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Majumder A, Gu Y, Chen YC, An X, Reinhard BM, Straub JE. Probing the Origins of the Disorder-to-Order Transition of a Modified Cholesterol in Ternary Lipid Bilayers. J Am Chem Soc 2024; 146:27725-27735. [PMID: 39315765 DOI: 10.1021/jacs.4c09495] [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: 09/25/2024]
Abstract
In a recent study, spectroscopic observations of modified cholesterol in both lipid-coated nanoparticles and liposomes provided evidence for a disorder-to-order orientational transition with increasing temperature. Below a critical temperature, in a membrane composed of modified cholesterol, saturated (DPPC) lipid, and anionic (DOPS) lipid, a roughly equal population of head-out and head-in conformations was observed. Surprisingly, as temperature was increased the modified cholesterol presented an abrupt transition to a population of all head-in orientations. Additionally, when saturated DPPC lipids were replaced by unsaturated DOPC the disorder-to-order transition was eliminated. To gain insight into this curious transition, we use all-atom molecular dynamics simulations to characterize the structure and fluctuations of lipid bilayers composed of saturated and unsaturated lipids, in the presence of normal and modified cholesterol. Free energy differences between head-out and head-in conformations are computed as a function of varying lipid membrane composition for normal and modified cholesterol. In bilayers primarily composed of DPPC, the orientation of modified cholesterol is observed to depend sensitively on the orientation of the surrounding normal or modified cholesterol molecules, suggesting cooperative Ising-like interactions favoring an ordered state. In bilayers primarily composed of DOPC, spontaneous flip-flop of modified cholesterol is observed, consistent with the measured small free energy barrier separating the head-in and head-out orientations. This combined experimental and computational study effectively characterizes the orientational dimorphism and provides novel insight into the fundamental nature of cholesterol interactions in membrane.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuanqing Gu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- The Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States
| | - Yi-Chen Chen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Xingda An
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- The Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States
| | - Björn M Reinhard
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- The Photonics Center, Boston University, 8 Saint Mary's Street, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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2
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Albani S, Eswaran VSB, Piergentili A, de Souza PCT, Lampert A, Rossetti G. Depletion of membrane cholesterol modifies structure, dynamic and activation of Na v1.7. Int J Biol Macromol 2024; 278:134219. [PMID: 39097041 DOI: 10.1016/j.ijbiomac.2024.134219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/05/2024]
Abstract
Cholesterol is a major component of plasma membranes and plays a significant role in actively regulating the functioning of several membrane proteins in humans. In this study, we focus on the role of cholesterol depletion on the voltage-gated sodium channel Nav1.7, which is primarily expressed in the peripheral sensory neurons and linked to various chronic inherited pain syndromes. Coarse-grained molecular dynamics simulations revealed key dynamic changes of Nav1.7 upon membrane cholesterol depletion: A loss of rigidity in the structural motifs linked to activation and fast-inactivation is observed, suggesting an easier transition of the channel between different gating states. In-vitro whole-cell patch clamp experiments on HEK293t cells expressing Nav1.7 validated these predictions at the functional level: Hyperpolarizing shifts in the voltage-dependence of activation and fast-inactivation were observed along with an acceleration of the time to peak and onset kinetics of fast inactivation. These results underline the critical role of membrane composition, and of cholesterol in particular, in influencing Nav1.7 gating characteristics. Furthermore, our results also point to cholesterol-driven changes of the geometry of drug-binding regions, hinting to a key role of the membrane environment in the regulation of drug effects.
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Affiliation(s)
- Simone Albani
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany; Faculty of Biology, RWTH Aachen University, Aachen, Germany
| | | | - Alessia Piergentili
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany; Faculty of Biology, RWTH Aachen University, Aachen, Germany; Department of Neurology, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Paulo Cesar Telles de Souza
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale, Supérieure de Lyon, 46 All'ee d'Italie, 69364 Lyon, France
| | - Angelika Lampert
- Institute of Neurophysiology, Uniklinik RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany.
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany; Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52425 Jülich, Germany; Department of Neurology, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany.
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3
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Liebl K, Voth GA. Lipid organization by the Caveolin-1 complex. Biophys J 2024:S0006-3495(24)00630-1. [PMID: 39306671 DOI: 10.1016/j.bpj.2024.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/26/2024] [Accepted: 09/19/2024] [Indexed: 09/25/2024] Open
Abstract
Caveolins are lipid-binding proteins that can organize membrane remodeling and oligomerize into the 8S complex. The CAV1-8S complex comprises a disk-like structure, about 15 nm in diameter, with a central beta barrel. Further oligomerization of 8S complexes remodels the membrane into caveolae vessels, with a dependence on cholesterol concentration. However, the molecular mechanisms behind membrane remodeling and cholesterol filtering are still not understood. Performing atomistic molecular dynamics simulations in combination with advanced sampling techniques, we describe how the CAV1-8S complex bends the membrane and accumulates cholesterol. Here, our simulations show an enhancing effect by the palmitoylations of CAV1, and we predict that the CAV1-8S complex can extract cholesterol molecules from the lipid bilayer and accommodate them in its beta barrel. Through backmapping to the all-atom level, we also conclude that the Martini v.2 coarse-grained force field overestimates membrane bending, as the atomistic simulations exhibit only very localized bending.
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Affiliation(s)
- Korbinian Liebl
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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Kennelly JP, Xiao X, Gao Y, Kim S, Hong SG, Villanueva M, Ferrari A, Vanharanta L, Nguyen A, Nagari RT, Burton NR, Tol MJ, Becker AP, Lee MJ, Ikonen E, Backus KM, Mack JJ, Tontonoz P. Cholesterol binding to VCAM-1 promotes vascular inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613543. [PMID: 39345495 PMCID: PMC11429921 DOI: 10.1101/2024.09.17.613543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Hypercholesterolemia has long been implicated in endothelial cell (EC) dysfunction, but the mechanisms by which excess cholesterol causes vascular pathology are incompletely understood. Here we used a cholesterol-mimetic probe to map cholesterol-protein interactions in primary human ECs and discovered that cholesterol binds to and stabilizes the adhesion molecule VCAM-1. We show that accessible plasma membrane (PM) cholesterol in ECs is acutely responsive to inflammatory stimuli and that the nonvesicular cholesterol transporter Aster-A regulates VCAM-1 stability in activated ECs by controlling the size of this pool. Deletion of Aster-A in ECs increases VCAM-1 protein, promotes immune cell recruitment to vessels, and impairs pulmonary immune homeostasis. Conversely, depleting cholesterol from the endothelium in vivo dampens VCAM-1 induction in response to inflammatory stimuli. These findings identify cholesterol binding to VCAM-1 as a key step during EC activation and provide a biochemical explanation for the ability of excess membrane cholesterol to promote immune cell recruitment to the endothelium.
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5
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Chiu PL, Orjuela JD, de Groot BL, Aponte Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 2024; 12:RP90851. [PMID: 39222068 PMCID: PMC11368405 DOI: 10.7554/elife.90851] [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: 09/04/2024] Open
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
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Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Juan D Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Biomedical Engineering Department, Universidad de los AndesBogotáColombia
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Camilo Aponte Santamaría
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
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6
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Tian L, Andrews C, Yan Q, Yang JJ. Molecular regulation of calcium-sensing receptor (CaSR)-mediated signaling. Chronic Dis Transl Med 2024; 10:167-194. [PMID: 39027195 PMCID: PMC11252437 DOI: 10.1002/cdt3.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 07/20/2024] Open
Abstract
Calcium-sensing receptor (CaSR), a family C G-protein-coupled receptor, plays a crucial role in regulating calcium homeostasis by sensing small concentration changes of extracellular Ca2+, Mg2+, amino acids (e.g., L-Trp and L-Phe), small peptides, anions (e.g., HCO3 - and PO4 3-), and pH. CaSR-mediated intracellular Ca2+ signaling regulates a diverse set of cellular processes including gene transcription, cell proliferation, differentiation, apoptosis, muscle contraction, and neuronal transmission. Dysfunction of CaSR with mutations results in diseases such as autosomal dominant hypocalcemia, familial hypocalciuric hypercalcemia, and neonatal severe hyperparathyroidism. CaSR also influences calciotropic disorders, such as osteoporosis, and noncalciotropic disorders, such as cancer, Alzheimer's disease, and pulmonary arterial hypertension. This study first reviews recent advances in biochemical and structural determination of the framework of CaSR and its interaction sites with natural ligands, as well as exogenous positive allosteric modulators and negative allosteric modulators. The establishment of the first CaSR protein-protein interactome network revealed 94 novel players involved in protein processing in endoplasmic reticulum, trafficking, cell surface expression, endocytosis, degradation, and signaling pathways. The roles of these proteins in Ca2+-dependent cellular physiological processes and in CaSR-dependent cellular signaling provide new insights into the molecular basis of diseases caused by CaSR mutations and dysregulated CaSR activity caused by its protein interactors and facilitate the design of therapeutic agents that target CaSR and other family C G-protein-coupled receptors.
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Affiliation(s)
- Li Tian
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Corey Andrews
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Qiuyun Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Jenny J. Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
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7
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Life Sci Alliance 2024; 7:e202402624. [PMID: 38925866 PMCID: PMC11208740 DOI: 10.26508/lsa.202402624] [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: 01/26/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
In Caenorhabditis elegans, inter-cellular transport of the small non-coding RNA causing systemic RNAi is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNAi defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the ChUP family. Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products-hSIDT1 and hSIDT2-mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain exists as two modules-a flexible lipid binding domain and a rigid transmembrane domain core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in ChUP family members.
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Affiliation(s)
- Vikas Navratna
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jaimin K Rana
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shyamal Mosalaganti
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI, USA
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8
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Shebanova A, Perrin QM, Zhu K, Gudlur S, Chen Z, Sun Y, Huang C, Lim ZW, Mondarte EA, Sun R, Lim S, Yu J, Miao Y, Parikh AN, Ludwig A, Miserez A. Cellular Uptake of Phase-Separating Peptide Coacervates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402652. [PMID: 39214144 DOI: 10.1002/advs.202402652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/07/2024] [Indexed: 09/04/2024]
Abstract
Peptide coacervates self-assembling via liquid-liquid phase separation are appealing intracellular delivery vehicles of macromolecular therapeutics (proteins, DNA, mRNA) owing to their non-cytotoxicity, high encapsulation capacity, and efficient cellular uptake. However, the mechanisms by which these viscoelastic droplets cross the cellular membranes remain unknown. Here, using multimodal imaging, data analytics, and biochemical inhibition assays, identify the key steps by which droplets enter the cell. find that the uptake follows a non-canonical pathway and instead integrates essential features of macropinocytosis and phagocytosis, namely active remodeling of the actin cytoskeleton and appearance of filopodia-like protrusions. Experiments using giant unilamellar vesicles show that the coacervates attach to the bounding membrane in a charge- and cholesterol-dependent manner but do not breach the lipid bilayer barrier. Cell uptake in the presence of small molecule inhibitors - interfering with actin and tubulin polymerization - confirm the active role of cytoskeleton remodeling, most prominently evident in electron microscopy imaging. These findings suggest a peculiar internalization mechanism for viscoelastic, glassy coacervate droplets combining features of non-specific uptake of fluids by macropinocytosis and particulate uptake of phagocytosis. The broad implications of this study will enable to enhance the efficacy and utility of coacervate-based strategies for intracellular delivery of macromolecular therapeutics.
