1
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Oliveira IS, Pinheiro GX, Sa MLB, Gurgel PHLO, Pizzol SU, Itri R, Henriques VB, Enoki TA. The Importance of Bilayer Asymmetry in Biological Membranes: Insights from Model Membranes. MEMBRANES 2025; 15:79. [PMID: 40137031 PMCID: PMC11943618 DOI: 10.3390/membranes15030079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 02/24/2025] [Accepted: 02/26/2025] [Indexed: 03/27/2025]
Abstract
This mini-review intends to highlight the importance of bilayer asymmetry. Biological membranes are complex structures that are a physical barrier separating the external environment from the cellular content. This complex bilayer comprises an extensive lipid repertory, suggesting that the different lipid structures might play a role in the membrane. Interestingly, this vast repertory of lipids is asymmetrically distributed between leaflets that form the lipid bilayer. Here, we discuss the properties of the plasma membrane from the perspective of experimental model membranes, consisting of simplified and controlled in vitro systems. We summarize some crucial features of the exoplasmic (outer) and cytoplasmic (inner) leaflets observed through investigations using symmetric and asymmetric membranes. Symmetric model membranes for the exoplasmic leaflet have a unique lipid composition that might form a coexistence of phases, namely the liquid disordered and liquid order phases. These phase domains may appear in different sizes and shapes depending on lipid composition and lipid-lipid interactions. In contrast, symmetric model membranes for the cytoplasmic leaflet form a fluid phase. We discuss the outcomes reported in the literature for asymmetric bilayers, which vary according to lipid compositions and, consequently, reflect different intra- and inter-leaflet interactions. Interestingly, the asymmetric bilayer could show induced domains in the inner leaflet, or it could decrease the tendency of the outer leaflet to phase separation. If cells regulate the lipid composition of the plasma membrane, they can adjust the existence and sizes of the domains by tuning the lipid composition.
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Affiliation(s)
| | | | | | | | | | | | | | - Thais A. Enoki
- Institute of Physics, University of Sao Paulo, Sao Paulo 05508-090, Brazil
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2
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Segars B, Makhoul-Mansour M, Beyrouthy J, Freeman EC. Measuring the Transmembrane Registration of Lipid Domains in Droplet Interface Bilayers through Tensiometry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:11228-11238. [PMID: 38753461 PMCID: PMC11140749 DOI: 10.1021/acs.langmuir.4c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
Diverse collections of lipids self-assemble into domains within biological membranes, and these domains are typically organized in both the transverse and lateral directions of the membrane. The ability of the membrane to link these domains across the membrane's interior grants cells control over features on the external cellular surface. Numerous hypothesized factors drive the cross-membrane (or transverse) coupling of lipid domains. In this work we seek to isolate these transverse lipid-lipid influences in a simple model system using droplet interface bilayers (DIBs) to better understand the associated mechanics. DIBs enable symmetric and asymmetric combinations of domain-forming lipid mixtures within a model bilayer, and the evolving energetics of the membrane may be tracked using drop-shape analysis. We find that symmetric distributions of domain-forming lipids produce long-lasting, gradual shifts in the DIB membrane energetics that are not observed in asymmetric distributions of the lipids where the domain-forming lipids are only within one leaflet. The approach selected for this work provides experimental measurement of the mismatch penalty associated with antiregistered lipid domains as well as measurements of the influence of rafts on DIB behaviors with suggestions for their future use as a model platform.
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Affiliation(s)
- Braydon
G. Segars
- School
of Environmental, Civil, Agricultural, and Mechanical Engineering, University of Georgia, 110 Riverbend Road, Athens, Georgia 30605, United States
| | - Michelle Makhoul-Mansour
- School
of Environmental, Civil, Agricultural, and Mechanical Engineering, University of Georgia, 110 Riverbend Road, Athens, Georgia 30605, United States
- Mechanical,
Agricultural, Biomedical, and Environmental Engineering Department,
Tickle College of Engineering, University
of Tennessee Knoxville, 1512 Middle Dr., Knoxville, Tennessee 37916, United States
| | - Joyce Beyrouthy
- School
of Environmental, Civil, Agricultural, and Mechanical Engineering, University of Georgia, 110 Riverbend Road, Athens, Georgia 30605, United States
| | - Eric C. Freeman
- School
of Environmental, Civil, Agricultural, and Mechanical Engineering, University of Georgia, 110 Riverbend Road, Athens, Georgia 30605, United States
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3
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Lee Y, Park S, Yuan F, Hayden CC, Wang L, Lafer EM, Choi SQ, Stachowiak JC. Transmembrane coupling of liquid-like protein condensates. Nat Commun 2023; 14:8015. [PMID: 38049424 PMCID: PMC10696066 DOI: 10.1038/s41467-023-43332-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Liquid-liquid phase separation of proteins occurs on both surfaces of cellular membranes during diverse physiological processes. In vitro reconstitution could provide insight into the mechanisms underlying these events. However, most existing reconstitution techniques provide access to only one membrane surface, making it difficult to probe transmembrane phenomena. To study protein phase separation simultaneously on both membrane surfaces, we developed an array of freestanding planar lipid membranes. Interestingly, we observed that liquid-like protein condensates on one side of the membrane colocalized with those on the other side, resulting in transmembrane coupling. Our results, based on lipid probe partitioning and mobility of lipids, suggest that protein condensates locally reorganize membrane lipids, a process which could be explained by multiple effects. These findings suggest a mechanism by which signals originating on one side of a biological membrane, triggered by protein phase separation, can be transferred to the opposite side.
