1
|
Soulié M, Deletraz A, Wehbie M, Mahler F, Chantemargue B, Bouchemal I, Le Roy A, Petit-Härtlein I, Fieschi F, Breyton C, Ebel C, Keller S, Durand G. Rigid Cyclic Fluorinated Detergents: Fine-Tuning the Hydrophilic-Lipophilic Balance Controls Self-Assembling and Biochemical Properties. ACS APPLIED MATERIALS & INTERFACES 2024; 16:32971-32982. [PMID: 38885044 DOI: 10.1021/acsami.4c03359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We report herein the synthesis of three detergents bearing a perfluorinated cyclohexyl group connected through a short, hydrogenated spacer (i.e., propyl, butyl, or pentyl) to a β-maltoside polar head that are, respectively, called FCymal-3, FCymal-4, and FCymal-5. Increasing the length of the spacer decreased the critical micellar concentration (CMC), as demonstrated by surface tension (SFT) and isothermal titration calorimetry (ITC), from 5 mM for FCymal-3 to 0.7 mM for FCymal-5. The morphology of the micelles was studied by dynamic light scattering (DLS), analytical ultracentrifugation (AUC), and small-angle X-ray scattering (SAXS), indicating heterogeneous rod-like shapes. While micelles of FCymal-3 and -4 have similar hydrodynamic diameters of ∼10 nm, those of FCymal-5 were twice as large. We also investigated the ability of the detergents to solubilize lipid membranes made of 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC). Molecular modeling indicated that the FCymal detergents generate disorder in lipid bilayers, with FCymal-3 being inserted more deeply into bilayers than FCymal-4 and -5. This was experimentally confirmed using POPC vesicles that were completely solubilized within 2 h with FCymal-3, whereas FCymal-5 required >8 h. A similar trend was noticed for the direct extraction of membrane proteins from E. coli membranes, with FCymal-3 being more potent than FCymal-5. An opposite trend was observed in terms of stabilization of the two model membrane proteins bacteriorhodopsin (bR) and SpNOX. In all three FCymal detergents, bR was stable for at least 2 months with no signs of aggregation. However, while the structural integrity of bR was fully preserved in FCymal-4 and -5, minor bleaching was observed in FCymal-3. Similarly, SpNOX exhibited the least activity in FCymal-3 and the highest activity in FCymal-5. By combining solubilizing and stabilizing potency, FCymal detergents push forward our expectations of the usefulness of fluorinated detergents for handling and investigating membrane proteins.
Collapse
Affiliation(s)
- Marine Soulié
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Anais Deletraz
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Moheddine Wehbie
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | | | - Ilham Bouchemal
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Grégory Durand
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| |
Collapse
|
2
|
Bhatt M, Lazzarin E, Alberto-Silva AS, Domingo G, Zerlotti R, Gradisch R, Bazzone A, Sitte HH, Stockner T, Bossi E. Unveiling the crucial role of betaine: modulation of GABA homeostasis via SLC6A1 transporter (GAT1). Cell Mol Life Sci 2024; 81:269. [PMID: 38884791 PMCID: PMC11335192 DOI: 10.1007/s00018-024-05309-w] [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: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
Betaine is an endogenous osmolyte that exhibits therapeutic potential by mitigating various neurological disorders. However, the underlying cellular and molecular mechanisms responsible for its neuroprotective effects remain puzzling.In this study, we describe a possible mechanism behind the positive impact of betaine in preserving neurons from excitotoxicity. Here we demonstrate that betaine at low concentration modulates the GABA uptake by GAT1 (slc6a1), the predominant GABA transporter in the central nervous system. This modulation occurs through the temporal inhibition of the transporter, wherein prolonged occupancy by betaine impedes the swift transition of the transporter to the inward conformation. Importantly, the modulatory effect of betaine on GAT1 is reversible, as the blocking of GAT1 disappears with increased extracellular GABA. Using electrophysiology, mass spectroscopy, radiolabelled cellular assay, and molecular dynamics simulation we demonstrate that betaine has a dual role in GAT1: at mM concentration acts as a slow substrate, and at µM as a temporal blocker of GABA, when it is below its K0.5. Given this unique modulatory characteristic and lack of any harmful side effects, betaine emerges as a promising neuromodulator of the inhibitory pathways improving GABA homeostasis via GAT1, thereby conferring neuroprotection against excitotoxicity.
Collapse
Affiliation(s)
- Manan Bhatt
- Department of Biotechnology and Life Science, Laboratory of Cellular and Molecular Physiology, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Erika Lazzarin
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Ana Sofia Alberto-Silva
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Guido Domingo
- Department of Biotechnology and Life Science, Laboratory of Cellular and Molecular Physiology, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Rocco Zerlotti
- Nanion Technologies GmbH, Ganghoferstr. 70a, 80339, Munich, Germany
| | - Ralph Gradisch
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Andre Bazzone
- Nanion Technologies GmbH, Ganghoferstr. 70a, 80339, Munich, Germany
| | - Harald H Sitte
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
- Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, Amman, 19328, Jordan
- Center for Addiction Research and Science, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Stockner
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Elena Bossi
- Department of Biotechnology and Life Science, Laboratory of Cellular and Molecular Physiology, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy.
- Centre for Neuroscience, University of Insubria, 21100, Varese, Italy.
| |
Collapse
|
3
|
Park P, Matsubara DK, Barzotto DR, Lima FS, Chaimovich H, Marrink SJ, Cuccovia IM. Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides. Sci Rep 2024; 14:9701. [PMID: 38678109 PMCID: PMC11055889 DOI: 10.1038/s41598-024-60601-w] [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: 09/30/2023] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Short-cationic alpha-helical antimicrobial peptides (SCHAMPs) are promising candidates to combat the growing global threat of antimicrobial resistance. They are short-sequenced, selective against bacteria, and have rapid action by destroying membranes. A full understanding of their mechanism of action will provide key information to design more potent and selective SCHAMPs. Molecular Dynamics (MD) simulations are invaluable tools that provide detailed insights into the peptide-membrane interaction at the atomic- and meso-scale level. We use atomistic and coarse-grained MD to look into the exact steps that four promising SCHAMPs-BP100, Decoralin, Neurokinin-1, and Temporin L-take when they interact with membranes. Following experimental set-ups, we explored the effects of SCHAMPs on anionic membranes and vesicles at multiple peptide concentrations. Our results showed all four peptides shared similar binding steps, initially binding to the membrane through electrostatic interactions and then flipping on their axes, dehydrating, and inserting their hydrophobic moieties into the membrane core. At higher concentrations, fully alpha-helical peptides induced membrane budding and protrusions. Our results suggest the carpet mode of action is fit for the description of SCHAMPs lysis activity and discuss the importance of large hydrophobic residues in SCHAMPs design and activity.
