1
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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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2
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Kiirikki AM, Antila HS, Bort LS, Buslaev P, Favela-Rosales F, Ferreira TM, Fuchs PFJ, Garcia-Fandino R, Gushchin I, Kav B, Kučerka N, Kula P, Kurki M, Kuzmin A, Lalitha A, Lolicato F, Madsen JJ, Miettinen MS, Mingham C, Monticelli L, Nencini R, Nesterenko AM, Piggot TJ, Piñeiro Á, Reuter N, Samantray S, Suárez-Lestón F, Talandashti R, Ollila OHS. Overlay databank unlocks data-driven analyses of biomolecules for all. Nat Commun 2024; 15:1136. [PMID: 38326316 PMCID: PMC10850068 DOI: 10.1038/s41467-024-45189-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.
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Affiliation(s)
- Anne M Kiirikki
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | - Hanne S Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Lara S Bort
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam-Golm, Germany
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, 99102, Zacatecas, Mexico
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Patrick F J Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), F-75005, Paris, France
- Université Paris Cité, F-75006, Paris, France
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | | | - Batuhan Kav
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
- ariadne.ai GmbH (Germany), Häusserstraße 3, 69115, Heidelberg, Germany
| | - Norbert Kučerka
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32, Bratislava, Slovakia
| | - Patrik Kula
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610, Prague, Czech Republic
| | - Milla Kurki
- School of Pharmacy, University of Eastern Finland, 70211, Kuopio, Finland
| | | | - Anusha Lalitha
- Institut Charles Gerhardt Montpellier (UMR CNRS 5253), Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, Cedex 05, France
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
| | - Jesper J Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 33612, Tampa, FL, USA
- Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, 33612, Tampa, FL, USA
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Cedric Mingham
- Hochschule Mannheim, University of Applied Sciences, 68163, Mannheim, Germany
| | - Luca Monticelli
- University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Lyon, France
| | - Ricky Nencini
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Alexey M Nesterenko
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
| | - Ángel Piñeiro
- Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Suman Samantray
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Fabián Suárez-Lestón
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
- Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
- MD.USE Innovations S.L., Edificio Emprendia, 15782, Santiago de Compostela, Spain
| | - Reza Talandashti
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - O H Samuli Ollila
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
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3
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Grad P, Edwards K, Gedda L, Agmo Hernández V. A closer look at calcium-induced interactions between phosphatidylserine-(PS) doped liposomes and the structural effects caused by inclusion of gangliosides or polyethylene glycol- (PEG) modified lipids. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184253. [PMID: 37979667 DOI: 10.1016/j.bbamem.2023.184253] [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: 08/07/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
The effects of polyethylene glycol- (PEG) modified lipids and gangliosides on the Ca2+ induced interaction between liposomes composed of palmitoyl-oleoyl phosphatidylethanolamine (POPE) and palmitoyl-oleoyl phosphatidylserine (POPS) was investigated at physiological ionic strength. Förster resonance energy transfer (FRET) studies complemented with dynamic light scattering (DLS) and cryo-transmission electron microscopy (Cryo-EM) show that naked liposomes tend to adhere, rupture, and collapse on each other's surfaces upon addition of Ca2+, eventually resulting in the formation of large multilamellar aggregates and bilayer sheets. Noteworthy, the presence of gangliosides or PEGylated lipids does not prevent the adhesion-rupture process, but leads to the formation of small, long-lived bilayer fragments/disks. PEGylated lipids seem to be more effective than gangliosides at stabilizing these structures. Attractive interactions arising from ion correlation are proposed to be a driving force for the liposome-liposome adhesion and rupture processes. The results suggest that, in contrast with the conclusions drawn from previous solely FRET-based studies, direct liposome-liposome fusion is not the dominating process triggered by Ca2+ in the systems studied.
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Affiliation(s)
- Philipp Grad
- Department of Chemistry-Ångström, Uppsala University, Box 573, 75123 Uppsala, Sweden
| | - Katarina Edwards
- Department of Chemistry-Ångström, Uppsala University, Box 573, 75123 Uppsala, Sweden.
| | - Lars Gedda
- Department of Chemistry-Ångström, Uppsala University, Box 573, 75123 Uppsala, Sweden.
| | - Víctor Agmo Hernández
- Department of Medicinal Chemistry, Uppsala University, Box 574, 75123 Uppsala, Sweden.
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4
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Żak A, Korshunova K, Rajtar N, Kulig W, Kepczynski M. Deciphering Lipid Arrangement in Phosphatidylserine/Phosphatidylcholine Mixed Membranes: Simulations and Experiments. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18995-19007. [PMID: 38096496 PMCID: PMC10753890 DOI: 10.1021/acs.langmuir.3c03061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/27/2023]
Abstract
Phosphatidylserine (PS) exposure on the plasma membrane is crucial for many cellular processes including apoptotic cell recognition, blood clotting regulation, cellular signaling, and intercellular interactions. In this study, we investigated the arrangement of PS headgroups in mixed PS/phosphatidylcholine (PC) bilayers, serving as a simplified model of the outer leaflets of mammalian cell plasma membranes. Combining atomistic-scale molecular dynamics (MD) simulations with Langmuir monolayer experiments, we unraveled the mutual miscibility of POPC and POPS lipids and the intricate intermolecular interactions inherent to these membranes as well as the disparities in position and orientation of PC and PS headgroups. Our experiments revealed micrometer-scale miscibility at all mole fractions of POPC and POPS, marked by modest deviations from ideal mixing with no apparent microscale phase separation. The MD simulations, meanwhile, demonstrated that these deviations were due to strong electrostatic interactions between like-lipid pairs (POPC-POPC and POPS-POPS), culminating in lateral segregation and nanoscale clustering. Notably, PS headgroups profoundly affect the ordering of the lipid acyl chains, leading to lipid elongation and subtle PS protrusion above the zwitterionic membrane. In addition, PC headgroups are more tilted with respect to the membrane normal, while PS headgroups align at a smaller angle, making them more exposed to the surface of the mixed PC/PS membranes. These findings provide a detailed molecular-level account of the organization of mixed PC/PS membranes, corroborated by experimental data. The insights gained here extend our comprehension of the physiological role of PSs.
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Affiliation(s)
- Agata Żak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Ksenia Korshunova
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Natan Rajtar
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Waldemar Kulig
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Mariusz Kepczynski
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
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5
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Jain H, Karathanou K, Bondar AN. Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes. Biomolecules 2023; 13:1238. [PMID: 37627303 PMCID: PMC10452392 DOI: 10.3390/biom13081238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.
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Affiliation(s)
- Honey Jain
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- IAS-5/INM-9, Forschungszentrum Jülich, Institute of Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany
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6
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Dorsch AD, da Silva Brito WA, Delcea M, Wende K, Bekeschus S. Lipid Corona Formation on Micro- and Nanoplastic Particles Modulates Uptake and Toxicity in A549 Cells. MATERIALS (BASEL, SWITZERLAND) 2023; 16:5082. [PMID: 37512356 PMCID: PMC10386368 DOI: 10.3390/ma16145082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Plastic waste is a global issue leaving no continents unaffected. In the environment, ultraviolet radiation and shear forces in water and land contribute to generating micro- and nanoplastic particles (MNPP), which organisms can easily take up. Plastic particles enter the human food chain, and the accumulation of particles within the human body is expected. Crossing epithelial barriers and cellular uptake of MNPP involves the interaction of plastic particles with lipids. To this end, we generated unilamellar vesicles from POPC (1-palmitoyl-2-oleoyl-glycero-3-phosphocholine) and POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine) and incubated them with pristine, carboxylated, or aminated polystyrene spheres (about 1 µm in diameter) to generate lipid coronas around the particles. Lipid coronas enhanced the average particle sizes and partially changed the MNPP zeta potential and polydispersity. In addition, lipid coronas led to significantly enhanced uptake of MNPP particles but not their cytotoxicity, as determined by flow cytometry. Finally, adding proteins to lipid corona nanoparticles further modified MNPP uptake by reducing the uptake kinetics, especially in pristine and carboxylated plastic samples. In conclusion, our study demonstrates for the first time the impact of different types of lipids on differently charged MNPP particles and the biological consequences of such modifications to better understand the potential hazards of plastic exposure.
