1
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Lombardo Pontillo A, Ferrari M, Rospiccio M, Buffo A. Molecular Modeling of the Adsorption of an Egg Yolk Protein on a Water-Oil Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38315870 DOI: 10.1021/acs.langmuir.3c03272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Egg yolk contains several molecular species with emulsifying properties, such as proteins and phospholipids. In particular, these molecules have both polar and nonpolar parts and thus can act as surfactants. One of the most surface-active proteins from egg yolk low-density lipoproteins is the so-called Apovitellenin-1. Experimental studies have been hindered by difficulties in isolating individual species from egg yolk lipoproteins. The purpose of this work was to assess the emulsifying properties of Apovitellenin-1 and any potential cooperative or competitive behavior in the presence of phospholipids. To do so, molecular simulations were carried out in a liquid-liquid interfacial system consisting of water and soybean oil, with varying concentrations of phospholipids and for different spatial configurations. To evaluate the conformational stability of the protein at the water-oil interface, the Gibbs free energy was computed from Metadynamics simulations as a function of the distance from the interface and of the radius of gyration. Moreover, a detailed analysis was also performed to determine which peptide residues were responsible for the protein adsorption at the oil-water interface as well as the lowering of the interfacial tension. Lastly, we combined the simulation results with a thermodynamic model to predict the interfacial tension behavior at increasing protein bulk concentration, which cannot be measured experimentally.
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Affiliation(s)
- Alessio Lombardo Pontillo
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Marco Ferrari
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Marcello Rospiccio
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Antonio Buffo
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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2
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Kabedev A, Bergström CAS, Larsson P. Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison. J Comput Aided Mol Des 2023; 38:5. [PMID: 38103089 PMCID: PMC10725378 DOI: 10.1007/s10822-023-00541-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important for the development of new delivery techniques and bioavailability improvement. A balance between accuracy and computational cost is a key factor for an extensive study of numerous compounds in diverse environments. In this study, we aimed to determine an optimal molecular dynamics (MD) protocol to evaluate small-molecule interactions with micelles composed of bile salts and phospholipids. MD simulations were used to produce free energy profiles for three drug molecules (danazol, probucol, and prednisolone) and one surfactant molecule (sodium caprate) as a function of the distance from the colloid center of mass. To address the challenges associated with such tasks, we compared different simulation setups, including freely assembled colloids versus pre-organized spherical micelles, full free energy profiles versus only a few points of interest, and a coarse-grained model versus an all-atom model. Our findings demonstrate that combining these techniques is advantageous for achieving optimal performance and accuracy when evaluating the solubilization capacity of micelles. All-atom (AA) and coarse-grained (CG) umbrella sampling (US) simulations and point-wise free energy (FE) calculations were compared to their efficiency to computationally analyze the solubilization of active pharmaceutical ingredients in intestinal fluid colloids.
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Affiliation(s)
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Swedish Drug Delivery Center, Uppsala University, Uppsala, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden.
- Swedish Drug Delivery Center, Uppsala University, Uppsala, Sweden.
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3
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Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z. Alchemical Free Energy Calculations on Membrane-Associated Proteins. J Chem Theory Comput 2023; 19:7437-7458. [PMID: 37902715 PMCID: PMC11017255 DOI: 10.1021/acs.jctc.3c00365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 10/31/2023]
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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Affiliation(s)
- Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Hryhory Sinenka
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Pierre Matricon
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique UPR 9080, CNRS and Université Paris Cité, 75005 Paris, France
| | - Grace Brannigan
- Center
for Computational and Integrative Biology, Rutgers University−Camden, Camden, New Jersey 08103, United States of America
- Department
of Physics, Rutgers University−Camden, Camden, New Jersey 08102, United States
of America
| | - Laura Pérez-Benito
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Vineet Pande
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Herman van Vlijmen
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Chris de Graaf
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Francesca Deflorian
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Gary Tresadern
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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4
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Sadžak A, Brkljača Z, Eraković M, Kriechbaum M, Maltar-Strmečki N, Přibyl J, Šegota S. Puncturing lipid membranes: onset of pore formation and the role of hydrogen bonding in the presence of flavonoids. J Lipid Res 2023; 64:100430. [PMID: 37611869 PMCID: PMC10518586 DOI: 10.1016/j.jlr.2023.100430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Products of lipid peroxidation induce detrimental structural changes in cell membranes, such as the formation of water pores, which occur in the presence of lipids with partially oxidized chains. However, the influence of another class of products, dicarboxylic acids, is still unclear. These products have greater mobility in the lipid bilayer, which enables their aggregation and the formation of favorable sites for the appearance of pores. Therefore, dodecanedioic acid (DDA) was selected as a model product. Additionally, the influence of several structurally different flavonoids on DDA aggregation via formation of hydrogen bonds with carboxyl groups was investigated. The molecular dynamics of DDA in DOPC lipid bilayer revealed the formation of aggregates extending over the hydrophobic region of the bilayer and increasing its polarity. Consequently, water penetration and the appearance of water wires was observed, representing a new step in the mechanism of pore formation. Furthermore, DDA molecules were found to interact with lipid polar groups, causing them to be buried in the bilayer. The addition of flavonoids to the system disrupted aggregate formation, resulting in the displacement of DDA molecules from the center of the bilayer. The placement of DDA and flavonoids in the lipid bilayer was confirmed by small-angle X-ray scattering. Atomic force microscopy and electron paramagnetic resonance were used to characterize the structural properties. The presence of DDA increased bilayer roughness and decreased the ordering of lipid chains, confirming its detrimental effects on the membrane surface, while flavonoids were found to reduce or reverse these changes.