Collapse
Affiliation(s)
- Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG, Groningen, the Netherlands
| | - Danilo K Matsubara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Domenico R Barzotto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG, Groningen, the Netherlands.
| | - Iolanda M Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| |
Collapse
|
4
|
Qiao Q, Wei G, Song Z. Structural diversity in the membrane-bound hIAPP dimer correlated with distinct membrane disruption mechanisms. Phys Chem Chem Phys 2024; 26:7090-7102. [PMID: 38345763 DOI: 10.1039/d3cp05887e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Amyloid deposits of the human islet amyloid polypeptide (hIAPP) have been identified in 90% of patients with type II diabetes. Cellular membranes accelerate the hIAPP fibrillation, and the integrity of membranes is also disrupted at the same time, leading to the apoptosis of β cells in pancreas. The molecular mechanism of hIAPP-induced membrane disruption, especially during the initial membrane disruption stage, has not been well understood yet. Herein, we carried out extensive all-atom molecular dynamics simulations investigating the hIAPP dimerization process in the anionic POPG membrane, to provide the detailed molecular mechanisms during the initial hIAPP aggregation stage in the membrane environment. Compared to the hIAPP monomer on the membrane, we observed not only an increase of α-helical structures, but also a substantial increase of β-sheet structures upon spontaneous dimerization. Moreover, the random coiled and α-helical dimer structures insert deep into the membrane interior with a few inter-chain contacts at the C-terminal region, while the β-sheet-rich structures reside on the membrane surface accompanied by strong inter-chain hydrophobic interactions. The coexistence of α and β structures constitutes a diverse structural ensemble of the membrane-bound hIAPP dimer. From α-helical to β-sheet structures, the degree of membrane disruption decreases gradually, and thus the membrane damage induced by random coiled and α-helical structures precedes that induced by β-sheet structures. We speculate that insertion of random coiled and α-helical structures contributes to the initial stage of membrane damage, while β-sheet structures on the membrane surface are more involved in the later stage of fibril-induced membrane disruption.
Collapse
Affiliation(s)
- Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai 200032, China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Fudan University, Shanghai 200438, China
| | - Zhijian Song
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai 200032, China
| |
Collapse
|
5
|
Gradisch R, Schlögl K, Lazzarin E, Niello M, Maier J, Mayer FP, Alves da Silva L, Skopec SMC, Blakely RD, Sitte HH, Mihovilovic MD, Stockner T. Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors. Nat Commun 2024; 15:417. [PMID: 38195746 PMCID: PMC10776687 DOI: 10.1038/s41467-023-44637-6] [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: 07/17/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
The presynaptic serotonin transporter (SERT) clears extracellular serotonin following vesicular release to ensure temporal and spatial regulation of serotonergic signalling and neurotransmitter homeostasis. Prescription drugs used to treat neurobehavioral disorders, including depression, anxiety, and obsessive-compulsive disorder, trap SERT by blocking the transport cycle. In contrast, illicit drugs of abuse like amphetamines reverse SERT directionality, causing serotonin efflux. Both processes result in increased extracellular serotonin levels. By combining molecular dynamics simulations with biochemical experiments and using a homologous series of serotonin analogues, we uncovered the coupling mechanism between the substrate and the transporter, which triggers the uptake of serotonin. Free energy analysis showed that only scaffold-bound substrates could initiate SERT occlusion through attractive long-range electrostatic interactions acting on the bundle domain. The associated spatial requirements define substrate and inhibitor properties, enabling additional possibilities for rational drug design approaches.
Collapse
Affiliation(s)
- Ralph Gradisch
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Katharina Schlögl
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060, Vienna, Austria
| | - Erika Lazzarin
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Marco Niello
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
- Genetics of Cognition Laboratory, Neuroscience area, Istituto Italiano di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Julian Maier
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Felix P Mayer
- Florida Atlantic University, Department of Biomedical Science, Jupiter, FL, 33458, USA
- Stiles-Nicholson Brain Institute, Jupiter, FL, 33458, USA
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Leticia Alves da Silva
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Sophie M C Skopec
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Randy D Blakely
- Florida Atlantic University, Department of Biomedical Science, Jupiter, FL, 33458, USA
- Stiles-Nicholson Brain Institute, Jupiter, FL, 33458, USA
| | - Harald H Sitte
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
- Al-Ahliyya Amman University, Hourani Center for Applied Scientific Research, Amman, Jordan
- Medical University of Vienna, Center for Addiction Research and Science, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Marko D Mihovilovic
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria.
| |
Collapse
|
6
|
Castelli M, Marchetti F, Osuna S, F. Oliveira AS, Mulholland AJ, Serapian SA, Colombo G. Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. J Am Chem Soc 2024; 146:901-919. [PMID: 38116743 PMCID: PMC10785808 DOI: 10.1021/jacs.3c11396] [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: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Protein functions are dynamically regulated by allostery, which enables conformational communication even between faraway residues, and expresses itself in many forms, akin to different "languages": allosteric control pathways predominating in an unperturbed protein are often unintuitively reshaped whenever biochemical perturbations arise (e.g., mutations). To accurately model allostery, unbiased molecular dynamics (MD) simulations require integration with a reliable method able to, e.g., detect incipient allosteric changes or likely perturbation pathways; this is because allostery can operate at longer time scales than those accessible by plain MD. Such methods are typically applied singularly, but we here argue their joint application─as a "multilingual" approach─could work significantly better. We successfully prove this through unbiased MD simulations (∼100 μs) of the widely studied, allosterically active oncotarget K-Ras4B, solvated and embedded in a phospholipid membrane, from which we decrypt allostery using four showcase "languages": Distance Fluctuation analysis and the Shortest Path Map capture allosteric hotspots at equilibrium; Anisotropic Thermal Diffusion and Dynamical Non-Equilibrium MD simulations assess perturbations upon, respectively, either superheating or hydrolyzing the GTP that oncogenically activates K-Ras4B. Chosen "languages" work synergistically, providing an articulate, mutually coherent, experimentally consistent picture of K-Ras4B allostery, whereby distinct traits emerge at equilibrium and upon GTP cleavage. At equilibrium, combined evidence confirms prominent allosteric communication from the membrane-embedded hypervariable region, through a hub comprising helix α5 and sheet β5, and up to the active site, encompassing allosteric "switches" I and II (marginally), and two proposed pockets. Upon GTP cleavage, allosteric perturbations mostly accumulate on the switches and documented interfaces.
Collapse
Affiliation(s)
- Matteo Castelli
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
- INSTM, via G. Giusti 9, 50121 Florence, Italy
- E4
Computer Engineering, via Martiri delle libertà 66, 42019 Scandiano (RE), Italy
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Girona, Catalonia E-17071, Spain
- ICREA, Barcelona, Catalonia E-08010, Spain
| | - A. Sofia F. Oliveira
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Adrian J. Mulholland
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Javanainen M, Heftberger P, Madsen JJ, Miettinen MS, Pabst G, Ollila OHS. Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions. J Chem Theory Comput 2023; 19:6342-6352. [PMID: 37616238 PMCID: PMC10536986 DOI: 10.1021/acs.jctc.3c00648] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 08/26/2023]
Abstract
Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.
