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Bartoš L, Drabinová M, Vácha R. Optimizing properties of translocation-enhancing transmembrane proteins. Biophys J 2024; 123:1240-1252. [PMID: 38615194 PMCID: PMC11140465 DOI: 10.1016/j.bpj.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/31/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024] Open
Abstract
Cell membranes act as semi-permeable barriers, often restricting the entry of large or hydrophilic molecules. Nonetheless, certain amphiphilic molecules, such as antimicrobial and cell-penetrating peptides, can cross these barriers. In this study, we demonstrate that specific properties of transmembrane proteins/peptides can enhance membrane permeation of amphiphilic peptides. Using coarse-grained molecular dynamics with free-energy calculations, we identify key translocation-enhancing attributes of transmembrane proteins/peptides: a continuous hydrophilic patch, charged residues preferably in the membrane center, and aromatic hydrophobic residues. By employing both coarse-grained and atomistic simulations, complemented by experimental validation, we show that these properties not only enhance peptide translocation but also speed up lipid flip-flop. The enhanced flip-flop reinforces the idea that proteins such as scramblases and insertases not only share structural features but also operate through identical biophysical mechanisms enhancing the insertion and translocation of amphiphilic molecules. Our insights offer guidelines for the designing of translocation-enhancing proteins/peptides that could be used in medical and biotechnological applications.
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Affiliation(s)
- Ladislav Bartoš
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martina Drabinová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic.
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2
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Xue Y, Zhou S, Yan L, Li Y, Xu X, Wang X, Minobe E, Kameyama M, Hao L, Hu H. Ahf-Caltide, a Novel Polypeptide Derived from Calpastatin, Protects against Oxidative Stress Injury by Stabilizing the Expression of Ca V1.2 Calcium Channel. Int J Mol Sci 2023; 24:15729. [PMID: 37958713 PMCID: PMC10648788 DOI: 10.3390/ijms242115729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Reperfusion after ischemia would cause massive myocardial injury, which leads to oxidative stress (OS). Calcium homeostasis imbalance plays an essential role in myocardial OS injury. CaV1.2 calcium channel mediates calcium influx into cardiomyocytes, and its activity is modulated by a region of calpastatin (CAST) domain L, CSL54-64. In this study, the effect of Ahf-caltide, derived from CSL54-64, on myocardial OS injury was investigated. Ahf-caltide decreased the levels of LDH, MDA and ROS and increased heart rate, coronary flow, cell survival and SOD activity during OS. In addition, Ahf-caltide permeated into H9c2 cells and increased CaV1.2, CaVβ2 and CAST levels by inhibiting protein degradation. At different Ca2+ concentrations (25 nM, 10 μM, 1 mM), the binding of CSL to the IQ motif in the C terminus of the CaV1.2 channel was increased in a H2O2 concentration-dependent manner. CSL54-64 was predicted to be responsible for the binding of CSL to CaV1.2. In conclusion, Ahf-caltide exerted a cardioprotective effect on myocardial OS injury by stabilizing CaV1.2 protein expression. Our study, for the first time, proposed that restoring calcium homeostasis by targeting the CaV1.2 calcium channel and its regulating factor CAST could be a novel treatment for myocardial OS injury.
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Affiliation(s)
- Yingchun Xue
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Shi Zhou
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Ling Yan
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Yuelin Li
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Xingrong Xu
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Xianghui Wang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Etsuko Minobe
- Department of Physiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan; (E.M.); (M.K.)
| | - Masaki Kameyama
- Department of Physiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan; (E.M.); (M.K.)
| | - Liying Hao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
| | - Huiyuan Hu
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110122, China; (Y.X.); (S.Z.); (L.Y.); (Y.L.); (X.X.); (X.W.)