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Affiliation(s)
- Anna Daniela Dorsch
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Walison Augusto da Silva Brito
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Department of General Pathology, State University of Londrina, Rodovia Celso Garcia Cid, Londrina 86057-970, Brazil
| | - Mihaela Delcea
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Kristian Wende
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Sander Bekeschus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Clinic and Policlinic for Dermatology and Venerology, Rostock University Medical Center, Strempelstr. 13, 18057 Rostock, Germany
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7
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Hmam O, Côté-Dubuc F, Badia A. Gold-Supported Lipid Membranes Formed by Redox-Triggered Vesicle Fusion on Binary Self-Assembled Monolayers: Ion-Pairing Association and Surface Hydrophilicity. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37223998 DOI: 10.1021/acsami.3c03526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The assembly of biomimetic, planar supported lipid bilayers (SLBs) by the popular vesicle fusion method, which relies on the spontaneous adsorption and rupture of small unilamellar vesicles from aqueous solution on a solid surface, typically works with a limited range of support materials and lipid systems. We previously reported a conceptual advance in the formation of SLBs from vesicles in the gel or fluid phase using the interfacial ion-pairing association of charged phospholipid headgroups with electrochemically generated cationic ferroceniums bound to a self-assembled monolayer (SAM) chemisorbed to gold. This redox-driven approach lays down a single bilayer membrane on the SAM-modified gold surface at room temperature within minutes and is compatible with both anionic and zwitterionic phospholipids. The present work explores the effects of the surface ferrocene concentration and hydrophobicity/hydrophilicity on the formation of continuous SLBs of dialkyl phosphatidylserine, dialkyl phosphatidylglycerol, and dialkyl phosphatidylcholine using binary SAMs of ferrocenylundecanethiolate (FcC11S) and dodecanethiolate (CH3C11S) or hydroxylundecanethiolate (HOC11S) comprising different surface mole fractions of ferrocene (χFcsurf). An increase in the surface hydrophilicity and surface free energy of the FcC11S/HOC11S SAM mitigates the decrease in the attractive ion-pairing interactions resulting from a reduced χFcsurf. SLBs of ≳80% area coverage form on the FcC11S/HOC11S SAM for all the phospholipid types down to χFcsurf of at least 0.2, composition yielding a water contact angle (θW) of 44 ± 4°. By contrast, a greater number of ion-pairing interactions is required on the hydrophobic FcC11S/CH3C11S surface to drive the vesicle fusion process; bilayers or bilayer patches form at χFcsurf ≳ 0.6 (θW = 97 ± 3°). These findings will aid in tailoring the surface chemistry of redox-active modified surfaces to widen the conditions that yield supported lipid membranes.
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Affiliation(s)
- Ons Hmam
- Département de chimie, Quebec Centre for Advanced Materials and Regroupement québécois sur les matériaux de pointe, Université de Montréal, Complexe des sciences, C.P. 6128, succursale Centre-ville, Montréal, Quebec H3C 3J7, Canada
| | - Félix Côté-Dubuc
- Département de chimie, Quebec Centre for Advanced Materials and Regroupement québécois sur les matériaux de pointe, Université de Montréal, Complexe des sciences, C.P. 6128, succursale Centre-ville, Montréal, Quebec H3C 3J7, Canada
| | - Antonella Badia
- Département de chimie, Quebec Centre for Advanced Materials and Regroupement québécois sur les matériaux de pointe, Université de Montréal, Complexe des sciences, C.P. 6128, succursale Centre-ville, Montréal, Quebec H3C 3J7, Canada
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8
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Martin A, Jemmett PN, Howitt T, Wood MH, Burley AW, Cox LR, Dafforn TR, Welbourn RJL, Campana M, Skoda MW, Thompson JJ, Hussain H, Rawle JL, Carlà F, Nicklin CL, Arnold T, Horswell SL. Effect of Anionic Lipids on Mammalian Plasma Cell Membrane Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2676-2691. [PMID: 36757323 PMCID: PMC9948536 DOI: 10.1021/acs.langmuir.2c03161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The effect of lipid composition on models of the inner leaflet of mammalian cell membranes has been investigated. Grazing incidence X-ray diffraction and X-ray and neutron reflectivity have been used to characterize lipid packing and solvation, while electrochemical and infrared spectroscopic methods have been employed to probe phase behavior in an applied electric field. Introducing a small quantity of the anionic lipid dimyristoylphosphatidylserine (DMPS) into bilayers of zwitterionic dimyristoylphosphatidylethanolamine (DMPE) results in a significant change in the bilayer response to an applied field: the tilt of the hydrocarbon chains increases before returning to the original tilt angle on detachment of the bilayer. Equimolar mixtures, with slightly closer chain packing, exhibit a similar but weaker response. The latter also tend to incorporate more solvent during this electrochemical phase transition, at levels similar to those of pure DMPS. Reflectivity measurements reveal greater solvation of lipid layers for DMPS > 30 mol %, matching the greater propensity for DMPS-rich bilayers to incorporate water. Taken together, the data indicate that the range of 10-35 mol % DMPS provides optimum bilayer properties (in flexibility and function as a barrier), which may explain why the DMPS content of cell membranes tends to be found within this range.
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Affiliation(s)
- Alexandra
L. Martin
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Philip N. Jemmett
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Thomas Howitt
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Mary H. Wood
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Andrew W. Burley
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Liam R. Cox
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Timothy R. Dafforn
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
| | - Rebecca J. L. Welbourn
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Mario Campana
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Maximilian W.
A. Skoda
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Joseph J. Thompson
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Hadeel Hussain
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Jonathan L. Rawle
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Francesco Carlà
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Christopher L. Nicklin
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
| | - Thomas Arnold
- ISIS
Pulsed Neutron and Muon Source, Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
- Diamond
Light Source, Harwell Science and Innovation
Campus, Chilton, Didcot, OxfordshireOX11 0DE, U.K.
- European
Spallation Source ERIC PO Box 176, SE-221 00Lund, Sweden
- Department
of Chemistry, University of Bath, Claverton Down, BathBA2 7AY, U.K.
| | - Sarah L. Horswell
- School of
Chemistry and School of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, U.K.
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9
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Pašalić L, Pem B, Bakarić D. Lamellarity-Driven Differences in Surface Structural Features of DPPS Lipids: Spectroscopic, Calorimetric and Computational Study. MEMBRANES 2023; 13:83. [PMID: 36676890 PMCID: PMC9865892 DOI: 10.3390/membranes13010083] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/27/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Although single-lipid bilayers are usually considered models of eukaryotic plasma membranes, their research drops drastically when it comes to exclusively anionic lipid membranes. Being a major anionic phospholipid in the inner leaflet of eukaryote membranes, phosphatidylserine-constituted lipid membranes were occasionally explored in the form of multilamellar liposomes (MLV), but their inherent instability caused a serious lack of efforts undertaken on large unilamellar liposomes (LUVs) as more realistic model membrane systems. In order to compensate the existing shortcomings, we performed a comprehensive calorimetric, spectroscopic and MD simulation study of time-varying structural features of LUV made from 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS), whereas the corresponding MLV were examined as a reference. A substantial uncertainty of UV/Vis data of LUV from which only Tm was unambiguously determined (53.9 ± 0.8 °C), along with rather high uncertainty on the high-temperature range of DPPS melting profile obtained from DSC (≈50-59 °C), presumably reflect distinguished surface structural features in LUV. The FTIR signatures of glycerol moiety and those originated from carboxyl group serve as a strong support that in LUV, unlike in MLV, highly curved surfaces occur continuously, whereas the details on the attenuation of surface features in MLV were unraveled by molecular dynamics.