Collapse
Affiliation(s)
- Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, 16000 Prague 6, Czech Republic
- Institute
of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Peter Heftberger
- Biophysics,
Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Jesper J. Madsen
- Global
and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, College of Public
Health, University of South Florida, Tampa, Florida 33612, United States
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Markus S. Miettinen
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
- Department
of Chemistry, University of Bergen, 5007 Bergen, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Georg Pabst
- Biophysics,
Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence
BioHealth—University of Graz, 8010 Graz, Austria
| | - O. H. Samuli Ollila
- Institute
of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
- VTT Technical Research Centre of Finland, 02150 Espoo, Finland
| |
Collapse
|
10
|
Roeters SJ, Strunge K, Pedersen KB, Golbek TW, Bregnhøj M, Zhang Y, Wang Y, Dong M, Nielsen J, Otzen DE, Schiøtt B, Weidner T. Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces. Nat Commun 2023; 14:5731. [PMID: 37723164 PMCID: PMC10507035 DOI: 10.1038/s41467-023-39843-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/23/2023] [Indexed: 09/20/2023] Open
Abstract
The amyloid aggregation of α-synuclein (αS), related to Parkinson's disease, can be catalyzed by lipid membranes. Despite the importance of lipid surfaces, the 3D-structure and orientation of lipid-bound αS is still not known in detail. Here, we report interface-specific vibrational sum-frequency generation (VSFG) experiments that reveal how monomeric αS binds to an anionic lipid interface over a large range of αS-lipid ratios. To interpret the experimental data, we present a frame-selection method ("ViscaSelect") in which out-of-equilibrium molecular dynamics simulations are used to generate structural hypotheses that are compared to experimental amide-I spectra via excitonic spectral calculations. At low and physiological αS concentrations, we derive flat-lying helical structures as previously reported. However, at elevated and potentially disease-related concentrations, a transition to interface-protruding αS structures occurs. Such an upright conformation promotes lateral interactions between αS monomers and may explain how lipid membranes catalyze the formation of αS amyloids at elevated protein concentrations.
Collapse
Affiliation(s)
- Steven J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
- Department of Anatomy and Neurosciences, Amsterdam UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Kris Strunge
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Kasper B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Thaddeus W Golbek
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Yuge Zhang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Yin Wang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
| |
Collapse
|
11
|
Nguyen JDM, da Hora GCA, Swanson JMJ. Mycolactone A vs. B: Multiscale Simulations Reveal the Roles of Localization and Association in Isomer-Specific Toxicity. Toxins (Basel) 2023; 15:486. [PMID: 37624243 PMCID: PMC10467071 DOI: 10.3390/toxins15080486] [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: 05/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Mycolactone is an exotoxin produced by Mycobacterium ulcerans that causes the neglected tropical skin disease Buruli ulcer. This toxin inhibits the Sec61 translocon in the endoplasmic reticulum (ER), preventing the host cell from producing several secretory and transmembrane proteins, resulting in cytotoxic and immunomodulatory effects. Interestingly, only one of the two dominant isoforms of mycolactone is cytotoxic. Here, we investigate the origin of this specificity by performing extensive molecular dynamics (MD) simulations with enhanced free energy sampling to query the association trends of the two isoforms with both the Sec61 translocon, using two distinct cryo-electron microscopy (cryo-EM) models as references, and the ER membrane, which serves as a toxin reservoir prior to association. Our results suggest that mycolactone B (the cytotoxic isoform) has a stronger association with the ER membrane than mycolactone A due to more favorable interactions with membrane lipids and water molecules. This could increase the reservoir of toxin proximal to the Sec61 translocon. In one model of Sec61 inhibited by mycolactone, we find that isomer B interacts more closely with residues thought to play a key role in signal peptide recognition and, thus, are essential for subsequent protein translocation. In the other model, we find that isomer B interacts more closely with the lumenal and lateral gates of the translocon, the dynamics of which are essential for protein translocation. These interactions induce a more closed conformation, which has been suggested to block signal peptide insertion and subsequent protein translocation. Collectively, these findings suggest that isomer B's unique cytotoxicity is a consequence of both increased localization to the ER membrane and channel-locking association with the Sec61 translocon, facets that could be targeted in the development of Buruli Ulcer diagnostics and Sec61-targeted therapeutics.
Collapse
Affiliation(s)
| | | | - Jessica M. J. Swanson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA; (J.D.M.N.); (G.C.A.d.H.)
| |
Collapse
|
12
|
Syrjänen JL, Epstein M, Gómez R, Furukawa H. Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red. Nat Commun 2023; 14:3821. [PMID: 37380652 PMCID: PMC10307800 DOI: 10.1038/s41467-023-39388-3] [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: 10/10/2022] [Accepted: 06/08/2023] [Indexed: 06/30/2023] Open
Abstract
Calcium homeostasis modulator 1 (CALHM1) is a voltage-dependent channel involved in neuromodulation and gustatory signaling. Despite recent progress in the structural biology of CALHM1, insights into functional regulation, pore architecture, and channel blockade remain limited. Here we present the cryo-EM structure of human CALHM1, revealing an octameric assembly pattern similar to the non-mammalian CALHM1s and the lipid-binding pocket conserved across species. We demonstrate by MD simulations that this pocket preferentially binds a phospholipid over cholesterol to stabilize its structure and regulate the channel activities. Finally, we show that residues in the amino-terminal helix form the channel pore that ruthenium red binds and blocks.
Collapse
Affiliation(s)
- Johanna L Syrjänen
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Max Epstein
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Ricardo Gómez
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Hiro Furukawa
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Matthes D, de Groot BL. Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. J Biol Chem 2023; 299:103034. [PMID: 36806684 PMCID: PMC10033322 DOI: 10.1016/j.jbc.2023.103034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Oligomeric aggregates of the amyloid-beta peptide(1-42) (Aβ42) are regarded as a primary cause of cytotoxicity related to membrane damage in Alzheimer's disease. However, a dynamical and structural characterization of pore-forming Aβ42 oligomers at atomic detail has not been feasible. Here, we used Aβ42 oligomer structures previously determined in a membrane-mimicking environment as putative model systems to study the pore formation process in phospholipid bilayers with all-atom molecular dynamics simulations. Multiple Aβ42 oligomer sizes, conformations, and N-terminally truncated isoforms were investigated on the multi-μs time scale. We found that pore formation and ion permeation occur via edge conductivity and exclusively for β-sandwich structures that feature exposed side-by-side β-strand pairs formed by residues 9 to 21 of Aβ42. The extent of pore formation and ion permeation depends on the insertion depth of hydrophilic residues 13 to 16 (HHQK domain) and thus on subtle differences in the overall stability, orientation, and conformation of the aggregates in the membrane. Additionally, we determined that backbone carbonyl and polar side-chain atoms from the edge strands directly contribute to the coordination sphere of the permeating ions. Furthermore, point mutations that alter the number of favorable side-chain contacts correlate with the ability of the Aβ42 oligomer models to facilitate ion permeation in the bilayer center. Our findings suggest that membrane-inserted, layered β-sheet edges are a key structural motif in pore-forming Aβ42 oligomers independent of their size and play a pivotal role in aggregate-induced membrane permeabilization.
