51
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Morris SNS, Deol KK, Lange M, Olzmann JA. A genome-wide CRISPR screen implicates plasma membrane asymmetry in exogenous C6-ceramide toxicity. Biol Open 2022; 11:283192. [PMID: 36409314 PMCID: PMC9793866 DOI: 10.1242/bio.059695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
The bioactive sphingolipid ceramide impacts diverse cellular processes (e.g. apoptosis and cell proliferation) through its effects on membrane dynamics and intracellular signaling pathways. The dysregulation of ceramide metabolism has been implicated in cancer evasion of apoptosis and targeting ceramide metabolism has potential therapeutic benefits as a strategy to kill cancer cells and slow tumor growth. However, the mechanisms of cancer cell resistance to ceramide-mediated cell death are vastly intertwined and incompletely understood. To shed light on this mystery, we performed a genome-wide CRISPR-Cas9 screen to systematically identify regulators of cancer resistance to the soluble short chain ceramide, C6 ceramide (C6-Cer). Our results reveal a complex landscape of genetic modifiers of C6-Cer toxicity, including genes associated with ceramide and sphingolipid metabolism, vesicular trafficking, and membrane biology. Furthermore, we find that loss of the phospholipid flippase subunit TMEM30A impairs the plasma membrane trafficking of its binding partner, the P4-type ATPase ATP11B, and depletion of TMEM30A or ATP11B disrupts plasma membrane asymmetry and promotes resistance to C6-Cer toxicity. Together, our findings provide a resource of genetic modifiers of C6-Cer toxicity and reveal an unexpected role of plasma membrane asymmetry in C6-Cer induced cell death.
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Affiliation(s)
- Siti Nur Sarah Morris
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Mike Lange
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA,Author for correspondence ()
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52
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Mohole M, Sengupta D, Chattopadhyay A. Synergistic and Competitive Lipid Interactions in the Serotonin 1A Receptor Microenvironment. ACS Chem Neurosci 2022; 13:3403-3415. [PMID: 36351047 DOI: 10.1021/acschemneuro.2c00422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The interaction of lipids with G-protein-coupled receptors (GPCRs) has been shown to modulate and dictate several aspects of GPCR organization and function. Diverse lipid interaction sites have been identified from structural biology, bioinformatics, and molecular dynamics studies. For example, multiple cholesterol interaction sites have been identified in the serotonin1A receptor, along with distinct and overlapping sphingolipid interaction sites. How these lipids interact with each other and what is the resultant effect on the receptor is still not clear. In this work, we have analyzed lipid-lipid crosstalk at the receptor of the serotonin1A receptor embedded in a membrane bilayer that mimics the neuronal membrane composition by long coarse-grain simulations. Using a set of similarity coefficients, we classified lipids that bind at the receptor together as synergistic cobinding, and those that bind individually as competitive. Our results show that certain lipids interact with the serotonin1A receptor in synergy with each other. Not surprisingly, the ganglioside GM1 and cholesterol show a synergistic cobinding, along with the relatively uncommon GM1-phosphatidylethanolamine (PE) and cholesterol-PE synergy. In contrast, certain lipid pairs such as cholesterol and sphingomyelin appear to be in competition at several sites, despite their coexistence in lipid nanodomains. In addition, we observed intralipid competition between two lipid tails, with the receptor exhibiting increased interactions with the unsaturated lipid tails. We believe our work represents an important step in understanding the diversity of GPCR-lipid interactions and exploring synergistic cobinding and competition in natural membranes.
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Affiliation(s)
- Madhura Mohole
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune411 008, India.,Academy of Scientific and Innovative Research, Ghaziabad201 002, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune411 008, India.,Academy of Scientific and Innovative Research, Ghaziabad201 002, India
| | - Amitabha Chattopadhyay
- Academy of Scientific and Innovative Research, Ghaziabad201 002, India.,CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad500 007, India
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53
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da Hora GCA, Nguyen JDM, Swanson JMJ. Can membrane composition traffic toxins? Mycolactone and preferential membrane interactions. Biophys J 2022; 121:4260-4270. [PMID: 36258678 PMCID: PMC9703097 DOI: 10.1016/j.bpj.2022.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022] Open
Abstract
Mycolactone is a cytotoxic and immunosuppressive macrolide produced by Mycobacterium ulcerans and the sole causative agent of the neglected tropical skin disease Buruli ulcer. The toxin acts by invading host cells and interacting with intracellular targets to disrupt multiple fundamental cellular processes. Mycolactone's amphiphilic nature enables strong interactions with lipophilic environments, including cellular membranes; however, the specificity of these interactions and the role of membranes in the toxin's pathogenicity remain unknown. It is likely that preferential interactions with lipophilic carriers play a key role in the toxin's distribution in the host, which, if understood, could provide insights to aid in the development of needed diagnostics for Buruli ulcer disease. In this work, molecular dynamics simulations were combined with enhanced free-energy sampling to characterize mycolactone's association with and permeation through models of the mammalian endoplasmic reticulum (ER) and plasma membranes (PMs). We find that increased order in the PMs not only leads to a different permeation mechanism compared with that in the ER membrane but also an energetic driving force for ER localization. Increased hydration, membrane deformation, and preferential interactions with unsaturated lipid tails stabilize the toxin in the ER membrane, while disruption of lipid packing is a destabilizing force in the PMs.
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Affiliation(s)
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah
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54
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Han S, Zhuang H, Arja RD, Reeves WH. A novel monocyte differentiation pattern in pristane-induced lupus with diffuse alveolar hemorrhage. eLife 2022; 11:e76205. [PMID: 36264674 PMCID: PMC9584606 DOI: 10.7554/elife.76205] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Pristane causes chronic peritoneal inflammation resulting in lupus, which in C57BL/6 mice is complicated by lung microvascular injury and diffuse alveolar hemorrhage (DAH). Mineral oil (MO) also causes inflammation, but not lupus or DAH. Since monocyte depletion prevents DAH, we examined the role of monocytes in the disease. Impaired bone marrow (BM) monocyte egress in Ccr2-/- mice abolished DAH, confirming the importance of monocyte recruitment to the lung. Circulating Ly6Chi monocytes from pristane-treated mice exhibited increased annexin-V staining in comparison with MO-treated controls without evidence of apoptosis, suggesting that pristane alters the distribution of phosphatidylserine in the plasma membrane before or shortly after monocyte egress from the BM. Plasma membrane asymmetry also was impaired in Nr4a1-regulated Ly6Clo/- 'patrolling' monocytes, which are derived from Ly6Chi precursors. Patrolling Ly6Clo/- monocytes normally promote endothelial repair, but their phenotype was altered in pristane-treated mice. In contrast to MO-treated controls, Nr4a1-regulated Ly6Clo/- monocytes from pristane-treated mice were CD138+, expressed more TremL4, a protein that amplifies TLR7 signaling, and exuberantly produced TNFα in response to TLR7 stimulation. TremL4 expression on these novel CD138+ monocytes was regulated by Nr4a1. Thus, monocyte CD138, high TremL4 expression, and annexin-V staining may define an activated/inflammatory subtype of patrolling monocytes associated with DAH susceptibility. By altering monocyte development, pristane exposure may generate activated Ly6Chi and Ly6Clo/- monocytes, contributing to lung microvascular endothelial injury and DAH susceptibility.
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Affiliation(s)
- Shuhong Han
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
| | - Haoyang Zhuang
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
| | - Rawad Daniel Arja
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
| | - Westley H Reeves
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
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55
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Varma M, Deserno M. Distribution of cholesterol in asymmetric membranes driven by composition and differential stress. Biophys J 2022; 121:4001-4018. [PMID: 35927954 PMCID: PMC9674969 DOI: 10.1016/j.bpj.2022.07.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Many lipid membranes of eukaryotic cells are asymmetric, which means the two leaflets differ in at least one physical property, such as lipid composition or lateral stress. Maintaining this asymmetry is helped by the fact that ordinary phospholipids rarely transition between leaflets, but cholesterol is an exception: its flip-flop times are in the microsecond range, so that its distribution between leaflets is determined by a chemical equilibrium. In particular, preferential partitioning can draw cholesterol into a more saturated leaflet, and phospholipid number asymmetry can force it out of a compressed leaflet. Combining highly coarse-grained membrane simulations with theoretical modeling, we investigate how these two driving forces play against each other until cholesterol's chemical potential is equilibrated. The theory includes two coupled elastic sheets and a Flory-Huggins mixing free energy with a χ parameter. We obtain a relationship between χ and the interaction strength between cholesterol and lipids in either of the two leaflets, and we find that it depends, albeit weakly, on lipid number asymmetry. The differential stress measurements under various asymmetry conditions agree with our theoretical predictions. Using the two kinds of asymmetries in combination, we find that it is possible to counteract the phospholipid number bias, and the resultant stress in the membrane, via the control of cholesterol mixing in the leaflets.