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Affiliation(s)
- Anja Sadžak
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mihael Eraković
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Manfred Kriechbaum
- Institute of Inorganic Chemistry, Graz University of Technology, Graz, Austria
| | | | - Jan Přibyl
- CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Suzana Šegota
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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5
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Ermilova I, Swenson J. Ionizable lipids penetrate phospholipid bilayers with high phase transition temperatures: perspectives from free energy calculations. Chem Phys Lipids 2023; 253:105294. [PMID: 37003484 DOI: 10.1016/j.chemphyslip.2023.105294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
The efficacies of modern gene-therapies strongly depend on their contents. At the same time the most potent formulations might not contain the best compounds. In this work we investigated the effect of phospholipids and their saturation on the binding ability of (6Z,9Z,28Z,31Z)-heptatriacont-6,9,28,31-tetraene-19-yl 4-(dimethylamino) butanoate (DLin-MC3-DMA) to model membranes at the neutral pH. We discovered that DLin-MC3-DMA has affinity to the most saturated monocomponent lipid bilayer 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and an aversion to the unsaturated one 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). The preference to a certain membrane was also well-correlated to the phase transition temperatures of phospholipid bilayers, and to their structural and dynamical properties. Additionally, in the case of the presence of DLin-MC3-DMA in the membrane with DOPC the ionizable lipid penetrated it, which indicates possible synergistic effects. Comparisons with other ionizable lipids were performed using a model lipid bilayer of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC). Particularly, the lipids heptadecan-9-yl 8-[2-hydroxyethyl-(6-oxo-6-undecoxyhexyl)amino]octanoate (SM-102) and [(4-Hydroxybutyl) azanediyl] di(hexane-6,1-diyl) bis(2-hexyldecanoate) (ALC-0315) from modern mRNA-vaccines against COVID-19 were investigated and force fields parameters were derived for those new lipids. It was discovered that ALC-0315 binds strongest to the membrane, while DLin-MC3-DMA is not able to reside in the bilayer center. The ability to penetrate the membrane POPC by SM-102 and ALC-0315 can be related to their saturation, comparing to DLin-MC3-DMA.
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Affiliation(s)
- Inna Ermilova
- Department of Physics, Chalmers Uiversity of Technology, SE 412 96, Gothenburg, Sweden.
| | - Jan Swenson
- Department of Physics, Chalmers Uiversity of Technology, SE 412 96, Gothenburg, Sweden.
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6
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Scrima S, Tiberti M, Campo A, Corcelle-Termeau E, Judith D, Foged MM, Clemmensen KKB, Tooze SA, Jäättelä M, Maeda K, Lambrughi M, Papaleo E. Unraveling membrane properties at the organelle-level with LipidDyn. Comput Struct Biotechnol J 2022; 20:3604-3614. [PMID: 35860415 PMCID: PMC9283888 DOI: 10.1016/j.csbj.2022.06.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/22/2022] Open
Abstract
Lipidomics of organelles could be used to design models for molecular simulations. The bottleneck is the analysis and rationalization of the data from simulations. LipidDyn is an automated pipeline to streamline the analyses of lipid bilayers. LipidDyn allows to collect analysis in a non-time-consuming and reproducible manner. We applied LipidDyn to different case studies to illustrate its potential.
Cellular membranes are formed from different lipids in various amounts and proportions depending on the subcellular localization. The lipid composition of membranes is sensitive to changes in the cellular environment, and its alterations are linked to several diseases. Lipids not only form lipid-lipid interactions but also interact with other biomolecules, including proteins. Molecular dynamics (MD) simulations are a powerful tool to study the properties of cellular membranes and membrane-protein interactions on different timescales and resolutions. Over the last few years, software and hardware for biomolecular simulations have been optimized to routinely run long simulations of large and complex biological systems. On the other hand, high-throughput techniques based on lipidomics provide accurate estimates of the composition of cellular membranes at the level of subcellular compartments. Lipidomic data can be analyzed to design biologically relevant models of membranes for MD simulations. Similar applications easily result in a massive amount of simulation data where the bottleneck becomes the analysis of the data. In this context, we developed LipidDyn, a Python-based pipeline to streamline the analyses of MD simulations of membranes of different compositions. Once the simulations are collected, LipidDyn provides average properties and time series for several membrane properties such as area per lipid, thickness, order parameters, diffusion motions, lipid density, and lipid enrichment/depletion. The calculations exploit parallelization, and the pipeline includes graphical outputs in a publication-ready form. We applied LipidDyn to different case studies to illustrate its potential, including membranes from cellular compartments and transmembrane protein domains. LipidDyn is available free of charge under the GNU General Public License from https://github.com/ELELAB/LipidDyn.
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Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Alessia Campo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elisabeth Corcelle-Termeau
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Delphine Judith
- Institut Cochin, Inserm U1016-CNRS, UMR8104, Université de Paris, Paris, France
| | - Mads Møller Foged
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | | | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
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7
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Gilbert J, Ermilova I, Nagao M, Swenson J, Nylander T. Effect of encapsulated protein on the dynamics of lipid sponge phase: a neutron spin echo and molecular dynamics simulation study. NANOSCALE 2022; 14:6990-7002. [PMID: 35470842 DOI: 10.1039/d2nr00882c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lipid membranes are highly mobile systems with hierarchical, time and length scale dependent, collective motions including thickness fluctuations, undulations, and topological membrane changes, which play an important role in membrane interactions. In this work we have characterised the effect of encapsulating two industrially important enzymes, β-galactosidase and aspartic protease, in lipid sponge phase nanoparticles on the dynamics of the lipid membrane using neutron spin echo (NSE) spectroscopy and molecular dynamics (MD) simulations. From NSE, reduced membrane dynamics were observed upon enzyme encapsulation, which were dependent on the enzyme concentration and type. By fitting the intermediate scattering functions (ISFs) with a modified Zilman and Granek model including nanoparticle diffusion, an increase in membrane bending rigidity was observed, with a larger effect for β-galactosidase than aspartic protease at the same concentration. MD simulations for the system with and without aspartic protease showed that the lipids relax more slowly in the system with protein due to the replacement of the lipid carbonyl-water hydrogen bonds with lipid-protein hydrogen bonds. This indicates that the most likely cause of the increase in membrane rigidity observed in the NSE measurements was dehydration of the lipid head groups. The dynamics of the protein itself were also studied, which showed a stable secondary structure of protein over the simulation, indicating no unfolding events occurred.