Collapse
Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| |
Collapse
|
15
|
Solbach F, Bernardi A, Bansal S, Budamagunta MS, Krep L, Leonhard K, Voss JC, Lam KS, Faller R. Determining structure and action mechanism of LBF14 by molecular simulation. J Biomol Struct Dyn 2022; 40:11977-11988. [PMID: 34424133 DOI: 10.1080/07391102.2021.1967783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The recently discovered, membrane-active peptide LBF14 contains several non-proteinogenic amino acids and is able to transform vesicles into tubule networks. The exact membrane interaction mechanism and detailed secondary structure are yet to be determined. We performed molecular dynamics simulations of LBF14 and let it fold de novo into its ensemble of native secondary structures. Histidine protonation state effects on secondary structure were investigated. An MD simulation of the peptide with a lipid bilayer was performed. Simulation results were compared to circular dichroism and electron paramagnetic resonance data of previous studies. LBF14 contains a conserved helical section in an otherwise random structure. Helical stability is influenced by histidine protonation. The peptide localized to the polar layer of the membrane, consistent with experimental results. While the overall secondary structure is unaffected by membrane interaction, Ramachandran plot analysis yielded two distinct peptide conformations during membrane interaction. This conformational change was accompanied by residue repositioning within the membrane. LBF14 only affected the local order in the membrane, and had no measurable effect on pressure. The simulation results are consistent with the previously proposed membrane interaction mechanism of LBF14 and can additionally explain the local interaction mechanism. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Florian Solbach
- Department of Chemical Engineering, University of California-Davis, Davis, CA, USA.,Chair of Technical Thermodynamics, RWTH Aachen University, Aachen, Germany
| | - Austen Bernardi
- Department of Chemical Engineering, University of California-Davis, Davis, CA, USA.,Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Shivani Bansal
- Department of Chemistry, University of California-Davis, Davis, CA, USA.,Department of Biochemistry and Molecular Medicine, School of Medicine, University of California-Davis, Davis, CA, USA
| | - Madhu S Budamagunta
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California-Davis, Davis, CA, USA
| | - Lukas Krep
- Chair of Technical Thermodynamics, RWTH Aachen University, Aachen, Germany
| | - Kai Leonhard
- Chair of Technical Thermodynamics, RWTH Aachen University, Aachen, Germany
| | - John C Voss
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California-Davis, Davis, CA, USA
| | - Kit S Lam
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - Roland Faller
- Department of Chemical Engineering, University of California-Davis, Davis, CA, USA
| |
Collapse
|
16
|
Braithwaite IM, Davis JH. Orientation of Cholesterol in Polyunsaturated Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15804-15816. [PMID: 36480923 DOI: 10.1021/acs.langmuir.2c02718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The local normal to the fluid liquid crystalline phase of the lipid membrane is an axis of motional symmetry for the molecules that make up the bilayer. The presence of cholesterol in the membrane increases not only the lipid hydrocarbon chain order but also the strength of the membrane's orienting potential. Cholesterol undergoes rapid reorientation about a diffusion axis that is roughly aligned with the long molecular axis, but there is also a slower reorientation of the diffusion axis, or "wobble", relative to the local bilayer normal. The extent of this second, slower motion depends on the degree of order of the lipids that make up the bilayer. We use 2H nuclear magnetic resonance of deuterium-labeled cholesterol to investigate quantitatively the effect of lipid chain unsaturation on cholesterol orientation in a series of phospholipid bilayers. We find that the hydrocarbon chains in membranes composed of polyunsaturated lipids are much more highly disordered than those in membranes composed of saturated lipids but that cholesterol remains aligned roughly along the bilayer normal.
Collapse
Affiliation(s)
| | - James H Davis
- Department of Physics, University of Guelph, Guelph, ON, CanadaN1G 2W1
| |
Collapse
|
17
|
Funnel metadynamics and behavioral studies reveal complex effect of D2AAK1 ligand on anxiety-like processes. Sci Rep 2022; 12:21192. [PMID: 36476619 PMCID: PMC9729218 DOI: 10.1038/s41598-022-25478-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Anxiety is a troublesome symptom for many patients, especially those suffering from schizophrenia. Its regulation involves serotonin receptors, targeted e.g. by antipsychotics or psychedelics such as LSD. 5-HT2A receptors are known for an extremely long LSD residence time, enabling minute doses to exert a long-lasting effect. In this work, we explore the changes in anxiety-like processes induced by the previously reported antipsychotic, D2AAK1. In vivo studies revealed that the effect of D2AAK1 on the anxiety is mediated through serotonin 5-HT1A and 5-HT2A receptors, and that it is time-dependent (anxiogenic after 30 min, anxiolytic after 60 min) and dose-dependent. The funnel metadynamics simulations suggest complicated ligand-5HT2AR interactions, involving an allosteric site located under the third extracellular loop, which is a possible explanation of the time-dependency. The binding of D2AAK1 at the allosteric site results in a broader opening of the extracellular receptor entry, possibly altering the binding kinetics of orthosteric ligands.
Collapse
|
18
|
Sousa CF, Kamal MAM, Richter R, Elamaldeniya K, Hartmann RW, Empting M, Lehr CM, Kalinina OV. Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane. J Chem Inf Model 2022; 62:5023-5033. [PMID: 36214845 DOI: 10.1021/acs.jcim.2c00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Passive diffusion across biomembranes is an important mechanism of permeation for multiple drugs, including antibiotics. However, this process is frequently neglected while studying drug uptake and, in our view, warrants further investigation. Here, we apply molecular dynamics simulations to investigate the impact of changes in molecular hydrophobicity on the permeability of a series of inhibitors of the quorum sensing of Pseudomonas aeruginosa, previously discovered by us, across a membrane model. Overall, we show that permeation across this membrane model does not correlate with the molecule's hydrophobicity. We demonstrate that using a simple model for permeation, based on the difference between the maximum and minimum of the free energy profile, outperforms the inhomogeneous solubility-diffusion model, yielding a permeability ranking that better agrees with the experimental results, especially for hydrophobic permeants. The calculated differences in permeability could not explain differences in in bacterio activity. Nevertheless, substantial differences in molecular orientation along the permeation pathway correlate with the in bacterio activity, emphasizing the importance of analyzing, at an atomistic level, the permeation pathway of these solutes.
Collapse
Affiliation(s)
- Carla F Sousa
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Mohamed A M Kamal
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Robert Richter
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Kalanika Elamaldeniya
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - Rolf W Hartmann
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany.,Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken66123, Germany
| | - Martin Empting
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,Antiviral & Antivirulence Drugs Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany
| | - Claus-Michael Lehr
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Olga V Kalinina
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany.,Medical Faculty, Saarland University, Homburg66421, Germany
| |
Collapse
|
19
|
Falginella FL, Kravec M, Drabinová M, Paclíková P, Bryja V, Vácha R. Binding of DEP domain to phospholipid membranes: More than just electrostatics. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183983. [PMID: 35750206 DOI: 10.1016/j.bbamem.2022.183983] [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: 01/05/2022] [Revised: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Over the past decades an extensive effort has been made to provide a more comprehensive understanding of Wnt signaling, yet many regulatory and structural aspects remain elusive. Among these, the ability of Dishevelled (DVL) protein to relocalize at the plasma membrane is a crucial step in the activation of all Wnt pathways. The membrane binding of DVL was suggested to be mediated by the preferential interaction of its C-terminal DEP domain with phosphatidic acid (PA). However, due to the scarcity and fast turnover of PA, we investigated the role on the membrane association of other more abundant phospholipids. The combined results from computational simulations and experimental measurements with various model phospholipid membranes, demonstrate that the membrane binding of DEP/DVL constructs is governed by the concerted action of generic electrostatics and finely-tuned intermolecular interactions with individual lipid species. In particular, while we confirmed the strong preference for PA lipid, we also observed a weak but non-negligible affinity for phosphatidylserine, the most abundant anionic phospholipid in the plasma membrane, and phosphatidylinositol 4,5-bisphosphate. The obtained molecular insight into DEP-membrane interaction helps to elucidate the relation between changes in the local membrane composition and the spatiotemporal localization of DVL and, possibly, other DEP-containing proteins.
Collapse
Affiliation(s)
- Francesco L Falginella
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marek Kravec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Martina Drabinová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Vítĕzslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno 612 65, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| |
Collapse
|
20
|
Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES 2022; 1864:183994. [PMID: 35724739 PMCID: PMC9212275 DOI: 10.1016/j.bbamem.2022.183994] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 01/20/2023]
Abstract
SARS-CoV-2 contains four structural proteins in its genome. These proteins aid in the assembly and budding of new virions at the ER-Golgi intermediate compartment (ERGIC). Current fundamental research efforts largely focus on one of these proteins – the spike (S) protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other structural proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length envelope (E) protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.
