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Veretenenko II, Trofimov YA, Krylov NA, Efremov RG. Nanoscale lipid domains determine the dynamic molecular portraits of mixed DOPC/DOPS bilayers in a fluid phase: A computational insight. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184376. [PMID: 39111381 DOI: 10.1016/j.bbamem.2024.184376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Lateral heterogeneity, or mosaicity, is a fundamental property inherent to cell membranes that is crucial for their functioning. While microscopic inhomogeneities (e.g. rafts) are easily detected experimentally, lipid domains with nanoscale dimensions (nanoclusters of nanodomains, NDs) resist reliable characterization by instrumental methods. In such a case, important insight can be gained via computer modeling. Here, NDs composed of lipid's head groups in the mixed zwitterionic dioleoylphosphatidylcholine (DOPC) and negatively charged dioleoylphosphatidylserine (DOPS) bilayers were studied by molecular dynamics. A new algorithm has been developed to identify NDs. Unlike most similar methods, it implicitly considers the heterogeneous distribution of lipid head atomic density and does not require subjectively chosen parameters. In DOPS-rich membranes, lipids form more compact and stable NDs due to strong interlipid interactions. In DOPC-rich systems, NDs arise due to the "packing" effect of weakly bound lipid heads. The clustering picture is related to the physical properties of the bilayer surface: DOPS-rich systems show more pronounced surface heterogeneity of hydrophilic/hydrophobic regions compared to DOPC-rich ones. The results obtained are important for the effective quantitative characterization of the "dynamic molecular portrait" of a membrane surface - its "fingerprint" characterizing dynamical distribution of its physicochemical properties.
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Affiliation(s)
- Irina I Veretenenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region 141701, Russia.
| | - Yury A Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Nikolay A Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region 141701, Russia; National Research University Higher School of Economics, Moscow 101000, Russia.
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Kefauver JM, Hakala M, Zou L, Alba J, Espadas J, Tettamanti MG, Gajić J, Gabus C, Campomanes P, Estrozi LF, Sen NE, Vanni S, Roux A, Desfosses A, Loewith R. Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain. Nature 2024; 632:664-671. [PMID: 39048819 PMCID: PMC11324527 DOI: 10.1038/s41586-024-07720-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Biological membranes are partitioned into functional zones termed membrane microdomains, which contain specific lipids and proteins1-3. The composition and organization of membrane microdomains remain controversial because few techniques are available that allow the visualization of lipids in situ without disrupting their native behaviour3,4. The yeast eisosome, composed of the BAR-domain proteins Pil1 and Lsp1 (hereafter, Pil1/Lsp1), scaffolds a membrane compartment that senses and responds to mechanical stress by flattening and releasing sequestered factors5-9. Here we isolated near-native eisosomes as helical tubules made up of a lattice of Pil1/Lsp1 bound to plasma membrane lipids, and solved their structures by helical reconstruction. Our structures reveal a striking organization of membrane lipids, and, using in vitro reconstitutions and molecular dynamics simulations, we confirmed the positioning of individual PI(4,5)P2, phosphatidylserine and sterol molecules sequestered beneath the Pil1/Lsp1 coat. Three-dimensional variability analysis of the native-source eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects the sequestration of these lipids. Collectively, our results support a mechanism in which stretching of the Pil1/Lsp1 lattice liberates lipids that would otherwise be anchored by the Pil1/Lsp1 coat, and thus provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain.
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Affiliation(s)
- Jennifer M Kefauver
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), El Entrego, Spain
| | - Markku Hakala
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Luoming Zou
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Josephine Alba
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Javier Espadas
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Maria G Tettamanti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jelena Gajić
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Caroline Gabus
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Leandro F Estrozi
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Nesli E Sen
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Robbie Loewith
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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Caselli L, Conti L, De Santis I, Berti D. Small-angle X-ray and neutron scattering applied to lipid-based nanoparticles: Recent advancements across different length scales. Adv Colloid Interface Sci 2024; 327:103156. [PMID: 38643519 DOI: 10.1016/j.cis.2024.103156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
Lipid-based nanoparticles (LNPs), ranging from nanovesicles to non-lamellar assemblies, have gained significant attention in recent years, as versatile carriers for delivering drugs, vaccines, and nutrients. Small-angle scattering methods, employing X-rays (SAXS) or neutrons (SANS), represent unique tools to unveil structure, dynamics, and interactions of such particles on different length scales, spanning from the nano to the molecular scale. This review explores the state-of-the-art on scattering methods applied to unveil the structure of lipid-based nanoparticles and their interactions with drugs and bioactive molecules, to inform their rational design and formulation for medical applications. We will focus on complementary information accessible with X-rays or neutrons, ranging from insights on the structure and colloidal processes at a nanoscale level (SAXS) to details on the lipid organization and molecular interactions of LNPs (SANS). In addition, we will review new opportunities offered by Time-resolved (TR)-SAXS and -SANS for the investigation of dynamic processes involving LNPs. These span from real-time monitoring of LNPs structural evolution in response to endogenous or external stimuli (TR-SANS), to the investigation of the kinetics of lipid diffusion and exchange upon interaction with biomolecules (TR-SANS). Finally, we will spotlight novel combinations of SAXS and SANS with complementary on-line techniques, recently enabled at Large Scale Facilities for X-rays and neutrons. This emerging technology enables synchronized multi-method investigation, offering exciting opportunities for the simultaneous characterization of the structure and chemical or mechanical properties of LNPs.