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10
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Heller WT. Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes. Biomolecules 2022; 12:1591. [PMID: 36358941 PMCID: PMC9687511 DOI: 10.3390/biom12111591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 09/23/2023] Open
Abstract
Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.
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Affiliation(s)
- William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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11
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Nasrollahpour M, Vafaee M, Razzaghi S. Structural and Dynamical Properties of Palmitoyl-Oleoyl Phosphatidylserine Lipid Nanotubes Containing Cholesterols and PEGylated Dioleoyl Phosphatidylethanolamine: A Coarse-Grained Molecular Dynamics Simulation. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Robertson MJ, Skiniotis G. Development of OPLS-AA/M Parameters for Simulations of G Protein-Coupled Receptors and Other Membrane Proteins. J Chem Theory Comput 2022; 18:4482-4489. [PMID: 35687850 DOI: 10.1021/acs.jctc.2c00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) and other membrane proteins are valuable drug targets, and their dynamic nature makes them attractive systems for study with molecular dynamics (MD) simulations and free energy approaches. Here, we report the development, implementation, and validation of OPLS-AA/M force field parameters to enable simulations of these systems. These efforts include the introduction of post-translational modifications including lipidations and phosphorylation. We also modify previously reported parameters for lipids to be more consistent with the OPLS-AA force field standard and extend their coverage. These new parameters are validated on a variety of test systems, with the results compared to high-level quantum mechanics calculations, experimental data, and simulations with other force fields. The results demonstrate that the new parameters reliably reproduce the behavior of membrane protein systems.
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Affiliation(s)
- Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
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13
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Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
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14
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Karathanou K, Bondar AN. Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183859. [PMID: 34999081 DOI: 10.1016/j.bbamem.2022.183859] [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: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.
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15
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New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition. Int J Mol Sci 2022; 23:ijms23052437. [PMID: 35269583 PMCID: PMC8910288 DOI: 10.3390/ijms23052437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/10/2022] Open
Abstract
The fourth enzymatic reaction in the de novo pyrimidine biosynthesis, the oxidation of dihydroorotate to orotate, is catalyzed by dihydroorotate dehydrogenase (DHODH). Enzymes belonging to the DHODH Class II are membrane-bound proteins that use ubiquinones as their electron acceptors. We have designed this study to understand the interaction of an N-terminally truncated human DHODH (HsΔ29DHODH) and the DHODH from Escherichia coli (EcDHODH) with ubiquinone (Q10) in supported lipid membranes using neutron reflectometry (NR). NR has allowed us to determine in situ, under solution conditions, how the enzymes bind to lipid membranes and to unambiguously resolve the location of Q10. Q10 is exclusively located at the center of all of the lipid bilayers investigated, and upon binding, both of the DHODHs penetrate into the hydrophobic region of the outer lipid leaflet towards the Q10. We therefore show that the interaction between the soluble enzymes and the membrane-embedded Q10 is mediated by enzyme penetration. We can also show that EcDHODH binds more efficiently to the surface of simple bilayers consisting of 1-palmitoyl, 2-oleoyl phosphatidylcholine, and tetraoleoyl cardiolipin than HsΔ29DHODH, but does not penetrate into the lipids to the same degree. Our results also highlight the importance of Q10, as well as lipid composition, on enzyme binding.
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16
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Abstract
![]()
We extend the modular AMBER lipid
force field to include anionic
lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin,
allowing the simulation of realistic cell membrane lipid compositions,
including raft-like domains. Head group torsion parameters are revised,
resulting in improved agreement with NMR order parameters, and hydrocarbon
chain parameters are updated, providing a better match with phase
transition temperature. Extensive validation runs (0.9 μs per
lipid type) show good agreement with experimental measurements. Furthermore,
the simulation of raft-like bilayers demonstrates the perturbing effect
of increasing PUFA concentrations on cholesterol molecules. The force
field derivation is consistent with the AMBER philosophy, meaning
it can be easily mixed with protein, small molecule, nucleic acid,
and carbohydrate force fields.
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Affiliation(s)
- Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ross C Walker
- GlaxoSmithKline PLC, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ian R Gould
- Department of Chemistry, Imperial College London, London, SW7 2AZ, U.K
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17
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Identifying Membrane Lateral Organization by Contrast-Matched Small Angle Neutron Scattering. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2402:163-177. [PMID: 34854044 DOI: 10.1007/978-1-0716-1843-1_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lipid domains in model membranes are routinely studied to provide insight into the physical interactions that drive raft formation in cellular membranes. Using small angle neutron scattering, contrast-matching techniques enable the detection of lipid domains ranging from tens to hundreds of nanometers which are not accessible to other techniques without the use of extrinsic probes. Here, we describe a probe-free experimental approach and model-free analysis to identify lipid domains in freely floating vesicles of ternary phase separating lipid mixtures.
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18
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Bohinc K, Špadina M, Reščič J, Shimokawa N, Spada S. Influence of Charge Lipid Head Group Structures on Electric Double Layer Properties. J Chem Theory Comput 2021; 18:448-460. [PMID: 34937343 PMCID: PMC8757465 DOI: 10.1021/acs.jctc.1c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this study we
derived a model for a multicomponent lipid monolayer
in contact with an aqueous solution by means of a generalized classical
density functional theory and Monte Carlo simulations. Some of the
important biological lipid systems were studied as monolayers composed
of head groups with different shapes and charge distributions. Starting
from the free energy of the system, which includes the electrostatic
interactions, additional internal degrees of freedom are included
as positional and orientational entropic contributions to the free
energy functional. The calculus of variation was used to derive Euler–Lagrange
equations, which were solved numerically by the finite element method.
The theory and Monte Carlo simulations predict that there are mainly
two distinct regions of the electric double layer: (1) the interfacial
region, with thickness less than or equal to the length of the fully
stretched conformation of the lipid head group, and (2) the outside
region, which follows the usual screening of the interface. In the
interfacial region, the electric double layer is strongly perturbed,
and electrostatic profiles and ion distributions have functionality
distinct to classical mean-field theories. Based purely on Coulomb
interactions, the theory suggests that the dominant effect on the
lipid head group conformation is from the charge density of the interface
and the structured lipid mole fraction in the monolayer, rather than
the salt concentration in the system.
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Affiliation(s)
- Klemen Bohinc
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Mario Špadina
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Naofumi Shimokawa
- Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Simone Spada
- National Institute of Oceanography and Applied Geophysics - OGS, 34010 Trieste, Italy
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19
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Lewis-Laurent A, Doktorova M, Heberle FA, Marquardt D. Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles. Biophys J 2021; 120:4639-4648. [PMID: 34571013 DOI: 10.1016/j.bpj.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022] Open
Abstract
Small-angle X-ray and neutron scattering are among the most powerful experimental techniques for investigating the structure of biological membranes. Much of the critical information contained in small-angle scattering (SAS) data is not easily accessible to researchers who have limited time to analyze results by hand or to nonexperts who may lack the necessary scientific background to process such data. Easy-to-use data visualization software can allow them to take full advantage of their SAS data and maximize the use of limited resources. To this end, we developed an internet-based application called Vesicle Viewer to visualize and analyze SAS data from unilamellar lipid bilayer vesicles. Vesicle Viewer utilizes a modified scattering density profile (SDP) analysis called EZ-SDP in which key bilayer structural parameters, such as area per lipid and bilayer thickness, are easily and robustly determined. Notably, we introduce a bilayer model that is able to describe an asymmetric bilayer, whether it be chemically or isotopically asymmetric. The application primarily uses Django, a Python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project; notable examples are Matplotlib (for graphs) and NumPy (for calculations). By eliminating the barrier of downloading and installing software, this web-based application will allow scientists to analyze their own vesicle scattering data using their preferred operating system. The web-based application can be found at https://vesicleviewer.dmarquardt.ca/.