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Affiliation(s)
- Jennifer Gilbert
- Division of Physical Chemistry, Department of Chemistry, Naturvetarvägen 14, Lund University, 22362 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Tommy Nylander
- Division of Physical Chemistry, Department of Chemistry, Naturvetarvägen 14, Lund University, 22362 Lund, Sweden.
- NanoLund, Lund University, Professorsgatan 1, 223 63 Lund, Sweden
- Lund Institute of Advanced Neutron and X-Ray Science, Scheelevägen 19, 223 70 Lund, Sweden
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8
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Licari G, Dehghani-Ghahnaviyeh S, Tajkhorshid E. Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes. J Chem Inf Model 2022; 62:986-996. [PMID: 35104125 PMCID: PMC8892574 DOI: 10.1021/acs.jcim.1c01388] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations of biological membranes have achieved such levels of sophistication that are commonly used to predict unresolved structures and various properties of lipids and to substantiate experimental data. While achieving sufficient sampling of lipid dynamics remains a major challenge, a commonly used method to improve lipid sampling, e.g., in terms of specific interactions with membrane-associated proteins, is to randomize the initial arrangement of lipid constituents in multiple replicas of simulations, without changing the overall lipid composition of the membrane of interest. Here, we introduce a method that can rapidly generate multiple replicas of lipid bilayers with different spatial and conformational configurations for any given lipid composition. The underlying algorithm, which allows one to shuffle lipids at any desired level, relies on the application of an external potential, here referred to as the "carving potential", that removes clashes/entanglements before lipid positions are exchanged (shuffled), thereby minimizing the energy penalty due to abrupt lipid repositioning. The method is implemented as "Membrane Mixer Plugin (MMP) 1.0" in VMD, with a convenient graphical user interface that guides the user in setting various options and parameters. The plugin is fully automated and generates new membrane replicas more rapidly and conveniently than other analogous tools. The plugin and its capabilities introduced here can be extended to include additional features in future versions.
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Affiliation(s)
- Giuseppe Licari
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States,Current address: Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharmaceuticals, Inc., Biberach An Der Riß, Germany,Contributed equally to this work
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States,Contributed equally to this work
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
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9
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Canner SW, Feller SE, Wassall SR. Molecular Organization of a Raft-like Domain in a Polyunsaturated Phospholipid Bilayer: A Supervised Machine Learning Analysis of Molecular Dynamics Simulations. J Phys Chem B 2021; 125:13158-13167. [PMID: 34812629 DOI: 10.1021/acs.jpcb.1c06511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous health benefits are associated with omega-3 polyunsaturated fatty acids (n-3 PUFA) consumed in fish oils. An understanding of the mechanism remains elusive. The plasma membrane as a site of action is the focus in this study. With large-scale all-atom MD simulations run on a model membrane (1050 lipid molecules), we observed the evolution over time (6 μs) of a circular (raft-like) domain composed of N-palmitoylsphingomyelin (PSM) and cholesterol embedded into a surrounding (non-raft) patch composed of polyunsaturated 1-palmitoyl-2-docosahexaenoylphosphatylcholine (PDPC) (1:1:1 mol). A supervised machine learning algorithm was developed to characterize the migration of each lipid based on molecular conformation and the local environment. PDPC molecules were seen to infiltrate the ordered raft-like domain in a small amount, while a small concentration of PSM and cholesterol molecules was seen to migrate into the disordered non-raft region. Enclosing the raft-like domain, a narrow (∼2 nm in width) interfacial zone composed of PDPC, PSM, and cholesterol that buffers the substantial difference in order (ΔSCD ≈ 0.12) between raft-like and non-raft environments was seen to form. Our results suggest that n-3 PUFA regulate the architecture of lipid rafts enriched in sphingolipids and cholesterol with a minimal effect on order within their interior in membranes.
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Affiliation(s)
- Samuel W Canner
- Department of Physics, IUPUI, Indianapolis, Indiana 46202-3273, United States.,Department of Computer and Information Science, IUPUI, Indianapolis, Indiana 46202-5132, United States
| | - Scott E Feller
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United States
| | - Stephen R Wassall
- Department of Physics, IUPUI, Indianapolis, Indiana 46202-3273, United States
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10
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Wilson KA, Wang L, O’Mara ML. Site of Cholesterol Oxidation Impacts Its Localization and Domain Formation in the Neuronal Plasma Membrane. ACS Chem Neurosci 2021; 12:3873-3884. [PMID: 34633798 DOI: 10.1021/acschemneuro.1c00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cholesterol is integral to the structure of mammalian cell membranes. Oxidation of cholesterol alters how it behaves in the membrane and influences the membrane biophysical properties. Elevated levels of oxidized cholesterol are associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, and Huntington's disease. Previous work has investigated the impact of oxidized cholesterol in the context of simple model membrane systems. However, there is a growing body of literature that shows that complex membranes possessing physiological phospholipid distributions have different properties from those of binary or trinary model membranes. In the current work, the impact of oxidized cholesterol on the biophysical properties of a complex neuronal plasma membrane is investigated using coarse-grained Martini molecular dynamics simulations. Comparison of the native neuronal membrane to neuronal membranes containing 10% tail-oxidized or 10% head-oxidized cholesterol shows that the site of oxidization changes the behavior of the oxidized cholesterol in the membrane. Furthermore, species-specific domain formation is observed between each oxidized cholesterol and minor lipid classes. Although both tail-oxidized and head-oxidized cholesterols modulate the biophysical properties of the membrane, smaller changes are observed in the complex neuronal membrane than seen in the previous work on simple binary or trinary model membranes. This work highlights the presence of compensatory effects of lipid diversity in the complex neuronal membrane. Overall, this study improves our molecular-level understanding of the effects of oxidized cholesterol on the properties of neuronal tissue and emphasizes the importance of studying membranes with realistic lipid compositions.