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Affiliation(s)
- Lucrezia Caselli
- Physical Chemistry 1, University of Lund, S-221 00 Lund, Sweden.
| | - Laura Conti
- Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ilaria De Santis
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Debora Berti
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy; Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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Collier CP, Bolmatov D, Elkins JG, Katsaras J. Nanoscopic lipid domains determined by microscopy and neutron scattering. Methods 2024; 223:127-135. [PMID: 38331125 DOI: 10.1016/j.ymeth.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.
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Affiliation(s)
- Charles P Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Neutron Scattering Division, Oak Ridge National Laboratorry, Oak Ridege, TN, USA
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Abstract
Pulmonary surfactant is a critical component of lung function in healthy individuals. It functions in part by lowering surface tension in the alveoli, thereby allowing for breathing with minimal effort. The prevailing thinking is that low surface tension is attained by a compression-driven squeeze-out of unsaturated phospholipids during exhalation, forming a film enriched in saturated phospholipids that achieves surface tensions close to zero. A thorough review of past and recent literature suggests that the compression-driven squeeze-out mechanism may be erroneous. Here, we posit that a surfactant film enriched in saturated lipids is formed shortly after birth by an adsorption-driven sorting process and that its composition does not change during normal breathing. We provide biophysical evidence for the rapid formation of an enriched film at high surfactant concentrations, facilitated by adsorption structures containing hydrophobic surfactant proteins. We examine biophysical evidence for and against the compression-driven squeeze-out mechanism and propose a new model for surfactant function. The proposed model is tested against existing physiological and pathophysiological evidence in neonatal and adult lungs, leading to ideas for biophysical research, that should be addressed to establish the physiological relevance of this new perspective on the function of the mighty thin film that surfactant provides.
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Affiliation(s)
- Fred Possmayer
- Department of Biochemistry, Western University, London, Ontario N6A 3K7, Canada
- Department of Obstetrics/Gynaecology, Western University, London, Ontario N6A 3K7, Canada
| | - Yi Y Zuo
- Department of Mechanical Engineering, University of Hawaii at Manon, Honolulu, Hawaii 96822, United States
- Department of Pediatrics, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii 96826, United States
| | - Ruud A W Veldhuizen
- Department of Physiology & Pharmacology, Western University, London, Ontario N6A 5C1, Canada
- Department of Medicine, Western University, London, Ontario N6A 3K7, Canada
- Lawson Health Research Institute, London, Ontario N6A 4V2, Canada
| | - Nils O Petersen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry, Western University, London, Ontario N6A 5B7, Canada
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Wiedmer SK, Riekkola ML. Field-flow fractionation - an excellent tool for fractionation, isolation and/or purification of biomacromolecules. J Chromatogr A 2023; 1712:464492. [PMID: 37944435 DOI: 10.1016/j.chroma.2023.464492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Field-flow fractionation (FFF) with its several variants, has developed into a mature methodology. The scope of the FFF investigations has expanded, covering both a wide range of basic studies and especially a wide range of analytical applications. Special attention of this review is given to the achievements of FFF with reference to recent applications in the fractionation, isolation, and purification of biomacromolecules, and from which especially those of (in alphabetical order) bacteria, cells, extracellular vesicles, liposomes, lipoproteins, nucleic acids, and viruses and virus-like particles. In evaluating the major approaches and trends demonstrated since 2012, the most significant biomacromolecule applications are compiled in tables. It is also evident that asymmetrical flow field-flow fractionation is by far the most dominant technique in the studies. The industry has also shown current interest in FFF and adopted it in some sophisticated fields. FFF, in combination with appropriate detectors, handles biomacromolecules in open channel in a gentle way due to the lack of shear forces and unwanted interactions caused by the stationary phase present in chromatography. In addition, in isolation and purification of biomacromolecules quite high yields can be achieved under optimal conditions.
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Affiliation(s)
- Susanne K Wiedmer
- Department of Chemistry, POB 55, 00014 University of Helsinki, Finland
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Spinozzi F, Barbosa LRS, Corucci G, Mariani P, Itri R. Small-angle scattering from flat bilayers containing correlated scattering length density inhomogeneities. J Appl Crystallogr 2023; 56:1348-1360. [PMID: 37791360 PMCID: PMC10543680 DOI: 10.1107/s1600576723006143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/12/2023] [Indexed: 10/05/2023] Open
Abstract
Model lipid bilayers have been widely employed as a minimal system to investigate the structural properties of biological membranes by small-angle X-ray (SAXS) and neutron scattering (SANS) techniques. These have nanometre resolution and can give information regarding membrane thickness and scattering length densities (SLDs) of polar and apolar regions. However, biological membranes are complex systems containing different lipids and protein species, in which lipid domains can be dynamically assembled and disassembled. Therefore, SLD variations can occur within the biomembrane. In this work, a novel method has been developed to simulate SAXS and SANS profiles obtained from large unilamellar vesicles containing SLD inhomogeneities that are spatially correlated over the membrane surface. Such inhomogeneities are represented by cylindrical entities with equivalent SLDs. Stacking of bilayers is also included in the model, with no correlation between horizontal and vertical order. The model is applied to a lipid bilayer containing SLD inhomogeneities representing pores, lipid domains, and transmembrane, partially immersed and anchored proteins. It is demonstrated that all the structural information from the host lipid bilayer and from the SLD inhomogeneity can be consistently retrieved by a combined analysis of experimental SAXS and SANS data through the methodology proposed here.
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Affiliation(s)
- Francesco Spinozzi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Leandro R. S. Barbosa
- Institute of Physics, University of São Paulo, São Paulo, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Campinas, São Paulo, Brazil
| | - Giacomo Corucci
- Institut Laue–Langevin, Grenoble, France
- École Doctorale de Physique, Université Grenoble Alpes, Saint-Martin-d’Héres, France
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Rosangela Itri
- Institute of Physics, University of São Paulo, São Paulo, Brazil
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