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Affiliation(s)
- Malavika Varma
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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56
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London E. Ordered Domain (Raft) Formation in Asymmetric Vesicles and Its Induction upon Loss of Lipid Asymmetry in Artificial and Natural Membranes. MEMBRANES 2022; 12:870. [PMID: 36135889 PMCID: PMC9503047 DOI: 10.3390/membranes12090870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
Lipid asymmetry, the difference in the lipid composition in the inner and outer lipid monolayers (leaflets) of a membrane, is an important feature of eukaryotic plasma membranes. Investigation of the biophysical consequences of lipid asymmetry has been aided by advances in the ability to prepare artificial asymmetric membranes, especially by use of cyclodextrin-catalyzed lipid exchange. This review summarizes recent studies with artificial asymmetric membranes which have identified conditions in which asymmetry can induce or suppress the ability of membranes to form ordered domains (rafts). A consequence of the latter effect is that, under some conditions, a loss of asymmetry can induce ordered domain formation. An analogous study in plasma membrane vesicles has demonstrated that asymmetry can also suppress domain formation in natural membranes. Thus, it is possible that a loss of asymmetry can induce domain formation in vivo.
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Affiliation(s)
- Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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57
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Hullin-Matsuda F, Colosetti P, Rabia M, Luquain-Costaz C, Delton I. Exosomal lipids from membrane organization to biomarkers: Focus on an endolysosomal-specific lipid. Biochimie 2022; 203:77-92. [DOI: 10.1016/j.biochi.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
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Lu F, Zhu Y, Zhang G, Liu Z. Renovation as innovation: Repurposing human antibacterial peptide LL-37 for cancer therapy. Front Pharmacol 2022; 13:944147. [PMID: 36081952 PMCID: PMC9445486 DOI: 10.3389/fphar.2022.944147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/22/2022] [Indexed: 01/10/2023] Open
Abstract
In many organisms, antimicrobial peptides (AMPs) display wide activities in innate host defense against microbial pathogens. Mammalian AMPs include the cathelicidin and defensin families. LL37 is the only one member of the cathelicidin family of host defense peptides expressed in humans. Since its discovery, it has become clear that they have pleiotropic effects. In addition to its antibacterial properties, many studies have shown that LL37 is also involved in a wide variety of biological activities, including tissue repair, inflammatory responses, hemotaxis, and chemokine induction. Moreover, recent studies suggest that LL37 exhibits the intricate and contradictory effects in promoting or inhibiting tumor growth. Indeed, an increasing amount of evidence suggests that human LL37 including its fragments and analogs shows anticancer effects on many kinds of cancer cell lines, although LL37 is also involved in cancer progression. Focusing on recent information, in this review, we explore and summarize how LL37 contributes to anticancer effect as well as discuss the strategies to enhance delivery of this peptide and selectivity for cancer cells.
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59
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Sun L, Pan F, Li S. Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties. MEMBRANES 2022; 12:membranes12080730. [PMID: 35893448 PMCID: PMC9394357 DOI: 10.3390/membranes12080730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023]
Abstract
The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated by using the phase diagrams based on the tail chain lengths for the two types of lipids. Several parameters, such as chain number and average radius of gyration, were employed to explore the structural formations of the membrane and perforated membrane in the dynamic processes. Interface tension was used to demonstrate the mechanical properties of the membrane and perforated membrane in the equilibrium state and dynamics processes. Results help us to understand the self-assembly mechanism of the biomolecule mixtures, which has a potential application for designing the lipid molecule-based bio-membranes in solutions.
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Affiliation(s)
| | - Fan Pan
- Correspondence: (F.P.); (S.L.)
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60
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Larsen AH. Molecular Dynamics Simulations of Curved Lipid Membranes. Int J Mol Sci 2022; 23:ijms23158098. [PMID: 35897670 PMCID: PMC9331392 DOI: 10.3390/ijms23158098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.
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61
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Almasieh M, Faris H, Levin LA. Pivotal roles for membrane phospholipids in axonal degeneration. Int J Biochem Cell Biol 2022; 150:106264. [PMID: 35868612 DOI: 10.1016/j.biocel.2022.106264] [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: 05/09/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Membrane phospholipids are critical components of several signaling pathways. Maintained in a variety of asymmetric distributions, their trafficking across the membrane can be induced by intra-, extra-, and intercellular events. A familiar example is the externalization of phosphatidylserine from the inner leaflet to the outer leaflet in apoptosis, inducing phagocytosis of the soma. Recently, it has been recognized that phospholipids in the axonal membrane may be a signal for axonal degeneration, regeneration, or other processes. This review focuses on key recent developments and areas for ongoing investigations. KEY FACTS: Phosphatidylserine externalization propagates along an axon after axonal injury and is delayed in the Wallerian degeneration slow (WldS) mutant. The ATP8A2 flippase mutant has spontaneous axonal degeneration. Microdomains of axonal degeneration in spheroid bodies have differential externalization of phosphatidylserine and phosphatidylethanolamine. Phospholipid trafficking could represent a mechanism for coordinated axonal degeneration and elimination, i.e. axoptosis, analogous to apoptosis of the cell body.
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Affiliation(s)
- Mohammadali Almasieh
- Department of Ophthalmology and Visual Sciences, McGill University, Montreal, Canada
| | - Hannah Faris
- Department of Ophthalmology and Visual Sciences, McGill University, Montreal, Canada
| | - Leonard A Levin
- Department of Ophthalmology and Visual Sciences, McGill University, Montreal, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada.
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62
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Sim JR, Shin DH, Park PG, Park SH, Bae JY, Lee Y, Kang DY, Kim YJ, Aum S, Noh SH, Hwang SJ, Cha HR, Kim CB, Ko SH, Park S, Jeon D, Cho S, Lee GE, Kim J, Moon YH, Kim JO, Nam JS, Kim CH, Moon S, Chung YW, Park MS, Ryu JH, Namkung W, Lee JM, Lee MG. Amelioration of SARS-CoV-2 infection by ANO6 phospholipid scramblase inhibition. Cell Rep 2022; 40:111117. [PMID: 35839776 PMCID: PMC9250890 DOI: 10.1016/j.celrep.2022.111117] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 05/27/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
As an enveloped virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delivers its viral genome into host cells via fusion of the viral and cell membranes. Here, we show that ANO6/TMEM16F-mediated cell surface exposure of phosphatidylserine is critical for SARS-CoV-2 entry and that ANO6-selective inhibitors are effective against SARS-CoV-2 infections. Application of the SARS-CoV-2 Spike pseudotyped virus (SARS2-PsV) evokes a cytosolic Ca2+ elevation and ANO6-dependent phosphatidylserine externalization in ACE2/TMPRSS2-positive mammalian cells. A high-throughput screening of drug-like chemical libraries identifies three different structural classes of chemicals showing ANO6 inhibitory effects. Among them, A6-001 displays the highest potency and ANO6 selectivity and it inhibits the single-round infection of SARS2-PsV in ACE2/TMPRSS2-positive HEK 293T cells. More importantly, A6-001 strongly inhibits authentic SARS-CoV-2-induced phosphatidylserine scrambling and SARS-CoV-2 viral replications in Vero, Calu-3, and primarily cultured human nasal epithelial cells. These results provide mechanistic insights into the viral entry process and offer a potential target for pharmacological intervention to protect against coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Ju-Ri Sim
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dong Hoon Shin
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Pil-Gu Park
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - So-Hyeon Park
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Youngchae Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dha-Yei Kang
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ye Jin Kim
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sowon Aum
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Shin Hye Noh
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea; Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hye-Ran Cha
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Cheong Bi Kim
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Si Hwan Ko
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sunghoon Park
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dongkyu Jeon
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Sungwoo Cho
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea
| | - Gee Eun Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jeonghun Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Young-Hye Moon
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Jae-Ouk Kim
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Jae-Sung Nam
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Chang-Hoon Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sungmin Moon
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Youn Wook Chung
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Wan Namkung
- College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Korea.