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Affiliation(s)
- Katie A. Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Lily Wang
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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11
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Fatafta H, Khaled M, Owen MC, Sayyed-Ahmad A, Strodel B. Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane. Proc Natl Acad Sci U S A 2021; 118:e2106210118. [PMID: 34544868 PMCID: PMC8488611 DOI: 10.1073/pnas.2106210118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Mounting evidence suggests that the neuronal cell membrane is the main site of oligomer-mediated neuronal toxicity of amyloid-β peptides in Alzheimer's disease. To gain a detailed understanding of the mutual interference of amyloid-β oligomers and the neuronal membrane, we carried out microseconds of all-atom molecular dynamics (MD) simulations on the dimerization of amyloid-β (Aβ)42 in the aqueous phase and in the presence of a lipid bilayer mimicking the in vivo composition of neuronal membranes. The dimerization in solution is characterized by a random coil to β-sheet transition that seems on pathway to amyloid aggregation, while the interactions with the neuronal membrane decrease the order of the Aβ42 dimer by attenuating its propensity to form a β-sheet structure. The main lipid interaction partners of Aβ42 are the surface-exposed sugar groups of the gangliosides GM1. As the neurotoxic activity of amyloid oligomers increases with oligomer order, these results suggest that GM1 is neuroprotective against Aβ-mediated toxicity.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Mohammed Khaled
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael C Owen
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | | | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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12
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Wilson KA, Wang L, Lin YC, O'Mara ML. Investigating the lipid fingerprint of SLC6 neurotransmitter transporters: a comparison of dDAT, hDAT, hSERT, and GlyT2. BBA ADVANCES 2021; 1:100010. [PMID: 37082011 PMCID: PMC10074915 DOI: 10.1016/j.bbadva.2021.100010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The local lipid annulus, or "fingerprint", of four SLC6 transporters (dDAT, hDAT, hSERT, and GlyT2) embedded in a complex neuronal membrane were compared and characterised using molecular dynamics. Our analysis included the development of new tools to improve membrane leaflet detection and the analysis of leaflet-dependent properties. Overall, the lipid fingerprints of the four transporters are comprised of similar lipids when grouped by headgroup or tail saturation. The enrichment and depletion of specific lipids, including sites of cholesterol contacts, varies between transporters. The subtle differences in lipid fingerprints results in varying membrane biophysical properties near the transporter. Our results highlight that the lipid-fingerprint of SLC6 transporters in complex membranes is highly dependent on membrane composition. Our results further characterize how the presence and identity of membrane proteins affects the complex interplay of lipid-protein interactions, influencing the local lipid environment and membrane biophysical properties.
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13
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Ermilova I, Swenson J. DOPC versus DOPE as a helper lipid for gene-therapies: molecular dynamics simulations with DLin-MC3-DMA. Phys Chem Chem Phys 2020; 22:28256-28268. [PMID: 33295352 DOI: 10.1039/d0cp05111j] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ionizable lipids are important compounds of modern therapeutic lipid nano-particles (LNPs). One of the most promising ionizable lipids (or amine lipids) is DLin-MC3-DMA. Depending on their pharmaceutical application these LNPs can also contain various helper lipids, such as phospho- and pegylated lipids, cholesterol and nucleic acids as a cargo. Due to their complex compositions the structures of these therapeutics have not been refined properly. Therefore, the role of each lipid in the pharmacological properties of LNPs has not been determined. In this work an atomistic model for the neutral form of DLin-MC3-DMA was derived and all-atom molecular dynamics (MD) simulations were carried out in order to investigate the effect of the phospholipid headgroup on the possible properties of the shell-membranes of LNPs. Bilayers containing either DOPC or DOPE lipids at two different ratios of DLin-MC3-DMA (5 mol% and 15 mol%) were constructed and simulated at neutral pH 7.4. The results from the analysis of MD trajectories revealed that DOPE lipid headgroups associated strongly with lipid tails and carbonyl oxygens of DLin-MC3-DMA, while for DOPC lipid headgroups no significant associations were observed. Furthermore, the strong associations between DOPE and DLin-MC3-DMA result in the positioning of DLin-MC3-DMA at the surface of the membrane. Such an interplay between the lipids slows down the lateral diffusion of all simulated bilayers, where a more dramatic decrease of the diffusion rate is observed in membranes with DOPE. This can explain the low water penetration of lipid bilayers with phosphatidylethanolamines and, probably, can relate to the bad transfection properties of LNPs with DOPE and DLin-MC3-DMA.