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Affiliation(s)
- Anastasia Shebanova
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Quentin Moana Perrin
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Kexin Zhu
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Sushanth Gudlur
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Zilin Chen
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Yue Sun
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Congxi Huang
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Zhi Wei Lim
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Evan Angelo Mondarte
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
| | - Ruoxuan Sun
- School of Chemistry, Chemical Engineering and Biotechnology, NTU, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Sierin Lim
- School of Chemistry, Chemical Engineering and Biotechnology, NTU, 70 Nanyang Drive, Singapore, 637457, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Jing Yu
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Yansong Miao
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Atul N Parikh
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 59 Nanyang Drive, Singapore, 636921, Singapore
- Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, CA, 95616, USA
| | - Alexander Ludwig
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, NTU, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Ali Miserez
- Centre for Sustainable Materials, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 637553, Singapore
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore
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9
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Bous J, Kinsolving J, Grätz L, Scharf MM, Voss JH, Selcuk B, Adebali O, Schulte G. Structural basis of frizzled 7 activation and allosteric regulation. Nat Commun 2024; 15:7422. [PMID: 39198452 PMCID: PMC11358414 DOI: 10.1038/s41467-024-51664-4] [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] [Received: 05/03/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
Frizzleds (ten paralogs: FZD1-10) belong to the class F of G protein-coupled receptors (GPCRs), which remains poorly understood despite its crucial role in multiple key biological functions including embryonic development, stem cell regulation, and homeostasis in the adult. FZD7, one of the most studied members of the family, is more specifically involved in the migration of mesendoderm cells during the development and renewal of intestinal stem cells in adults. Moreover, FZD7 has been highlighted for its involvement in tumor development predominantly in the gastrointestinal tract. This study reports the structure of inactive FZD7, without any stabilizing mutations, determined by cryo-electron microscopy (cryo-EM) at 1.9 Å resolution. We characterize a fluctuating water pocket in the core of the receptor important for FZD7 dynamics. Molecular dynamics simulations are used to investigate the temporal distribution of those water molecules and their importance for potential conformational changes in FZD7. Moreover, we identify lipids interacting with the receptor core and a conserved cholesterol-binding site, which displays a key role in FZD7 association with a transducer protein, Disheveled (DVL), and initiation of downstream signaling and signalosome formation.
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Affiliation(s)
- Julien Bous
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden.
| | - Julia Kinsolving
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Lukas Grätz
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena M Scharf
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Hendrik Voss
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Berkay Selcuk
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ogün Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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10
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Stefanski KM, Wilkinson MC, Sanders CR. Roles for PMP22 in Schwann cell cholesterol homeostasis in health and disease. Biochem Soc Trans 2024; 52:1747-1756. [PMID: 38979632 DOI: 10.1042/bst20231359] [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] [Received: 04/02/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024]
Abstract
Underexpression, overexpression, and point mutations in peripheral myelin protein 22 (PMP22) cause most cases of Charcot-Marie-Tooth disease (CMTD). While its exact functions remain unclear, PMP22 is clearly essential for formation and maintenance of healthy myelin in the peripheral nervous system. This review explores emerging evidence for roles of PMP22 in cholesterol homeostasis. First, we highlight dysregulation of lipid metabolism in PMP22-based forms of CMTD and recently-discovered interactions between PMP22 and cholesterol biosynthesis machinery. We then examine data that demonstrates PMP22 and cholesterol co-traffic in cells and co-localize in lipid rafts, including how disease-causing PMP22 mutations result in aberrations in cholesterol localization. Finally, we examine roles for interactions between PMP22 and ABCA1 in cholesterol efflux. Together, this emerging body of evidence suggests that PMP22 plays a role in facilitating enhanced cholesterol synthesis and trafficking necessary for production and maintenance of healthy myelin.
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Affiliation(s)
- Katherine M Stefanski
- Department of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240-7917, U.S.A
| | - Mason C Wilkinson
- Department of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240-7917, U.S.A
| | - Charles R Sanders
- Department of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, TN 37240-7917, U.S.A
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11
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Shikha D, Dalai R, Kumar S, Goswami C. Residues of TRPM8 at the Lipid-Water-Interface have Coevolved with Cholesterol Interaction and are Relevant for Diverse Health Disorders. J Membr Biol 2024:10.1007/s00232-024-00319-y. [PMID: 39150496 DOI: 10.1007/s00232-024-00319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024]
Abstract
TRPM8 is a non-selective cation channel that is expressed in several tissues and cells and also has a unique property to be activated by low-temperature. In this work, we have analyzed the conservation of amino acids that are present in the lipid-water-interface (LWI) region of TRPM8, the region which experiences a microenvironment near the membrane surface. We demonstrate that the amino acids present in the LWI region are more conserved than the transmembrane or even full-length TRPM8, suggesting strong selection pressure in these residues. TRPM8 also has several conserved cholesterol-binding motifs where cholesterol can bind in different modes and energies. We suggest that mutations and/or physiological conditions can potentially alter these TRPM8-cholesterol complexes and can lead to physiological disorders or even apparently irreversible diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Deep Shikha
- School of Biological Sciences, National Institute of Science Education and Research, An OCC of Homi Bhabha National Institute, Khordha, Jatni, Odisha, 752050, India
| | - Ritesh Dalai
- School of Biological Sciences, National Institute of Science Education and Research, An OCC of Homi Bhabha National Institute, Khordha, Jatni, Odisha, 752050, India
| | - Shamit Kumar
- School of Biological Sciences, National Institute of Science Education and Research, An OCC of Homi Bhabha National Institute, Khordha, Jatni, Odisha, 752050, India
| | - Chandan Goswami
- School of Biological Sciences, National Institute of Science Education and Research, An OCC of Homi Bhabha National Institute, Khordha, Jatni, Odisha, 752050, India.
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12
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Bell TA, Luce BE, Hakim P, Ananda VY, Dardari H, Nguyen TH, Monshizadeh A, Chao LH. Prominin 1 and Tweety Homology 1 both induce extracellular vesicle formation. eLife 2024; 13:e100061. [PMID: 39136554 PMCID: PMC11405016 DOI: 10.7554/elife.100061] [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] [Received: 05/27/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024] Open
Abstract
Prominin 1 (Prom1) is a five-transmembrane pass integral membrane protein that associates with curved regions of the plasma membrane. Prom1 interacts with membrane cholesterol and actively remodels the plasma membrane. Membrane-bending activity is particularly evident in photoreceptors, where Prom1 loss-of-function mutations cause failure of outer segment homeostasis, leading to cone-rod retinal dystrophy (CRRD). The Tweety Homology (Ttyh) protein family has been proposed to be homologous to Prominin, but it is not known whether Ttyh proteins have an analogous membrane-bending function. Here, we characterize the membrane-bending activity of human Prom1 and Ttyh1 in native bilayer membranes. We find that Prom1 and Ttyh1 both induce formation of extracellular vesicles (EVs) in cultured mammalian cells and that the EVs produced are physically similar. Ttyh1 is more abundant in EV membranes than Prom1 and produces EVs with membranes that are more tubulated than Prom1 EVs. We further show that Prom1 interacts more stably with membrane cholesterol than Ttyh1 and that this may contribute to membrane-bending inhibition in Prom1 EVs. Intriguingly, a loss-of-function mutation in Prom1 associated with CRRD induces particularly stable cholesterol binding. These experiments provide mechanistic insight into Prominin function in CRRD and suggest that Prom and Ttyh belong to a single family of functionally related membrane-bending, EV-generating proteins.
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Affiliation(s)
- Tristan A Bell
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Bridget E Luce
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Pusparanee Hakim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Virly Y Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Hiba Dardari
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Tran H Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Arezu Monshizadeh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States
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13
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Chahinian H, Yahi N, Fantini J. Glutamate, Gangliosides, and the Synapse: Electrostatics at Work in the Brain. Int J Mol Sci 2024; 25:8583. [PMID: 39201269 PMCID: PMC11354842 DOI: 10.3390/ijms25168583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/02/2024] [Accepted: 08/04/2024] [Indexed: 09/02/2024] Open
Abstract
The synapse is a piece of information transfer machinery replacing the electrical conduction of nerve impulses at the end of the neuron. Like many biological mechanisms, its functioning is heavily affected by time constraints. The solution selected by evolution is based on chemical communication that, in theory, cannot compete with the speed of nerve conduction. Nevertheless, biochemical and biophysical compensation mechanisms mitigate this intrinsic weakness: (i) through the high concentrations of neurotransmitters inside the synaptic vesicles; (ii) through the concentration of neurotransmitter receptors in lipid rafts, which are signaling platforms; indeed, the presence of raft lipids, such as gangliosides and cholesterol, allows a fine tuning of synaptic receptors by these lipids; (iii) through the negative electrical charges of the gangliosides, which generate an attractive (for cationic neurotransmitters, such as serotonin) or repulsive (for anionic neurotransmitters, such as glutamate) electric field. This electric field controls the flow of glutamate in the tripartite synapse involving pre- and post-synaptic neurons and the astrocyte. Changes in the expression of brain gangliosides can disrupt the functioning of the glutamatergic synapse, causing fatal diseases, such as Rett syndrome. In this review, we propose an in-depth analysis of the role of gangliosides in the glutamatergic synapse, highlighting the primordial and generally overlooked role played by the electric field of synaptic gangliosides.
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Affiliation(s)
| | | | - Jacques Fantini
- Faculty of Sciences, Department of Biology, University of Aix-Marseille, INSERM UA16, 13015 Marseille, France; (H.C.); (N.Y.)