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
| | - Min Goo Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea; Severance Biomedical Science Institute, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea.
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63
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Zhang Y, Zhu X, Zhang H, Yan J, Xu P, Wu P, Wu S, Bai C. Mechanism Study of Proteins under Membrane Environment. MEMBRANES 2022; 12:membranes12070694. [PMID: 35877897 PMCID: PMC9322369 DOI: 10.3390/membranes12070694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
Membrane proteins play crucial roles in various physiological processes, including molecule transport across membranes, cell communication, and signal transduction. Approximately 60% of known drug targets are membrane proteins. There is a significant need to deeply understand the working mechanism of membrane proteins in detail, which is a challenging work due to the lack of available membrane structures and their large spatial scale. Membrane proteins carry out vital physiological functions through conformational changes. In the current study, we utilized a coarse-grained (CG) model to investigate three representative membrane protein systems: the TMEM16A channel, the family C GPCRs mGlu2 receptor, and the P4-ATPase phospholipid transporter. We constructed the reaction pathway of conformational changes between the two-end structures. Energy profiles and energy barriers were calculated. These data could provide reasonable explanations for TMEM16A activation, the mGlu2 receptor activation process, and P4-ATPase phospholipid transport. Although they all belong to the members of membrane proteins, they behave differently in terms of energy. Our work investigated the working mechanism of membrane proteins and could give novel insights into other membrane protein systems of interest.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Xiaohong Zhu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China;
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
- Correspondence: (S.W.); (C.B.)
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
- Chenzhu Biotechnology Co., Ltd., Hangzhou 310005, China
- Correspondence: (S.W.); (C.B.)
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64
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Maeda R, Tamagaki-Asahina H, Sato T, Yanagawa M, Sako Y. Threonine phosphorylation regulates the molecular assembly and signaling of EGFR in cooperation with membrane lipids. J Cell Sci 2022; 135:275916. [PMID: 35791809 DOI: 10.1242/jcs.260355] [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: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022] Open
Abstract
The cytoplasmic domain of the receptor tyrosine kinases (RTKs) plays roles as a phosphorylation enzyme and a protein scaffold but the allocation of these two functions is not fully understood. We here analyzed assembly of the transmembrane (TM)-juxtamembrane (JM) region of EGFR, one of the best studied species of RTKs, by combining single-pair FRET imaging and a nanodisc technique. The JM domain of EGFR contains a threonine residue (Thr654) that is phosphorylated after ligand association. We observed that the TM-JM peptides of EGFR form anionic lipid-induced dimers and cholesterol-induced oligomers. The two forms involve distinct molecular interactions, with a bias towards oligomer formation upon threonine phosphorylation. We further analyzed the functions and oligomerization of whole EGFR molecules, with or without a substitution of Thr654 to alanine, in living cells. The results suggested an autoregulatory mechanism in which Thr654 phosphorylation causes a switch of the major function of EGFR from kinase activation dimers to scaffolding oligomers.
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Affiliation(s)
- Ryo Maeda
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama 351-0198, Japan
| | | | - Takeshi Sato
- Kyoto Pharmaceutical University, 5, Misasagi-cho, Yamashina, Kyoto, 607-8414, Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN CPR, Wako, Saitama 351-0198, Japan.,CREST JST, 4-1-8, Honcho, Kawaguchi, 332-0012, Japan
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65
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Notti RQ, Walz T. Native-like environments afford novel mechanistic insights into membrane proteins. Trends Biochem Sci 2022; 47:561-569. [PMID: 35331611 PMCID: PMC9847468 DOI: 10.1016/j.tibs.2022.02.008] [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: 12/14/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 01/21/2023]
Abstract
Advances in cryogenic electron microscopy (cryo-EM) enabled routine near-atomic structure determination of membrane proteins, while nanodisc technology has provided a way to provide membrane proteins with a native or native-like lipid environment. After giving a brief history of membrane mimetics, we present example structures of membrane proteins in nanodiscs that revealed information not provided by structures obtained in detergent. We describe how the lipid environment surrounding the membrane protein can be custom designed during nanodisc assembly and how it can be modified after assembly to test functional hypotheses. Because nanodiscs most closely replicate the physiologic environment of membrane proteins and often afford novel mechanistic insights, we propose that nanodiscs ought to become the standard for structural studies on membrane proteins.
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Affiliation(s)
- Ryan Q. Notti
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, New York, NY 10065,Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, New York, NY 10065,Correspondence: (Walz, T.)
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66
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Abstract
Lipid-DNA conjugates have emerged as highly useful tools to modify the cell membranes. These conjugates generally consist of a lipid anchor for membrane modification and a functional DNA nanostructure for membrane analysis or regulation. There are several unique properties of these lipid-DNA conjugates, especially including their programmability, fast and efficient membrane insertion, and precise sequence-specific assembly. These unique properties have enabled a broad range of biophysical applications on live cell membranes. In this review, we will mainly focus on recent tremendous progress, especially during the past three years, in regulating the biophysical features of these lipid-DNA conjugates and their key applications in studying cell membrane biophysics. Some insights into the current challenges and future directions of this interdisciplinary field have also been provided.
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67
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Pinto BI, Bassetto CAZ, Bezanilla F. Optocapacitance: physical basis and its application. Biophys Rev 2022; 14:569-577. [PMID: 35528029 PMCID: PMC9042976 DOI: 10.1007/s12551-022-00943-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/13/2022] [Indexed: 12/22/2022] Open
Abstract
The observation that membrane capacitance increases with temperature has led to the development of new methods of neuronal stimulation using light. The optocapacitive effect refers to a light-induced change in capacitance produced by the heating of the membrane through a photothermal effect. This change in capacitance manifests as a current, named optocapacitive current that depolarizes cells and therefore can be used to stimulate excitable tissues. Here, we discuss how optocapacitance arises from basic membrane properties, the characteristics of the optocapacitive current, its use for neuronal stimulation, and the challenges for its application in vivo.
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Affiliation(s)
- Bernardo I. Pinto
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637 USA
| | - Carlos A. Z. Bassetto
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637 USA
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637 USA ,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
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68
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Sang L, Yang L, Ge Q, Xie S, Zhou T, Lin A. Subcellular distribution, localization, and function of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1729. [PMID: 35413151 DOI: 10.1002/wrna.1729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/06/2022]
Abstract
Eukaryotic cells contain subcellular organelles with spatiotemporal regulation to coordinate various biochemical reactions. The various organelles perform their essential biological functions by employing specific biomolecules, including nucleic acids. Recent studies have revealed that noncoding RNAs (ncRNAs) are highly compartmentalized in cells and that their spatial distribution is intimately related to their functions. Dysregulation of subcellular ncRNAs can disrupt cellular homeostasis and cause human diseases. Mitochondria are responsible for energy generation to fuel cell growth and proliferation. Therefore, identifying mitochondria-associated ncRNAs helps to reveal new regulatory mechanisms and physiological functions of mitochondria. In this review, we summarize the latest advances in subcellular ncRNAs derived from either the nuclear or mitochondrial genome. We also discuss available biological approaches for investigating organelle-specific ncRNAs. Exploring the distribution and function of subcellular ncRNAs may facilitate the understanding of endomembrane dynamics and provide potential strategies for clinical transformation. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Lingjie Sang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luojia Yang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiwei Ge
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Xie
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Aifu Lin
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China
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69
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Bag N, London E, Holowka DA, Baird BA. Transbilayer Coupling of Lipids in Cells Investigated by Imaging Fluorescence Correlation Spectroscopy. J Phys Chem B 2022; 126:2325-2336. [PMID: 35294838 DOI: 10.1021/acs.jpcb.2c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasma membranes host numerous receptors, sensors, and ion channels involved in cellular signaling. Phase separation within the plasma membrane has emerged as a key biophysical regulator of signaling reactions in multiple physiological and pathological contexts. There is much evidence that plasma membrane composition supports the coexistence of liquid-ordered (Lo) and liquid-disordered (Ld) phases or domains at physiological conditions. However, this phase/domain separation is nanoscopic and transient in live cells. It has been recently proposed that transbilayer coupling between the inner and outer leaflets of the plasma membrane is driven by their asymmetric lipid distribution and by dynamic cytoskeleton-lipid composites that contribute to the formation and transience of Lo/Ld phase separation in live cells. In this Perspective, we highlight new approaches to investigate how transbilayer coupling may influence phase separation. For quantitative evaluation of the impact of these interactions, we introduce an experimental strategy centered around Imaging Fluorescence Correlation Spectroscopy (ImFCS), which measures membrane diffusion with very high precision. To demonstrate this strategy, we choose two well-established model systems for transbilayer interactions: cross-linking by multivalent antigen of immunoglobulin E bound to receptor FcεRI and cross-linking by cholera toxin B of GM1 gangliosides. We discuss emerging methods to systematically perturb membrane lipid composition, particularly exchange of outer leaflet lipids with exogenous lipids using methyl alpha cyclodextrin. These selective perturbations may be quantitatively evaluated with ImFCS and other high-resolution biophysical tools to discover novel principles of lipid-mediated phase separation in live cells in the context of their pathophysiological relevance.