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Affiliation(s)
- Inna Ermilova
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
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14
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Flavonol clustering in model lipid membranes: DSC, AFM, force spectroscopy and MD simulations study. Colloids Surf B Biointerfaces 2020; 193:111147. [PMID: 32526654 DOI: 10.1016/j.colsurfb.2020.111147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/06/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022]
Abstract
We here report on flavonols (myricetin (MCE) and its glycoside myricitrin (MCI)) - 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane interactions focusing on the effects of flavonol clustering on the membrane thermotropic and nanomechanical properties. Atomic force microscopy (AFM), force spectroscopy (FS) and differential scanning calorimetry (DSC) together with molecular dynamics (MD) simulations provided a consistent picture of flavonol - DMPC membrane interactions. DMPC membrane as a supported lipid bilayer preserved its integrity even at higher flavonol molar fraction x. When present at x = 0.1 - 0.3, MCE and MCI both slightly improve DMPC bilayer fluidity which is evidenced by the decrease in the main phase transition temperature Tm. MCE is found within the interior of the bilayer, while MCI incorporates in the head group-water interface region. AFM and FS confirmed clusters as protrusions with an average height of 0.012 μm and average diameters of 0.60 and 0.24 μm for MCE and MCI clusters, respectively. The average membrane thickness in DMPC fluid phase decreases for 7% at xMCE = 0.30, while only 4% at xMCI = 0.27. The induced membrane changes are dependent on the chemical and physical properties of inserted flavonols. The hypothesis regarding the tendency of flavonol to clustering in membranes by increasing flavonol molar fraction has been confirmed.
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15
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Zalygin A, Solovyeva D, Vaskan I, Henry S, Schaefer M, Volynsky P, Tuzikov A, Korchagina E, Ryzhov I, Nizovtsev A, Mochalov K, Efremov R, Shtykova E, Oleinikov V, Bovin N. Structure of Supramers Formed by the Amphiphile Biotin-CMG-DOPE. ChemistryOpen 2020; 9:641-648. [PMID: 32499990 PMCID: PMC7266497 DOI: 10.1002/open.201900276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/02/2020] [Indexed: 11/10/2022] Open
Abstract
The synthetic function-spacer-lipid (FSL) amphiphile biotin-CMG-DOPE is widely used for delicate ligation of living cells with biotin residues under physiological conditions. Since this molecule has an "apolar-polar-hydrophobic" gemini structure, the supramolecular organization is expected to differ significantly from the classical micelle. Its organization is investigated with experimental methods and molecular dynamics simulations (MDS). Although the linear length of a single biotin-CMG-DOPE molecule is 9.5 nm, the size of the dominant supramer globule is only 14.6 nm. Investigations found that while the DOPE tails form a hydrophobic core, the polar CMG spacer folds back upon itself and predominantly places the biotin reside inside the globule or planar layer. MDS demonstrates that <10 % of biotin residues on the highly water dispersible globules and only 1 % of biotin residues in layer coatings are in an linear conformation and exposing biotin into the aqueous medium. This explains why in biotin-CMG-DOPE apolar biotin residues both in water dispersible globules and coatings on solid surfaces are still capable of interacting with streptavidin.
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Affiliation(s)
- Anton Zalygin
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Daria Solovyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Ivan Vaskan
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute)Kashirskoe shosse 31Moscow115409Russian Federation
| | - Stephen Henry
- School of EngineeringComputer & Mathematical SciencesAuckland University of TechnologyAuckland1010New Zealand
| | - Marcel Schaefer
- School of EngineeringComputer & Mathematical SciencesAuckland University of TechnologyAuckland1010New Zealand
| | - Pavel Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Alexander Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Elena Korchagina
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Ivan Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Alexey Nizovtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Konstantin Mochalov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Roman Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
- National Research University Higher School of EconomicsMyasnitskaya Str. 20Moscow101000Russian Federation
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of SciencesMoscow119333Russian Federation
- Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscow119991Russian Federation
| | - Vladimir Oleinikov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute)Kashirskoe shosse 31Moscow115409Russian Federation
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
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16
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Furlan AL, Laurin Y, Botcazon C, Rodríguez-Moraga N, Rippa S, Deleu M, Lins L, Sarazin C, Buchoux S. Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane. PLANTS 2020; 9:plants9050648. [PMID: 32443858 PMCID: PMC7285231 DOI: 10.3390/plants9050648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/20/2022]
Abstract
Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.
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Affiliation(s)
- Aurélien L. Furlan
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Yoann Laurin
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Camille Botcazon
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Nely Rodríguez-Moraga
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sébastien Buchoux
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Correspondence: ; Tel.: +33-(0)3-2282-7473
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17
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Batishchev OV, Alekseeva AS, Tretiakova DS, Galimzyanov TR, Chernyadyev AY, Onishchenko NR, Volynsky PE, Boldyrev IA. Cyclopentane rings in hydrophobic chains of a phospholipid enhance the bilayer stability to electric breakdown. SOFT MATTER 2020; 16:3216-3223. [PMID: 32161934 DOI: 10.1039/c9sm02001b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Archaeal lipids ensure unprecedented stability of archaea membranes in extreme environments. Here, we incorporate a characteristic structural feature of an archaeal lipid, the cyclopentane ring, into hydrocarbon chains of a short-chain (C12) phosphatidylcholine to explore whether the insertion would allow such a lipid (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, diC12cp-PC) to form stable bilayers at room temperature. According to fluorescence-based assays, in water diC12cp-PC formed liquid-crystalline bilayers at room temperature. Liposomes produced from diC12cp-PC retained calcein for over a week when stored at +4 °C. diC12cp-PC could also form model bilayer lipid membranes that were by an order of magnitude more stable to electrical breakdown than egg PC membranes. Molecular dynamics simulation showed that the cyclopentane fragment fixes five carbon atoms (or four C-C bonds), which is compensated by the higher mobility of the rest of the chain. This was found to be the reason for the remarkable stability of the diC12cp-PC bilayer: restricted conformational mobility of a chain segment increases the membrane bending modulus (compared to a normal hydrocarbon chain of the same length). Here, higher stiffness practically does not affect the line tension of a membrane pore edge. Rather it makes it more difficult for diC12cp-PC to rearrange in order to line the edge of a hydrophilic pore; therefore, fewer pores are formed.