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Affiliation(s)
- Yohan Lee
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Sujin Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Feng Yuan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
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4
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Pinigin KV, Akimov SA. The Membrane-Mediated Interaction of Liquid-Ordered Lipid Domains in the Presence of Amphipathic Peptides. MEMBRANES 2023; 13:816. [PMID: 37887988 PMCID: PMC10608175 DOI: 10.3390/membranes13100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
The lipid membranes of living cells are composed of a large number of lipid types and can undergo phase separation with the formation of nanometer-scale liquid-ordered lipid domains, also called rafts. Raft coalescence, i.e., the fusion of lipid domains, is involved in important cell processes, such as signaling and trafficking. In this work, within the framework of the theory of elasticity of lipid membranes, we explore how amphipathic peptides adsorbed on lipid membranes may affect the domain-domain fusion processes. We show that the elastic deformations of lipid membranes drive amphipathic peptides to the boundary of lipid domains, which leads to an increase in the average energy barrier of the domain-domain fusion, even if the surface concentration of amphipathic peptides is low and the domain boundaries are only partially occupied by the peptides. This inhibition of the fusion of lipid domains may lead to negative side effects of using amphipathic peptides as antimicrobial agents.
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Affiliation(s)
- Konstantin V. Pinigin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Sergey A. Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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5
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Maleš P, Butumović M, Erceg I, Brkljača Z, Bakarić D. Influence of DPPE surface undulations on melting temperature determination: UV/Vis spectroscopic and MD study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184072. [PMID: 36216096 DOI: 10.1016/j.bbamem.2022.184072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/09/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022]
Abstract
One of the most distinguished quantities that describes lipid main phase transition, i.e. the transition from the gel (Lβ(')) to the fluid (Lα) phase, is its melting temperature (Tm). Because melting is accompanied by a large change in enthalpy the, Lβ(') → Lα transition can be monitored by various calorimetric, structural and spectroscopic techniques and Tm should be the same regardless of the metric monitored or the technique employed. However, in the case of DPPE multilamellar aggregates there is a small but systematic deviation of Tm values determined by DSC and FTIR spectroscopy. The aim of this paper is to explain this discrepancy by combined UV/Vis spectroscopic and MD computational approach. Multivariate analysis performed on temperature-dependent UV/Vis spectra of DPPE suspensions demonstrated that at 55 ± 1 °C certain phenomenon causes a small but detectable change in suspension turbidity, whereas a dominant change in the latter is registered at 63.2 ± 0.4 °C that coincides with Tm value determined from DSC curve. If this effect should be ignored, the overall data give Tm value the same as FTIR spectra data (61.0 ± 0.4 °C). As the classical MD simulations suggest that about 10° below Tm certain undulations appear at the surface of DPPE bilayers, we concluded that certain discontinuities in curvature fluctuations arise at reported temperature which are to some extent coupled with lipid melting. Ultimately, such events and the associated changes in curvature affect Tm value measured by different techniques.
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Affiliation(s)
- Petra Maleš
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Marija Butumović
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ina Erceg
- Division for Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Zlatko Brkljača
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Danijela Bakarić
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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6
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Maleš P, Pem B, Petrov D, Jurašin DD, Bakarić D. Deciphering the origin of the melting profile of unilamellar phosphatidylcholine liposomes by measuring the turbidity of its suspensions. SOFT MATTER 2022; 18:6703-6715. [PMID: 36017811 DOI: 10.1039/d2sm00878e] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The elucidation of the thermal properties of phosphatidylcholine liposomes is often based on the analysis of the thermal capacity profiles of multilamellar liposomes (MLV), which may qualitatively disagree with those of unilamellar liposomes (LUV). Experiments and interpretation of LUV liposomes is further complicated by aggregation and lamellarization of lipid bilayers in a short time period, which makes it almost impossible to distinguish the signatures of the two types of bilayers. To characterize independently MLV and LUV of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the latter were prepared with the addition of small amounts of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylglycerol (DPPG) which, due to the sterical hindrance and negative charge at a given pH value, cause LUV repellence and contribute to their stability. Differential scanning calorimetry curves and temperature-dependent UV/Vis spectra of the prepared MLV and LUV were measured. Multivariate analysis of spectrophotometric data determined the phase transition temperatures (pretransition at Tp and the main phase transition at Tm), and based on the changes in turbidities, the thickness of the lipid bilayer in LUV was determined. The obtained data suggested that the curvature change is a key distinguishing factor in MLV and LUV heat capacity profiles. By combining the experimental results and those obtained by MD simulations, the interfacial water layer was characterized and its contribution to the thermal properties of LUV was discussed.