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Affiliation(s)
- Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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70
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Maltan L, Andova AM, Derler I. The Role of Lipids in CRAC Channel Function. Biomolecules 2022; 12:biom12030352. [PMID: 35327543 PMCID: PMC8944985 DOI: 10.3390/biom12030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/28/2022] Open
Abstract
The composition and dynamics of the lipid membrane define the physical properties of the bilayer and consequently affect the function of the incorporated membrane transporters, which also applies for the prominent Ca2+ release-activated Ca2+ ion channel (CRAC). This channel is activated by receptor-induced Ca2+ store depletion of the endoplasmic reticulum (ER) and consists of two transmembrane proteins, STIM1 and Orai1. STIM1 is anchored in the ER membrane and senses changes in the ER luminal Ca2+ concentration. Orai1 is the Ca2+-selective, pore-forming CRAC channel component located in the plasma membrane (PM). Ca2+ store-depletion of the ER triggers activation of STIM1 proteins, which subsequently leads to a conformational change and oligomerization of STIM1 and its coupling to as well as activation of Orai1 channels at the ER-PM contact sites. Although STIM1 and Orai1 are sufficient for CRAC channel activation, their efficient activation and deactivation is fine-tuned by a variety of lipids and lipid- and/or ER-PM junction-dependent accessory proteins. The underlying mechanisms for lipid-mediated CRAC channel modulation as well as the still open questions, are presented in this review.
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71
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Requirement of Xk and Vps13a for the P2X7-mediated phospholipid scrambling and cell lysis in mouse T cells. Proc Natl Acad Sci U S A 2022; 119:2119286119. [PMID: 35140185 PMCID: PMC8851519 DOI: 10.1073/pnas.2119286119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/12/2022] Open
Abstract
A high extracellular adenosine triphosphate (ATP) concentration rapidly and reversibly exposes phosphatidylserine (PtdSer) in T cells by binding to the P2X7 receptor, which ultimately leads to necrosis. Using mouse T cell transformants expressing P2X7, we herein performed CRISPR/Cas9 screening for the molecules responsible for P2X7-mediated PtdSer exposure. In addition to Eros, which is required for the localization of P2X7 to the plasma membrane, this screening identified Xk and Vps13a as essential components for this process. Xk is present at the plasma membrane, and its paralogue, Xkr8, functions as a phospholipid scramblase. Vps13a is a lipid transporter in the cytoplasm. Blue-native polyacrylamide gel electrophoresis indicated that Xk and Vps13a interacted at the membrane. A null mutation in Xk or Vps13a blocked P2X7-mediated PtdSer exposure, the internalization of phosphatidylcholine, and cytolysis. Xk and Vps13a formed a complex in mouse splenic T cells, and Xk was crucial for ATP-induced PtdSer exposure and cytolysis in CD25+CD4+ T cells. XK and VPS13A are responsible for McLeod syndrome and chorea-acanthocytosis, both characterized by a progressive movement disorder and cognitive and behavior changes. Our results suggest that the phospholipid scrambling activity mediated by XK and VPS13A is essential for maintaining homeostasis in the immune and nerve systems.
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72
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Ge Y, Boopathy S, Nguyen TH, Lugo CM, Chao LH. Absence of Cardiolipin From the Outer Leaflet of a Mitochondrial Inner Membrane Mimic Restricts Opa1-Mediated Fusion. Front Mol Biosci 2022; 8:769135. [PMID: 35004847 PMCID: PMC8728091 DOI: 10.3389/fmolb.2021.769135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Cardiolipin is a tetra-acylated di-phosphatidylglycerol lipid enriched in the matrix-facing (inner) leaflet of the mitochondrial inner membrane. Cardiolipin plays an important role in regulating mitochondria function and dynamics. Yet, the mechanisms connecting cardiolipin distribution and mitochondrial protein function remain indirect. In our previous work, we established an in vitro system reconstituting mitochondrial inner membrane fusion mediated by Opa1. We found that the long form of Opa1 (l-Opa1) works together with the proteolytically processed short form (s-Opa1) to mediate fast and efficient membrane fusion. Here, we extend our reconstitution system to generate supported lipid bilayers with asymmetric cardiolipin distribution. Using this system, we find the presence of cardiolipin on the inter-membrane space-facing (outer) leaflet is important for membrane tethering and fusion. We discuss how the presence of cardiolipin in this leaflet may influence protein and membrane properties, and future applications for this approach.
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Affiliation(s)
- Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Sivakumar Boopathy
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Tran H Nguyen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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73
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López‐Andarias J, Eblighatian K, Pasquer QTL, Assies L, Sakai N, Hoogendoorn S, Matile S. Photocleavable Fluorescent Membrane Tension Probes: Fast Release with Spatiotemporal Control in Inner Leaflets of Plasma Membrane, Nuclear Envelope, and Secretory Pathway. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Javier López‐Andarias
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Krikor Eblighatian
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Quentin T. L. Pasquer
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Lea Assies
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Sascha Hoogendoorn
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
| | - Stefan Matile
- Department of Organic Chemistry National Centre of Competence in Research (NCCR) Chemical Biology University of Geneva Geneva Switzerland
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74
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Perez-Salas U, Garg S, Gerelli Y, Porcar L. Deciphering lipid transfer between and within membranes with time-resolved small-angle neutron scattering. CURRENT TOPICS IN MEMBRANES 2021; 88:359-412. [PMID: 34862031 DOI: 10.1016/bs.ctm.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This review focuses on time-resolved neutron scattering, particularly time-resolved small angle neutron scattering (TR-SANS), as a powerful in situ noninvasive technique to investigate intra- and intermembrane transport and distribution of lipids and sterols in lipid membranes. In contrast to using molecular analogues with potentially large chemical tags that can significantly alter transport properties, small angle neutron scattering relies on the relative amounts of the two most abundant isotope forms of hydrogen: protium and deuterium to detect complex membrane architectures and transport processes unambiguously. This review discusses advances in our understanding of the mechanisms that sustain lipid asymmetry in membranes-a key feature of the plasma membrane of cells-as well as the transport of lipids between membranes, which is an essential metabolic process.
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Affiliation(s)
- Ursula Perez-Salas
- Physics Department, University of Illinois at Chicago, Chicago, IL, United States.
| | - Sumit Garg
- Physics Department, University of Illinois at Chicago, Chicago, IL, United States
| | - Yuri Gerelli
- Department of Life and Environmental Sciences, Universita` Politecnica delle Marche, Ancona, Italy
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75
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The interaction of steroids with phospholipid bilayers and membranes. Biophys Rev 2021; 14:163-179. [DOI: 10.1007/s12551-021-00918-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
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76
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Mutants of the white ABCG Transporter in Drosophila melanogaster Have Deficient Olfactory Learning and Cholesterol Homeostasis. Int J Mol Sci 2021; 22:ijms222312967. [PMID: 34884779 PMCID: PMC8657504 DOI: 10.3390/ijms222312967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
Drosophila's white gene encodes an ATP-binding cassette G-subfamily (ABCG) half-transporter. White is closely related to mammalian ABCG family members that function in cholesterol efflux. Mutants of white have several behavioral phenotypes that are independent of visual defects. This study characterizes a novel defect of white mutants in the acquisition of olfactory memory using the aversive olfactory conditioning paradigm. The w1118 mutants learned slower than wildtype controls, yet with additional training, they reached wildtype levels of performance. The w1118 learning phenotype is also found in the wapricot and wcoral alleles, is dominant, and is rescued by genomic white and mini-white transgenes. Reducing dietary cholesterol strongly impaired olfactory learning for wildtype controls, while w1118 mutants were resistant to this deficit. The w1118 mutants displayed higher levels of cholesterol and cholesterol esters than wildtype under this low-cholesterol diet. Increasing levels of serotonin, dopamine, or both in the white mutants significantly improved w1118 learning. However, serotonin levels were not lower in the heads of the w1118 mutants than in wildtype controls. There were also no significant differences found in synapse numbers within the w1118 brain. We propose that the w1118 learning defect may be due to inefficient biogenic amine signaling brought about by altered cholesterol homeostasis.