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Affiliation(s)
- Oleg V Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Anna S Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Daria S Tretiakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Timur R Galimzyanov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia and National University of Science and Technology MISiS, Moscow, 119049, Russia
| | - Andrey Yu Chernyadyev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Natalia R Onishchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Pavel E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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18
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Mineev KS, Volynsky PE, Galimzyanov TR, Tretiakova DS, Bobrov MY, Alekseeva AS, Boldyrev IA. Archaeal cyclopentane fragment in a surfactant's hydrophobic tail decreases the Krafft point. SOFT MATTER 2020; 16:1333-1341. [PMID: 31934706 DOI: 10.1039/c9sm02000d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Archaea are prokaryotic microorganisms famous for their ability to adapt to extreme environments, including low and high temperatures. Archaeal lipids often are macrocycles with two polar heads and a hydrophobic core that contains methyl groups and in-line cycles. Here we present the design of novel general-purpose surfactants that have inherited features of archaeal lipids. These are C12 and C14 carboxylic acids containing in-line cyclopentanes. The cyclopentanes disturb the chain packing, which results in remarkable expansion of the operational range of the surfactant into the low-temperature region. We report synthesis and properties of these novel archaea-like surfactants and details of their chain packing derived from thermodynamics model predictions, molecular dynamics simulations, and experimental data on CMC and Krafft points.
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Affiliation(s)
- Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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19
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Ermilova I, Lyubartsev AP. Modelling of interactions between Aβ(25-35) peptide and phospholipid bilayers: effects of cholesterol and lipid saturation. RSC Adv 2020; 10:3902-3915. [PMID: 35492630 PMCID: PMC9048594 DOI: 10.1039/c9ra06424a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/14/2019] [Indexed: 11/25/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in neuronal membranes is a known promoter of Alzheimer’s disease. To gain insight into the molecular details of Aβ peptide aggregation and its effect on model neuronal membranes, we carried out molecular dynamics simulations of the Aβ(25–35) fragment of the amyloid precursor protein in phospholipid bilayers composed of either fully saturated or highly unsaturated lipids, in the presence or absence of cholesterol. It was found that the peptide does not penetrate through any of the considered membranes, but can reside in the headgroup region and upper part of the lipid tails showing a clear preference to a polyunsaturated cholesterol-free membrane. Due to the ordering and condensing effect upon addition of cholesterol, membranes become more rigid facilitating peptide aggregation on the surface. Except for the case of the cholesterol-free saturated lipid bilayer, the peptides have a small effect on the membrane structure and ordering. It was also found that the most “active” amino-acid for peptide–lipid and peptide–cholesterol interaction is methionine-35, followed by asparagine-27 and serine-26, which form hydrogen bonds between peptides and polar atoms of lipid headgroups. These amino acids are also primarily responsible for peptide aggregation. This work will be relevant for designing strategies to develop drugs to combat Alzheimer’s disease. Molecular dynamics simulations of Aβ(25–35) peptides in phospholipid bilayers are carried out to investigate the effect of polyunsaturated lipids and cholesterol on aggregation of the peptides. ![]()
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Affiliation(s)
- Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm University Stockholm Sweden +46 8161193
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University Stockholm Sweden +46 8161193
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20
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Ntarakas N, Ermilova I, Lyubartsev AP. Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:813-824. [PMID: 31655893 PMCID: PMC6853862 DOI: 10.1007/s00249-019-01407-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/02/2019] [Accepted: 10/13/2019] [Indexed: 12/05/2022]
Abstract
Aggregation of amyloid-\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β (Aβ) peptides, cleaved from the amyloid precursor protein, is known as a precursor of the Alzheimer’s disease (AD). It is also known that Alzheimer’s disease is characterized by a substantial decrease of the amount of polyunsaturated lipids in the neuronal membranes of the frontal gray matter. To get insight into possible interconnection of these phenomena, we have carried out molecular dynamics simulations of two fragments of A\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β peptide, A\documentclass[12pt]{minimal}
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\begin{document}$$_{1-28}$$\end{document}1-28 and A\documentclass[12pt]{minimal}
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\begin{document}$$_{26-40}$$\end{document}26-40, in four different lipid bilayers: two monocomponent ones (14:0-14:0 PC, 18:0-22:6 PC), and two bilayers containing mixtures of 18:0-18:0 PE, 22:6-22:6 PE, 16:0-16:0 PC and 18:1-18:1 PC lipids of composition mimicking neuronal membranes in a “healthy” and “AD” brain. The simulations showed that the presence of lipids with highly unsaturated 22:6cis fatty acids chains strongly affects the interaction of amyloid-\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β peptides with lipid membranes. The polyunsaturated lipids cause stronger adsorption of A\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β-peptides by the membrane and lead to weaker binding between peptides when the latter form aggregates. This difference in the behaviour observed in monocomponent bilayers is propagated in a similar fashion to the mixed membranes mimicking composition of neuronal membranes in “healthy” and “AD” brains, with “healthy” membrane having higher fraction of polyunsaturated lipids. Our simulations give strong indication that it can be physical–chemical background of the interconnection between amyloid fibrillization causing Alzheimer’s disease, and content of polyunsaturated lipids in the neuronal membranes.
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Affiliation(s)
- Nikolaos Ntarakas
- Department of Materials and Environmental Chemistry, Stockholm's University, 10691, Stockholm, Sweden
| | - Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm's University, 10691, Stockholm, Sweden
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm's University, 10691, Stockholm, Sweden.