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3
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Nakao H, Nagao M, Yamada T, Imamura K, Nozaki K, Ikeda K, Nakano M. Impact of transmembrane peptides on individual lipid motions and collective dynamics of lipid bilayers. Colloids Surf B Biointerfaces 2023; 228:113396. [PMID: 37311269 DOI: 10.1016/j.colsurfb.2023.113396] [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: 03/22/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
The fluid nature of lipid bilayers is indispensable for the dynamic regulation of protein function and membrane morphology in biological membranes. Membrane-spanning domains of proteins interact with surrounding lipids and alter the physical properties of lipid bilayers. However, there is no comprehensive view of the effects of transmembrane proteins on the membrane's physical properties. Here, we investigated the effects of transmembrane peptides with different flip-flop-promoting abilities on the dynamics of a lipid bilayer employing complemental fluorescence and neutron scattering techniques. The quasi-elastic neutron scattering and fluorescence experiments revealed that lateral diffusion of the lipid molecules and the acyl chain motions were inhibited by the inclusion of transmembrane peptides. The neutron spin-echo spectroscopy measurements indicated that the lipid bilayer became more rigid but more compressible and the membrane viscosity increased when the transmembrane peptides were incorporated into the membrane. These results suggest that the inclusion of rigid transmembrane structures hinders individual and collective lipid motions by slowing down lipid diffusion and increasing interleaflet coupling. The present study provides a clue for understanding how the local interactions between lipids and proteins change the collective dynamics of the lipid bilayers, and therefore, the function of biological membranes.
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Affiliation(s)
- Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Michihiro Nagao
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, MD 20899-6102, USA; Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742-2115, USA; Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Koki Imamura
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Koichi Nozaki
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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4
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The Role of Transmembrane Proteins in Plant Growth, Development, and Stress Responses. Int J Mol Sci 2022; 23:ijms232113627. [PMID: 36362412 PMCID: PMC9655316 DOI: 10.3390/ijms232113627] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Transmembrane proteins participate in various physiological activities in plants, including signal transduction, substance transport, and energy conversion. Although more than 20% of gene products are predicted to be transmembrane proteins in the genome era, due to the complexity of transmembrane domains they are difficult to reliably identify in the predicted protein, and they may have different overall three-dimensional structures. Therefore, it is challenging to study their biological function. In this review, we describe the typical structures of transmembrane proteins and their roles in plant growth, development, and stress responses. We propose a model illustrating the roles of transmembrane proteins during plant growth and response to various stresses, which will provide important references for crop breeding.
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Nakao H, Nakano M. Flip-Flop Promotion Mechanisms by Model Transmembrane Peptides. Chem Pharm Bull (Tokyo) 2022; 70:519-523. [DOI: 10.1248/cpb.c22-00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama
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6
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Nakano M, Nakao H, Yoshida S, Fukuda M, Imai M, Ikeda K. Energetic and Structural Insights into Phospholipid Transfer from Membranes with Different Curvatures by Time-Resolved Neutron Scattering. J Phys Chem Lett 2022; 13:6024-6030. [PMID: 35748601 DOI: 10.1021/acs.jpclett.2c01080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding how lipid dynamics change with membrane curvature is important given that biological membranes constantly change their curvature and morphology through membrane fusion and endo-/exocytosis. Here, we used time-resolved small-angle neutron scattering and time-resolved fluorescence to characterize the properties and dynamics of phospholipids in vesicles with different curvatures. Dissociation of phospholipids from vesicles required traversing an energy barrier comprising positive enthalpy and negative entropy. However, lipids in membranes with high positive curvature have dense acyl chain packing and loose headgroup packing, leading to hydrophobic hydration due to water penetration into the membrane. These properties were found to lower the hydrophobic hydration enhancement associated with phospholipid dissociation and mitigate the acyl chain packing of lipids adjacent to the space created by the lipid dissociation, resulting in an increase in activation entropy. The results of this study provide important insights into the functions of biomembranes in relation to their dynamic structural changes.
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Affiliation(s)
- Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Shigeharu Yoshida
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masakazu Fukuda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Manjiro Imai
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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7
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Nakao H, Kimura Y, Sakai A, Ikeda K, Nakano M. Development of membrane-insertable lipid scrambling peptides: A time-resolved small-angle neutron scattering study. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:024301. [PMID: 33758768 PMCID: PMC7980860 DOI: 10.1063/4.0000045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/26/2021] [Indexed: 05/14/2023]
Abstract
Phospholipid transbilayer movement (flip-flop) in the plasma membrane is regulated by membrane proteins to maintain cell homeostasis and interact with other cells. The promotion of flip-flop by phospholipid scramblases causes the loss of membrane lipid asymmetry, which is involved in apoptosis, blood coagulation, and viral infection. Therefore, compounds that can artificially control flip-flop in the plasma membrane are of biological and medical interest. Here, we have developed lipid scrambling transmembrane peptides that can be inserted into the membrane. Time-resolved small-angle neutron scattering measurements revealed that the addition of peptides containing a glutamine residue at the center of the hydrophobic sequence to lipid vesicles induces the flip-flop of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. Peptides without the glutamine residue had no effect on the flip-flop. Because the glutamine-containing peptides exhibited scramblase activity in monomeric form, the polar glutamine residue would be exposed to the hydrocarbon region of the membrane, perturbing the membrane and promoting the lipid flip-flop. These scrambling peptides would be valuable tools to regulate lipid flip-flop in the plasma membrane.