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Affiliation(s)
- Aislyn Lewis-Laurent
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | | | - Drew Marquardt
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada; Department of Physics, University of Windsor, Windsor, Ontario, Canada.
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20
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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21
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Nasedkin A, Ermilova I, Swenson J. Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:927-940. [PMID: 34215900 PMCID: PMC8448678 DOI: 10.1007/s00249-021-01553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Microtubules are essential parts of the cytoskeleton that are built by polymerization of tubulin heterodimers into a hollow tube. Regardless that their structures and functions have been comprehensively investigated in a modern soft matter, it is unclear how properties of tubulin heterodimer influence and promote the self-assembly. A detailed knowledge of such structural mechanisms would be helpful in drug design against neurodegenerative diseases, cancer, diabetes etc. In this work atomistic molecular dynamics simulations were used to investigate the fundamental dynamics of tubulin heterodimers in a sheet and a short microtubule utilizing well-equilibrated structures. The breathing motions of the tubulin heterodimers during assembly show that the movement at the lateral interface between heterodimers (wobbling) dominates in the lattice. The simulations of the protofilament curvature agrees well with recently published experimental data, showing curved protofilaments at polymerization of the microtubule plus end. The tubulin heterodimers exposed at the microtubule minus end were less curved and displayed altered interactions at the site of sheet closure around the outmost heterodimers, which may slow heterodimer binding and polymerization, providing a potential explanation for the limited dynamics observed at the minus end.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
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22
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Frewein MPK, Doktorova M, Heberle FA, Scott HL, Semeraro EF, Porcar L, Pabst G. Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase. Symmetry (Basel) 2021; 13. [PMID: 35530371 PMCID: PMC9075682 DOI: 10.3390/sym13081441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.
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Affiliation(s)
- Moritz P. K. Frewein
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- Institut Laue-Langevin, 38043 Grenoble, France
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Haden L. Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Enrico F. Semeraro
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | | | - Georg Pabst
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-380-4989
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23
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Silin VI, Hoogerheide DP. pH dependent electrical properties of the inner- and outer- leaflets of biomimetic cell membranes. J Colloid Interface Sci 2021; 594:279-289. [PMID: 33765647 DOI: 10.1016/j.jcis.2021.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
Composition and asymmetry of lipid membranes provide a means for regulation of trans-membrane permeability of ions and small molecules. The pH dependence of these processes plays an important role in the functioning and survival of cells. In this work, we study the pH dependence of membrane electrical resistance and capacitance using electrochemical impedance spectroscopy (EIS), surface plasmon resonance (SPR) and neutron reflectometry (NR) measurements of biomimetic tethered bilayer lipid membranes (tBLMs). tBLMs were prepared with single-component phospholipid compositions, as well as mixtures of phospholipids (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingomyelin and cholesterol) that mimic the inner- and outer- leaflets of plasma cell membranes. We found that all studied tBLMs have a resistance maximum at pHs near the pKas of the phospholipids. SPR and NR indicated that surface concentration of phospholipids and the thickness of the hydrophobic part of the membrane did not change versus pH. We postulate that these maxima are the result of protonation of the phosphate oxygen of the phospholipids and that hydronium ions play a major role in the conductance at pHs < pKas while sodium ions play the major role at pHs > pKas. An additional sharp resistance maximum of the PE tBLMs found at pH 5.9 and most likely represents the phosphatidylethanolamine's isoelectric point. The data show the key roles of the characteristic parts of phospholipid molecules: terminal group (choline, carboxyl, amine), phosphate, glycerol and ester oxygens on the permeability and selectivity of ions through the membrane. The interactions between these groups lead to significant differences in the electrical properties of biomimetic models of inner- and outer- leaflets of the plasma cell membranes.
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Affiliation(s)
- Vitalii I Silin
- University of Maryland, Institute for Bioscience and Biotechnology Research, Rockville MD 20850, USA.
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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24
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Song DH, Garcia G, Situ K, Chua BA, Hong MLO, Do EA, Ramirez CM, Harui A, Arumugaswami V, Morizono K. Development of a blocker of the universal phosphatidylserine- and phosphatidylethanolamine-dependent viral entry pathways. Virology 2021; 560:17-33. [PMID: 34020328 DOI: 10.1016/j.virol.2021.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022]
Abstract
Envelope phosphatidylserine (PtdSer) and phosphatidylethanolamine (PtdEtr) have been shown to mediate binding of enveloped viruses. However, commonly used PtdSer binding molecules such as Annexin V cannot block PtdSer-mediated viral infection. Lack of reagents that can conceal envelope PtdSer and PtdEtr and subsequently inhibit infection hinders elucidation of the roles of the envelope phospholipids in viral infection. Here, we developed sTIM1dMLDR801, a reagent capable of blocking PtdSer- and PtdEtr-dependent infection of enveloped viruses. Using sTIM1dMLDR801, we found that envelope PtdSer and/or PtdEtr can support ZIKV infection of not only human but also mosquito cells. In a mouse model for ZIKV infection, sTIM1dMLDR801 reduced ZIKV load in serum and the spleen, indicating envelope PtdSer and/or PtdEtr support in viral infection in vivo. sTIM1dMLDR801 will enable elucidation of the roles of envelope PtdSer and PtdEtr in infection of various virus species, thereby facilitating identification of their receptors and transmission mechanisms.
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Affiliation(s)
- Da-Hoon Song
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Kathy Situ
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Bernadette A Chua
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Madeline Lauren O Hong
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Elyza A Do
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Christina M Ramirez
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| | - Airi Harui
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
| | - Kouki Morizono
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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25
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Kinnun JJ, Scott HL, Ashkar R, Katsaras J. Biomembrane Structure and Material Properties Studied With Neutron Scattering. Front Chem 2021; 9:642851. [PMID: 33987167 PMCID: PMC8110834 DOI: 10.3389/fchem.2021.642851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, United States.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Shull-Wollan Center, Oak Ridge, TN, United States.,Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, United States
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26
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Vasquez-Montes V, Ladokhin AS. Expanding MPEx Hydropathy Analysis to Account for Electrostatic Contributions to Protein Interactions with Anionic Membranes. J Membr Biol 2021; 254:109-117. [PMID: 33564913 DOI: 10.1007/s00232-021-00170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022]
Abstract
Hydropathy plots are a crucial tool to guide experimental design, as they generate predictions of protein-membrane interactions and their bilayer topology. The predictions are based on experimentally determined hydrophobicity scales, which provide an estimate for the propensity and stability of these interactions. A significant improvement to the accuracy of hydropathy analyses was provided by the development of the popular Wimley-White interfacial and octanol hydrophobicity scales. These scales have been previously incorporated into the freely available MPEx (Membrane Protein Explorer) online application. Here, we introduce a substantial update to MPEx that allows for the consideration of electrostatic contributions to the bilayer partitioning free energy. This component originates from the Coulombic attraction or repulsion of charges between proteins and membranes. Its inclusion in hydropathy calculations increases the accuracy of hydropathy plot predictions and extends their use to more complex systems (i.e., anionic membranes). We illustrate the application of this analysis to studies on the membrane selectivity of antimicrobial peptides, the membrane partitioning of ion-channel gating modifiers, and the amyloid proteins α-synuclein and Tau, as well as pH-dependent bilayer interactions of diphtheria toxin and apoptotic inhibitor Bcl-xL.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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27
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Qian S, Sharma VK, Clifton LA. Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15189-15211. [PMID: 33300335 DOI: 10.1021/acs.langmuir.0c02516] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H2O/D2O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.