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14
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Liebl K, Voth GA. Lipid Organization by the Caveolin-1 Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602986. [PMID: 39026816 PMCID: PMC11257593 DOI: 10.1101/2024.07.10.602986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Caveolins are lipid-binding proteins that can organize membrane remodeling and oligomerize into the 8S-complex. The CAV1 8S-complex comprises a disk-like structure, about 15nm in diameter, with a central beta barrel. Further oligomerization of 8S-complexes remodels the membrane into caveolae vessels, with a dependence on cholesterol concentration. However, the molecular mechanisms behind membrane remodeling and cholesterol filtering are still not understood. Performing atomistic Molecular Dynamics simulations in combination with advanced sampling techniques, we describe how the CAV1-8S complex bends the membrane and accumulates cholesterol. Here, our simulations show an enhancing effect by the palmitoylations of CAV1, and we predict that the CAV1-8S complex can extract cholesterol molecules from the lipid bilayer and accommodate them in its beta barrel. Through backmapping to the all-atom level we also conclude that the Martini v2 coarse-grained forcefield overestimates membrane bending, as the atomistic simulations exhibit only very localized bending.
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Affiliation(s)
- Korbinian Liebl
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
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15
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Miya V, Kumar C, Breed AA, Idicula-Thomas S, Pathak BR. Mammalian cysteine-rich secretory proteins interact with plasma membrane Ca 2+ exporter PMCA4b. Andrology 2024; 12:1096-1110. [PMID: 37882330 DOI: 10.1111/andr.13549] [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] [Received: 06/24/2023] [Revised: 09/28/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Mammalian cysteine-rich secretory proteins (CRISPs) are predominantly expressed in the male reproductive tract. Knockout mice lacking two or more CRISPs show defects in sperm transport, sperm-egg interaction and Ca2+ homeostasis. CRISPs play redundant and specific roles via their binding partners. To understand this, a comprehensive analysis of CRISP interactome needs to be undertaken. OBJECTIVES This study aimed to analyse CRISP4 binding partners on the plasma membrane of rat caudal spermatozoa. MATERIALS AND METHODS Total proteins from rat caudal spermatozoa were subjected to immunoprecipitation using anti-CRISP4 antibody followed by liquid chromatography-mass spectrophotometry analysis. Plasma membrane localised proteins were shortlisted, and a key target was validated by co-immunoprecipitation and co-localisation. Co-transfection followed by co-immunoprecipitation was carried out for studying the interaction of full-length as well as deletion mutants of CRISPs with human plasma membrane calcium ATPase, isoform b (hPMCA4b). Calcium assays were performed using Fura-2-AM. The cholesterol binding ability of different CRISPs was evaluated in silico. RESULTS The membrane-specific interactome of rat CRISP4 (rCRISP4) from caudal spermatozoa revealed PMCA4b as a novel binding partner, and their interaction was validated in rat spermatozoa. Human CRISP1 (hCRISP1) and hCRISP3 also interacted with PMCA4b via the N-terminal domain. Interestingly, hCRISP1 and rCRISP4 delayed PMCA4b-mediated calcium extrusion but hCRISP3 did not. In silico analysis demonstrated that hCRISP1 and rCRISP4 have higher binding affinity towards cholesterol than hCRISP3. The secretion profile of different CRISPs also showed that the ratio of secreted to cell-associated proteins was highest for hCRISP3. CONCLUSION Our study identifies PMCA4b as a target of multiple mammalian CRISPs and unravels a new role of CRISPs in regulating calcium homeostasis. Differences in the interaction of different CRISPs with cholesterol may regulate their enrichment in the lipid rafts and redistribution in the membrane post-capacitation, thereby affecting their interaction with PMCA4b.
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Affiliation(s)
- Vaidehi Miya
- Division of Cellular and Structural Biology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, India
| | - Chandan Kumar
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, India
| | - Ananya A Breed
- Division of Cellular and Structural Biology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, India
| | - Bhakti R Pathak
- Division of Cellular and Structural Biology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai, India
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16
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Bepler T, Barrera MD, Rooney MT, Xiong Y, Kuang H, Goodell E, Goodwin MJ, Harbron E, Fu R, Mihailescu M, Narayanan A, Cotten ML. Antiviral activity of the host defense peptide piscidin 1: investigating a membrane-mediated mode of action. Front Chem 2024; 12:1379192. [PMID: 38988727 PMCID: PMC11233706 DOI: 10.3389/fchem.2024.1379192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024] Open
Abstract
Outbreaks of viral diseases are on the rise, fueling the search for antiviral therapeutics that act on a broad range of viruses while remaining safe to human host cells. In this research, we leverage the finding that the plasma membranes of host cells and the lipid bilayers surrounding enveloped viruses differ in lipid composition. We feature Piscidin 1 (P1), a cationic host defense peptide (HDP) that has antimicrobial effects and membrane activity associated with its N-terminal region where a cluster of aromatic residues and copper-binding motif reside. While few HDPs have demonstrated antiviral activity, P1 acts in the micromolar range against several enveloped viruses that vary in envelope lipid composition. Notably, it inhibits HIV-1, a virus that has an envelope enriched in cholesterol, a lipid associated with higher membrane order and stability. Here, we first document through plaque assays that P1 boasts strong activity against SARS-CoV-2, which has an envelope low in cholesterol. Second, we extend previous studies done with homogeneous bilayers and devise cholesterol-containing zwitterionic membranes that contain the liquid disordered (Ld; low in cholesterol) and ordered (Lo, rich in cholesterol) phases. Using dye leakage assays and cryo-electron microscopy on vesicles, we show that P1 has dramatic permeabilizing capability on the Lo/Ld, an effect matched by a strong ability to aggregate, fuse, and thin the membranes. Differential scanning calorimetry and NMR experiments demonstrate that P1 mixes the lipid content of vesicles and alters the stability of the Lo. Structural studies by NMR indicate that P1 interacts with the Lo/Ld by folding into an α-helix that lies parallel to the membrane surface. Altogether, these results show that P1 is more disruptive to phase-separated than homogenous cholesterol-containing bilayers, suggesting an ability to target domain boundaries. Overall, this multi-faceted research highlights how a peptide that interacts strongly with membranes through an aromatic-rich N-terminal motif disrupt viral envelope mimics. This represents an important step towards the development of novel peptides with broad-spectrum antiviral activity.
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Affiliation(s)
- Tristan Bepler
- New York Structural Biology Center, New York, NY, United States
| | - Michael D. Barrera
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Mary T. Rooney
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, United States
| | - Evan Goodell
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Matthew J. Goodwin
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Elizabeth Harbron
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Aarthi Narayanan
- Department of Biology, George Mason University, Manassas, VA, United States
| | - Myriam L. Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
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17
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Lihan M, Tajkhorshid E. Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. J Chem Inf Model 2024; 64:4822-4834. [PMID: 38844760 DOI: 10.1021/acs.jcim.4c00619] [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: 06/25/2024]
Abstract
Cholesterol (CHL) plays an integral role in modulating the function and activity of various mammalian membrane proteins. Due to the slow dynamics of lipids, conventional computational studies of protein-CHL interactions rely on either long-time scale atomistic simulations or coarse-grained approximations to sample the process. A highly mobile membrane mimetic (HMMM) has been developed to enhance lipid diffusion and thus used to facilitate the investigation of lipid interactions with peripheral membrane proteins and, with customized in silico solvents to replace phospholipid tails, with integral membrane proteins. Here, we report an updated HMMM model that is able to include CHL, a nonphospholipid component of the membrane, henceforth called HMMM-CHL. To this end, we had to optimize the effect of the customized solvents on CHL behavior in the membrane. Furthermore, the new solvent is compatible with simulations using force-based switching protocols. In the HMMM-CHL, both improved CHL dynamics and accelerated lipid diffusion are integrated. To test the updated model, we have applied it to the characterization of protein-CHL interactions in two membrane protein systems, the human β2-adrenergic receptor (β2AR) and the mitochondrial voltage-dependent anion channel 1 (VDAC-1). Our HMMM-CHL simulations successfully identified CHL binding sites and captured detailed CHL interactions in excellent consistency with experimental data as well as other simulation results, indicating the utility of the improved model in applications where an enhanced sampling of protein-CHL interactions is desired.
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Affiliation(s)
- Muyun Lihan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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18
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Zhekova HR, Ramirez Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. Biophys J 2024; 123:1705-1721. [PMID: 38760929 PMCID: PMC11214021 DOI: 10.1016/j.bpj.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 04/09/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024] Open
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO3-, CO32-, Cl-, Na+, K+, NH3, and H+, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl-/HCO3- exchanger) and NBCe1 (Na+-CO32-cotransporter). Previous computational studies of the outward-facing state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1, and NDCBE (an Na+-CO32-/Cl- exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. The recently resolved inward-facing state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, phosphatidylcholine, and sphingomyelin in the three studied proteins, and their potential roles in the SLC4 transport function, conformational transition, and protein dimerization are discussed.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Daniel P Ramirez Echemendía
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexander Pushkin
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Ira Kurtz
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Brain Research Institute, University of California, Los Angeles, Los Angeles, California.
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19
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572875. [PMID: 38187772 PMCID: PMC10769365 DOI: 10.1101/2023.12.21.572875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In C. elegans, inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNA interference-defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the cholesterol uptake family (ChUP). Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products - hSIDT1 and hSIDT2 - mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain (ECD) of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain (TMD) exists as two modules - a flexible lipid binding domain (LBD) and a rigid TMD core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in cholesterol uptake (ChUP) family members.
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Affiliation(s)
- Vikas Navratna
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Arvind Kumar
- Thermo Fisher Scientific, Waltham, Massachusetts, 02451, United States
| | - Jaimin K. Rana
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, Michigan, 48109, United States
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20
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Delgado-Coello B, Luna-Reyes I, Méndez-Acevedo KM, Bravo-Martínez J, Montalvan-Sorrosa D, Mas-Oliva J. Analysis of cholesterol-recognition motifs of the plasma membrane Ca 2+-ATPase. J Bioenerg Biomembr 2024; 56:205-219. [PMID: 38436904 PMCID: PMC11116186 DOI: 10.1007/s10863-024-10010-5] [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] [Received: 01/09/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
The plasma membrane Ca2+-ATPase (PMCA) is crucial for the fine tuning of intracellular calcium levels in eukaryotic cells. In this study, we show the presence of CARC sequences in all human and rat PMCA isoforms and we performed further analysis by molecular dynamics simulations. This analysis focuses on PMCA1, containing three CARC motifs, and PMCA4, with four CARC domains. In PMCA1, two CARC motifs reside within transmembrane domains, while the third is situated at the intracellular interface. The simulations depict more stable RMSD values and lower RMSF fluctuations in the presence of cholesterol, emphasizing its potential stabilizing effect. In PMCA4, a distinct dynamic was found. Notably, the total energy differences between simulations with cholesterol and phospholipids are pronounced in PMCA4 compared to PMCA1. RMSD values for PMCA4 indicate a more energetically favorable conformation in the presence of cholesterol, suggesting a robust interaction between CARCs and this lipid in the membranes. Furthermore, RMSF analysis for CARCs in both PMCA isoforms exhibit lower values in the presence of cholesterol compared to POPC alone. The analysis of H-bond occupancy and total energy values strongly suggests the potential interaction of CARCs with cholesterol. Given the crucial role of PMCAs in physiological calcium regulation and their involvement in diverse pathological processes, this study underscores the significance of CARC motifs and their interaction with cholesterol in elucidating PMCA function. These insights into the energetic preferences associated with CARC-cholesterol interactions offer valuable implications for understanding PMCA function in maintaining calcium homeostasis and addressing potential associated pathologies.