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Affiliation(s)
| | | | | | | | - Minoru Nakano
- Author to whom correspondence should be addressed: . Tel.: +81 76 434 7565. Fax: +81 76 434 7568
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8
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Nielsen JE, Bjørnestad VA, Pipich V, Jenssen H, Lund R. Beyond structural models for the mode of action: How natural antimicrobial peptides affect lipid transport. J Colloid Interface Sci 2021; 582:793-802. [DOI: 10.1016/j.jcis.2020.08.094] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022]
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9
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Bubnis G, Grubmüller H. Sequential Water and Headgroup Merger: Membrane Poration Paths and Energetics from MD Simulations. Biophys J 2020; 119:2418-2430. [PMID: 33189685 PMCID: PMC7822740 DOI: 10.1016/j.bpj.2020.10.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/07/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023] Open
Abstract
Membrane topology changes such as poration, stalk formation, and hemifusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here, we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free-energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our molecular dynamics simulations, we developed a “gizmo” potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid headgroups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes.
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Affiliation(s)
- Greg Bubnis
- Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany; Weill Institute for Neurosciences and Department of Neurology, University of California San Francisco, San Francisco, California.
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
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Nakao H, Sugimoto Y, Ikeda K, Saito H, Nakano M. Structural Feature of Lipid Scrambling Model Transmembrane Peptides: Same-Side Positioning of Hydrophilic Residues and Their Deeper Position. J Phys Chem Lett 2020; 11:1662-1667. [PMID: 32058725 DOI: 10.1021/acs.jpclett.0c00175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phospholipid scramblases that catalyze lipid transbilayer movement are associated with intercellular signaling and lipid homeostasis. Although several studies have shown that the hydrophilic residue-rich groove of the proteins mediates lipid scrambling, the interactions between the groove and the lipid bilayers remain poorly understood. Here we have revealed the structural features of model transmembrane peptides that conduct lipid scrambling as well as the interactions between the peptides and the surrounding lipids by means of experimental and simulation techniques. Peptides with two strongly hydrophilic residues located on the same side of the helices and at a deeper position in the membrane exhibited high scramblase activities. All-atom molecular dynamics simulations showed that the interactions between the hydrophilic residues and lipid head groups regulate the membrane thinning and disorder near the peptides in an order that correlates with the scramblase activity of the peptides. These results provide a basis for understanding the lipid scrambling mechanisms by transmembrane regions.