Collapse
|
21
|
sPLA2 Wobbles on the Lipid Bilayer between Three Positions, Each Involved in the Hydrolysis Process. Toxins (Basel) 2022; 14:toxins14100669. [PMID: 36287938 PMCID: PMC9610741 DOI: 10.3390/toxins14100669] [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] [Received: 08/25/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Secreted phospholipases A2 (sPLA2s) are peripheral membrane enzymes that hydrolyze phospholipids in the sn-2 position. The action of sPLA2 is associated with the work of two active sites. One, the interface binding site (IBS), is needed to bind the enzyme to the membrane surface. The other one, the catalytic site, is needed to hydrolyze the substrate. The interplay between sites, how the substrate protrudes to, and how the hydrolysis products release from, the catalytic site remains in the focus of investigations. Here, we report that bee venom PLA2 has two additional interface binding modes and enzyme activity through constant switching between three different orientations (modes of binding), only one of which is responsible for substrate uptake from the bilayer. The finding was obtained independently using atomic force microscopy and molecular dynamics. Switching between modes has biological significance: modes are steps of the enzyme moving along the membrane, product release in biological milieu, and enzyme desorption from the bilayer surface.
Collapse
|
22
|
The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nat Commun 2022; 13:5385. [PMID: 36104315 PMCID: PMC9474542 DOI: 10.1038/s41467-022-32797-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/12/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractAggregation of amyloidogenic proteins is a characteristic of multiple neurodegenerative diseases. Atomic resolution of small molecule binding to such pathological protein aggregates is of interest for the development of therapeutics and diagnostics. Here we investigate the interaction between α-synuclein fibrils and anle138b, a clinical drug candidate for disease modifying therapy in neurodegeneration and a promising scaffold for positron emission tomography tracer design. We used nuclear magnetic resonance spectroscopy and the cryogenic electron microscopy structure of α-synuclein fibrils grown in the presence of lipids to locate anle138b within a cavity formed between two β-strands. We explored and quantified multiple binding modes of the compound in detail using molecular dynamics simulations. Our results reveal stable polar interactions between anle138b and backbone moieties inside the tubular cavity of the fibrils. Such cavities are common in other fibril structures as well.
Collapse
|
23
|
Kumar A, Kindig K, Rao S, Zaki AM, Basak S, Sansom MSP, Biggin PC, Chakrapani S. Structural basis for cannabinoid-induced potentiation of alpha1-glycine receptors in lipid nanodiscs. Nat Commun 2022; 13:4862. [PMID: 35982060 PMCID: PMC9388682 DOI: 10.1038/s41467-022-32594-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/08/2022] [Indexed: 11/23/2022] Open
Abstract
Nociception and motor coordination are critically governed by glycine receptor (GlyR) function at inhibitory synapses. Consequentially, GlyRs are attractive targets in the management of chronic pain and in the treatment of several neurological disorders. High-resolution mechanistic details of GlyR function and its modulation are just emerging. While it has been known that cannabinoids such as Δ9-tetrahydrocannabinol (THC), the principal psychoactive constituent in marijuana, potentiate GlyR in the therapeutically relevant concentration range, the molecular mechanism underlying this effect is still not understood. Here, we present Cryo-EM structures of full-length GlyR reconstituted into lipid nanodisc in complex with THC under varying concentrations of glycine. The GlyR-THC complexes are captured in multiple conformational states that reveal the basis for THC-mediated potentiation, manifested as different extents of opening at the level of the channel pore. Taken together, these structural findings, combined with molecular dynamics simulations and functional analysis, provide insights into the potential THC binding site and the allosteric coupling to the channel pore.
Collapse
Affiliation(s)
- Arvind Kumar
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Kayla Kindig
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Sandip Basak
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
24
|
Structural and dynamic mechanisms of GABA A receptor modulators with opposing activities. Nat Commun 2022; 13:4582. [PMID: 35933426 PMCID: PMC9357065 DOI: 10.1038/s41467-022-32212-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
γ-Aminobutyric acid type A (GABAA) receptors are pentameric ligand-gated ion channels abundant in the central nervous system and are prolific drug targets for treating anxiety, sleep disorders and epilepsy. Diverse small molecules exert a spectrum of effects on γ-aminobutyric acid type A (GABAA) receptors by acting at the classical benzodiazepine site. They can potentiate the response to GABA, attenuate channel activity, or counteract modulation by other ligands. Structural mechanisms underlying the actions of these drugs are not fully understood. Here we present two high-resolution structures of GABAA receptors in complex with zolpidem, a positive allosteric modulator and heavily prescribed hypnotic, and DMCM, a negative allosteric modulator with convulsant and anxiogenic properties. These two drugs share the extracellular benzodiazepine site at the α/γ subunit interface and two transmembrane sites at β/α interfaces. Structural analyses reveal a basis for the subtype selectivity of zolpidem that underlies its clinical success. Molecular dynamics simulations provide insight into how DMCM switches from a negative to a positive modulator as a function of binding site occupancy. Together, these findings expand our understanding of how GABAA receptor allosteric modulators acting through a common site can have diverging activities. GABAA receptors are important targets for anxiety, sedation and anesthesia. Here, the authors present structures bound by zolpidem (Ambien), the most prescribed hypnotic in the US, and DMCM, a negative modulator, providing insights into receptor modulation.
Collapse
|
25
|
Lu Y, Salsbury F, Derreumaux P. Impact of A2T and D23N mutations on C99 homodimer conformations. J Chem Phys 2022; 157:085102. [DOI: 10.1063/5.0101622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix modified the structures and fluctuations of C99. In this study, we performed atomistic molecular dynamics simulations of the homodimer of the 55-residue congener of the C-terminal domain of the amyloid protein precursor, C99(1-55), in a POPC-cholesterol lipid bilayer, and we compared the conformational ensemble of WT sequence to those of the A2T and D23N variants. These mutations are particularly interesting as the protective Alzheimer's disease (AD) A2T mutation is known to decrease Aβ production, whereas the early onset AD D23N mutation does not affect Aβ production. We found noticeable differences in the structural ensembles of the three sequences. In particular, A2T varies from both WT and D23N by having long-range effects on the population of the extracellular justamembrane helix, the interface between the G29xxx-G33xxx-G37 motifs and the fluctuations of the transmembrane helical topologies.