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Affiliation(s)
- Blanca Delgado-Coello
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apdo. Postal 70-243, Ciudad de México, C.P. 04510, México.
| | - Ismael Luna-Reyes
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apdo. Postal 70-243, Ciudad de México, C.P. 04510, México
| | - Kevin M Méndez-Acevedo
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apdo. Postal 70-243, Ciudad de México, C.P. 04510, México
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Jorge Bravo-Martínez
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Danai Montalvan-Sorrosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jaime Mas-Oliva
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apdo. Postal 70-243, Ciudad de México, C.P. 04510, México.
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21
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Beverley KM, Barbera N, Levitan I. Dual pattern of cholesterol-induced decoupling of residue-residue interactions of Kir2.2. J Struct Biol 2024; 216:108091. [PMID: 38641256 DOI: 10.1016/j.jsb.2024.108091] [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: 07/13/2023] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024]
Abstract
Cholesterol is a negative regulator of a variety of ion channels. We have previously shown that cholesterol suppresses Kir2.2 channels via residue-residue uncoupling on the inter-subunit interfaces within the close state of the channels (3JYC). In this study, we extend this analysis to the other known structure of Kir2.2 that is closer to the open state of Kir2.2 channels (3SPI) and provide additional analysis of the residue distances between the uncoupled residues and cholesterol binding domains in the two conformation states of the channels. We found that the general phenomenon of cholesterol binding leading to uncoupling between specific residues is conserved in both channel states but the specific pattern of the uncoupling residues is distinct between the two states and implies different mechanisms. Specifically, we found that cholesterol binding in the 3SPI state results in an uncoupling of residues in three distinct regions; the transmembrane domain, membrane-cytosolic interface, and the cytosolic domain, with the first two regions forming an envelope around PI(4,5)P2 and cholesterol binding sites and the distal region overlapping with the subunit-subunit interface characterized in our previous study of the disengaged state. We also found that this uncoupling is dependent upon the number of cholesterol molecules bound to the channel. We further generated a mutant channel Kir2.2P187V with a single point mutation in a residue proximal to the PI(4,5)P2 binding site, which is predicted to be uncoupled from other residues in its vicinity upon cholesterol binding and found that this mutation abrogates the sensitivity of Kir2.2 to cholesterol changes in the membrane. These findings suggest that cholesterol binding to this conformation state of Kir2.2 channels may destabilize the PI(4,5)P2 interactions with the channels while in the disengaged state the destabilization occurs where the subunits interact. These findings give insight into the structural mechanistic basis for the functional effects of cholesterol binding to the Kir2.2 channel.
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Affiliation(s)
- Katie M Beverley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Nicolas Barbera
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; Center for Public Health Genomics, Department of Biomedical Engineering, School of Engineering &Applied Science, University of Virginia, Charlottesville, VA 22904, USA
| | - Irena Levitan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
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22
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Hirano Y, Ohto U, Ichi I, Sato R, Miyake K, Shimizu T. Cryo-EM analysis reveals human SID-1 transmembrane family member 1 dynamics underlying lipid hydrolytic activity. Commun Biol 2024; 7:664. [PMID: 38811802 PMCID: PMC11137008 DOI: 10.1038/s42003-024-06346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Two mammalian homologs of systemic RNA interference defective protein 1 (SID-1) (SIDT1/2) are suggested to function as double-stranded RNA (dsRNA) transporters for extracellular dsRNA uptake or for release of incorporated dsRNA from lysosome to cytoplasm. SIDT1/2 is also suggested to be involved in cholesterol transport and lipid metabolism. Here, we determine the cryo-electron microscopy structures of human SIDT1, homodimer in a side-by-side arrangement, with two distinct conformations, the cholesterol-bound form and the unbound form. Our structures reveal that the membrane-spanning region of SIDT1 harbors conserved histidine and aspartate residues coordinating to putative zinc ion, in a structurally similar manner to alkaline ceramidases or adiponectin receptors that require zinc for ceramidase activity. We identify that SIDT1 has a ceramidase activity that is attenuated by cholesterol binding. Observations from two structures suggest that cholesterol molecules serve as allosteric regulator that binds the transmembrane region of SIDT1 and induces the conformation change and the reorientation of the catalytic residues. This study represents a contribution to the elucidation of the cholesterol-mediated mechanisms of lipid hydrolytic activity and RNA transport in the SID-1 family proteins.
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Affiliation(s)
- Yoshinori Hirano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ikuyo Ichi
- Natural Science Division, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610, Japan
- Institute for Human Life Innovation, Faculty of Core Research, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Ryota Sato
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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23
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Jalalypour F, Howard RJ, Lindahl E. Allosteric Cholesterol Site in Glycine Receptors Characterized through Molecular Simulations. J Phys Chem B 2024; 128:4996-5007. [PMID: 38747451 PMCID: PMC11129184 DOI: 10.1021/acs.jpcb.4c01703] [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: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/24/2024]
Abstract
Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the glycine agonist, interactions with lipids and other compounds in the surrounding membrane environment modulate their function, but molecular details of these interactions remain unclear, in particular, for cholesterol. Here, we report coarse-grained simulations in a model neuronal membrane for three zebrafish glycine receptor structures representing apparent resting, open, and desensitized states. We then converted the systems to all-atom models to examine detailed lipid interactions. Cholesterol bound to the receptor at an outer-leaflet intersubunit site, with a preference for the open and desensitized versus resting states, indicating that it can bias receptor function. Finally, we used short atomistic simulations and iterative amino acid perturbations to identify residues that may mediate allosteric gating transitions. Frequent cholesterol contacts in atomistic simulations clustered with residues identified by perturbation analysis and overlapped with mutations influencing channel function and pathology. Cholesterol binding at this site was also observed in a recently reported pig heteromeric glycine receptor. These results indicate state-dependent lipid interactions relevant to allosteric transitions of glycine receptors, including specific amino acid contacts applicable to biophysical modeling and pharmaceutical design.
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Affiliation(s)
- Farzaneh Jalalypour
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | - Rebecca J. Howard
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Erik Lindahl
- Science
for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 17121 Solna, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
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24
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Bell TA, Luce BE, Hakim P, Ananda VY, Dardari H, Nguyen TH, Monshizadeh A, Chao LH. Prominin 1 and Tweety Homology 1 both induce extracellular vesicle formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.566258. [PMID: 37986829 PMCID: PMC10659291 DOI: 10.1101/2023.11.08.566258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Prominin-1 (Prom1) is a five-transmembrane-pass integral membrane protein that associates with curved regions of the plasma membrane. Prom1 interacts with membrane cholesterol and actively remodels the plasma membrane. Membrane bending activity is particularly evident in photoreceptors, where Prom1 loss-of-function mutations cause failure of outer segment homeostasis, leading to cone-rod retinal dystrophy (CRRD). The Tweety Homology (Ttyh) protein family has been proposed to be homologous to Prominin, but it is not known whether Ttyh proteins have an analogous membrane-bending function. Here, we characterize the membrane-bending activity of human Prom1 and Ttyh1 in native bilayer membranes. We find that Prom1 and Ttyh1 both induce formation of extracellular vesicles (EVs) in cultured mammalian cells and that the EVs produced are physically similar. Ttyh1 is more abundant in EV membranes than Prom1 and produces EVs with membranes that are more tubulated than Prom1 EVs. We further show that Prom1 interacts more stably with membrane cholesterol than Ttyh1 and that this may contribute to membrane bending inhibition in Prom1 EVs. Intriguingly, a loss-of-function mutation in Prom1 associated with CRRD induces particularly stable cholesterol binding. These experiments provide mechanistic insight into Prominin function in CRRD and suggest that Prom and Ttyh belong to a single family of functionally related membrane-bending, EV-generating proteins.
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Affiliation(s)
- Tristan A. Bell
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115
- Current Address: Generate Biomedicines, 101 South St, Somerville, MA, 02143
| | - Bridget E. Luce
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Pusparanee Hakim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Virly Y. Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Hiba Dardari
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Tran H. Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Arezu Monshizadeh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Luke H. Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115
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25
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Chiu PL, Orjuela JD, de Groot BL, Aponte-Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.16.540959. [PMID: 37292626 PMCID: PMC10245776 DOI: 10.1101/2023.05.16.540959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
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26
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Sengupta S, Yaeger JD, Schultz MM, Francis KR. Dishevelled localization and function are differentially regulated by structurally distinct sterols. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.593701. [PMID: 38798572 PMCID: PMC11118412 DOI: 10.1101/2024.05.14.593701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The Dishevelled (DVL) family of proteins form supramolecular protein and lipid complexes at the cytoplasmic interface of the plasma membrane to regulate tissue patterning, proliferation, cell polarity, and oncogenic processes through DVL-dependent signaling, such as Wnt/β-catenin. While DVL binding to cholesterol is required for its membrane association, the specific structural requirements and cellular impacts of DVL-sterol association are unclear. We report that intracellular sterols which accumulate within normal and pathological conditions cause aberrant DVL activity. In silico and molecular analyses suggested orientation of the β- and α-sterol face within the DVL-PDZ domain regulates DVL-sterol binding. Intracellular accumulation of naturally occurring sterols impaired DVL2 plasma membrane association, inducing DVL2 nuclear localization via Foxk2. Changes to intracellular sterols also selectively impaired DVL2 protein-protein interactions This work identifies sterol specificity as a regulator of DVL signaling, suggests intracellular sterols cause distinct impacts on DVL activity, and supports a role for intracellular sterol homeostasis in cell signaling.