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Affiliation(s)
- Petra Maleš
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Barbara Pem
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Dražen Petrov
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Darija Domazet Jurašin
- Division for Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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7
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Sharma A, Seal A, Iyer SS, Srivastava A. Enthalpic and entropic contributions to interleaflet coupling drive domain registration and antiregistration in biological membrane. Phys Rev E 2022; 105:044408. [PMID: 35590589 DOI: 10.1103/physreve.105.044408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Biological membrane is a complex self-assembly of lipids, sterols, and proteins organized as a fluid bilayer of two closely stacked lipid leaflets. Differential molecular interactions among its diverse constituents give rise to heterogeneities in the membrane lateral organization. Under certain conditions, heterogeneities in the two leaflets can be spatially synchronized and exist as registered domains across the bilayer. Several contrasting theories behind mechanisms that induce registration of nanoscale domains have been suggested. Following a recent study showing the effect of position of lipid tail unsaturation on domain registration behavior, we decided to develop an analytical theory to elucidate the driving forces that create and maintain domain registry across leaflets. Towards this, we formulated a Hamiltonian for a stacked lattice system where site variables capture the lipid molecular properties such as the position of unsaturation and various other interactions that could drive phase separation and interleaflet coupling. We solve the Hamiltonian using Monte Carlo simulations and create a complete phase diagram that reports the presence or absence of registered domains as a function of various Hamiltonian parameters. We find that the interleaflet coupling should be described as a competing enthalpic contribution due to interaction of lipid tail termini, primarily due to saturated-saturated interactions, and an interleaflet entropic contribution from overlap of unsaturated tail termini. A higher position of unsaturation is seen to provide weaker interleaflet coupling. Thermodynamically stable nanodomains could also be observed for certain points in the parameter space in our bilayer model, which were further verified by carrying out extended Monte Carlo simulations. These persistent noncoalescing registered nanodomains close to the lower end of the accepted nanodomain size range also point towards a possible "nanoscale" emulsion description of lateral heterogeneities in biological membrane leaflets.
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Affiliation(s)
- Akshara Sharma
- Department of Physics, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India
| | - Aniruddha Seal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, Khurda, Odisha 752050, India
| | - Sahithya S Iyer
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India
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8
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Saitov A, Kalutsky MA, Galimzyanov TR, Glasnov T, Horner A, Akimov SA, Pohl P. Determinants of Lipid Domain Size. Int J Mol Sci 2022; 23:ijms23073502. [PMID: 35408861 PMCID: PMC8998648 DOI: 10.3390/ijms23073502] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
Lipid domains less than 200 nm in size may form a scaffold, enabling the concerted function of plasma membrane proteins. The size-regulating mechanism is under debate. We tested the hypotheses that large values of spontaneous monolayer curvature are incompatible with micrometer-sized domains. Here, we used the transition of photoswitchable lipids from their cylindrical conformation to a conical conformation to increase the negative curvature of a bilayer-forming lipid mixture. In contrast to the hypothesis, pre-existing micrometer-sized domains did not dissipate in our planar bilayers, as indicated by fluorescence images and domain mobility measurements. Elasticity theory supports the observation by predicting the zero free energy gain for splitting large domains into smaller ones. It also indicates an alternative size-determining mechanism: The cone-shaped photolipids reduce the line tension associated with lipid deformations at the phase boundary and thus slow down the kinetics of domain fusion. The competing influence of two approaching domains on the deformation of the intervening lipids is responsible for the kinetic fusion trap. Our experiments indicate that the resulting local energy barrier may restrict the domain size in a dynamic system.
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Affiliation(s)
- Ali Saitov
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, 4020 Linz, Austria; (A.S.); (A.H.)
| | - Maksim A. Kalutsky
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia; (M.A.K.); (T.R.G.); (S.A.A.)
