyama
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Hooi Ting Hu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Toshifumi Fujioka
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; Kazusa DNA Research Institute, 2-6-7 Kazusa, kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sohei Yamada
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Hiroki Kawana
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Daisuke Saigusa
- Tohoku University Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Hiroki Ikeda
- Department of Embryology, Nara Medical University, Kashihara 634-0813, Nara, Japan
| | - Rie Kurata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kayoko Oono-Yakura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Manabu Kitamata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazuki Kida
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Tomoya Hikita
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
| | - Kiyohito Mizutani
- Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Kazuma Yasuhara
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, Minatojima-minaminachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Chitose Oneyama
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara 634-0813, Nara, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Junken Aoki
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yoshimi Takai
- Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-0011, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma 630-0192, Japan.
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12
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Stroh KS, Risselada HJ. Quantifying Membrane Curvature Sensing of Peripheral Proteins by Simulated Buckling and Umbrella Sampling. J Chem Theory Comput 2021; 17:5276-5286. [PMID: 34261315 DOI: 10.1021/acs.jctc.1c00021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane curvature plays an essential role in the organization and trafficking of membrane associated proteins. Comparison or prediction of the experimentally resolved protein concentrations adopted at different membrane curvatures requires direct quantification of the relative partitioning free energy. Here, we present a highly efficient and simple to implement a free-energy calculation method which is able to directly resolve the relative partitioning free energy of proteins as a direct function of membrane curvature, i.e., a curvature sensing profile, within (coarse-grained) molecular dynamics simulations. We demonstrate its utility by resolving these profiles for two known curvature sensing peptides, namely ALPS and α-synuclein, for a membrane curvature ranging from -1/6.5 to +1/6.5 nm-1. We illustrate that the difference in relative partitioning (binding) free energy between these two extrema is only about 13 kBT for both peptides, illustrating that the driving force of curvature sensing is subtle. Furthermore, we illustrate that ALPS and α-synuclein sense curvature via a contrasting mechanism, which is differentially affected by membrane composition. In addition, we demonstrate that the intrinsic spontaneous curvature of both of these peptides lies beyond the range of membrane curvature accessible in micropipette aspiration experiments, being about 1/7 nm -1. Our approach offers an efficient and simple to implement in silico tool for exploring and screening the membrane curvature sensing mechanisms of proteins.
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Affiliation(s)
- Kai Steffen Stroh
- Institute for Theoretical Physics, Georg-August University Göttingen, Göttingen, Germany
| | - Herre Jelger Risselada
- Institute for Theoretical Physics, Georg-August University Göttingen, Göttingen, Germany.,Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Leibniz Institute for Surface Engineering, Leipzig, Germany
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13
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Liaci AM, Steigenberger B, Telles de Souza PC, Tamara S, Gröllers-Mulderij M, Ogrissek P, Marrink SJ, Scheltema RA, Förster F. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Mol Cell 2021; 81:3934-3948.e11. [PMID: 34388369 DOI: 10.1016/j.molcel.2021.07.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre-proteins with exquisite specificity. Although the determinants of this process have been established empirically, the molecular details of SP recognition and removal remain elusive. Here, we show that the human SPC exists in two functional paralogs with distinct proteolytic subunits. We determined the atomic structures of both paralogs using electron cryo-microscopy and structural proteomics. The active site is formed by a catalytic triad and abuts the ER membrane, where a transmembrane window collectively formed by all subunits locally thins the bilayer. Molecular dynamics simulations indicate that this unique architecture generates specificity for SPs based on the length of their hydrophobic segments.
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Affiliation(s)
- A Manuel Liaci
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Paulo Cesar Telles de Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands; Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS and University of Lyon, Lyon, France
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Mariska Gröllers-Mulderij
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Patrick Ogrissek
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands; Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands.
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