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77
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Loss of plasma membrane lipid asymmetry can induce ordered domain (raft) formation. J Lipid Res 2021; 63:100155. [PMID: 34843684 PMCID: PMC8953672 DOI: 10.1016/j.jlr.2021.100155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/22/2022] Open
Abstract
In some cases, lipids in one leaflet of an asymmetric artificial lipid vesicle suppress the formation of ordered lipid domains (rafts) in the opposing leaflet. Whether this occurs in natural membranes is unknown. Here, we investigated this issue using plasma membrane vesicles (PMVs) from rat leukemia RBL-2H3 cells. Membrane domain formation and order was assessed by fluorescence resonance energy transfer and fluorescence anisotropy. We found that ordered domains in PMVs prepared from cells by N-ethyl maleimide (NEM) treatment formed up to ∼37°C, whereas ordered domains in symmetric vesicles formed from the extracted PMV lipids were stable up to 55°C, indicating the stability of ordered domains was substantially decreased in intact PMVs. This behavior paralleled lesser ordered domain stability in artificial asymmetric lipid vesicles relative to the corresponding symmetric vesicles, suggesting intact PMVs exhibit some degree of lipid asymmetry. This was supported by phosphatidylserine mislocalization on PMV outer leaflets as judged by annexin binding, which indicated NEM-induced PMVs are much more asymmetric than PMVs formed by dithiothreitol/paraformaldehyde treatment. Destroying asymmetry by reconstitution of PMVs using detergent dilution also showed stabilization of domain formation, even though membrane proteins remained associated with reconstituted vesicles. Similar domain stabilization was observed in artificial asymmetric lipid vesicles after destroying asymmetry via detergent reconstitution. Proteinase K digestion of proteins had little effect on domain stability in NEM PMVs. We conclude that loss of PMV lipid asymmetry can induce ordered domain formation. The dynamic control of lipid asymmetry in cells may regulate domain formation in plasma membranes.
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78
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Park S, Im W, Pastor RW. Developing initial conditions for simulations of asymmetric membranes: a practical recommendation. Biophys J 2021; 120:5041-5059. [PMID: 34653389 DOI: 10.1016/j.bpj.2021.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/09/2021] [Accepted: 10/08/2021] [Indexed: 01/03/2023] Open
Abstract
It has been proposed that the surface tension difference between leaflets (or differential stress) in asymmetric bilayers is generally nonvanishing. This implies that there is no unique approach to generate initial conditions for simulations of asymmetric bilayers in the absence of experimentally derived constraints. Current generation methods include individual area per lipid (APL) based, leaflet surface area (SA) matching, and zero leaflet tension based (0-DS). This work adds a bilayer-based approach that aims for achieving partial chemical equilibrium by interleaflet switching of selected lipids via P21 periodic boundary conditions. Based on a recently proposed theoretical framework, we obtained expressions for tensions in asymmetric bilayers from both the bending and area strains. We also developed a quantitative measure for the energetic penalty from the differential stress. The impacts of APL-, SA-, and 0-DS-based approaches on mechanical properties are assessed for two different asymmetric bilayers. The lateral pressure profile and its moments differ significantly for each method, whereas the area compressibility modulus is relatively insensitive. Application of P21 periodic boundary conditions (APL/P21, SA/P21, and 0-DS/P21) results in better agreement in mechanical properties between asymmetric bilayers generated by APL-, SA-, and 0-DS-based approaches, in which changes are the smallest for bilayers from the SA-based method. The estimated differential stress from the theory shows good agreement with that from the simulations. These simulation results and the good agreement between the predicted and observed differential stress further support the theoretical framework in which bilayer mechanical properties are outcomes of the interplay between intrinsic bending and asymmetric lipid packing. Based on the simulation results and theoretical predictions, the SA/P21-based, or at least the SA-based (when the differential stress is small), approach is recommended as a practical method for developing initial conditions for asymmetric bilayer simulations.
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Affiliation(s)
- Sooyhung Park
- Department of Biological Sciences, Bethlehem, Pennsylvania; Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania.
| | - Wonpil Im
- Department of Biological Sciences, Bethlehem, Pennsylvania; Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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79
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Tang S, Davoudi Z, Wang G, Xu Z, Rehman T, Prominski A, Tian B, Bratlie KM, Peng H, Wang Q. Soft materials as biological and artificial membranes. Chem Soc Rev 2021; 50:12679-12701. [PMID: 34636824 DOI: 10.1039/d1cs00029b] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past few decades have seen emerging growth in the field of soft materials for synthetic biology. This review focuses on soft materials involved in biological and artificial membranes. The biological membranes discussed here are mainly those involved in the structure and function of cells and organelles. As building blocks in medicine, non-native membranes including nanocarriers (NCs), especially liposomes and DQAsomes, and polymeric membranes for scaffolds are constructed from amphiphilic combinations of lipids, proteins, and carbohydrates. Artificial membranes can be prepared using synthetic, soft materials and molecules and then incorporated into structures through self-organization to form micelles or niosomes. The modification of artificial membranes can be realized using traditional chemical methods such as click reactions to target the delivery of NCs and control the release of therapeutics. The biomembrane, a lamellar structure inlaid with ion channels, receptors, lipid rafts, enzymes, and other functional units, separates cells and organelles from the environment. An active domain inserted into the membrane and organelles for energy conversion and cellular communication can target disease by changing the membrane's composition, structure, and fluidity and affecting the on/off status of the membrane gates. The biological membrane targets analyzing pathological mechanisms and curing complex diseases, which inspires us to create NCs with artificial membranes.
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Affiliation(s)
- Shukun Tang
- Department of Pharmaceutics, Daqing Branch, Harbin Medical University, Research and Development of Natural Products Key Laboratory of Harbin Medical University, 39 Xin Yang Road, Daqing, 163319, China.
| | - Zahra Davoudi
- Department of Chemical and Biological Engineering, Iowa State University, 1014 Sweeney Hall, Ames, IA 50011, USA.
| | - Guangtian Wang
- Department of Pharmaceutics, Daqing Branch, Harbin Medical University, Research and Development of Natural Products Key Laboratory of Harbin Medical University, 39 Xin Yang Road, Daqing, 163319, China.
| | - Zihao Xu
- Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011, USA
| | - Tanzeel Rehman
- Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011, USA
| | - Aleksander Prominski
- The James Franck Institute, Department of Chemistry, The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Bozhi Tian
- The James Franck Institute, Department of Chemistry, The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kaitlin M Bratlie
- Department of Chemical and Biological Engineering, Iowa State University, 1014 Sweeney Hall, Ames, IA 50011, USA. .,Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011, USA
| | - Haisheng Peng
- Department of Pharmaceutics, Daqing Branch, Harbin Medical University, Research and Development of Natural Products Key Laboratory of Harbin Medical University, 39 Xin Yang Road, Daqing, 163319, China.
| | - Qun Wang
- Department of Chemical and Biological Engineering, Iowa State University, 1014 Sweeney Hall, Ames, IA 50011, USA.
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80
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Abe M, Makino A, Murate M, Hullin-Matsuda F, Yanagawa M, Sako Y, Kobayashi T. PMP2/FABP8 induces PI(4,5)P 2-dependent transbilayer reorganization of sphingomyelin in the plasma membrane. Cell Rep 2021; 37:109935. [PMID: 34758297 DOI: 10.1016/j.celrep.2021.109935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/20/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022] Open
Abstract
Sphingomyelin (SM) is a mammalian lipid mainly distributed in the outer leaflet of the plasma membrane (PM). We show that peripheral myelin protein 2 (PMP2), a member of the fatty-acid-binding protein (FABP) family, can localize at the PM and controls the transbilayer distribution of SM. Genetic screening with genome-wide small hairpin RNA libraries identifies PMP2 as a protein involved in the transbilayer movement of SM. A biochemical assay demonstrates that PMP2 is a phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-binding protein. PMP2 induces the tubulation of model membranes in a PI(4,5)P2-dependent manner, accompanied by the modification of the transbilayer membrane distribution of lipids. In the PM of PMP2-overexpressing cells, inner-leaflet SM is increased whereas outer-leaflet SM is reduced. PMP2 is a causative protein of Charcot-Marie-Tooth disease (CMT). A mutation in PMP2 associated with CMT increases its affinity for PI(4,5)P2, inducing membrane tubulation and the subsequent transbilayer movement of lipids.