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21
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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22
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Capelli R, Bochicchio A, Piccini G, Casasnovas R, Carloni P, Parrinello M. Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations. J Chem Theory Comput 2019; 15:3354-3361. [DOI: 10.1021/acs.jctc.9b00118] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Riccardo Capelli
- INM-9/IAS-5 Computational Biomedicine, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-54245 Jülich, Germany
| | - Anna Bochicchio
- INM-9/IAS-5 Computational Biomedicine, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-54245 Jülich, Germany
| | - GiovanniMaria Piccini
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Ticino, Switzerland
| | - Rodrigo Casasnovas
- INM-9/IAS-5 Computational Biomedicine, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-54245 Jülich, Germany
- JARA-HPC, Forschungszentrum Jülich, D-54245 Jülich, Germany
| | - Paolo Carloni
- INM-9/IAS-5 Computational Biomedicine, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-54245 Jülich, Germany
- Department of Physics, RWTH Aachen University, D-52078 Aachen, Germany
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Ticino, Switzerland
- Istituto Italiano
di Tecnologia, Via Morego 30, I-16163 Genova, Italy
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23
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Lu Y, Shi XF, Nguyen PH, Sterpone F, Salsbury FR, Derreumaux P. Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. J Phys Chem B 2019; 123:2687-2696. [PMID: 30813725 DOI: 10.1021/acs.jpcb.9b00431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The omega-3 and omega-6 polyunsaturated fatty acids are two important components of cell membranes in human brains. When incorporated into phospholipids, omega-3 slows the progression of Alzheimer's disease (AD), whereas omega-6 is linked to increased risk of AD. Little is known on the amyloid-β (Aβ) conformations in membranes rich in omega-3 and omega-6 phospholipids. Herein, the structural properties of the Aβ29-42 dimer embedded in both fatty acid membranes were comparatively studied to a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) bilayer using all-atom molecular dynamics (MD) simulations. Starting from α-helix, both omega-6 and omega-3 membranes promote new orientations and conformations of the dimer, in agreement with the observed dependence of Aβ production upon addition of these two fatty acids. This conformational result is corroborated by atomistic MD simulations of the dimer of the 99 amino acid C-terminal fragment of amyloid precursor protein spanning the residues 15-55. Starting from β-sheet, omega-6 membrane promotes helical and disordered structures of Aβ29-42 dimer, whereas omega-3 membrane preserves the β-sheet structures differing however from those observed in POPC. Remarkably, the mixture of the two fatty acids and POPC depicts another conformational ensemble of the Aβ29-42 dimer. This finding demonstrates that variation in the abundance of the molecular phospholipids, which changes with age, modulates membrane-embedded Aβ oligomerization.
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Affiliation(s)
- Yan Lu
- School of Physics and Optoelectronic Engineering , Xidian University , Xi'an 710071 , China
| | - Xiao-Feng Shi
- School of Physics and Optoelectronic Engineering , Xidian University , Xi'an 710071 , China
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS , Université Paris Diderot, Sorbonne Paris Cite , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS , Université Paris Diderot, Sorbonne Paris Cite , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Freddie R Salsbury
- Department of Physics , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Pharmacy , Ton Duc Thang University , Ho Chi Minh City , Vietnam
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24
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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25
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Smith DJ, Klauda JB, Sodt AJ. Simulation Best Practices for Lipid Membranes [Article v1.0]. LIVING JOURNAL OF COMPUTATIONAL MOLECULAR SCIENCE 2019; 1:5966. [PMID: 36204133 PMCID: PMC9534443 DOI: 10.33011/livecoms.1.1.5966] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
We establish a reliable and robust standardization of settings for practical molecular dynamics (MD) simulations of pure and mixed (single- and multi-component) lipid bilayer membranes. In lipid membranes research, particle-based molecular simulations are a powerful tool alongside continuum theory, lipidomics, and model, in vitro, and in vivo experiments. Molecular simulations can provide precise and reproducible spatiotemporal (atomic- and femtosecond-level) information about membrane structure, mechanics, thermodynamics, kinetics, and dynamics. Yet the simulation of lipid membranes can be a daunting task, given the uniqueness of lipid membranes relative to conventional liquid-liquid and solid-liquid interfaces, the immense and complex thermodynamic and statistical mechanical theory, the diversity of multiscale lipid models, limitations of modern computing power, the difficulty and ambiguity of simulation controls, finite size effects, competitive continuum simulation alternatives, and the desired application, including vesicle experiments and biological membranes. These issues can complicate an essential understanding of the field of lipid membranes, and create major bottlenecks to simulation advancement. In this article, we clarify these issues and present a consistent, thorough, and user-friendly framework for the design of state-of-the-art lipid membrane MD simulations. We hope to allow early-career researchers to quickly overcome common obstacles in the field of lipid membranes and reach maximal impact in their simulations.
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Affiliation(s)
- David J. Smith
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering and Biophysics Program, University of Maryland, College Park, MD, USA
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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26
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Huber RG, Carpenter TS, Dube N, Holdbrook DA, Ingólfsson HI, Irvine WA, Marzinek JK, Samsudin F, Allison JR, Khalid S, Bond PJ. Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions. Methods Mol Biol 2019; 2003:1-30. [PMID: 31218611 DOI: 10.1007/978-1-4939-9512-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lipid membranes play a crucial role in living systems by compartmentalizing biological processes and forming a barrier between these processes and the environment. Naturally, a large apparatus of biomolecules is responsible for construction, maintenance, transport, and degradation of these lipid barriers. Additional classes of biomolecules are tasked with transport of specific substances or transduction of signals from the environment across lipid membranes. In this article, we intend to describe a set of techniques that enable one to build accurate models of lipid systems and their associated proteins, and to simulate their dynamics over a variety of time and length scales. We discuss the methods and challenges that allow us to derive structural, mechanistic, and thermodynamic information from these models. We also show how these models have recently been applied in research to study some of the most complex lipid-protein systems to date, including bacterial and viral envelopes, neuronal membranes, and mammalian signaling systems.