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Affiliation(s)
- Sonali Sengupta
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD, 57104, USA
| | - Jazmine D.W. Yaeger
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD, 57104, USA
| | - Maycie M. Schultz
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD, 57104, USA
| | - Kevin R. Francis
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD, 57104, USA
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, SD, 57105, USA
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27
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Enkavi G, Girych M, Moliner R, Vattulainen I, Castrén E. TrkB transmembrane domain: bridging structural understanding with therapeutic strategy. Trends Biochem Sci 2024; 49:445-456. [PMID: 38433044 DOI: 10.1016/j.tibs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024]
Abstract
TrkB (neuronal receptor tyrosine kinase-2, NTRK2) is the receptor for brain-derived neurotrophic factor (BDNF) and is a critical regulator of activity-dependent neuronal plasticity. The past few years have witnessed an increasing understanding of the structure and function of TrkB, including its transmembrane domain (TMD). TrkB interacts with membrane cholesterol, which bidirectionally regulates TrkB signaling. Additionally, TrkB has recently been recognized as a binding target of antidepressant drugs. A variety of different antidepressants, including typical and rapid-acting antidepressants, as well as psychedelic compounds, act as allosteric potentiators of BDNF signaling through TrkB. This suggests that TrkB is the common target of different antidepressant compounds. Although more research is needed, current knowledge suggests that TrkB is a promising target for further drug development.
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Affiliation(s)
- Giray Enkavi
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Rafael Moliner
- Neuroscience Center/HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Eero Castrén
- Neuroscience Center/HiLIFE, University of Helsinki, Helsinki, Finland.
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28
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Hutchinson K, Schlessinger A. Comprehensive Characterization of LAT1 Cholesterol-Binding Sites. J Chem Theory Comput 2024; 20:3349-3358. [PMID: 38597304 DOI: 10.1021/acs.jctc.3c01391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The human L-type amino acid transporter 1 (LAT1; SLC7A5), is an amino acid exchanger protein, primarily found in the blood-brain barrier, placenta, and testis, where it plays a key role in amino acid homeostasis. Cholesterol is an essential lipid that has been highlighted to play a role in regulating the activity of membrane transporters, such as LAT1, yet little is known about the molecular mechanisms driving this phenomenon. Here we perform a comprehensive computational analysis to investigate cholesterol's role in LAT1 structure and function, focusing on four cholesterol-binding sites (CHOL1-4) identified in a recent LAT1-apo inward-open conformation cryo-EM structure. Through a series of independent molecular dynamics (MD) simulations, molecular docking, MM/GBSA free energy calculations, and other analysis tools, we explored the interactions between LAT1 and cholesterol. Our findings suggest that CHOL3 forms the most stable and favorable interactions with LAT1. Principal component analysis (PCA) and center of mass (COM) distance assessments show that CHOL3 binding stabilizes the inward-open state of LAT1 by preserving the spatial arrangement of the hash and bundle domains. Additionally, we propose an alternative cholesterol-binding site for originally assigned CHOL1. Overall, this study improves the understanding of cholesterol's modulatory effect on LAT1 and proposes candidate sites for the discovery of future allosteric ligands with rational design.
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Affiliation(s)
- Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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29
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Isu UH, Badiee SA, Polasa A, Tabari SH, Derakhshani-Molayousefi M, Moradi M. Cholesterol Dependence of the Conformational Changes in Metabotropic Glutamate Receptor 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589854. [PMID: 38659864 PMCID: PMC11042357 DOI: 10.1101/2024.04.17.589854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Metabotropic glutamate receptors (mGluRs) are class C G protein-coupled receptors that function as obligate dimers in regulating neurotransmission and synaptic plasticity in the central nervous system. The mGluR1 subtype has been shown to be modulated by the membrane lipid environment, particularly cholesterol, though the molecular mechanisms remain elusive. In this study, we employed all-atom molecular dynamics simulations to investigate the effects of cholesterol on the conformational dynamics of the mGluR1 seven-transmembrane (7TM) domain in an inactive state model. Simulations were performed with three different cholesterol concentrations (0%, 10%, and 25%) in a palmitoyl-oleoyl phosphatidylcholine (POPC) lipid bilayer system. Our results demonstrate that cholesterol induces conformational changes in the mGluR1 dimer more significantly than in the individual protomers. Notably, cholesterol modulates the dynamics and conformations of the TM1 and TM2 helices at the dimer interface. Interestingly, an intermediate cholesterol concentration of 10% elicits more pronounced conformational changes compared to both cholesterol-depleted (0%) and cholesterol-enriched (25%) systems. Specific electrostatic interaction unique to the 10% cholesterol system further corroborate these conformational differences. Given the high sequence conservation of the 7TM domains across mGluR subtypes, the cholesterol-dependent effects observed in mGluR1 are likely applicable to other members of this receptor family. Our findings provide atomistic insights into how cholesterol modulates the conformational landscape of mGluRs, which could impact their function and signaling mechanisms.
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30
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Lingwood C. Is cholesterol both the lock and key to abnormal transmembrane signals in Autism Spectrum Disorder? Lipids Health Dis 2024; 23:114. [PMID: 38643132 PMCID: PMC11032007 DOI: 10.1186/s12944-024-02075-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 04/22/2024] Open
Abstract
Disturbances in cholesterol homeostasis have been associated with ASD. Lipid rafts are central in many transmembrane signaling pathways (including mTOR) and changes in raft cholesterol content affect their order function. Cholesterol levels are controlled by several mechanisms, including endoplasmic reticulum associated degradation (ERAD) of the rate limiting HMGCoA reductase. A new approach to increase cholesterol via temporary ERAD blockade using a benign bacterial toxin-derived competitor for the ERAD translocon is suggested.A new lock and key model for cholesterol/lipid raft dependent signaling is proposed in which the rafts provide both the afferent and efferent 'tumblers' across the membrane to allow 'lock and key' receptor transmembrane signals.
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Affiliation(s)
- Clifford Lingwood
- Division of Molecular Medicine, Research Institute, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Departments of Biochemistry and Laboratory Medicine & Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada.
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31
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Kuwashima Y, Yanagawa M, Maekawa M, Abe M, Sako Y, Arita M. TRPV4-dependent Ca 2+ influx determines cholesterol dynamics at the plasma membrane. Biophys J 2024; 123:867-884. [PMID: 38433447 PMCID: PMC10995426 DOI: 10.1016/j.bpj.2024.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024] Open
Abstract
The activities of the transient receptor potential vanilloid 4 (TRPV4), a Ca2+-permeable nonselective cation channel, are controlled by its surrounding membrane lipids (e.g., cholesterol, phosphoinositides). The transmembrane region of TRPV4 contains a cholesterol recognition amino acid consensus (CRAC) motif and its inverted (CARC) motif located in the plasmalemmal cytosolic leaflet. TRPV4 localizes in caveolae, a bulb-shaped cholesterol-rich domain at the plasma membrane. Here, we visualized the spatiotemporal interactions between TRPV4 and cholesterol at the plasma membrane in living cells by dual-color single-molecule imaging using total internal reflection fluorescence microscopy. To this aim, we labeled cholesterol at the cytosolic leaflets of the plasma membrane using a cholesterol biosensor, D4H. Our single-molecule tracking analysis showed that the TRPV4 molecules colocalize with D4H-accessible cholesterol molecules mainly in the low fluidity membrane domains in which both molecules are highly clustered. Colocalization of TRPV4 and D4H-accessible cholesterol was observed both inside and outside of caveolae. Agonist-evoked TRPV4 activation remarkably decreased colocalization probability and association rate between TRPV4 and D4H-accessible cholesterol molecules. Interestingly, upon TRPV4 activation, the particle density of D4H-accessible cholesterol molecules was decreased and the D4H-accessible cholesterol molecules in the fast-diffusing state were increased at the plasma membrane. The introduction of skeletal dysplasia-associated R616Q mutation into the CRAC/CARC motif of TRPV4, which reduced the interaction with cholesterol clusters, could not alter the D4H-accessible cholesterol dynamics. Mechanistically, TRPV4-mediated Ca2+ influx and the C-terminal calmodulin-binding site of TRPV4 are essential for modulating the plasmalemmal D4H-accessible cholesterol dynamics. We propose that TRPV4 remodels its surrounding plasmalemmal environment by manipulating cholesterol dynamics through Ca2+ influx.
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Affiliation(s)
- Yutaro Kuwashima
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan; Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Masashi Maekawa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan.
| | - Makoto Arita
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan; Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan.
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32
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Zhang BC, Laursen MF, Hu L, Hazrati H, Narita R, Jensen LS, Hansen AS, Huang J, Zhang Y, Ding X, Muyesier M, Nilsson E, Banasik A, Zeiler C, Mogensen TH, Etzerodt A, Agger R, Johannsen M, Kofod-Olsen E, Paludan SR, Jakobsen MR. Cholesterol-binding motifs in STING that control endoplasmic reticulum retention mediate anti-tumoral activity of cholesterol-lowering compounds. Nat Commun 2024; 15:2760. [PMID: 38553448 PMCID: PMC10980718 DOI: 10.1038/s41467-024-47046-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
The cGAS-STING pathway plays a crucial role in anti-tumoral responses by activating inflammation and reprogramming the tumour microenvironment. Upon activation, STING traffics from the endoplasmic reticulum (ER) to Golgi, allowing signalling complex assembly and induction of interferon and inflammatory cytokines. Here we report that cGAMP stimulation leads to a transient decline in ER cholesterol levels, mediated by Sterol O-Acyltransferase 1-dependent cholesterol esterification. This facilitates ER membrane curvature and STING trafficking to Golgi. Notably, we identify two cholesterol-binding motifs in STING and confirm their contribution to ER-retention of STING. Consequently, depletion of intracellular cholesterol levels enhances STING pathway activation upon cGAMP stimulation. In a preclinical tumour model, intratumorally administered cholesterol depletion therapy potentiated STING-dependent anti-tumoral responses, which, in combination with anti-PD-1 antibodies, promoted tumour remission. Collectively, we demonstrate that ER cholesterol sets a threshold for STING signalling through cholesterol-binding motifs in STING and we propose that this could be exploited for cancer immunotherapy.
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Affiliation(s)
- Bao-Cun Zhang
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Marlene F Laursen
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Lili Hu
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Hossein Hazrati
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
- Department of Forensic Medicine, Aarhus University, DK-8200, Aarhus N, Denmark
| | - Ryo Narita
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Lea S Jensen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Aida S Hansen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jinrong Huang
- Department of Biology, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - Yan Zhang
- Department of Engineering, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Xiangning Ding
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | | | - Emil Nilsson
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Agnieszka Banasik
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Christina Zeiler
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, DK-8200, Aarhus N, Denmark
| | - Anders Etzerodt
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Ralf Agger
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University, DK-8200, Aarhus N, Denmark
| | - Emil Kofod-Olsen
- Department of Health Science and Technology, Aalborg University, DK-9220, Aalborg, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Martin R Jakobsen
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C, Denmark.