Collapse
Affiliation(s)
- Yan Lu
- School of Physics, Xidian University, China
| | | | | |
Collapse
|
26
|
Kania A, Bratek M, Majta J, Sarapata K, Gałan W, Markiewicz M, Wójcik-Augustyn A. The importance of atomic partial charges in the reproduction of intermolecular interactions for the triacetin - a model of glycerol backbone. Chem Phys Lipids 2022; 245:105203. [DOI: 10.1016/j.chemphyslip.2022.105203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 11/03/2022]
|
27
|
Hou Y, Xu B, Chen SL, Gan W, Yuan Q, Lin X. Understanding the different cross-membrane transport kinetics of two charged molecules on the DOPG lipid surface with second harmonic generation and MD simulation. SOFT MATTER 2022; 18:4305-4314. [PMID: 35620962 DOI: 10.1039/d2sm00167e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A clear physical picture of the dynamic behavior of molecules on the surface of the lipid membrane is highly desired and has attracted great attention from researchers. In this study, a step forward in this direction based on previous studies was presented with second harmonic generation (SHG) and molecular dynamic (MD) simulation. Specifically, details on the orientation flipping and cross-membrane transport of two charged molecules, 4-(4-diethylaminostyry)-1-methyl-pyridinium iodide (D289) and malachite green (MG), on the surface of 2-dioleoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DOPG) lipids were presented. Firstly, the orientation flipping of the two molecules on the surface of lipids before their cross-membrane transport was confirmed by the MD simulation. Then, the concentration dependent rate of the cross membrane transport for MG/D289 was analyzed. It was found that a simplified model could satisfactorily interpret the faster cross-membrane transport of MG under higher bulk concentrations. A different concentration dependent dynamics was observed with D289 and the reason behind it was also discussed. With this investigation, the surface structures and dynamics of D289 and MG on the DOPG lipid surface were clearly presented.
Collapse
Affiliation(s)
- Yi Hou
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Shenzhen 518055, Guangdong, Harbin 150001, Heilongjiang, China.
| | - Baomei Xu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Shenzhen 518055, Guangdong, Harbin 150001, Heilongjiang, China.
| | - Shun-Li Chen
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structure Materials of Guangdong Province, Shantou University, Shantou 515063, Guangdong, China
| | - Wei Gan
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Shenzhen 518055, Guangdong, Harbin 150001, Heilongjiang, China.
| | - Qunhui Yuan
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, Guangdong, China.
| | - Xi Lin
- School of Materials Science and Engineering, and Institute of Materials Genome & Big Data, Harbin Institute of Technology(Shenzhen), University Town, Shenzhen 518055, China.
| |
Collapse
|
28
|
Ginez LD, Osorio A, Vázquez-Ramírez R, Arenas T, Mendoza L, Camarena L, Poggio S. Changes in fluidity of the E. coli outer membrane in response to temperature, divalent cations and polymyxin-B show two different mechanisms of membrane fluidity adaptation. FEBS J 2022; 289:3550-3567. [PMID: 35038363 DOI: 10.1111/febs.16358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 12/28/2022]
Abstract
The outer membrane (OM) is an essential component of the Gram-negative bacterial cell envelope. Restricted diffusion of integral OM proteins and lipopolysaccharide (LPS) that constitute the outer leaflet of the OM support a model in which the OM is in a semi-crystalline state. The low fluidity of the OM has been suggested to be an important property of this membrane that even contributes to cell rigidity. The LPS characteristics strongly determine the properties of the OM and the LPS layer fluidity has been measured using different techniques that require specific conditions or are technically challenging. Here, we characterize the Escherichia coli LPS fluidity by evaluating the lateral diffusion of the styryl dye FM4-64FX in fluorescence recovery after photobleaching experiments. This technique allowed us to determine the effect of different conditions and genetic backgrounds on the LPS fluidity. Our results show that a fraction of the LPS can slowly diffuse and that the fluidity of the LPS layer adapts by modifying the diffusion of the LPS and the fraction of mobile LPS molecules.
Collapse
Affiliation(s)
- Luis David Ginez
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Aurora Osorio
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Ricardo Vázquez-Ramírez
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Thelma Arenas
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Luis Mendoza
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Laura Camarena
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Sebastian Poggio
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| |
Collapse
|
29
|
Mancino AS, Glass WG, Yan Y, Biggin PC, Bowie D. Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms. J Gen Physiol 2022; 154:213074. [PMID: 35297947 PMCID: PMC8939363 DOI: 10.1085/jgp.202112906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is an important cellular mechanism that fine tunes the gating properties of both voltage- and ligand-gated ion-channels. The cardiac voltage-gated sodium channel, Nav1.5, is subject to alternative splicing of the DI S3–S4 linker, which generates two types of channels with different activation properties. Here, we show that the gating differences between the adult (mH1) and neonatal (Nav1.5e) isoforms of Nav1.5 are mediated by two amino acid residues: Thr/Ser at position 207 and Asp/Lys at position 211. Electrophysiological experiments, in conjunction with molecular dynamics simulations, revealed that each residue contributes equally to the overall gating shifts in activation, but that the underlying structural mechanisms are different. Asp/Lys at position 211 acts through electrostatic interactions, whereas Thr/Ser at position 207 is predicted to alter the hydrogen bond network at the top of the S3 helix. These distinct structural mechanisms work together to modify movement of the voltage-sensitive S4 helix to bring about channel activation. Interestingly, mutation of the homologous Asp and Thr residues of the skeletal muscle isoform, Nav1.4, to Lys and Ser, respectively, confers a similar gating shift in channel activation, suggesting that these residues may fulfill a conserved role across other Nav channel family members.
Collapse
Affiliation(s)
- Adamo S Mancino
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec, Canada
| | - William G Glass
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Yuhao Yan
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec, Canada
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec, Canada
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Żuk J, Bartuzi D, Miszta P, Kaczor AA. The Role of Lipids in Allosteric Modulation of Dopamine D 2 Receptor-In Silico Study. Molecules 2022; 27:molecules27041335. [PMID: 35209123 PMCID: PMC8874991 DOI: 10.3390/molecules27041335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022] Open
Abstract
The dopamine D2 receptor, belonging to the class A G protein-coupled receptors (GPCRs), is an important drug target for several diseases, including schizophrenia and Parkinson’s disease. The D2 receptor can be activated by the natural neurotransmitter dopamine or by synthetic ligands, which in both cases leads to the receptor coupling with a G protein. In addition to receptor modulation by orthosteric or allosteric ligands, it has been shown that lipids may affect the behaviour of membrane proteins. We constructed a model of a D2 receptor with a long intracellular loop (ICL3) coupled with Giα1 or Giα2 proteins, embedded in a complex asymmetric membrane, and simulated it in complex with positive, negative or neutral allosteric ligands. In this study, we focused on the influence of ligand binding and G protein coupling on the membrane–receptor interactions. We show that there is a noticeable interplay between the cell membrane, G proteins, D2 receptor and its modulators.
Collapse
Affiliation(s)
- Justyna Żuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland; (J.Ż.); (D.B.)
| | - Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland; (J.Ż.); (D.B.)
| | - Przemysław Miszta
- Faculty of Chemistry, Biological, Chemical Research Centre, University of Warsaw, PL-02093 Warsaw, Poland;
| | - Agnieszka A. Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland; (J.Ż.); (D.B.)
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
- Correspondence: ; Tel.: +48-81-448-72-73
| |
Collapse
|
32
|
Liu H, Pei Y. Atomistic Molecular Dynamics Simulation Study on the Interaction between Atomically Precise Thiolate-Protected Gold Nanoclusters and Phospholipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1653-1661. [PMID: 35080404 DOI: 10.1021/acs.langmuir.1c02001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The interaction of atomically precise monolayer thiolate (SR) protected gold nanoclusters (Au NCs) with the phospholipid membranes has been studied by the all-atom molecular dynamics (AAMD) simulations. The effect of cluster size, type, and the surface charge density of protection ligand was studied. The simulation results show gold nanoclusters with different size and surface modifications have much different transmembrane behaviors. The Au25(SR)18 cluster was found to possess the best affinity to the phospholipid membranes among six atomically accurate clusters Au25(SR)18, Au36(SR)24, Au44(SR)28, Au68(SR)32, Au144(SR)60, and Au314(SR)96. Using the Au25 NC as a model, this work also found that the aggregation mode of the surface ligands and the surface charge density are the important factors affecting the interaction between the gold nanoclusters and the phospholipid membranes. Moreover, the balance of hydrophilic and hydrophobic ligands on the surface of Au NCs is beneficial to the high permeability.