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Affiliation(s)
- Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Namita Dube
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Daniel A Holdbrook
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - William A Irvine
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Jane R Allison
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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27
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Schumann-Gillett A, O'Mara ML. The effects of oxidised phospholipids and cholesterol on the biophysical properties of POPC bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:210-219. [DOI: 10.1016/j.bbamem.2018.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/04/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
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28
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Ermilova I, Lyubartsev AP. Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees. SOFT MATTER 2018; 15:78-93. [PMID: 30520494 DOI: 10.1039/c8sm01937a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cholesterol is an essential component of all animal cell membranes and plays an important role in maintaining the membrane structure and physical-chemical properties necessary for correct cell functioning. The presence of cholesterol is believed to be responsible for domain formation (lipid rafts) due to different interactions of cholesterol with saturated and unsaturated lipids. In order to get detailed atomistic insight into the behaviour of cholesterol in bilayers composed of lipids with varying degrees of unsaturation, we have carried out a series of molecular dynamics simulations of saturated and polyunsaturated lipid bilayers with different contents of cholesterol, as well as well-tempered metadynamics simulations with a single cholesterol molecule in these bilayers. From these simulations we have determined distributions of cholesterol across the bilayer, its orientational properties, free energy profiles, and specific interactions of molecular groups able to form hydrogen bonds. Both molecular dynamics and metadynamics simulations showed that the most unsaturated bilayer with 22:6 fatty acid chains shows behaviour which is most different from other lipids. In this bilayer, cholesterol is relatively often found in a "flipped" configuration with the hydroxyl group oriented towards the membrane middle plane. This bilayer has also the highest (least negative) binding free energy among liquid phase bilayers, and the lowest reorientation barrier. Furthermore, cholesterol molecules in this bilayer are often found to form head-to-tail contacts which may lead to specific clustering behaviour. Overall, our simulations support ideas that there can be a subtle interconnection between the contents of highly unsaturated fatty acids and cholesterol, deficiency or excess of each of them is related to many human afflictions and diseases.
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Affiliation(s)
- Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm Universtity, Stockholm, Sweden.
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm Universtity, Stockholm, Sweden.
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29
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Goossens K, De Winter H. Molecular Dynamics Simulations of Membrane Proteins: An Overview. J Chem Inf Model 2018; 58:2193-2202. [PMID: 30336018 DOI: 10.1021/acs.jcim.8b00639] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulations of membrane proteins have been rising in popularity in the past decade. Advancements in technology and force fields made it possible to simulate behavior of membrane proteins. Membrane protein simulations can now be used as supporting evidence for experimental findings, for elucidating protein mechanisms, and validating protein crystal structures. Unrelated to experimental data, these simulations can also serve to investigate larger scale processes like protein sorting, protein-membrane interactions, and more. In this review, the history as well as the state-of-the-art methodologies in membrane protein simulations will be summarized. An emphasis will be put on how to set up the system and on the current models for the different components of the simulation system. An overview of the available tools for membrane protein simulation will be given, and current limitations and prospects will also be discussed.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
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30
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Taiwo BJ, Olubiyi OO, Wang X, Fisusi FA, Akinniyi GA, Van Heerden FR, Strodel B. Schistosomiasis: Snail-vector control, molecular modelling and dynamic studies of bioactive N-acetylglycoside saponins from Tetrapleura tetraptera. Comput Biol Chem 2018; 77:363-372. [PMID: 30466045 DOI: 10.1016/j.compbiolchem.2018.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/31/2018] [Accepted: 09/16/2018] [Indexed: 10/28/2022]
Abstract
Schistosomiasis, a chronic neglected tropical disease caused by the Schistosoma spp. parasite, is associated with disabling patient symptoms. The new focus of the WHO roadmap on 'transmission control, wherever possible' offers drug development opportunities for intermediate-host control to prevent human-to-snail-to-human parasite transmission. Reports on the analysis of the impact of 'chemical-based mollusciciding' have concluded that constant application of molluscicides may contribute significantly towards the elimination of schistosomiasis in endemic areas. In South-Western Nigeria, Tetrapleura tetraptera is a tree whose fruit has been widely used in snail vector control. The presence of molluscicidal N-acetyl triterpene glycosides in the fruit has been reported. In this study, a bioactivity-directed fractionation of the fruit extract was performed to isolate the most potent molluscicidal saponin from the fruit. In an attempt to provide mechanistic insight into the observed activity, in silico screening was performed, profiling the molluscicidal N-acetyl triterpene glycosides reported from the fruit against two potential therapeutic targets in the mollusk used, NADH-ubiquinone oxidoreductase (NAD1) and retinoid X receptor. The docking predicted binary complexes of the saponins, which were subjected to explicit solvent conformational sampling from which patterns of structural stability were obtained. The binding energies alone did not account for the potency of the saponins indicating the influence of other factor like pharmacokinetic parameters. The study concluded that there is a preferential suitability of ND1's MWFE site for the rational design and development of novel molluscicidal agents.
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Affiliation(s)
- Bamigboye J Taiwo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy Obafemi Awolowo University, Ile Ife, Osun State, Nigeria.
| | - Olujide O Olubiyi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy Obafemi Awolowo University, Ile Ife, Osun State, Nigeria.
| | - Xue Wang
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University, Dusseldorf, Germany.
| | - Funmilola A Fisusi
- Drug Research and Production Unit, Faculty of Pharmacy, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria.
| | - Ganiyu Akintayo Akinniyi
- Drug Research and Production Unit, Faculty of Pharmacy, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria.
| | - Fanie R Van Heerden
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University, Dusseldorf, Germany.
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