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Timur R. Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia; (M.A.K.); (T.R.G.); (S.A.A.)
| | - Toma Glasnov
- Institute of Chemistry, University of Graz, 8010 Graz, Austria;
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, 4020 Linz, Austria; (A.S.); (A.H.)
| | - Sergey A. Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia; (M.A.K.); (T.R.G.); (S.A.A.)
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, 4020 Linz, Austria; (A.S.); (A.H.)
- Correspondence:
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9
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Pohl P. Biophysical Reviews' "Meet the Councilor Series"-a profile of Peter Pohl. Biophys Rev 2021; 13:839-844. [PMID: 35035592 PMCID: PMC8724173 DOI: 10.1007/s12551-021-00897-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 10/30/2022] Open
Abstract
It is my pleasure to write a few words to introduce myself to the readers of Biophysical Reviews as part of the "Meet the Councilor Series." Currently, I am serving the second period as IUPAB councilor after having been elected first in 2017. Initially, I studied Biophysics in Moscow (Russia) and later Medicine in Halle (Germany). My scientific carrier took me from the Medical School of the Martin Luther University of Halle-Wittenberg, via the Leibniz Institute for Molecular Pharmacology (Berlin) and the Institute for Biology at the Humboldt University (Berlin) to the Physics Department of the Johannes Kepler University in Linz (Austria). My key research interests lie in the molecular mechanisms of transport phenomena occurring at the lipid membrane, including (i) spontaneous and facilitated transport of water and other small molecules across membranes in reconstituted systems, (ii) proton migration along the membrane surface, (iii) protein translocation, and (iv) bilayer mechanics. Training of undergraduate, graduate, and postdoctoral researchers from diverse academic disciplines has been-and shall remain-a consistent part of my work.
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Affiliation(s)
- Peter Pohl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
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10
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Pinigin KV, Galimzyanov TR, Akimov SA. Amphipathic Peptides Impede Lipid Domain Fusion in Phase-Separated Membranes. MEMBRANES 2021; 11:membranes11110797. [PMID: 34832026 PMCID: PMC8618981 DOI: 10.3390/membranes11110797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022]
Abstract
Cell membranes are heterogeneous in lipid composition which leads to the phase separation with the formation of nanoscopic liquid-ordered domains, also called rafts. There are multiple cell processes whereby the clustering of these domains into a larger one might be involved, which is responsible for such important processes as signal transduction, polarized sorting, or immune response. Currently, antimicrobial amphipathic peptides are considered promising antimicrobial, antiviral, and anticancer therapeutic agents. Here, within the framework of the classical theory of elasticity adapted for lipid membranes, we investigate how the presence of the peptides in a phase-separated membrane influences the fusion of the domains. We show that the peptides tend to occupy the boundaries of liquid-ordered domains and significantly increase the energy barrier of the domain-domain fusion, which might lead to misregulation of raft clustering and adverse consequences for normal cell processes.
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11
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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: 61] [Impact Index Per Article: 15.3] [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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12
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Kinnun JJ, Bolmatov D, Lavrentovich MO, Katsaras J. Lateral heterogeneity and domain formation in cellular membranes. Chem Phys Lipids 2020; 232:104976. [PMID: 32946808 PMCID: PMC7491465 DOI: 10.1016/j.chemphyslip.2020.104976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022]
Abstract
As early as the development of the fluid mosaic model for cellular membranes, researchers began observing the telltale signs of lateral heterogeneity. Over the decades this has led to the development of the lipid raft hypothesis and the ensuing controversy that has unfolded, as a result. Here, we review the physical concepts behind domain formation in lipid membranes, both of their structural and dynamic origins. This, then leads into a discussion of coarse-grained, phenomenological approaches that describe the wide range of phases associated with lipid lateral heterogeneity. We use these physical concepts to describe the interaction between raft-lipid species, such as long-chain saturated lipids, sphingomyelin, and cholesterol, and non-raft forming lipids, such as those with short acyl chains or unsaturated fatty acids. While debate has persisted on the biological relevance of lipid domains, recent research, described here, continues to identify biological roles for rafts and new experimental approaches have revealed the existence of lipid domains in living systems. Given the recent progress on both the biological and structural aspects of raft formation, the research area of membrane lateral heterogeneity will not only expand, but will continue to produce exciting results.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.
| | - Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
| | - Maxim O Lavrentovich
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
| | - John Katsaras
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States; Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
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13
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Sarmento MJ, Ricardo JC, Amaro M, Šachl R. Organization of gangliosides into membrane nanodomains. FEBS Lett 2020; 594:3668-3697. [DOI: 10.1002/1873-3468.13871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Maria J. Sarmento
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences Prague 8 Czech Republic
| | - Joana C. Ricardo
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences Prague 8 Czech Republic
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences Prague 8 Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences Prague 8 Czech Republic
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14
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Akimov SA, Molotkovsky RJ, Kuzmin PI, Galimzyanov TR, Batishchev OV. Continuum Models of Membrane Fusion: Evolution of the Theory. Int J Mol Sci 2020; 21:E3875. [PMID: 32485905 PMCID: PMC7312925 DOI: 10.3390/ijms21113875] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Starting from fertilization, through tissue growth, hormone secretion, synaptic transmission, and sometimes morbid events of carcinogenesis and viral infections, membrane fusion regulates the whole life of high organisms. Despite that, a lot of fusion processes still lack well-established models and even a list of main actors. A merger of membranes requires their topological rearrangements controlled by elastic properties of a lipid bilayer. That is why continuum models based on theories of membrane elasticity are actively applied for the construction of physical models of membrane fusion. Started from the view on the membrane as a structureless film with postulated geometry of fusion intermediates, they developed along with experimental and computational techniques to a powerful tool for prediction of the whole process with molecular accuracy. In the present review, focusing on fusion processes occurring in eukaryotic cells, we scrutinize the history of these models, their evolution and complication, as well as open questions and remaining theoretical problems. We show that modern approaches in this field allow continuum models of membrane fusion to stand shoulder to shoulder with molecular dynamics simulations, and provide the deepest understanding of this process in multiple biological systems.
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Affiliation(s)
- Sergey A. Akimov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (R.J.M.); (P.I.K.); (T.R.G.); (O.V.B.)
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15
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Sarmento MJ, Hof M, Šachl R. Interleaflet Coupling of Lipid Nanodomains - Insights From in vitro Systems. Front Cell Dev Biol 2020; 8:284. [PMID: 32411705 PMCID: PMC7198703 DOI: 10.3389/fcell.2020.00284] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/02/2020] [Indexed: 01/09/2023] Open
Abstract
The plasma membrane is a complex system, consisting of two layers of lipids and proteins compartmentalized into small structures called nanodomains. Despite the asymmetric composition of both leaflets, coupling between the layers is surprisingly strong. This can be evidenced, for example, by recent experimental studies performed on phospholipid giant unilamellar vesicles showing that nanodomains formed in the outer layer are perfectly registered with those in the inner leaflet. Similarly, microscopic phase separation in one leaflet can induce phase separation in the opposing leaflet that would otherwise be homogeneous. In this review, we summarize the current theoretical and experimental knowledge that led to the current view that domains are – irrespective of their size – commonly registered across the bilayer. Mechanisms inducing registration of nanodomains suggested by theory and calculations are discussed. Furthermore, domain coupling is evidenced by experimental studies based on the sparse number of methods that can resolve registered from independent nanodomains. Finally, implications that those findings using model membrane studies might have for cellular membranes are discussed.
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Affiliation(s)
- Maria J Sarmento
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova, Prague, Czechia
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova, Prague, Czechia
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova, Prague, Czechia
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16
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Saitov A, Akimov SA, Galimzyanov TR, Glasnov T, Pohl P. Ordered Lipid Domains Assemble via Concerted Recruitment of Constituents from Both Membrane Leaflets. PHYSICAL REVIEW LETTERS 2020; 124:108102. [PMID: 32216409 PMCID: PMC7115998 DOI: 10.1103/physrevlett.124.108102] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Lipid rafts serve as anchoring platforms for membrane proteins. Thus far they escaped direct observation by light microscopy due to their small size. Here we used differently colored dyes as reporters for the registration of both ordered and disordered lipids from the two leaves of a freestanding bilayer. Photoswitchable lipids dissolved or reformed the domains. Measurements of domain mobility indicated the presence of 120 nm wide ordered and 40 nm wide disordered domains. These sizes are in line with the predicted roles of line tension and membrane undulation as driving forces for alignment.