Collapse
Affiliation(s)
- Hengzhi Liu
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan, Hunan Province 411105, China
| | - Yong Pei
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan, Hunan Province 411105, China
| |
Collapse
|
33
|
Ponleitner M, Szöllősi D, El-Kasaby A, Koban F, Freissmuth M, Stockner T. Thermal Unfolding of the Human Serotonin Transporter: Differential Effect by Stabilizing and Destabilizing Mutations and Cholesterol on Thermodynamic and Kinetic Stability. Mol Pharmacol 2022; 101:95-105. [PMID: 34866045 DOI: 10.1124/molpharm.121.000413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/21/2021] [Indexed: 11/22/2022] Open
Abstract
Folding-deficient mutants of solute carrier 6 (SLC6) family members have been linked to human diseases. The serotonin transporter [(SERT)/SLC6A4] is an important drug target in the treatment of depression, anxiety, and obsessive-compulsive disorders and-with structural information in several conformational states-one of the best understood transporters. Here, we surmised that thermal unfolding offered a glimpse on the folding energy landscape of SLC6 transporters. We carried out molecular dynamic (MD) simulations to understand the mechanistic basis for enhanced and reduced stability, respectively, of the thermostabilized variant SERT-Y110A/I291A/T439S, which had previously been used for crystallization of human SERT in the outward-facing state, and of the folding-deficient SERT-P601A/G602A. We also examined the hydrophobic mismatch caused by the absence of cholesterol to explore the contribution of cholesterol to protein stability. When compared with wild type SERT, the thermodynamic and kinetic stability of SERT-Y110A/I291A/T439S was enhanced. In the other instances, changes in these two components were not correlated: the mutations in SERT-P601A/G602A led to a drop in thermodynamic but an increase in kinetic stability. The divergence was even more pronounced after cholesterol depletion, which reduced thermodynamic stability but increased the kinetic stability of wild type SERT to a level comparable to that of SERT-Y110A/I291A/T439S. We conclude that the low cholesterol content of the endoplasmic reticulum facilitates progression of the folding trajectory by reducing the energy difference between folding intermediates and the native state. SIGNIFICANCE STATEMENT: Point mutations in solute carrier 6 (SLC6) family members cause folding diseases. The serotonin transporter [(SERT)/SLC6A4] is a target for antidepressants and the best understood SLC6. This study produced molecular dynamics simulations and examined thermal unfolding of wild type and mutant SERT variants to understand their folding energy landscape. In the folding-deficient SERT-P012A/G602A, changes in kinetic and thermodynamic stability were not correlated. Similarly, cholesterol depletion lowered thermodynamic but enhanced kinetic stability. These observations allow for rationalizing the action of pharmacochaperones.
Collapse
Affiliation(s)
- Markus Ponleitner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Daniel Szöllősi
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Ali El-Kasaby
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Florian Koban
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Austria
| |
Collapse
|
34
|
Allosteric modulation of dopamine D 2L receptor in complex with G i1 and G i2 proteins: the effect of subtle structural and stereochemical ligand modifications. Pharmacol Rep 2022; 74:406-424. [PMID: 35064921 PMCID: PMC8964653 DOI: 10.1007/s43440-021-00352-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 12/28/2022]
Abstract
Background Allosteric modulation of G protein-coupled receptors (GPCRs) is nowadays one of the hot topics in drug discovery. In particular, allosteric modulators of D2 receptor have been proposed as potential modern therapeutics to treat schizophrenia and Parkinson’s disease. Methods To address some subtle structural and stereochemical aspects of allosteric modulation of D2 receptor, we performed extensive in silico studies of both enantiomers of two compounds (compound 1 and compound 2), and one of them (compound 2) was synthesized as a racemate in-house and studied in vitro. Results Our molecular dynamics simulations confirmed literature reports that the R enantiomer of compound 1 is a positive allosteric modulator of the D2L receptor, while its S enantiomer is a negative allosteric modulator. Moreover, based on the principal component analysis (PCA), we hypothesized that both enantiomers of compound 2 behave as silent allosteric modulators, in line with our in vitro studies. PCA calculations suggest that the most pronounced modulator-induced receptor rearrangements occur at the transmembrane helix 7 (TM7). In particular, TM7 bending at the conserved P7.50 and G7.42 was observed. The latter resides next to the Y7.43, which is a significant part of the orthosteric binding site. Moreover, the W7.40 conformation seems to be affected by the presence of the positive allosteric modulator. Conclusions Our work reveals that allosteric modulation of the D2L receptor can be affected by subtle ligand modifications. A change in configuration of a chiral carbon and/or minor structural modulator modifications are solely responsible for the functional outcome of the allosteric modulator. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s43440-021-00352-x.
Collapse
|
35
|
Occlusion of the human serotonin transporter is mediated by serotonin-induced conformational changes in the bundle domain. J Biol Chem 2022; 298:101613. [PMID: 35065961 PMCID: PMC8867121 DOI: 10.1016/j.jbc.2022.101613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
The human serotonin transporter (hSERT) terminates neurotransmission by removing serotonin (5HT) from the synaptic cleft, an essential process for proper functioning of serotonergic neurons. Structures of the hSERT have revealed its molecular architecture in four conformations, including the outward-open and occluded states, and show the transporter’s engagement with co-transported ions and the binding mode of inhibitors. In this study, we investigated the molecular mechanism by which the hSERT occludes and sequesters the substrate 5HT. This first step of substrate uptake into cells is a structural change consisting of the transition from the outward-open to the occluded state. Inhibitors such as the antidepressants citalopram, fluoxetine, and sertraline inhibit this step of the transport cycle. Using molecular dynamics simulations, we reached a fully occluded state, in which the transporter-bound 5HT becomes fully shielded from both sides of the membrane by two closed hydrophobic gates. Analysis of 5HT-triggered occlusion showed that bound 5HT serves as an essential trigger for transporter occlusion. Moreover, simulations revealed a complex sequence of steps and showed that movements of bundle domain helices are only partially correlated. 5HT-triggered occlusion is initially dominated by movements of transmembrane helix 1b, while in the final step, only transmembrane helix 6a moves and relaxes an intermediate change in its secondary structure.
Collapse
|
36
|
Szöllősi D, Stockner T. Sodium Binding Stabilizes the Outward-Open State of SERT by Limiting Bundle Domain Motions. Cells 2022; 11:cells11020255. [PMID: 35053371 PMCID: PMC8773566 DOI: 10.3390/cells11020255] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
The human serotonin transporter (hSERT) removes the neurotransmitter serotonin from the synaptic cleft by reuptake into the presynaptic nerve terminal. A number of neurologic diseases are associated with dysfunction of the hSERT, and several medications for their treatment are hSERT blockers, including citalopram, fluoxetine, and paroxetine. The substrate transport is energized by the high concentration of external NaCl. We showed through molecular dynamics simulations that the binding of NaCl stabilized the hSERT in the substrate-binding competent conformation, which was characterized by an open access path to the substrate-binding site through the outer vestibule. Importantly, the binding of NaCl reduced the dynamics of the hSERT by decreasing the internal fluctuations of the bundle domain as well as the movement of the bundle domain relative to the scaffold domain. In contrast, the presence of only the bound chloride ion did not reduce the high domain mobility of the apo state.