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Affiliation(s)
- Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Veerendra Kumar Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, U.K. OX11 0QX
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28
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Lombardo D, Calandra P, Kiselev MA. Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments. Molecules 2020; 25:E5624. [PMID: 33260426 PMCID: PMC7730346 DOI: 10.3390/molecules25235624] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Scattering techniques represent non-invasive experimental approaches and powerful tools for the investigation of structure and conformation of biomaterial systems in a wide range of distances, ranging from the nanometric to micrometric scale. More specifically, small-angle X-rays and neutron scattering and light scattering techniques represent well-established experimental techniques for the investigation of the structural properties of biomaterials and, through the use of suitable models, they allow to study and mimic various biological systems under physiologically relevant conditions. They provide the ensemble averaged (and then statistically relevant) information under in situ and operando conditions, and represent useful tools complementary to the various traditional imaging techniques that, on the contrary, reveal more local structural information. Together with the classical structure characterization approaches, we introduce the basic concepts that make it possible to examine inter-particles interactions, and to study the growth processes and conformational changes in nanostructures, which have become increasingly relevant for an accurate understanding and prediction of various mechanisms in the fields of biotechnology and nanotechnology. The upgrade of the various scattering techniques, such as the contrast variation or time resolved experiments, offers unique opportunities to study the nano- and mesoscopic structure and their evolution with time in a way not accessible by other techniques. For this reason, highly performant instruments are installed at most of the facility research centers worldwide. These new insights allow to largely ameliorate the control of (chemico-physical and biologic) processes of complex (bio-)materials at the molecular length scales, and open a full potential for the development and engineering of a variety of nano-scale biomaterials for advanced applications.
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Affiliation(s)
- Domenico Lombardo
- CNR-IPCF, Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici, 98158 Messina, Italy
| | - Pietro Calandra
- CNR-ISMN, Consiglio Nazionale delle Ricerche, Istituto Studio Materiali Nanostrutturati, 00015 Roma, Italy;
| | - Mikhail A. Kiselev
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980 Moscow, Russia;
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29
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Lipid headgroups alter huntingtin aggregation on membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183497. [PMID: 33130095 DOI: 10.1016/j.bbamem.2020.183497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022]
Abstract
Huntington's Disease is a fatal neurodegenerative disorder caused by expansion of a glutamine repeat region (polyQ) beyond a critical threshold within exon1 of the huntingtin protein (htt). As a consequence of polyQ expansion, htt associates into a variety of aggregate species that are thought to underlie cellular toxicity. Within cells, htt associates with numerous membranous organelles and surfaces that exert influence on the aggregation process. In particular, the first 17 amino acids at the N-terminus of htt (Nt17) serve as a lipid-binding domain that is intrinsically disordered in bulk solution but adopts an amphipathic α-helical structure upon binding membranes. Beyond this, Nt17 is implicated in initiating htt fibrillization. As the interaction between Nt17 and lipid membranes is likely influenced by lipid properties, the impact of lipid headgroups on htt-exon1 aggregation, membrane activity, and the ability to form protein:lipid complexes was determined. Htt-exon1 with a disease-length polyQ domain (46Q) was exposed to lipid vesicles comprised of lipids with either zwitterionic (POPC and POPE) or anionic (POPG and POPS) headgroups. With zwitterionic head groups, large lipid to peptide ratios were required to have a statistically significant impact on htt aggregation. Anionic lipids enhanced htt fibrillization, even at low lipid:protein ratios, and this was accompanied by changes in aggregate morphology. Despite the larger impact of anionic lipids, htt-exon1(46Q) was more membrane active with zwitterionic lipid systems. The ability of Nt17 to form complexes with lipids was also mediated by lipid headgroups as zwitterionic ionic lipids more readily associated with multimeric forms of Nt17 in comparison with anionic lipids. Collectively, these results highlight the complexity of htt/membrane interactions and the resulting impact on the aggregation process.
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30
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Doktorova M, Kučerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. J Phys Chem B 2020; 124:5186-5200. [PMID: 32468822 DOI: 10.1021/acs.jpcb.0c03389] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.
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Affiliation(s)
- Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 814 99 Bratislava, Slovakia
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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31
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Lam K, Tajkhorshid E. Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics. Biophys J 2020; 119:24-34. [PMID: 32533943 DOI: 10.1016/j.bpj.2020.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022] Open
Abstract
Organic fluorophores, such as Cy3 and Cy5, have been widely used as chemical labels to probe the structure and dynamics of membrane proteins. Although a number of previous studies have reported on the possibility of some of the water-soluble fluorophores to interact with lipid bilayers, detailed fluorophore-lipid interactions and, more importantly, the potential effect of such interactions on the natural dynamics of the labeled membrane proteins have not been well studied. We have performed a large set of all-atom molecular dynamics simulations employing the highly mobile membrane mimetic model to describe spontaneous partitioning of the fluorophores into lipid bilayers with different lipid compositions. Spontaneous membrane partitioning of Cy3 and Cy5 fluorophores captured in these simulations proceeds in two steps. Electrostatic interaction between the fluorophores and the lipid headgroups facilitates the initial, fast membrane association of the fluorophores, followed by slow insertion of hydrophobic moieties into the lipid bilayer core. After the conversion of the resulting membrane-bound systems to full-membrane representations, biased-exchange umbrella sampling simulations are performed for free energy calculations, revealing a higher energy barrier for partitioning into negatively charged (phosphatidylserine or phosphatidylcholine) membranes than purely zwitterionic (phosphatidylcholine or phosphatidylethanolamine) ones. Furthermore, the potential effect of fluorophore-lipid interactions on membrane proteins has been examined by covalently linking Cy5 to single- and multipass transmembrane helical proteins. Equilibrium simulations show strong position-dependent effects of Cy5-tagging on the structure and natural dynamics of membrane proteins. Interactions between the tagged protein and Cy5 were also observed. Our results suggest that fluorophore-lipid interactions can affect the structure and dynamics of membrane proteins to various extents, especially in systems with higher structural flexibility.
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Affiliation(s)
- Kin Lam
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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32
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Marquardt D, Heberle FA, Pan J, Cheng X, Pabst G, Harroun TA, Kučerka N, Katsaras J. The structures of polyunsaturated lipid bilayers by joint refinement of neutron and X-ray scattering data. Chem Phys Lipids 2020; 229:104892. [PMID: 32061581 DOI: 10.1016/j.chemphyslip.2020.104892] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/18/2020] [Accepted: 02/10/2020] [Indexed: 11/29/2022]
Abstract
We present the detailed structural analysis of polyunsaturated fatty acid-containing phospholipids namely, 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC) and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC). A newly developed molecular dynamics (MD) simulation parsing scheme for lipids containing fatty acids with multiple double bonds was implemented into the scattering density profile (SDP) model to simultaneously refine differently contrasted neutron and X-ray scattering data. SDP analyses of scattering data at 30 °C yielded lipid areas of 71.1 Å2 and 70.4 Å2 for PDPC and SDPC bilayers, respectively, and a model free analysis of PDPC at 30 °C resulted in a lipid area of 72 Å2. In addition to bilayer structural parameters, using area-constrained MD simulations we determined the area compressibility modulus, KA, to be 246.4 mN/m, a value similar to other neutral phospholipids.
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Affiliation(s)
- Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada; Department of Physics, University of Windsor, Windsor, ON, Canada.
| | | | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, OH, USA
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, 8010 Graz, Austria
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, ON, Canada
| | - Norbert Kučerka
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Russia and Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Slovakia
| | - John Katsaras
- Department of Physics, Brock University, St. Catharines, ON, Canada; The Bredesen Center, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Large Scale Structures Group, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA.
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33
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Wilson KA, Wang L, MacDermott-Opeskin H, O'Mara ML. The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane. Aust J Chem 2020. [DOI: 10.1071/ch19353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools and techniques, the role of the major lipid species, insights gained into lipid bilayer structure and function from molecular dynamics simulations, and recent progress towards the computational modelling of the physiological complexity of eukaryotic lipid bilayers.