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33
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Pleskač P, Fargeas CA, Veselska R, Corbeil D, Skoda J. Emerging roles of prominin-1 (CD133) in the dynamics of plasma membrane architecture and cell signaling pathways in health and disease. Cell Mol Biol Lett 2024; 29:41. [PMID: 38532366 DOI: 10.1186/s11658-024-00554-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Prominin-1 (CD133) is a cholesterol-binding membrane glycoprotein selectively associated with highly curved and prominent membrane structures. It is widely recognized as an antigenic marker of stem cells and cancer stem cells and is frequently used to isolate them from biological and clinical samples. Recent progress in understanding various aspects of CD133 biology in different cell types has revealed the involvement of CD133 in the architecture and dynamics of plasma membrane protrusions, such as microvilli and cilia, including the release of extracellular vesicles, as well as in various signaling pathways, which may be regulated in part by posttranslational modifications of CD133 and its interactions with a variety of proteins and lipids. Hence, CD133 appears to be a master regulator of cell signaling as its engagement in PI3K/Akt, Src-FAK, Wnt/β-catenin, TGF-β/Smad and MAPK/ERK pathways may explain its broad action in many cellular processes, including cell proliferation, differentiation, and migration or intercellular communication. Here, we summarize early studies on CD133, as they are essential to grasp its novel features, and describe recent evidence demonstrating that this unique molecule is involved in membrane dynamics and molecular signaling that affects various facets of tissue homeostasis and cancer development. We hope this review will provide an informative resource for future efforts to elucidate the details of CD133's molecular function in health and disease.
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Affiliation(s)
- Petr Pleskač
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Christine A Fargeas
- Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
- Tissue Engineering Laboratories, Medizinische Fakultät der Technischen Universität Dresden, Dresden, Germany
| | - Renata Veselska
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Denis Corbeil
- Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.
- Tissue Engineering Laboratories, Medizinische Fakultät der Technischen Universität Dresden, Dresden, Germany.
| | - Jan Skoda
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.
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Jiang W, Jin WL, Xu AM. Cholesterol metabolism in tumor microenvironment: cancer hallmarks and therapeutic opportunities. Int J Biol Sci 2024; 20:2044-2071. [PMID: 38617549 PMCID: PMC11008265 DOI: 10.7150/ijbs.92274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/27/2024] [Indexed: 04/16/2024] Open
Abstract
Cholesterol is crucial for cell survival and growth, and dysregulation of cholesterol homeostasis has been linked to the development of cancer. The tumor microenvironment (TME) facilitates tumor cell survival and growth, and crosstalk between cholesterol metabolism and the TME contributes to tumorigenesis and tumor progression. Targeting cholesterol metabolism has demonstrated significant antitumor effects in preclinical and clinical studies. In this review, we discuss the regulatory mechanisms of cholesterol homeostasis and the impact of its dysregulation on the hallmarks of cancer. We also describe how cholesterol metabolism reprograms the TME across seven specialized microenvironments. Furthermore, we discuss the potential of targeting cholesterol metabolism as a therapeutic strategy for tumors. This approach not only exerts antitumor effects in monotherapy and combination therapy but also mitigates the adverse effects associated with conventional tumor therapy. Finally, we outline the unresolved questions and suggest potential avenues for future investigations on cholesterol metabolism in relation to cancer.
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Affiliation(s)
- Wen Jiang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, P. R. China
| | - Wei-Lin Jin
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou 730000, P. R. China
| | - A-Man Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, P. R. China
- Anhui Public Health Clinical Center, Hefei 230022, P. R. China
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Ayuyan AG, Cherny VV, Chaves G, Musset B, Cohen FS, DeCoursey TE. Interaction with stomatin directs human proton channels into cholesterol-dependent membrane domains. Biophys J 2024:S0006-3495(24)00168-1. [PMID: 38444158 DOI: 10.1016/j.bpj.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/24/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024] Open
Abstract
Many membrane proteins are modulated by cholesterol. Here we report profound effects of cholesterol depletion and restoration on the human voltage-gated proton channel, hHV1, in excised patches but negligible effects in the whole-cell configuration. Despite the presence of a putative cholesterol-binding site, a CARC motif in hHV1, mutation of this motif did not affect cholesterol effects. The murine HV1 lacks a CARC sequence but displays similar cholesterol effects. These results argue against a direct effect of cholesterol on the HV1 protein. However, the data are fully explainable if HV1 preferentially associates with cholesterol-dependent lipid domains, or "rafts." The rafts would be expected to concentrate in the membrane/glass interface and to be depleted from the electrically accessible patch membrane. This idea is supported by evidence that HV1 channels can diffuse between seal and patch membranes when suction is applied. Simultaneous truncation of the large intracellular N and C termini of hHV1 greatly attenuated the cholesterol effect, but C truncation alone did not; this suggests that the N terminus is the region of attachment to lipid domains. Searching for abundant raft-associated proteins led to stomatin. Co-immunoprecipitation experiment results were consistent with hHV1 binding to stomatin. The stomatin-mediated association of HV1 with cholesterol-dependent lipid domains provides a mechanism for cells to direct HV1 to subcellular locations where it is needed, such as the phagosome in leukocytes.
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Affiliation(s)
- Artem G Ayuyan
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois.
| | - Vladimir V Cherny
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois
| | - Gustavo Chaves
- Institut für Physiologie, Pathophysiologie und Biophysik, CPPB, Paracelsus Medical University, Nürnberg, Germany
| | - Boris Musset
- Institut für Physiologie, Pathophysiologie und Biophysik, CPPB, Paracelsus Medical University, Nürnberg, Germany
| | - Fredric S Cohen
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois
| | - Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University, Chicago, Illinois.
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Kattar A, V. Lage E, Casas M, Concheiro A, Alvarez-Lorenzo C. Langmuir monolayer studies of non-ionic surfactants and DOTMA for the design of ophthalmic niosomes. Heliyon 2024; 10:e25887. [PMID: 38380035 PMCID: PMC10877279 DOI: 10.1016/j.heliyon.2024.e25887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
The worldwide increase in diabetes entails a rise in associated diseases, with diabetic retinopathy on the forefront of the ocular complications. To overcome the challenges posed by ocular barriers, self-assembled nanocarriers have gathered increasing attention in recent years, with niosomes revealing themselves to be suitable for the delivery of a variety of drugs. This study investigated the mechanical properties of Langmuir monolayers comprising cholesterol, Tween 60, and 1,2-di-O-octadecenyl-3-trimethylammonium propane (DOTMA), both individually and in binary and ternary systems. The cholesterol monolayer was characterized by an L-shaped isotherm, reflecting two surface aggregation states. Tween 60 exhibited expanded conformation and progressive aggregation, transitioning through a phase change. The addition of cholesterol to Tween 60 resulted in a subtle reduction in surface compressional modulus. The compression isotherms highlighted the stabilizing effect of cholesterol on the monolayer, affecting the film's resistance to compression. The introduction of DOTMA in Tween 60 monolayers revealed concentration-dependent effects, where the compression resistance of the film was proportional to DOTMA concentration. Ternary systems of cholesterol, DOTMA and Tween 60 exhibited unique behavior, with DOTMA enhancing film stability and cholesterol modulating this effect. Temperature and subphase ionic strength variations further exacerbated the effects of DOTMA concentration. Brewster Angle Microscopy confirmed the absence of microdomains in the compressed monolayer, supporting the hypothesis of a monolayer collapse. Overall, the research provided valuable insights into the intricate interactions and mechanical behavior of these surfactant systems and the feasibility of obtaining cationic niosome-based drug delivery.
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Affiliation(s)
- Axel Kattar
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma Group (GI-1645), Facultad de Farmacia, and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Instituto de Materiales (iMATUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Emílio V. Lage
- Department of Physical Chemistry, Biomembranes Lab, Faculty of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Matilde Casas
- Instituto de Materiales (iMATUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Department of Physical Chemistry, Biomembranes Lab, Faculty of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Angel Concheiro
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma Group (GI-1645), Facultad de Farmacia, and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Instituto de Materiales (iMATUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma Group (GI-1645), Facultad de Farmacia, and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Instituto de Materiales (iMATUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Hawes E, Claxton D, Oeser J, O’Brien R. Identification of structural motifs critical for human G6PC2 function informed by sequence analysis and an AlphaFold2-predicted model. Biosci Rep 2024; 44:BSR20231851. [PMID: 38095063 PMCID: PMC10776900 DOI: 10.1042/bsr20231851] [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] [Received: 10/26/2023] [Revised: 11/22/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
G6PC2 encodes a glucose-6-phosphatase (G6Pase) catalytic subunit, primarily expressed in pancreatic islet β cells, which modulates the sensitivity of insulin secretion to glucose and thereby regulates fasting blood glucose (FBG). Mutational analyses were conducted to validate an AlphaFold2 (AF2)-predicted structure of human G6PC2 in conjunction with a novel method to solubilize and purify human G6PC2 from a heterologous expression system. These analyses show that residues forming a predicted intramolecular disulfide bond are essential for G6PC2 expression and that residues forming part of a type 2 phosphatidic acid phosphatase (PAP2) motif are critical for enzyme activity. Additional mutagenesis shows that residues forming a predicted substrate cavity modulate enzyme activity and substrate specificity and residues forming a putative cholesterol recognition amino acid consensus (CRAC) motif influence protein expression or enzyme activity. This CRAC motif begins at residue 219, the site of a common G6PC2 non-synonymous single-nucleotide polymorphism (SNP), rs492594 (Val219Leu), though the functional impact of this SNP is disputed. In microsomal membrane preparations, the L219 variant has greater activity than the V219 variant, but this difference disappears when G6PC2 is purified in detergent micelles. We hypothesize that this was due to a differential association of the two variants with cholesterol. This concept was supported by the observation that the addition of cholesteryl hemi-succinate to the purified enzymes decreased the Vmax of the V219 and L219 variants ∼8-fold and ∼3 fold, respectively. We anticipate that these observations should support the rational development of G6PC2 inhibitors designed to lower FBG.