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Affiliation(s)
- Mitsuhiro Abe
- Lipid Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan.
| | - Asami Makino
- Lipid Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Motohide Murate
- Lipid Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France
| | - Françoise Hullin-Matsuda
- Lipid Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Université de Lyon, CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon 1, 69495 Pierre-Benite, France
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Toshihide Kobayashi
- Lipid Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Cellular Informatics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France.
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81
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López-Andarias J, Eblighatian K, Pasquer QTL, Assies L, Sakai N, Hoogendoorn S, Matile S. Photocleavable Fluorescent Membrane Tension Probes: Fast Release with Spatiotemporal Control in Inner Leaflets of Plasma Membrane, Nuclear Envelope, and Secretory Pathway. Angew Chem Int Ed Engl 2021; 61:e202113163. [PMID: 34734671 PMCID: PMC9299180 DOI: 10.1002/anie.202113163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Indexed: 12/25/2022]
Abstract
Mechanosensitive flipper probes are attracting interest as fluorescent reporters of membrane order and tension in biological systems. We introduce PhotoFlippers, which contain a photocleavable linker and an ultralong tether between mechanophore and various targeting motifs. Upon irradiation, the original probe is released and labels the most ordered membrane that is accessible by intermembrane transfer. Spatiotemporal control from photocleavable flippers is essential to access open, dynamic or elusive membrane motifs without chemical or physical interference. For instance, fast release with light is shown to place the original small‐molecule probes into the innermost leaflet of the nuclear envelope to image changes in membrane tension, at specific points in time of membrane trafficking along the secretory pathway, or in the inner leaflet of the plasma membrane to explore membrane asymmetry. These results identify PhotoFlippers as useful chemistry tools to enable research in biology.
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Affiliation(s)
- Javier López-Andarias
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Krikor Eblighatian
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Quentin T L Pasquer
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Lea Assies
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sascha Hoogendoorn
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) Chemical Biology, University of Geneva, Geneva, Switzerland
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82
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Palaia I, Paraschiv A, Debets VE, Storm C, Šarić A. Durotaxis of Passive Nanoparticles on Elastic Membranes. ACS NANO 2021; 15:15794-15802. [PMID: 34550677 DOI: 10.1101/2021.04.01.438065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in nonuniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically nonuniform elastic membrane. We observe a nonmonotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.
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Affiliation(s)
- Ivan Palaia
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Vincent E Debets
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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83
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Kinnebrew M, Luchetti G, Sircar R, Frigui S, Viti LV, Naito T, Beckert F, Saheki Y, Siebold C, Radhakrishnan A, Rohatgi R. Patched 1 reduces the accessibility of cholesterol in the outer leaflet of membranes. eLife 2021; 10:e70504. [PMID: 34698632 PMCID: PMC8654371 DOI: 10.7554/elife.70504] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
A long-standing mystery in vertebrate Hedgehog signaling is how Patched 1 (PTCH1), the receptor for Hedgehog ligands, inhibits the activity of Smoothened, the protein that transmits the signal across the membrane. We previously proposed (Kinnebrew et al., 2019) that PTCH1 inhibits Smoothened by depleting accessible cholesterol from the ciliary membrane. Using a new imaging-based assay to directly measure the transport activity of PTCH1, we find that PTCH1 depletes accessible cholesterol from the outer leaflet of the plasma membrane. This transport activity is terminated by binding of Hedgehog ligands to PTCH1 or by dissipation of the transmembrane potassium gradient. These results point to the unexpected model that PTCH1 moves cholesterol from the outer to the inner leaflet of the membrane in exchange for potassium ion export in the opposite direction. Our study provides a plausible solution for how PTCH1 inhibits SMO by changing the organization of cholesterol in membranes and establishes a general framework for studying how proteins change cholesterol accessibility to regulate membrane-dependent processes in cells.
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Affiliation(s)
- Maia Kinnebrew
- Department of Biochemistry and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Giovanni Luchetti
- Department of Biochemistry and Medicine, Stanford University School of MedicineStanfordUnited States
- Department of Physiological Chemistry, GenentechSouth San FranciscoUnited States
| | - Ria Sircar
- Department of Biochemistry and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Sara Frigui
- Department of Biochemistry and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Lucrezia Vittoria Viti
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Tomoki Naito
- Lee Kong Chian School of Medicine, Nanyang Technological UniversitySingaporeSingapore
| | - Francis Beckert
- Department of Biochemistry and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological UniversitySingaporeSingapore
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Arun Radhakrishnan
- Department of Molecular Genetics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Rajat Rohatgi
- Department of Biochemistry and Medicine, Stanford University School of MedicineStanfordUnited States
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84
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Palaia I, Paraschiv A, Debets VE, Storm C, Šarić A. Durotaxis of Passive Nanoparticles on Elastic Membranes. ACS NANO 2021; 15:15794-15802. [PMID: 34550677 DOI: 10.1021/acsnano.1c02777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in nonuniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically nonuniform elastic membrane. We observe a nonmonotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.
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Affiliation(s)
- Ivan Palaia
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Vincent E Debets
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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85
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Bai L, Jain BK, You Q, Duan HD, Takar M, Graham TR, Li H. Structural basis of the P4B ATPase lipid flippase activity. Nat Commun 2021; 12:5963. [PMID: 34645814 PMCID: PMC8514546 DOI: 10.1038/s41467-021-26273-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
P4 ATPases are lipid flippases that are phylogenetically grouped into P4A, P4B and P4C clades. The P4A ATPases are heterodimers composed of a catalytic α-subunit and accessory β-subunit, and the structures of several heterodimeric flippases have been reported. The S. cerevisiae Neo1 and its orthologs represent the P4B ATPases, which function as monomeric flippases without a β-subunit. It has been unclear whether monomeric flippases retain the architecture and transport mechanism of the dimeric flippases. Here we report the structure of a P4B ATPase, Neo1, in its E1-ATP, E2P-transition, and E2P states. The structure reveals a conserved architecture as well as highly similar functional intermediate states relative to dimeric flippases. Consistently, structure-guided mutagenesis of residues in the proposed substrate translocation path disrupted Neo1’s ability to establish membrane asymmetry. These observations indicate that evolutionarily distant P4 ATPases use a structurally conserved mechanism for substrate transport. The P4 ATPase lipid flippases play a crucial role in membrane biogenesis. Here the authors report the structure of the monomeric P4B ATPase Neo1 in several states, clarifying the mechanism of substrate transport.
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Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China.
| | - Bhawik K Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Qinglong You
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - H Diessel Duan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Mehmet Takar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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86
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Steck TL, Tabei SMA, Lange Y. A basic model for cell cholesterol homeostasis. Traffic 2021; 22:471-481. [PMID: 34528339 DOI: 10.1111/tra.12816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/26/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
Cells manage their cholesterol by negative feedback using a battery of sterol-responsive proteins. How these activities are coordinated so as to specify the abundance and distribution of the sterol is unclear. We present a simple mathematical model that addresses this question. It assumes that almost all of the cholesterol is associated with phospholipids in stoichiometric complexes. A small fraction of the sterol is uncomplexed and thermodynamically active. It equilibrates among the organelles, setting their sterol level according to the affinity of their phospholipids. The activity of the homeostatic proteins in the cytoplasmic membranes is then set by their fractional saturation with uncomplexed cholesterol in competition with the phospholipids. The high-affinity phospholipids in the plasma membrane (PM) are filled to near stoichiometric equivalence, giving it most of the cell sterol. Notably, the affinity of the phospholipids in the endomembranes (EMs) is lower by orders of magnitude than that of the phospholipids in the PM. Thus, the small amount of sterol in the EMs rests far below stoichiometric capacity. Simulations match a variety of experimental data. The model captures the essence of cell cholesterol homeostasis, makes coherent a diverse set of experimental findings, provides a surprising prediction and suggests new experiments.