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Affiliation(s)
- Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yuta Sugimoto
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroaki Saito
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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11
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Abstract
The lipid bilayer, together with embedded proteins, is the central structure in biomembranes. While artificial lipid bilayers are useful to model natural membranes, they are generally symmetric, with the same membrane lipid composition in each lipid monolayer (leaflet). In contrast, natural membranes are often asymmetric, with different lipids in each leaflet. To prepare asymmetric lipid vesicles, we developed cyclodextrin-catalyzed phospholipid exchange procedures. The basic method is that an excess of vesicles with one set of lipids (the donor vesicles) is mixed with a second set of vesicles (acceptor vesicles) with a different set of lipids. Cyclodextrin is introduced into the external aqueous solution, so that lipids in the outer leaflet of the vesicles bind to it and are shuttled between the vesicles. At equilibrium, the lipids in the outer leaflet of the acceptor vesicles are replaced by those from the donor vesicles. The exchanged acceptor vesicles are then isolated. Asymmetric vesicles are versatile in terms of vesicle sizes and lipid compositions that can be prepared. Measuring asymmetry is often difficult. A variety of assays can be used to measure the extent of asymmetry, but most are specific for one particular membrane lipid type or class, and there are none that can be used in all situations. Studies using asymmetric vesicles have begun to explore how asymmetry influences lipid movement across the bilayer, the formation of ordered lipid domains, coupling between the physical properties in each leaflet, and membrane protein conformation. Lipid domain formation stands out as one of the most important properties in which asymmetry is likely to be crucial. Lipid bilayers can exist in both liquidlike and solid/ordered-like states depending on lipid structure, and in lipid vesicles with a mixture of lipids highly ordered and disordered domains can coexist. However, until very recently, such studies only had been carried out in symmetric artificial membranes. Whether ordered domains (often called lipid rafts) and disordered lipid domains coexist in asymmetric cell membranes remains controversial partly because lipids favoring the formation of an ordered state are largely restricted to the leaflet facing the external environment. Studies using asymmetric vesicles have recently shown that each leaflet can influence the physical behavior of the other, i.e., that the domain forming properties in each leaflet tend to be coupled, with consequences highly dependent upon the details of lipid structure. Future studies investigating the dependence of coupling and properties upon the details of lipid composition should clarify the potential of natural membranes to form lipid domains. In addition, we recently extended the exchange method to living mammalian cells, using exchange to efficiently replace virtually the entire phospholipid and sphingolipid population of the plasma membrane outer leaflet with exogenous lipids without harming cells. This should allow detailed studies of the functional impact of lipid structure, asymmetry, domain organization, and interactions with membrane proteins in living cells.
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Affiliation(s)
- Erwin London
- Department of Biochemistry and Cell Biology and Department of Chemistry Stony Brook University, Stony Brook, New York 11794, United States
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Manna M, Nieminen T, Vattulainen I. Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes. Annu Rev Biophys 2019; 48:421-439. [DOI: 10.1146/annurev-biophys-052118-115553] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell signaling controls essentially all cellular processes. While it is often assumed that proteins are the key architects coordinating cell signaling, recent studies have shown more and more clearly that lipids are also involved in signaling processes in a number of ways. Lipids do, for instance, act as messengers, modulate membrane receptor conformation and dynamics, and control membrane receptor partitioning. Further, through structural modifications such as oxidation, the functions of lipids as part of signaling processes can be modified. In this context, in this article we discuss the understanding recently revealed by atomistic and coarse-grained computer simulations of nanoscale processes and underlying physicochemical principles related to lipids’ functions in cellular signaling.
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Affiliation(s)
- Moutusi Manna
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462 066, India
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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13
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Nakano M. Evaluation of Interbilayer and Transbilayer Transfer Dynamics of Phospholipids Using Time-Resolved Small-Angle Neutron Scattering. Chem Pharm Bull (Tokyo) 2019; 67:316-320. [DOI: 10.1248/cpb.c18-00942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Minoru Nakano
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama
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14
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Patel SJ, Van Lehn RC. Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer. J Phys Chem B 2018; 122:10337-10348. [PMID: 30376710 DOI: 10.1021/acs.jpcb.8b06613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cell membrane largely prevents the passive diffusion of charged molecules due to the large free energy barrier associated with translocating charged groups across the hydrophobic lipid bilayer core. Despite this barrier, some peptides can interconvert between transmembrane and surface-adsorbed states by "flipping" charged flanking loops across the bilayer on a surprisingly rapid second-minute time scale. The transmembrane helices of some multispanning membrane proteins undergo similar reorientation processes, suggesting that loop-flipping may be a mechanism for regulating membrane protein topology; however, the molecular mechanisms underlying this behavior remain unknown. In this work, we study the loop-flipping behavior exhibited by a peptide with a hydrophobic transmembrane helix, charged flanking loops, and a central, membrane-exposed aspartate residue of varying protonation state. We utilize all-atom temperature accelerated molecular dynamics simulations to predict the likelihood of loop-flipping without predefining specific loop-flipping pathways. We demonstrate that this approach can identify multiple possible flipping pathways, with the prevalence of each pathway depending on the protonation state of the central residue. In particular, we find that a charged central residue facilitates loop-flipping by stabilizing membrane water defects, enabling the "self-catalysis" of charge translocation. These findings provide detailed molecular-level insights into charged loop-flipping pathways that may generalize to other charge translocation processes, such as lipid flip-flop or the large-scale conformational rearrangements of multispanning membrane proteins.
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Affiliation(s)
- Samarthaben J Patel
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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