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34
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Melcr J, Ferreira TM, Jungwirth P, Ollila OHS. Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization. J Chem Theory Comput 2019; 16:738-748. [PMID: 31762275 DOI: 10.1021/acs.jctc.9b00824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphatidylserine (PS) lipids are important signaling molecules and the most common negatively charged lipids in eukaryotic membranes. The signaling can be often regulated by calcium, but its interactions with PS headgroups are not fully understood. Classical molecular dynamics (MD) simulations can potentially give detailed description of lipid-ion interactions, but the results strongly depend on the used force field. Here, we apply the electronic continuum correction (ECC) to the Amber Lipid17 parameters of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS) lipid to improve its interactions with K+, Na+, and Ca2+ ions. The partial charges of the headgroup, glycerol backbone, and carbonyls of POPS, bearing a unit negative charge, were scaled with a factor of 0.75, derived for monovalent ions, and the Lennard-Jones σ parameters of the same segments were scaled with a factor of 0.89. The resulting ECC-POPS model gives more realistic interactions with Na+ and Ca2+ cations than the original Amber Lipid17 parameters when validated using headgroup order parameters and the "electrometer concept". In ECC-lipids simulations, populations of complexes of Ca2+ cations with more than two PS lipids are negligible, and interactions of Ca2+ cations with only carboxylate groups are twice more likely than with only phosphate groups, while interactions with carbonyls almost entirely involve other groups as well. Our results pave the way for more realistic MD simulations of biomolecular systems with anionic membranes, allowing signaling processes involving PS and Ca2+ to be elucidated.
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Affiliation(s)
- Josef Melcr
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , CZ-16610 Prague 6 , Czech Republic.,Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials , University of Groningen , 9747 AG Groningen , The Netherlands
| | - Tiago M Ferreira
- NMR Group-Institut for Physics , Martin-Luther University Halle-Wittenberg , 06120 Halle , Germany
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , CZ-16610 Prague 6 , Czech Republic
| | - O H Samuli Ollila
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , CZ-16610 Prague 6 , Czech Republic.,Institute of Biotechnology , University of Helsinki , Helsinki FI-00014 , Finland
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35
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Quantitative accounting of dye leakage and photobleaching in single lipid vesicle measurements: Implications for biomacromolecular interaction analysis. Colloids Surf B Biointerfaces 2019; 182:110338. [DOI: 10.1016/j.colsurfb.2019.06.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/08/2019] [Accepted: 06/28/2019] [Indexed: 02/05/2023]
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36
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Antila H, Buslaev P, Favela-Rosales F, Ferreira TM, Gushchin I, Javanainen M, Kav B, Madsen JJ, Melcr J, Miettinen MS, Määttä J, Nencini R, Ollila OHS, Piggot TJ. Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. J Phys Chem B 2019; 123:9066-9079. [DOI: 10.1021/acs.jpcb.9b06091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Fernando Favela-Rosales
- Departamento de Investigación, Tecnológico Nacional de México, Campus Zacatecas Occidente, C. P. 99102 Zacatecas, México
| | - Tiago M. Ferreira
- NMR Group - Institute for Physics, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Batuhan Kav
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jesper J. Madsen
- Department of Chemistry, The University of Chicago, 60637 Chicago, Illinois, United States of America
- Department of Global Health, College of Public Health, University of South Florida, 33612 Tampa, Florida, United States of America
| | - Josef Melcr
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Markus S. Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jukka Määttä
- Department of Chemistry and Materials Science, Aalto University, 00076 Espoo, Finland
| | - Ricky Nencini
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Thomas J. Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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Scott HL, Skinkle A, Kelley EG, Waxham MN, Levental I, Heberle FA. On the Mechanism of Bilayer Separation by Extrusion, or Why Your LUVs Are Not Really Unilamellar. Biophys J 2019; 117:1381-1386. [PMID: 31586522 DOI: 10.1016/j.bpj.2019.09.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/18/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Extrusion through porous filters is a widely used method for preparing biomimetic model membranes. Of primary importance in this approach is the efficient production of single bilayer (unilamellar) vesicles that eliminate the influence of interlamellar interactions and strictly define the bilayer surface area available to external reagents such as proteins. Submicroscopic vesicles produced using extrusion are widely assumed to be unilamellar, and large deviations from this assumption would impact interpretations from many model membrane experiments. Using three probe-free methods-small angle X-ray and neutron scattering and cryogenic electron microscopy-we report unambiguous evidence of extensive multilamellarity in extruded vesicles composed of neutral phosphatidylcholine lipids, including for the common case of neutral lipids dispersed in physiological buffer and extruded through 100-nm diameter pores. In such preparations, only ∼35% of lipids are externally accessible and this fraction is highly dependent on preparation conditions. Charged lipids promote unilamellarity as does decreasing solvent ionic strength, indicating the importance of electrostatic interactions in determining the lamellarity of extruded vesicles. Smaller extrusion pore sizes also robustly increase the fraction of unilamellar vesicles, suggesting a role for membrane bending. Taken together, these observations suggest a mechanistic model for extrusion, wherein the formation of unilamellar vesicles involves competition between bilayer bending and adhesion energies. The findings presented here have wide-ranging implications for the design and interpretation of model membrane studies, especially ensemble-averaged observations relying on the assumption of unilamellarity.
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Affiliation(s)
- Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Allison Skinkle
- Department of Biosciences, Rice University, Houston, Texas; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas.
| | - Frederick A Heberle
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas.
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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 2019; 114:146-157. [PMID: 29320681 PMCID: PMC5773765 DOI: 10.1016/j.bpj.2017.11.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [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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Vasquez-Montes V, Vargas-Uribe M, Pandey NK, Rodnin MV, Langen R, Ladokhin AS. Lipid-modulation of membrane insertion and refolding of the apoptotic inhibitor Bcl-xL. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:691-700. [PMID: 31004798 DOI: 10.1016/j.bbapap.2019.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Bcl-xL is a member of the Bcl-2 family of apoptotic regulators, responsible for inhibiting the permeabilization of the mitochondrial outer membrane, and a promising anti-cancer target. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (a) a soluble folded conformation, (b) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (c) refolded membrane-inserted conformations, for which no structural data are available. Previous studies established that in the cell Bcl-xL exists in a dynamic equilibrium between soluble and membranous states, however, no direct evidence exists in support of either anchored or inserted conformation of the membranous state in vivo. In this in vitro study, we employed a combination of fluorescence and EPR spectroscopy to characterize structural features of the bilayer-inserted conformation of Bcl-xL and the lipid modulation of its membrane insertion transition. Our results indicate that the core hydrophobic helix α6 inserts into the bilayer without adopting a transmembrane orientation. This insertion disrupts the packing of Bcl-xL and releases the regulatory N-terminal BH4 domain (α1) from the rest of the protein structure. Our data demonstrate that both insertion and refolding of Bcl-xL are modulated by lipid composition, which brings the apparent pKa of insertion to the threshold of physiological pH. We hypothesize that conformational rearrangements associated with the bilayer insertion of Bcl-xL result in its switching to a so-called non-canonical mode of apoptotic inhibition. Presented results suggest that the alteration in lipid composition before and during apoptosis can serve as an additional factor regulating the permeabilization of the mitochondrial outer membrane.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nitin K Pandey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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40
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Scott HL, Heberle FA, Katsaras J, Barrera FN. Phosphatidylserine Asymmetry Promotes the Membrane Insertion of a Transmembrane Helix. Biophys J 2019; 116:1495-1506. [PMID: 30954213 DOI: 10.1016/j.bpj.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/13/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022] Open
Abstract
The plasma membrane (PM) contains an asymmetric distribution of lipids between the inner and outer bilayer leaflets. A lipid of special interest in eukaryotic membranes is the negatively charged phosphatidylserine (PS). In healthy cells, PS is actively sequestered to the inner leaflet of the PM, but PS redistributes to the outer leaflet when the cell is damaged or at the onset of apoptosis. However, the influence of PS asymmetry on membrane protein structure and folding are poorly understood. The pH low insertion peptide (pHLIP) adsorbs to the membrane surface at a neutral pH, but it inserts into the membrane at an acidic pH. We have previously observed that in symmetric vesicles, PS affects the membrane insertion of pHLIP by lowering the pH midpoint of insertion. Here, we studied the effect of PS asymmetry on the membrane interaction of pHLIP. We developed a modified protocol to create asymmetric vesicles containing PS and employed Annexin V labeled with an Alexa Fluor 568 fluorophore as a new probe to quantify PS asymmetry. We observed that the membrane insertion of pHLIP was promoted by the asymmetric distribution of negatively charged PS, which causes a surface charge difference between bilayer leaflets. Our results indicate that lipid asymmetry can modulate the formation of an α-helix on the membrane. A corollary is that model studies using symmetric bilayers to mimic the PM may fail to capture important aspects of protein-membrane interactions.