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Affiliation(s)
- Ali Saitov
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria
| | - Sergey A Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy prospekt, Moscow 119071, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy prospekt, Moscow 119071, Russia
| | - Toma Glasnov
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria
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17
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Pinigin KV, Kondrashov OV, Jiménez-Munguía I, Alexandrova VV, Batishchev OV, Galimzyanov TR, Akimov SA. Elastic deformations mediate interaction of the raft boundary with membrane inclusions leading to their effective lateral sorting. Sci Rep 2020; 10:4087. [PMID: 32139760 PMCID: PMC7058020 DOI: 10.1038/s41598-020-61110-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
Liquid-ordered lipid domains represent a lateral inhomogeneity in cellular membranes. These domains have elastic and physicochemical properties different from those of the surrounding membrane. In particular, their thickness exceeds that of the disordered membrane. Thus, elastic deformations arise at the domain boundary in order to compensate for the thickness mismatch. In equilibrium, the deformations lead to an incomplete register of monolayer ordered domains: the elastic energy is minimal if domains in opposing monolayers lie on the top of each other, and their boundaries are laterally shifted by about 3 nm. This configuration introduces a region, composed of one ordered and one disordered monolayers, with an intermediate bilayer thickness. Besides, a jump in a local monolayer curvature takes place in this intermediate region, concentrating here most of the elastic stress. This region can participate in a lateral sorting of membrane inclusions by offering them an optimal bilayer thickness and local curvature conditions. In the present study, we consider the sorting of deformable lipid inclusions, undeformable peripheral and deeply incorporated peptide inclusions, and undeformable transmembrane inclusions of different molecular geometry. With rare exceptions, all types of inclusions have an affinity to the ordered domain boundary as compared to the bulk phases. The optimal lateral distribution of inclusions allows relaxing the elastic stress at the boundary of domains.
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Affiliation(s)
- Konstantin V Pinigin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Oleg V Kondrashov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Irene Jiménez-Munguía
- National University of Science and Technology "MISiS", 4 Leninskiy prospect, Moscow, 119049, Russia
| | | | - Oleg V Batishchev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Sergey A Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia.
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18
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Ermakov YA, Sokolov VS, Akimov SA, Batishchev OV. Physicochemical and Electrochemical Aspects of the Functioning of Biological Membranes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420030085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Pohl EE, Jovanovic O. The Role of Phosphatidylethanolamine Adducts in Modification of the Activity of Membrane Proteins under Oxidative Stress. Molecules 2019; 24:E4545. [PMID: 31842328 PMCID: PMC6943717 DOI: 10.3390/molecules24244545] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/11/2022] Open
Abstract
Reactive oxygen species (ROS) and their derivatives, reactive aldehydes (RAs), have been implicated in the pathogenesis of many diseases, including metabolic, cardiovascular, and inflammatory disease. Understanding how RAs can modify the function of membrane proteins is critical for the design of therapeutic approaches in the above-mentioned pathologies. Over the last few decades, direct interactions of RA with proteins have been extensively studied. Yet, few studies have been performed on the modifications of membrane lipids arising from the interaction of RAs with the lipid amino group that leads to the formation of adducts. It is even less well understood how various multiple adducts affect the properties of the lipid membrane and those of embedded membrane proteins. In this short review, we discuss a crucial role of phosphatidylethanolamine (PE) and PE-derived adducts as mediators of RA effects on membrane proteins. We propose potential PE-mediated mechanisms that explain the modulation of membrane properties and the functions of membrane transporters, channels, receptors, and enzymes. We aim to highlight this new area of research and to encourage a more nuanced investigation of the complex nature of the new lipid-mediated mechanism in the modification of membrane protein function under oxidative stress.
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Affiliation(s)
- Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna A-1210, Austria
| | - Olga Jovanovic
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna A-1210, Austria
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20
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The Effect of Transmembrane Protein Shape on Surrounding Lipid Domain Formation by Wetting. Biomolecules 2019; 9:biom9110729. [PMID: 31726783 PMCID: PMC6920788 DOI: 10.3390/biom9110729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022] Open
Abstract
Signal transduction through cellular membranes requires the highly specific and coordinated work of specialized proteins. Proper functioning of these proteins is provided by an interplay between them and the lipid environment. Liquid-ordered lipid domains are believed to be important players here, however, it is still unclear whether conditions for a phase separation required for lipid domain formation exist in cellular membranes. Moreover, membrane leaflets are compositionally asymmetric, that could be an obstacle for the formation of symmetric domains spanning the lipid bilayer. We theoretically show that the presence of protein in the membrane leads to the formation of a stable liquid-ordered lipid phase around it by the mechanism of protein wetting by lipids, even in the absence of conditions necessary for the global phase separation in the membrane. Moreover, we show that protein shape plays a crucial role in this process, and protein conformational rearrangement can lead to changes in the size and characteristics of surrounding lipid domains.
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21
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Heerklotz H, London E. Kiss and Run Asymmetric Vesicles to Investigate Coupling. Biophys J 2019; 117:1009-1011. [PMID: 31477242 DOI: 10.1016/j.bpj.2019.07.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022] Open
Affiliation(s)
- Heiko Heerklotz
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Signalling Research Centers BIOSS and CIBSS, Freiburg, Germany.
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York.