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Affiliation(s)
- Theodore L Steck
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - S M Ali Tabei
- Department of Physics, University of Northern Iowa, Cedar Falls, Iowa, USA
| | - Yvonne Lange
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
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87
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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88
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Smith P, Lorenz CD. LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations. J Chem Theory Comput 2021; 17:5907-5919. [PMID: 34450002 DOI: 10.1021/acs.jctc.1c00447] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic-a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble-an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London WC2R 2LS, U.K
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89
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Chen Y, Wang Z, Ji Y, He L, Wang X, Li S. Asymmetric Lipid Membranes under Shear Flows: A Dissipative Particle Dynamics Study. MEMBRANES 2021; 11:655. [PMID: 34564472 PMCID: PMC8465239 DOI: 10.3390/membranes11090655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/20/2021] [Indexed: 12/03/2022]
Abstract
We investigate the phase behavior of the asymmetric lipid membranes under shear flows, using the dissipative particle dynamics simulation. Two cases, the weak and strong shear flows, are considered for the asymmetric lipid microstructures. Three typical asymmetric structures, the membranes, tubes, and vesicle, are included in the phase diagrams, where the effect of two different types of lipid chain length on the formation of asymmetric membranes is evaluated. The dynamic processes are demonstrated for the asymmetric membranes by calculating the average radius of gyration and shape factor. The result indicates that different shear flows will affect the shape of the second type of lipid molecules; the shape of the first type of lipid molecules is more stable than that of the second type of lipid molecules. The mechanical properties are investigated for the asymmetric membranes by analyzing the interface tension. The results reveal an absolute pressure at the junctions of different types of particles under the weak shear flow; the other positions are almost in a state of no pressure; there is almost no pressure inside the asymmetric lipid membrane structure under the strong shear flow. The findings will help us to understand the potential applications of asymmetric lipid microstructures in the biological and medical fields.
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Affiliation(s)
| | | | | | | | | | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou 325035, China; (Y.C.); (Z.W.); (Y.J.); (L.H.); (X.W.)
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90
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Thallmair S, Javanainen M, Fábián B, Martinez-Seara H, Marrink SJ. Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. J Phys Chem B 2021; 125:9537-9546. [PMID: 34398598 PMCID: PMC8404198 DOI: 10.1021/acs.jpcb.1c03665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Molecular dynamics
(MD) simulations have become an indispensable
tool to investigate phase separation in model membrane systems. In
particular, simulations based on coarse-grained (CG) models have found
widespread use due to their increased computational efficiency, allowing
for simulations of multicomponent lipid bilayers undergoing phase
separation into liquid-ordered and liquid-disordered domains. Here,
we show that a significant temperature difference between molecule
types can artificially arise in CG MD membrane simulations with the
standard Martini simulation parameters in GROMACS. In particular,
the linear constraint solver (LINCS) algorithm does not converge with
its default settings, resulting in serious temperature differences
between molecules in a time step-dependent manner. We demonstrate
that the underlying reason for this behavior is the presence of highly
constrained moieties, such as cholesterol. Their presence can critically
impact numerous structural and dynamic membrane properties obtained
from such simulations. Furthermore, any preference of these molecules
toward a certain membrane phase can lead to spatial temperature gradients,
which can amplify the degree of phase separation or even induce it
in compositions that would otherwise mix well. We systematically investigated
the effect of the integration time step and LINCS settings on membrane
properties. Our data show that for cholesterol-containing membranes,
a time step of 20 fs should be combined with at least lincs_iter = 2 and lincs_order = 12, while using a time
step of 30 fs requires at least lincs_iter =
3 and lincs_order = 12 to bring the temperature
differences to a level where they do not perturb central membrane
properties. Moreover, we show that in cases where stricter LINCS settings
are computationally too demanding, coupling the lipids in multiple
groups to the temperature bath offers a practical workaround to the
problem, although the validity of this approach should be further
verified. Finally, we show that similar temperature gradients can
also emerge in atomistic simulations using the CHARMM force field
in combination with settings that allow for a 5 fs integration step.
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Affiliation(s)
- Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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91
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Schneider-Schaulies S, Schumacher F, Wigger D, Schöl M, Waghmare T, Schlegel J, Seibel J, Kleuser B. Sphingolipids: Effectors and Achilles Heals in Viral Infections? Cells 2021; 10:cells10092175. [PMID: 34571822 PMCID: PMC8466362 DOI: 10.3390/cells10092175] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022] Open
Abstract
As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.
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Affiliation(s)
- Sibylle Schneider-Schaulies
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Fabian Schumacher
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
| | - Dominik Wigger
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
| | - Marie Schöl
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Trushnal Waghmare
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Jan Schlegel
- Department for Biotechnology and Biophysics, University of Wuerzburg, 97074 Würzburg, Germany;
| | - Jürgen Seibel
- Department for Organic Chemistry, University of Wuerzburg, 97074 Würzburg, Germany;
| | - Burkhard Kleuser
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
- Correspondence: ; Tel.: +49-30-8386-9823
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92
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Phospholipids: Identification and Implication in Muscle Pathophysiology. Int J Mol Sci 2021; 22:ijms22158176. [PMID: 34360941 PMCID: PMC8347011 DOI: 10.3390/ijms22158176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/29/2022] Open
Abstract
Phospholipids (PLs) are amphiphilic molecules that were essential for life to become cellular. PLs have not only a key role in compartmentation as they are the main components of membrane, but they are also involved in cell signaling, cell metabolism, and even cell pathophysiology. Considered for a long time to simply be structural elements of membranes, phospholipids are increasingly being viewed as sensors of their environment and regulators of many metabolic processes. After presenting their main characteristics, we expose the increasing methods of PL detection and identification that help to understand their key role in life processes. Interest and importance of PL homeostasis is growing as pathogenic variants in genes involved in PL biosynthesis and/or remodeling are linked to human diseases. We here review diseases that involve deregulation of PL homeostasis and present a predominantly muscular phenotype.
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93
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Abstract
Cell membranes - primarily composed of lipids, sterols, and proteins - form a dynamic interface between living cells and their environment. They act as a mechanical barrier around the cell while selectively facilitating material transport, signal transduction, and various other functions necessary for the cell viability. The complex functionality of cell membranes and the hierarchical motions and responses they exhibit demand a thorough understanding of the origin of different membrane dynamics and how they are influenced by molecular additives and environmental cues. These dynamic modes include single-molecule diffusion, thermal fluctuations, and large-scale membrane deformations, to name a few. This review highlights advances in investigating structure-driven dynamics associated with model cell membranes, with a particular focus on insights gained from neutron scattering and spectroscopy experiments. We discuss the uniqueness of neutron contrast variation and its remarkable potential in probing selective membrane structure and dynamics on spatial and temporal scales over which key biological functions occur. We also present a summary of current and future opportunities in synergistic combinations of neutron scattering with molecular dynamics (MD) simulations to gain further understanding of the molecular mechanisms underlying complex membrane functions.
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Affiliation(s)
- Sudipta Gupta
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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94
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Scott HL, Kennison KB, Enoki TA, Doktorova M, Kinnun JJ, Heberle FA, Katsaras J. Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry. Symmetry (Basel) 2021; 13. [PMID: 35498375 PMCID: PMC9053528 DOI: 10.3390/sym13081356] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma membranes (PMs) is not symmetric. Despite this, model membrane studies have largely relied on chemically symmetric model membranes for the study of lipid–lipid and lipid–protein interactions. This is primarily due to the difficulty in preparing stable, asymmetric model membranes that are amenable to biophysical studies. However, in the last 20 years, efforts have been made in producing more biologically faithful model membranes. Here, we review several recently developed experimental and computational techniques for the robust generation of asymmetric model membranes and highlight a new and particularly promising technique to study membrane asymmetry.
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Affiliation(s)
- Haden L. Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Kristen B. Kennison
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Thais A. Enoki
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Jacob J. Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - John Katsaras
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
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95
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Ristovski M, Farhat D, Bancud SEM, Lee JY. Lipid Transporters Beam Signals from Cell Membranes. MEMBRANES 2021; 11:562. [PMID: 34436325 PMCID: PMC8399137 DOI: 10.3390/membranes11080562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
Lipid composition in cellular membranes plays an important role in maintaining the structural integrity of cells and in regulating cellular signaling that controls functions of both membrane-anchored and cytoplasmic proteins. ATP-dependent ABC and P4-ATPase lipid transporters, two integral membrane proteins, are known to contribute to lipid translocation across the lipid bilayers on the cellular membranes. In this review, we will highlight current knowledge about the role of cholesterol and phospholipids of cellular membranes in regulating cell signaling and how lipid transporters participate this process.