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Affiliation(s)
- Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge, Tennessee
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge, Tennessee; Large Scale Structures Group, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics, Brock University, St. Catharines, Ontario, Canada
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
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41
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Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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42
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Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019; 21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aggregation of misfolded oligomeric amyloid-beta (Aβ) peptides on lipid membranes has been identified as a primary event in Alzheimer's pathogenesis. However, the structural and dynamical features of this membrane assisted Aβ aggregation have not been well characterized. The microscopic characterization of dynamic molecular-level interactions in peptide aggregation pathways has been challenging both computationally and experimentally. In this work, we explore differential patterns of membrane-induced Aβ 16-22 (K-L-V-F-F-A-E) aggregation from the microscopic perspective of molecular interactions. Physics-based coarse-grained molecular dynamics (CG-MD) simulations were employed to investigate the effect of lipid headgroup charge - zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPC) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine: POPS) - on Aβ 16-22 peptide aggregation. Our analyses present an extensive overview of multiple pathways for peptide absorption and biomechanical forces governing peptide folding and aggregation. In agreement with experimental observations, anionic POPS molecules promote extended configurations in Aβ peptides that contribute towards faster emergence of ordered β-sheet-rich peptide assemblies compared to POPC, suggesting faster fibrillation. In addition, lower cumulative rates of peptide aggregation in POPS due to higher peptide-lipid interactions and slower lipid diffusion result in multiple distinct ordered peptide aggregates that can serve as nucleation seeds for subsequent Aβ aggregation. This study provides an in-silico assessment of experimentally observed aggregation patterns, presents new morphological insights and highlights the importance of lipid headgroup chemistry in modulating the peptide absorption and aggregation process.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
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43
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Hallock MJ, Greenwood AI, Wang Y, Morrissey JH, Tajkhorshid E, Rienstra CM, Pogorelov TV. Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane. Biochemistry 2018; 57:6897-6905. [PMID: 30456950 DOI: 10.1021/acs.biochem.8b01069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The plasma membrane of the cell is a complex, tightly regulated, heterogeneous environment shaped by proteins, lipids, and small molecules. Ca2+ ions are important cellular messengers, spatially separated from anionic lipids. After cell injury, disease, or apoptotic events, anionic lipids are externalized to the outer leaflet of the plasma membrane and encounter Ca2+, resulting in dramatic changes in the plasma membrane structure and initiation of signaling cascades. Despite the high chemical and biological significance, the structures of lipid-Ca2+ nanoclusters are still not known. Previously, we demonstrated by solid-state nuclear magnetic resonance (NMR) spectroscopy that upon binding to Ca2+, individual phosphatidylserine lipids populate two distinct yet-to-be-characterized structural environments. Here, we concurrently employ extensive all-atom molecular dynamics (MD) simulations with our accelerated membrane mimetic and detailed NMR measurements to identify lipid-Ca2+ nanocluster conformations. We find that major structural characteristics of these nanoclusters, including interlipid pair distances and chemical shifts, agree with observable NMR parameters. Simulations reveal that lipid-ion nanoclusters are shaped by two characteristic, long-lived lipid structures induced by divalent Ca2+. Using ab initio quantum mechanical calculations of chemical shifts on MD-captured lipid-ion complexes, we show that computationally observed conformations are validated by experimental NMR data. Both NMR measurements of diluted specifically labeled lipids and MD simulations reveal that the basic structural unit that reshapes the membrane is a Ca2+-coordinated phosphatidylserine tetramer. Our combined computational and experimental approach presented here can be applied to other complex systems in which charged membrane-active molecular agents leave structural signatures on lipids.
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Affiliation(s)
- Michael J Hallock
- School of Chemical Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Alexander I Greenwood
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yan Wang
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - James H Morrissey
- Department of Biological Chemistry , University of Michigan Medical School , Ann Arbor , Michigan 48103 , United States
| | - Emad Tajkhorshid
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Chad M Rienstra
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Taras V Pogorelov
- School of Chemical Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,National Center for Supercomputing Applications , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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44
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Quan H, Kim Y, Park HC, Yang HC. Effects of phosphatidylserine-containing supported lipid bilayers on the polarization of macrophages. J Biomed Mater Res A 2018; 106:2625-2633. [PMID: 29781181 DOI: 10.1002/jbm.a.36454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/24/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022]
Abstract
Placement of dental implants initiates inflammatory foreign body response, in which macrophages play a central role and affect the subsequent tissue healing process such as bone formation. The purpose of this study was to fabricate phosphatidylserine (PS)-containing supported lipid bilayers (SLBs) on a titanium surface to regulate the polarization of macrophages, a critical factor that affects following tissue healing and regeneration. The fluorescent recovery after photobleaching images showed that the percentage of PS had a critical influence on the fluidity, and 20% PS had the highest fluidity. Furthermore, more expanded and elongated cells were observed in the SLB-coated groups. transforming growth factor-β1 and vascular endothelial growth factor, the key cytokine markers of M2 macrophage polarization, were increased in the SLB-coated groups, especially in the 20% PS group. Consistently, cells cultured on the SLB-coated titanium exhibited the distribution of CD206+ , which is a M2 macrophage specific maker. The results of this study demonstrated M2 polarization of macrophages on PS-SLB-coated titanium discs, which suggests the application of PS-SLB as an immune-regulating coating material to improve tissue reactions to dental implants. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2625-2633, 2018.
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Affiliation(s)
- Hongxuan Quan
- Department of Dental Biomaterials Science, Dental Research Institute and BK21 Plus Program, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Yongjoon Kim
- Department of Dental Biomaterials Science, Dental Research Institute and BK21 Plus Program, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Hee Chul Park
- Department of Dental Biomaterials Science, Dental Research Institute and BK21 Plus Program, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Hyeong-Cheol Yang
- Department of Dental Biomaterials Science, Dental Research Institute and BK21 Plus Program, School of Dentistry, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
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45
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The impact of deuteration on natural and synthetic lipids: A neutron diffraction study. Colloids Surf B Biointerfaces 2018; 168:126-133. [PMID: 29433911 DOI: 10.1016/j.colsurfb.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/09/2018] [Accepted: 02/03/2018] [Indexed: 12/19/2022]
Abstract
The structural investigation of cellular membranes requires access to model systems where the molecular complexity is representative of the cellular environment and that allow for the exploitation of structural techniques. Neutron scattering, and in particular neutron diffraction can provide unique and detailed information on the structure of lipid membranes. However, deuterated samples are desirable to fully exploit this powerful method. Recently, the extraction of lipids from microorganisms grown in deuterated media was demonstrated to be both an attracting route to obtain complex lipid mixtures resembling the composition of natural membranes, and to producing deuterated molecules in a very convenient way. A full characterization of these deuterated extracts is hence pivotal for their use in building up model membrane systems. Here we report the structural characterization of lipid extracts obtained from Pichia pastoris by means of neutron diffraction measurements. In particular, we compare the structure of membranes extracted from yeast cells grown in a standard culture medium and in a corresponding deuterated culture medium. The results show that the different molecular composition of the deuterated and protiated lipid extracts induce different structural organization of the lipid membranes. In addition, we compare these membranes composed of extracted yeast lipids with stacked bilayers prepared from synthetic lipid mixtures.