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22
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 466] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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23
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Vinklárek IS, Vel'as L, Riegerová P, Skála K, Mikhalyov I, Gretskaya N, Hof M, Šachl R. Experimental Evidence of the Existence of Interleaflet Coupled Nanodomains: An MC-FRET Study. J Phys Chem Lett 2019; 10:2024-2030. [PMID: 30964299 DOI: 10.1021/acs.jpclett.9b00390] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plasma membranes of living cells are compartmentalized into small submicroscopic structures (nanodomains) having potentially relevant biological functions. Despite this, structural features of these nanodomains remain elusive, primarily due to the difficulties in characterizing such small dynamic entities. It is unclear whether nanodomains found in the upper bilayer leaflet are transversally registered with those found in the lower leaflet. Experiments performed on larger microscopic domains indicate that the coupling between the leaflets is strong, forcing the domains to be in perfect registration, but can the same thing be said about the biologically more relevant nanodomains? This work provides experimental evidence that even small nanodomains of variable sizes between 10 and 160 nm are interleaflet coupled. Importantly, the alternative scenarios of partially registered, independent, or antiregistered nanodomains could be excluded.
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Affiliation(s)
- Ivo S Vinklárek
- Department of Biophysical Chemistry , J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague , Czech Republic
| | - Lukáš Vel'as
- Department of Biophysical Chemistry , J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague , Czech Republic
| | - Petra Riegerová
- Department of Biophysical Chemistry , J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague , Czech Republic
| | - Kristián Skála
- Department of Biophysical Chemistry , J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague , Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science , Charles University , Hlavova 8 , CZ-12840 Prague , Czech Republic
| | - Ilya Mikhalyov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Science , Moscow GSP-7 , Russia
| | - Natalia Gretskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Science , Moscow GSP-7 , Russia
| | - Martin Hof
- Department of Biophysical Chemistry , J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague , Czech Republic
| | - Radek Šachl
- Department of Biophysical Chemistry , J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague , Czech Republic
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24
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Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. J Membr Biol 2018; 251:609-631. [PMID: 30350011 PMCID: PMC6244758 DOI: 10.1007/s00232-018-0050-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences and Centre of Excellence "Biomaterials Chemistry", Linnæus University, Kalmar, Sweden.
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, UK
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mikkel Christensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark.,Sino-Danish Center for Education and Research, Beijing, China
| | - João T S Coimbra
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Simona Concilio
- Department of Industrial Engineering, University of Salerno, Fisciano, SA, Italy
| | - Csaba Daday
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | | | - Konstantina Karathanou
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | | | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Antara Mazumdar
- GBB Institute, University of Groningen, Groningen, The Netherlands
| | - Richard Naftalin
- Physiology and Vascular Biology Departments, King's College London School of Medicine, London, UK
| | - Mónica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires, Argentina
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Peter Quinn
- Biochemistry Department, King's College London, London, UK
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
| | - Lucia Sessa
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down Bath, BA2 7AY, UK.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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25
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Effects of Passive Phospholipid Flip-Flop and Asymmetric External Fields on Bilayer Phase Equilibria. Biophys J 2018; 115:1956-1965. [PMID: 30393103 DOI: 10.1016/j.bpj.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
Compositional asymmetry between the leaflets of bilayer membranes modifies their phase behavior and is thought to influence other important features such as mechanical properties and protein activity. We address here how phase behavior is affected by passive phospholipid flip-flop, such that the compositional asymmetry is not fixed. We predict transitions from "pre-flip-flop" behavior to a restricted set of phase equilibria that can persist in the presence of passive flip-flop. Surprisingly, such states are not necessarily symmetric. We further account for external symmetry breaking, such as a preferential substrate interaction, and show how this can stabilize strongly asymmetric equilibrium states. Our theory explains several experimental observations of flip-flop-mediated changes in phase behavior and shows how domain formation and compositional asymmetry can be controlled in concert, by manipulating passive flip-flop rates and applying external fields.
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26
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Thallmair S, Ingólfsson HI, Marrink SJ. Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. J Phys Chem Lett 2018; 9:5527-5533. [PMID: 30192549 PMCID: PMC6151656 DOI: 10.1021/acs.jpclett.8b01877] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/07/2018] [Indexed: 05/25/2023]
Abstract
The plasma membrane is a highly complex multicomponent system that is central to the functioning of cells. Cholesterol, a key lipid component of the plasma membrane, promotes the formation of nanodomains. These nanodomains are often correlated across the two membrane leaflets, but the underlying physical mechanism remains unclear. Using coarse-grained molecular dynamics simulations, we investigate the influence of cholesterol flip-flop on membrane properties, in particular, the interleaflet coupling of cholesterol-enriched domains. We show that the cholesterol density correlation between the leaflets of an average mammalian plasma membrane is significantly reduced by suppressing interleaflet cholesterol population. Our results suggest an amplifying role of cholesterol in signal transduction across the leaflets.