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Affiliation(s)
- Miliça Ristovski
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
- Translational and Molecular Medicine Program, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Danny Farhat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
- Biomedical Sciences Program, Faculty of Science, University of Ottawa, Ottawa, ON K1H 6N5, Canada
| | - Shelly Ellaine M. Bancud
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
- Translational and Molecular Medicine Program, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
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96
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Tei R, Baskin JM. Induced proximity tools for precise manipulation of lipid signaling. Curr Opin Chem Biol 2021; 65:93-100. [PMID: 34304140 DOI: 10.1016/j.cbpa.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/03/2021] [Accepted: 06/18/2021] [Indexed: 01/07/2023]
Abstract
Lipids are highly dynamic molecules that, due to their hydrophobicity, are spatially confined to membrane environments. From these locations, certain privileged lipids serve as signaling molecules. For understanding the biological functions of subcellular pools of signaling lipids, induced proximity tools have been invaluable. These methods involve controlled heterodimerization, by either small-molecule or light triggers, of functional proteins. In the arena of lipid signaling, induced proximity tools can recruit lipid-metabolizing enzymes to manipulate lipid signaling and create artificial tethers between organelle membranes to control lipid trafficking pathways at membrane contact sites. Here, we review recent advances in methodology development and biological application of chemical-induced and light-induced proximity tools for manipulating lipid metabolism, trafficking, and signaling.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853, USA.
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97
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Zheng Y, Ding Y, Zheng X, Zhang C, Zhang Y, Xiang Y, Tong A. Long-Term Dynamic Imaging of Cellular Processes Using an AIE Lipid Order Probe in the Dual-Color Mode. Anal Chem 2021; 93:10272-10281. [PMID: 34219453 DOI: 10.1021/acs.analchem.1c01681] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lipid order in the cytoplasm membrane of eukaryotic cells undergoes dynamic changes in almost all cellular processes. Dynamically monitoring these changes is of essential biological significance and remains challenging. This work provides the first aggregation-induced emission probe, TPNPDA-C15, with highly three-dimensional specificity to cell membranes for fluorescent imaging of lipid order of live cells. TPNPDA-C15 displays red fluorescence enhancement with the viscosity increase while emits yellow fluorescence when aggregates form. Imaging analyses of giant unilamellar vesicles and live cells under osmotic shock by the probe demonstrate its sensitive response to the degree of phospholipids packing on artificial and cell membranes. Taking advantage of its superior low photocytotoxicity and high photostability, TPNPDA-C15 is further applied for long-term dynamic imaging of entire live cell physiological processes including apoptosis, ferroptosis, and mitosis in the dual-color mode. With the analysis of fluorescence signal changes in the two fluorescence channels, TPNPDA-C15 serves as a robust fluorescent probe for the imaging study of cellular dynamics.
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Affiliation(s)
- Yue Zheng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Yiwen Ding
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Xiaokun Zheng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Chu Zhang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Yanli Zhang
- Imaging Core Facility, Technology Center for Protein Science, Tsinghua University, Beijing 100084, P. R. China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
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98
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Wu E, Guo X, Teng X, Zhang R, Li F, Cui Y, Zhang D, Liu Q, Luo J, Wang J, Chen R. Discovery of Plasma Membrane-Associated RNAs through APEX-seq. Cell Biochem Biophys 2021; 79:905-917. [PMID: 34028638 DOI: 10.1007/s12013-021-00991-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2021] [Indexed: 02/08/2023]
Abstract
In addition to nucleic acids, a variety of other biomolecules have also been found on the plasma membrane. Although researchers have realized that RNA has the ability to bind to membrane vesicles in vitro, little is known about whether and how RNA connects to the plasma membrane of the cell. The combination of high-throughput sequencing and in situ labeling methods provides an innovative approach for large-scale identification of subcellular RNAs. Here, we applied the recently published method APEX-seq and identified 75 RNAs related to the plasma membrane, in which lncRNA PMAR72 (plasma membrane-associated RNA AL121772.1) has a considerable affinity with sphingomyelin (SM) and localizes within distinct membrane foci. Our findings will provide some new evidence to elaborate the relationship between RNA and the plasma membrane of mammalian cells.
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Affiliation(s)
- Erzhong Wu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuzhen Guo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ruijin Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fahui Li
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ya Cui
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Dongdong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Qinghua Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Jiangyun Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
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99
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Factor Xa inhibitors: critical considerations for clinical development and testing. J Thromb Thrombolysis 2021; 52:397-402. [PMID: 33991266 PMCID: PMC8122197 DOI: 10.1007/s11239-021-02455-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 12/25/2022]
Abstract
The selection of factor (F) X and its activated protease FXa for targeted inhibition to prevent and treat thrombotic conditions is based on an understanding of coagulation biochemistry, sequential steps that occur on tissue factor bearing cells and the interface of coagulation proteins, platelets, mononuclear cells and the nuclear constituents of inflammatory cells. The goal for developing direct oral FXa inhibitors was to achieve rapid, selective, predictable, safe and effective anticoagulation across a broad group of patients expected to derive benefit. The history and development in patient care are exemplars of knowledge, translation and collaboration between the public and private sectors.
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100
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Kabelka I, Vácha R. Advances in Molecular Understanding of α-Helical Membrane-Active Peptides. Acc Chem Res 2021; 54:2196-2204. [PMID: 33844916 DOI: 10.1021/acs.accounts.1c00047] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological membranes separate the interior of cells or cellular compartments from their outer environments. This barrier function of membranes can be disrupted by membrane-active peptides, some of which can spontaneously penetrate through the membranes or open leaky transmembrane pores. However, the origin of their activity/toxicity is not sufficiently understood for the development of more potent peptides. To this day, there are no design rules that would be generally valid, and the role of individual amino acids tends to be sequence-specific.In this Account, we describe recent progress in understanding the design principles that govern the activity of membrane-active peptides. We focus on α-helical amphiphilic peptides and their ability to (1) translocate across phospholipid bilayers, (2) form transmembrane pores, or (3) act synergistically, i.e., to produce a significantly more potent effect in a mixture than the individual components.We refined the description of peptide translocation using computer simulations and demonstrated the effect of selected residues. Our simulations showed the necessity to explicitly include charged residues in the translocation description to correctly sample the membrane perturbations they can cause. Using this description, we calculated the translocation of helical peptides with and without the kink induced by the proline/glycine residue. The presence of the kink had no effect on the translocation barrier, but it decreased the peptide affinity to the membrane and reduced the peptide stability inside the membrane. Interestingly, the effects were mainly caused by the peptide's increased polarity, not the higher flexibility of the kink.Flexibility plays a crucial role in pore formation and affects distinct pore structures in different ways. The presence of a kink destabilizes barrel-stave pores, because the kink prevents the tight packing of peptides in the bundle, which is characteristic of the barrel-stave structure. In contrast, the kink facilitates the formation of toroidal pores, where the peptides are only loosely arranged and do not need to closely assemble. The exact position of the kink in the sequence further determines the preferred arrangement of peptides in the pore, i.e., an hourglass or U-shaped structure. In addition, we demonstrated that two self-associated (via termini) helical peptides could mimic the behavior of peptides with a helix-kink-helix motif.Finally, we review the recent findings on the peptide synergism of the archetypal mixture of Magainin 2 and PGLa peptides. We focused on a bacterial plasma membrane mimic that contains negatively charged lipids and lipids with negative intrinsic curvature. We showed that the synergistic action of peptides was highly dependent on the lipid composition. When the lipid composition and peptide/lipid ratios were changed, the systems exhibited more complex behavior than just the previously reported pore formation. We observed membrane adhesion, fusion, and even the formation of the sponge phase in this regime. Furthermore, enhanced adhesion/partitioning to the membrane was reported to be caused by lipid-induced peptide aggregation.In conclusion, the provided molecular insight into the complex behavior of membrane-active peptides provides clues for the design and modification of antimicrobial peptides or toxins.
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Affiliation(s)
- Ivo Kabelka
- CEITEC − Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC − Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University Kamenice 5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
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