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Affiliation(s)
- Emily M. Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - Derek P. Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, U.S.A
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Beverley KM, Levitan I. Cholesterol regulation of mechanosensitive ion channels. Front Cell Dev Biol 2024; 12:1352259. [PMID: 38333595 PMCID: PMC10850386 DOI: 10.3389/fcell.2024.1352259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
The purpose of this review is to evaluate the role of cholesterol in regulating mechanosensitive ion channels. Ion channels discussed in this review are sensitive to two types of mechanical signals, fluid shear stress and/or membrane stretch. Cholesterol regulates the channels primarily in two ways: 1) indirectly through localizing the channels into cholesterol-rich membrane domains where they interact with accessory proteins and/or 2) direct binding of cholesterol to the channel at specified putative binding sites. Cholesterol may also regulate channel function via changes of the biophysical properties of the membrane bilayer. Changes in cholesterol affect both mechanosensitivity and basal channel function. We focus on four mechanosensitive ion channels in this review Piezo, Kir2, TRPV4, and VRAC channels. Piezo channels were shown to be regulated by auxiliary proteins that enhance channel function in high cholesterol domains. The direct binding mechanism was shown in Kir2.1 and TRPV4 where cholesterol inhibits channel function. Finally, cholesterol regulation of VRAC was attributed to changes in the physical properties of lipid bilayer. Additional studies should be performed to determine the physiological implications of these sterol effects in complex cellular environments.
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Affiliation(s)
- Katie M. Beverley
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Irena Levitan
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
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Area-Gomez E, Schon EA. Towards a Unitary Hypothesis of Alzheimer's Disease Pathogenesis. J Alzheimers Dis 2024; 98:1243-1275. [PMID: 38578892 DOI: 10.3233/jad-231318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
The "amyloid cascade" hypothesis of Alzheimer's disease (AD) pathogenesis invokes the accumulation in the brain of plaques (containing the amyloid-β protein precursor [AβPP] cleavage product amyloid-β [Aβ]) and tangles (containing hyperphosphorylated tau) as drivers of pathogenesis. However, the poor track record of clinical trials based on this hypothesis suggests that the accumulation of these peptides is not the only cause of AD. Here, an alternative hypothesis is proposed in which the AβPP cleavage product C99, not Aβ, is the main culprit, via its role as a regulator of cholesterol metabolism. C99, which is a cholesterol sensor, promotes the formation of mitochondria-associated endoplasmic reticulum (ER) membranes (MAM), a cholesterol-rich lipid raft-like subdomain of the ER that communicates, both physically and biochemically, with mitochondria. We propose that in early-onset AD (EOAD), MAM-localized C99 is elevated above normal levels, resulting in increased transport of cholesterol from the plasma membrane to membranes of intracellular organelles, such as ER/endosomes, thereby upregulating MAM function and driving pathology. By the same token, late-onset AD (LOAD) is triggered by any genetic variant that increases the accumulation of intracellular cholesterol that, in turn, boosts the levels of C99 and again upregulates MAM function. Thus, the functional cause of AD is upregulated MAM function that, in turn, causes the hallmark disease phenotypes, including the plaques and tangles. Accordingly, the MAM hypothesis invokes two key interrelated elements, C99 and cholesterol, that converge at the MAM to drive AD pathogenesis. From this perspective, AD is, at bottom, a lipid disorder.
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Affiliation(s)
- Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY, USA
- Centro de Investigaciones Biológicas "Margarita Salas", Spanish National Research Council, Madrid, Spain
| | - Eric A Schon
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Genetics and Development>, Columbia University, New York, NY, USA
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Naglekar A, Chattopadhyay A, Sengupta D. Palmitoylation of the Glucagon-like Peptide-1 Receptor Modulates Cholesterol Interactions at the Receptor-Lipid Microenvironment. J Phys Chem B 2023; 127:11000-11010. [PMID: 38111968 DOI: 10.1021/acs.jpcb.3c05930] [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: 12/20/2023]
Abstract
The G protein-coupled receptor (GPCR) superfamily of cell surface receptors has been shown to be functionally modulated by post-translational modifications. The glucagon-like peptide receptor-1 (GLP-1R), which is a drug target in diabetes and obesity, undergoes agonist-dependent palmitoyl tail conjugation. The palmitoylation in the C-terminal domain of GLP-1R has been suggested to modulate the receptor-lipid microenvironment. In this work, we have performed coarse-grain molecular dynamics simulations of palmitoylated and nonpalmitoylated GLP-1R to analyze the differential receptor-lipid interactions. Interestingly, the placement and dynamics of the C-terminal domain of GLP-1R are found to be directly dependent on the palmitoyl tail. We observe that both cholesterol and phospholipids interact with the receptor but display differential interactions in the presence and absence of the palmitoyl tail. We characterize important cholesterol-binding sites and validate sites that have been previously reported in experimentally resolved structures of the receptor. We show that the receptor acts like a conduit for cholesterol flip-flop by stabilizing cholesterol in the membrane core. Taken together, our work represents an important step in understanding the molecular effects of lipid modifications in GPCRs.
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Affiliation(s)
- Amit Naglekar
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitabha Chattopadhyay
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Iwaya C, Suzuki A, Iwata J. Loss of Sc5d results in micrognathia due to a failure in osteoblast differentiation. J Adv Res 2023:S2090-1232(23)00395-8. [PMID: 38086515 DOI: 10.1016/j.jare.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 01/01/2024] Open
Abstract
INTRODUCTION Mutations in genes related to cholesterol metabolism, or maternal diet and health status, affect craniofacial bone formation. However, the precise role of intracellular cholesterol metabolism in craniofacial bone development remains unclear. OBJECTIVE The aim of this study is to determine how cholesterol metabolism aberrations affect craniofacial bone development. METHODS Mice with a deficiency in Sc5d, which encodes an enzyme involved in cholesterol synthesis, were analyzed with histology, micro computed tomography (microCT), and cellular and molecular biological methods. RESULTS Sc5d null mice exhibited mandible hypoplasia resulting from defects in osteoblast differentiation. The activation of the hedgehog and WNT/β-catenin signaling pathways, which induce expression of osteogenic genes Col1a1 and Spp1, was compromised in the mandible of Sc5d null mice due to a failure in the formation of the primary cilium, a cell surface structure that senses extracellular cues. Treatments with an inducer of hedgehog or WNT/β-catenin signaling or with simvastatin, a drug that restores abnormal cholesterol production, partially rescued the defects in osteoblast differentiation seen in Sc5d mutant cells. CONCLUSION Our results indicate that loss of Sc5d results in mandibular hypoplasia through defective primary cilia-mediated hedgehog and WNT/β-catenin signaling pathways.
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Affiliation(s)
- Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA; Center for Craniofacial Research, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA; Center for Craniofacial Research, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA; Center for Craniofacial Research, The University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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Samhan-Arias AK, Poejo J, Marques-da-Silva D, Martínez-Costa OH, Gutierrez-Merino C. Are There Lipid Membrane-Domain Subtypes in Neurons with Different Roles in Calcium Signaling? Molecules 2023; 28:7909. [PMID: 37894616 PMCID: PMC10708093 DOI: 10.3390/molecules28237909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Lipid membrane nanodomains or lipid rafts are 10-200 nm diameter size cholesterol- and sphingolipid-enriched domains of the plasma membrane, gathering many proteins with different roles. Isolation and characterization of plasma membrane proteins by differential centrifugation and proteomic studies have revealed a remarkable diversity of proteins in these domains. The limited size of the lipid membrane nanodomain challenges the simple possibility that all of them can coexist within the same lipid membrane domain. As caveolin-1, flotillin isoforms and gangliosides are currently used as neuronal lipid membrane nanodomain markers, we first analyzed the structural features of these components forming nanodomains at the plasma membrane since they are relevant for building supramolecular complexes constituted by these molecular signatures. Among the proteins associated with neuronal lipid membrane nanodomains, there are a large number of proteins that play major roles in calcium signaling, such as ionotropic and metabotropic receptors for neurotransmitters, calcium channels, and calcium pumps. This review highlights a large variation between the calcium signaling proteins that have been reported to be associated with isolated caveolin-1 and flotillin-lipid membrane nanodomains. Since these calcium signaling proteins are scattered in different locations of the neuronal plasma membrane, i.e., in presynapses, postsynapses, axonal or dendritic trees, or in the neuronal soma, our analysis suggests that different lipid membrane-domain subtypes should exist in neurons. Furthermore, we conclude that classification of lipid membrane domains by their content in calcium signaling proteins sheds light on the roles of these domains for neuronal activities that are dependent upon the intracellular calcium concentration. Some examples described in this review include the synaptic and metabolic activity, secretion of neurotransmitters and neuromodulators, neuronal excitability (long-term potentiation and long-term depression), axonal and dendritic growth but also neuronal cell survival and death.
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Affiliation(s)
- Alejandro K. Samhan-Arias
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), C/Arturo Duperier 4, 28029 Madrid, Spain;
- Instituto de Investigaciones Biomédicas ‘Sols-Morreale’ (CSIC-UAM), C/Arturo Duperier 4, 28029 Madrid, Spain
| | - Joana Poejo
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain;
| | - Dorinda Marques-da-Silva
- LSRE—Laboratory of Separation and Reaction Engineering and LCM—Laboratory of Catalysis and Materials, School of Management and Technology, Polytechnic Institute of Leiria, Morro do Lena-Alto do Vieiro, 2411-901 Leiria, Portugal;
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- School of Technology and Management, Polytechnic Institute of Leiria, Morro do Lena-Alto do Vieiro, 2411-901 Leiria, Portugal
| | - Oscar H. Martínez-Costa
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), C/Arturo Duperier 4, 28029 Madrid, Spain;
- Instituto de Investigaciones Biomédicas ‘Sols-Morreale’ (CSIC-UAM), C/Arturo Duperier 4, 28029 Madrid, Spain
| | - Carlos Gutierrez-Merino
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain;
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Das T, Hang HC. Discovery and Characterization of IFITM S-Palmitoylation. Viruses 2023; 15:2329. [PMID: 38140570 PMCID: PMC10747768 DOI: 10.3390/v15122329] [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] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Interferon-induced transmembrane proteins (IFITM1, 2 and 3) are important host antiviral defense factors. They are active against viruses like the influenza A virus (IAV), dengue virus (DENV), Ebola virus (EBOV), Zika virus (ZIKV) and severe acute respiratory syndrome coronavirus (SARS-CoV). In this review, we focus on IFITM3 S-palmitoylation, a reversible lipid modification, and describe its role in modulating IFITM3 antiviral activity. Our laboratory discovered S-palmitoylation of IFITMs using chemical proteomics and demonstrated the importance of highly conserved fatty acid-modified Cys residues in IFITM3 antiviral activity. Further studies showed that site-specific S-palmitoylation at Cys72 is important for IFITM3 trafficking to restricted viruses (IAV and EBOV) and membrane-sterol interactions. Thus, site-specific lipid modification of IFITM3 directly regulates its antiviral activity, cellular trafficking, and membrane-lipid interactions.