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Affiliation(s)
- Sebastian Thallmair
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
| | - Helgi I. Ingólfsson
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, 94550 California, United States
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
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27
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Steer D, Leung SSW, Meiselman H, Topgaard D, Leal C. Structure of Lung-Mimetic Multilamellar Bodies with Lipid Compositions Relevant in Pneumonia. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7561-7574. [PMID: 29847137 DOI: 10.1021/acs.langmuir.8b01359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The hierarchical assembly of lipids, as modulated by composition and environment, plays a significant role in the function of biological membranes and a myriad of diseases. Elevated concentrations of calcium ions and cardiolipin (CL), an anionic tetra-alkyl lipid found in mitochondria and some bacterial cell membranes, have been implicated in pneumonia recently. However, their impact on the physicochemical properties of lipid assemblies in lungs and how it impairs alveoli function is still unknown. We use small- and wide-angle X-ray scattering (S/WAXS) and solid-state nuclear magnetic resonance (ssNMR) to probe the structure and dynamics of lung-mimetic multilamellar bodies (MLBs) in the presence of Ca2+ and CL. We conjecture that CL overexpressed in the hypophase of alveoli strongly affects the structure of lung-lipid bilayers and their stacking in the MLBs. Specifically, S/WAXS data revealed that CL induces significant shrinkage of the water-layer separating the concentric bilayers in multilamellar aggregates. ssNMR measurements indicate that this interbilayer tightening is due to undulation repulsion damping as CL renders the glycerol backbone of the membranes significantly more static. In addition to MLB dehydration, CL promotes intrabilayer phase separation into saturated-rich and unsaturated-rich lipid domains that couple across multiple layers. Expectedly, addition of Ca2+ screens the electrostatic repulsion between negatively charged lung membranes. However, when CL is present, addition of Ca2+ results in an apparent interbilayer expansion likely due to local structural defects. Combining S/WAXS and ssNMR on systems with compositions pertinent to healthy and unhealthy lung membranes, we propose how alteration of the physiochemical properties of MLBs can critically impact the breathing cycle.
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Affiliation(s)
| | | | | | - Daniel Topgaard
- Division of Physical Chemistry, Center of Chemistry and Chemical Engineering , Lund University , SE-221 00 Lund , Sweden
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Eicher B, Marquardt D, Heberle FA, Letofsky-Papst I, Rechberger GN, Appavou MS, Katsaras J, Pabst G. Intrinsic Curvature-Mediated Transbilayer Coupling in Asymmetric Lipid Vesicles. Biophys J 2018; 114:146-157. [PMID: 29320681 PMCID: PMC5773765 DOI: 10.1016/j.bpj.2017.11.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/30/2017] [Accepted: 11/09/2017] [Indexed: 11/16/2022] Open
Abstract
We measured the effect of intrinsic lipid curvature, J0, on structural properties of asymmetric vesicles made of palmitoyl-oleoyl-phosphatidylethanolamine (POPE; J0<0) and palmitoyl-oleoyl-phosphatidylcholine (POPC; J0∼0). Electron microscopy and dynamic light scattering were used to determine vesicle size and morphology, and x-ray and neutron scattering, combined with calorimetric experiments and solution NMR, yielded insights into leaflet-specific lipid packing and melting processes. Below the lipid melting temperature we observed strong interleaflet coupling in asymmetric vesicles with POPE inner bilayer leaflets and outer leaflets enriched in POPC. This lipid arrangement manifested itself by lipids melting cooperatively in both leaflets, and a rearrangement of lipid packing in both monolayers. On the other hand, no coupling was observed in vesicles with POPC inner bilayer leaflets and outer leaflets enriched in POPE. In this case, the leaflets melted independently and did not affect each other's acyl chain packing. Furthermore, we found no evidence for transbilayer structural coupling above the melting temperature of either sample preparation. Our results are consistent with the energetically preferred location of POPE residing in the inner leaflet, where it also resides in natural membranes, most likely causing the coupling of both leaflets. The loss of this coupling in the fluid bilayers is most likely the result of entropic contributions.
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Affiliation(s)
- Barbara Eicher
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz; BioTechMed-Graz, Graz, Austria
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Frederick A Heberle
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Ilse Letofsky-Papst
- Institute for Electron Microscopy and Nanoanalysis and Center for Electron Microscopy, Graz University of Technology, NAWI Graz
| | - Gerald N Rechberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria; Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Garching, Germany; Forschungszentrum Jülich GmbH, Institut für Festkörperforschung, Jülich Center for Neutron Science at FRM II Outstation, Garching, Germany
| | - John Katsaras
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz; BioTechMed-Graz, Graz, Austria.
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