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46
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Lubart Q, Vitet H, Dalonneau F, Le Roy A, Kowalski M, Lourdin M, Ebel C, Weidenhaupt M, Picart C. Role of Phosphorylation in Moesin Interactions with PIP 2-Containing Biomimetic Membranes. Biophys J 2018; 114:98-112. [PMID: 29320700 PMCID: PMC5912500 DOI: 10.1016/j.bpj.2017.10.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/08/2017] [Accepted: 10/17/2017] [Indexed: 12/26/2022] Open
Abstract
Moesin, a protein of the ezrin, radixin, and moesin family, which links the plasma membrane to the cytoskeleton, is involved in multiple physiological and pathological processes, including viral budding and infection. Its interaction with the plasma membrane occurs via a key phosphoinositide, the phosphatidyl(4,5)inositol-bisphosphate (PIP2), and phosphorylation of residue T558, which has been shown to contribute, in cellulo, to a conformationally open protein. We study the impact of a double phosphomimetic mutation of moesin (T235D, T558D), which mimics the phosphorylation state of the protein, on protein/PIP2/microtubule interactions. Analytical ultracentrifugation in the micromolar range showed moesin in the monomer and dimer forms, with wild-type (WT) moesin containing a slightly larger fraction (∼30%) of dimers than DD moesin (10-20%). Only DD moesin was responsive to PIP2 in its micellar form. Quantitative cosedimentation assays using large unilamellar vesicles and quartz crystal microbalance on supported lipid bilayers containing PIP2 reveal a specific cooperative interaction for DD moesin with an ability to bind two PIP2 molecules simultaneously, whereas WT moesin was able to bind only one. In addition, DD moesin could subsequently interact with microtubules, whereas WT moesin was unable to do so. Altogether, our results point to an important role of these two phosphorylation sites in the opening of moesin: since DD moesin is intrinsically in a more open conformation than WT moesin, this intermolecular interaction is reinforced by its binding to PIP2. We also highlight important differences between moesin and ezrin, which appear to be finely regulated and to exhibit distinct molecular behaviors.
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Affiliation(s)
- Quentin Lubart
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Helene Vitet
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Fabien Dalonneau
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Aline Le Roy
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Mathieu Kowalski
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Morgane Lourdin
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Christine Ebel
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Marianne Weidenhaupt
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Catherine Picart
- CNRS UMR 5628 (LMGP), University Grenoble Alpes, CEA, CNRS, Grenoble, France; Institut National Polytechnique de Grenoble, University Grenoble Alpes, CEA, CNRS, Grenoble, France.
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47
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Doktorova M, Heberle FA, Kingston RL, Khelashvili G, Cuendet MA, Wen Y, Katsaras J, Feigenson GW, Vogt VM, Dick RA. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties. Biophys J 2017; 113:2004-2015. [PMID: 29117524 DOI: 10.1016/j.bpj.2017.08.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 01/28/2023] Open
Abstract
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Yi Wen
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - John Katsaras
- 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; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Volker M Vogt
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Robert A Dick
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.
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Doktorova M, Heberle FA, Kingston RL, Khelashvili G, Cuendet MA, Wen Y, Katsaras J, Feigenson GW, Vogt VM, Dick RA. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties. Biophys J 2017. [PMID: 29117524 DOI: 10.1016/j.bpj.2017.08.055.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Yi Wen
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - John Katsaras
- 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; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Volker M Vogt
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York
| | - Robert A Dick
- Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.
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49
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Ermakov YA, Kamaraju K, Dunina-Barkovskaya A, Vishnyakova KS, Yegorov YE, Anishkin A, Sukharev S. High-Affinity Interactions of Beryllium(2+) with Phosphatidylserine Result in a Cross-Linking Effect Reducing Surface Recognition of the Lipid. Biochemistry 2017; 56:5457-5470. [PMID: 28872302 DOI: 10.1021/acs.biochem.7b00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Beryllium has multiple industrial applications, but its manufacture is associated with a serious occupational risk of developing chronic inflammation in the lungs known as berylliosis, or chronic beryllium disease. Although the Be2+-induced abnormal immune responses have recently been linked to a specific MHC-II allele, the nature of long-lasting granulomas is not fully understood. Here we show that Be2+ binds with a micromolar affinity to phosphatidylserine (PS), the major surface marker of apoptotic cells. Isothermal titration calorimetry indicates that, like that of Ca2+, binding of Be2+ to PS liposomes is largely entropically driven, likely by massive desolvation. Be2+ exerts a compacting effect on PS monolayers, suggesting cross-linking through coordination by both phosphates and carboxyls in multiple configurations, which were visualized in molecular dynamics simulations. Electrostatic modification of PS membranes by Be2+ includes complete neutralization of surface charges at ∼30 μM, accompanied by an increase in the boundary dipole potential. The data suggest that Be2+ can displace Ca2+ from the surface of PS, and being coordinated in a tight shell of four oxygens, it can mask headgroups from Ca2+-mediated recognition by PS receptors. Indeed, 48 μM Be2+ added to IC-21 cultured macrophages specifically suppresses binding and engulfment of PS-coated silica beads or aged erythrocytes. We propose that Be2+ adsorption at the surface of apoptotic cells may potentially prevent normal phagocytosis, thus causing accumulation of secondary necrotic foci and the resulting chronic inflammation.
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Affiliation(s)
- Yuri A Ermakov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences , Leninsky Prospect 31, Moscow 117071, Russia
| | - Kishore Kamaraju
- Department of Biology, University of Maryland , College Park, Maryland 20742, United States
| | | | - Khava S Vishnyakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov Street 32, Moscow 119991, Russia
| | - Yegor E Yegorov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov Street 32, Moscow 119991, Russia
| | - Andriy Anishkin
- Department of Biology, University of Maryland , College Park, Maryland 20742, United States
| | - Sergei Sukharev
- Department of Biology, University of Maryland , College Park, Maryland 20742, United States
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50
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Heberle FA, Pabst G. Complex biomembrane mimetics on the sub-nanometer scale. Biophys Rev 2017; 9:353-373. [PMID: 28717925 PMCID: PMC5578918 DOI: 10.1007/s12551-017-0275-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/26/2017] [Indexed: 12/12/2022] Open
Abstract
Biomimetic lipid vesicles are indispensable tools for gaining insight into the biophysics of cell physiology on the molecular level. The level of complexity of these model systems has steadily increased, and now spans from domain-forming lipid mixtures to asymmetric lipid bilayers. Here, we review recent progress in the development and application of elastic neutron and X-ray scattering techniques for studying these systems in situ and under physiologically relevant conditions on the nanometer to sub-nanometer length scales. In particular, we focus on: (1) structural details of coexisting liquid-ordered and liquid-disordered domains, including their thickness and lipid packing mismatch as a function of a size transition from nanoscopic to macroscopic domains; (2) membrane-mediated protein partitioning into lipid domains; (3) the role of the aqueous medium in tuning interactions between membranes and domains; and (4) leaflet-specific structure in asymmetric bilayers and passive lipid flip-flop.
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Affiliation(s)
- Frederick A Heberle
- The Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA.,Joint Institute for Biological Sciences and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, 8010, Graz, Austria. .,BioTechMed-Graz, 8010, Graz, Austria.
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