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Affiliation(s)
- Tandrila Das
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Howard C. Hang
- Departments of Immunology and Microbiology and Chemistry, Scripps Research, La Jolla, CA 92037, USA
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Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. J Chem Theory Comput 2023; 19:7387-7404. [PMID: 37796943 DOI: 10.1021/acs.jctc.3c00547] [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] [Indexed: 10/07/2023]
Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
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Affiliation(s)
- Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Ana C Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tugba Nur Ozturk
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Rúa de Jenaro de la Fuente, 15705 Santiago de Compostela, Spain
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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45
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Kulshrestha A, Punnathanam SN, Roy R, Ayappa KG. Cholesterol catalyzes unfolding in membrane-inserted motifs of the pore forming protein cytolysin A. Biophys J 2023; 122:4068-4081. [PMID: 37740492 PMCID: PMC10598289 DOI: 10.1016/j.bpj.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/20/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023] Open
Abstract
Plasma membrane-induced protein folding and conformational transitions play a central role in cellular homeostasis. Several transmembrane proteins are folded in the complex lipid milieu to acquire a specific structure and function. Bacterial pore forming toxins (PFTs) are proteins expressed by a large class of pathogenic bacteria that exploit the plasma membrane environment to efficiently undergo secondary structure changes, oligomerize, and form transmembrane pores. Unregulated pore formation causes ion imbalance, leading to cell death and infection. Determining the free energy landscape of these membrane-driven-driven transitions remains a challenging problem. Although cholesterol recognition is required for lytic activity of several proteins in the PFT family of toxins, the regulatory role of cholesterol for the α-PFT, cytolysin A expressed by Escherichia coli remains unexplained. In a recent free energy computation, we showed that the β tongue, a critical membrane-inserted motif of the ClyA toxin, has an on-pathway partially unfolded intermediate that refolds into the helix-turn-helix motif of the pore state. To understand the molecular role played by cholesterol, we carry out string-method-based computations in membranes devoid of cholesterol, which reveals an increase of ∼30 times in the free energy barrier for the loss of β sheet secondary structure when compared with membranes containing cholesterol. Specifically, the tyrosine-cholesterol interaction was found to be critical to creating the unfolded intermediate. Cholesterol also increases the packing and hydrophobicity of the bilayer, resulting in enhanced interactions of the bound protein before complete membrane insertion. Our study illustrates that cholesterol is critical to catalyzing and stabilizing the membrane-inserted unfolded state of the β tongue motif of ClyA, opening up fresh insights into cholesterol-assisted unfolding of membrane proteins.
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Affiliation(s)
- Avijeet Kulshrestha
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India
| | - Sudeep N Punnathanam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India; Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India.
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46
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Girych M, Kulig W, Enkavi G, Vattulainen I. How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harb Perspect Biol 2023; 15:a041419. [PMID: 37487628 PMCID: PMC10547395 DOI: 10.1101/cshperspect.a041419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized by the fact that in many neuropathological diseases there are significant deviations in the lipid composition of nerve membranes compared to healthy individuals. The lipid composition of neuromembranes can significantly affect the function of receptors by regulating the physical properties of the membrane or by affecting specific interactions between receptors and lipids. In addition, it is worth noting that the ligand-binding pocket of many receptors is located inside the cell membrane, due to which lipids can even modulate the binding of ligands to their receptors. These mechanisms highlight the importance of lipids in the regulation of membrane receptor activation and function. In this article, we focus on two major protein families: G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) and discuss how lipids affect their function in neuronal membranes, elucidating the basic mechanisms underlying neuronal function and dysfunction.
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Affiliation(s)
- Mykhailo Girych
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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47
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Regmi D, Shen F, Stanic A, Islam M, Du D. Effect of phospholipid liposomes on prion fragment (106-128) amyloid formation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184199. [PMID: 37454869 DOI: 10.1016/j.bbamem.2023.184199] [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: 03/16/2023] [Revised: 06/08/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Misfolding and aggregation of cellular prion protein (PrPc) is a major molecular process involved in the pathogenesis of prion diseases. Here, we studied the aggregation properties of a prion fragment peptide PrP(106-128). The results show that the peptide aggregates in a concentration-dependent manner in an aqueous solution and that the aggregation is sensitive to pH and the preformed amyloid seeds. Furthermore, we show that the zwitterionic POPC liposomes moderately inhibit the aggregation of PrP(106-128), whereas POPC/cholesterol (8:2) vesicles facilitate peptide aggregation likely due to the increase of the lipid packing order and membrane rigidity in the presence of cholesterol. In addition, anionic lipid vesicles of POPG and POPG/cholesterol above a certain concentration accelerate the aggregation of the peptide remarkably. The strong electrostatic interactions between the N-terminal region of the peptide and POPG may constrain the conformational plasticity of the peptide, preventing insertion of the peptide into the inner side of the membrane and thus promoting fibrillation on the membrane surface. The results suggest that the charge properties of the membrane, the composition of the liposomes, and the rigidity of lipid packing are critical in determining peptide adsorption on the membrane surface and the efficiency of the membrane in catalyzing peptide oligomeric nucleation and amyloid formation. The peptide could be used as an improved model molecule to investigate the mechanistic role of the crucial regions of PrP in aggregation in a membrane-rich environment and to screen effective inhibitors to block key interactions between these regions and membranes for preventing PrP aggregation.
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Affiliation(s)
- Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Aleksander Stanic
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA.
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48
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Sampieri A, Asanov A, Méndez-Acevedo KM, Vaca L. SIDT2 Associates with Apolipoprotein A1 (ApoA1) and Facilitates ApoA1 Secretion in Hepatocytes. Cells 2023; 12:2353. [PMID: 37830567 PMCID: PMC10571540 DOI: 10.3390/cells12192353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023] Open
Abstract
SIDT2 is a lysosomal protein involved in the degradation of nucleic acids and the transport of cholesterol between membranes. Previous studies identified two "cholesterol recognition/interaction amino acid consensus" (CRAC) motifs in SIDT1 and SIDT2 members. We have previously shown that the first CRAC motif (CRAC-1) is essential for protein translocation to the PM upon cholesterol depletion in the cell. In the present study, we show that SIDT2 and the apolipoprotein A1 (ApoA1) form a complex which requires the second CRAC-2 motif in SIDT2 to be established. The overexpression of SIDT2 and ApoA1 results in enhanced ApoA1 secretion by HepG2 cells. This is not observed when overexpressing the SIDT2 with the CRAC-2 domain mutated to render it unfunctional. All these results provide evidence of a novel role for SIDT2 as a protein forming a complex with ApoA1 and enhancing its secretion to the extracellular space.
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Affiliation(s)
- Alicia Sampieri
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City 04510, Mexico;
| | | | - Kevin Manuel Méndez-Acevedo
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City 04510, Mexico;
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49
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Iyer DR, Venkatraman J, Tanguy E, Vitale N, Mahapatra NR. Chromogranin A and its derived peptides: potential regulators of cholesterol homeostasis. Cell Mol Life Sci 2023; 80:271. [PMID: 37642733 PMCID: PMC11072126 DOI: 10.1007/s00018-023-04908-3] [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] [Received: 03/03/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
Chromogranin A (CHGA), a member of the granin family of proteins, has been an attractive therapeutic target and candidate biomarker for several cardiovascular, neurological, and inflammatory disorders. The prominence of CHGA stems from the pleiotropic roles of several bioactive peptides (e.g., catestatin, pancreastatin, vasostatins) generated by its proteolytic cleavage and by their wide anatomical distribution. These peptides are emerging as novel modulators of cardiometabolic diseases that are often linked to high blood cholesterol levels. However, their impact on cholesterol homeostasis is poorly understood. The dynamic nature of cholesterol and its multitudinous roles in almost every aspect of normal body function makes it an integral component of metabolic physiology. A tightly regulated coordination of cholesterol homeostasis is imperative for proper functioning of cellular and metabolic processes. The deregulation of cholesterol levels can result in several pathophysiological states. Although studies till date suggest regulatory roles for CHGA and its derived peptides on cholesterol levels, the mechanisms by which this is achieved still remain unclear. This review aims to aggregate and consolidate the available evidence linking CHGA with cholesterol homeostasis in health and disease. In addition, we also look at common molecular regulatory factors (viz., transcription factors and microRNAs) which could govern the expression of CHGA and genes involved in cholesterol homeostasis under basal and pathological conditions. In order to gain further insights into the pathways mediating cholesterol regulation by CHGA/its derived peptides, a few prospective signaling pathways are explored, which could act as primers for future studies.
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Affiliation(s)
- Dhanya R Iyer
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Janani Venkatraman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Emeline Tanguy
- Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212 and Université de Strasbourg, 5 Rue Blaise Pascal, 67000, Strasbourg, France
| | - Nicolas Vitale
- Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212 and Université de Strasbourg, 5 Rue Blaise Pascal, 67000, Strasbourg, France.
| | - Nitish R Mahapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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50
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Kim M, Bezprozvanny I. Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function. Int J Mol Sci 2023; 24:12980. [PMID: 37629160 PMCID: PMC10455549 DOI: 10.3390/ijms241612980] [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] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The sigma 1 receptor (S1R) is a 223-amino-acid-long transmembrane endoplasmic reticulum (ER) protein. The S1R plays an important role in neuronal health and it is an established therapeutic target for neurodegenerative and neuropsychiatric disorders. Despite its importance in physiology and disease, the biological function of S1R is poorly understood. To gain insight into the biological and signaling functions of S1R, we took advantage of recently reported crystal structures of human and Xenopus S1Rs and performed structural modeling of S1R interactions with ligands and cholesterol in the presence of the membrane. By combining bioinformatics analysis of S1R sequence and structural modelling approaches, we proposed a model that suggests that S1R may exist in two distinct conformations-"dynamic monomer" (DM) and "anchored monomer" (AM). We further propose that equilibrium between AM and DM conformations of S1R is essential for its biological function in cells, with AM conformation facilitating the oligomerization of S1R and DM conformation facilitating deoligomerization. Consistent with experimental evidence, our hypothesis predicts that increased levels of membrane cholesterol and S1R antagonists should promote the oligomeric state of S1R, but S1R agonists and pathogenic mutations should promote its deoligomerization. Obtained results provide mechanistic insights into signaling functions of S1R in cells, and the proposed model may help to explain neuroprotective effects of S1R modulators.
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Affiliation(s)
- Meewhi Kim
- Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Ilya Bezprozvanny
- Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Laboratory of Molecular Neurodegeneration, Peter the Great St Petersburg State Polytechnical University, 195251 St. Petersburg, Russia
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