Collapse
|
37
|
Hsieh MK, Yu Y, Klauda JB. All-Atom Modeling of Complex Cellular Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3-17. [PMID: 34962814 DOI: 10.1021/acs.langmuir.1c02084] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.
Collapse
|
38
|
Antila HS, Wurl A, Ollila OS, Miettinen MS, Ferreira TM. Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes. Biophys J 2022; 121:68-78. [PMID: 34902330 PMCID: PMC8758420 DOI: 10.1016/j.bpj.2021.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023] Open
Abstract
Cells use homeostatic mechanisms to ensure an optimal composition of distinct types of lipids in cellular membranes. The hydrophilic region of biological lipid membranes is mainly composed of several types of phospholipid headgroups that interact with incoming molecules, nanoparticles, and viruses, whereas the hydrophobic region consists of a distribution of acyl chains and sterols affecting membrane fluidity/rigidity related properties and forming an environment for membrane-bound molecules such as transmembrane proteins. A fundamental open question is to what extent the motions of these regions are coupled and, consequently, how strongly the interactions of phospholipid headgroups with other molecules depend on the properties and composition of the membrane hydrophobic core. We combine advanced solid-state nuclear magnetic resonance spectroscopy with high-fidelity molecular dynamics simulations to demonstrate how the rotational dynamics of choline headgroups remain nearly unchanged (slightly faster) with incorporation of cholesterol into a phospholipid membrane, contrasting the well-known extreme slowdown of the other phospholipid segments. Notably, our results suggest a new paradigm in which phospholipid dipole headgroups interact as quasi-freely rotating flexible dipoles at the interface, independent of the properties in the hydrophobic region.
Collapse
Affiliation(s)
- Hanne S. Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany,Corresponding author
| | - Anika Wurl
- NMR Group, Institute for Physics, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Markus S. Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Tiago M. Ferreira
- NMR Group, Institute for Physics, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany,Corresponding author
| |
Collapse
|
39
|
Franco LR, Park P, Chaimovich H, Coutinho K, Cuccovia IM, Lima FS. Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration. RSC Adv 2022; 12:4573-4588. [PMID: 35425494 PMCID: PMC8981376 DOI: 10.1039/d1ra06267k] [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] [Received: 08/18/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
MD simulations reveal that BP100 peptide induces local membrane thinning and negative curvature, slows lipid dynamics and increases the water life time in the lipid hydrophobic core and transmembrane water transport in the direction of the peptide.
Collapse
Affiliation(s)
| | - Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Iolanda M. Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S. Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
| |
Collapse
|
40
|
Schneemilch M, Quirke N. Predicting nanoparticle uptake by biological membranes: theory and simulation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1996574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - N. Quirke
- Department of Chemistry, Imperial College, London, UK
| |
Collapse
|
41
|
Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae. Sci Rep 2021; 11:17333. [PMID: 34462478 PMCID: PMC8405694 DOI: 10.1038/s41598-021-96757-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 08/05/2021] [Indexed: 11/08/2022] Open
Abstract
The use of lignocellulosic-based fermentation media will be a necessary part of the transition to a circular bio-economy. These media contain many inhibitors to microbial growth, including acetic acid. Under industrially relevant conditions, acetic acid enters the cell predominantly through passive diffusion across the plasma membrane. The lipid composition of the membrane determines the rate of uptake of acetic acid, and thicker, more rigid membranes impede passive diffusion. We hypothesized that the elongation of glycerophospholipid fatty acids would lead to thicker and more rigid membranes, reducing the influx of acetic acid. Molecular dynamics simulations were used to predict the changes in membrane properties. Heterologous expression of Arabidopsis thaliana genes fatty acid elongase 1 (FAE1) and glycerol-3-phosphate acyltransferase 5 (GPAT5) increased the average fatty acid chain length. However, this did not lead to a reduction in the net uptake rate of acetic acid. Despite successful strain engineering, the net uptake rate of acetic acid did not decrease. We suggest that changes in the relative abundance of certain membrane lipid headgroups could mitigate the effect of longer fatty acid chains, resulting in a higher net uptake rate of acetic acid.
Collapse
|
42
|
Abstract
Molecular simulations of biological molecules require an accurate description of molecular interactions through a force field (FF). The focus of this Perspective is on all-atom lipid FFs. Recent additions to the CHARMM36 lipid FF continue to expand a researcher's ability to probe membrane structure and function with a wide variety of biologically important lipids. Currently, there is an effort to reduce the assumptions in all-atom lipid FFs. The inclusion of long-range dispersion interaction through particle-mesh Ewald is allowing for more accurate descriptions of lipid bilayer and monolayer properties without additional computational cost. Soon, simulations with lipid FFs will no longer depend on short-range cutoffs and will accurately represent long-range dispersion. This requires efficient FF parametrization with an automated approach due to FF complexity. In addition, polarizable FFs for lipids will be important for the next generation of simulations that accurately represent how molecule interactions respond to a varied environment.
Collapse
|
43
|
Dynamic "Molecular Portraits" of Biomembranes Drawn by Their Lateral Nanoscale Inhomogeneities. Int J Mol Sci 2021; 22:ijms22126250. [PMID: 34200697 PMCID: PMC8230387 DOI: 10.3390/ijms22126250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/22/2023] Open
Abstract
To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called "dynamic molecular portrait". The latter reflects a combination of time-dependent surface distributions of various physicochemical properties, inherent in both model lipid bilayers and natural multi-component cell membranes. One of the most important features of biomembranes is their mosaicity, which is expressed in the constant presence of lateral inhomogeneities, the sizes and lifetimes of which vary in a wide range-from 1 to 103 nm and from 0.1 ns to milliseconds. In addition to the relatively well-studied macroscopic domains (so-called "rafts"), the analysis of micro- and nanoclusters (or domains) that form an instantaneous picture of the distribution of structural, dynamic, hydrophobic, electrical, etc., properties at the membrane-water interface is attracting increasing interest. This is because such nanodomains (NDs) have been proven to be crucial for the proper membrane functioning in cells. Therefore, an understanding with atomistic details the phenomena associated with NDs is required. The present mini-review describes the recent results of experimental and in silico studies of spontaneously formed NDs in lipid membranes. The main attention is paid to the methods of ND detection, characterization of their spatiotemporal parameters, the elucidation of the molecular mechanisms of their formation. Biological role of NDs in cell membranes is briefly discussed. Understanding such effects creates the basis for rational design of new prospective drugs, therapeutic approaches, and artificial membrane materials with specified properties.
Collapse
|
44
|
Szöllősi D, Stockner T. Investigating the Mechanism of Sodium Binding to SERT Using Direct Simulations. Front Cell Neurosci 2021; 15:673782. [PMID: 34040506 PMCID: PMC8141550 DOI: 10.3389/fncel.2021.673782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
The serotonin transporter (SERT) terminates neurotransmission by transporting serotonin from the synapse into the pre-synaptic nerve terminal. Altered SERT function leads to several neurological diseases including depression, anxiety, mood disorders, and attention deficit hyperactivity disorders (ADHD). Accordingly SERT is the target for their pharmacological treatments, but also targeted by multiple drugs of abuse. Transport of serotonin by SERT is energized by the transmembrane electrochemical gradient of sodium. We used extensive molecular dynamics simulations to investigate the process of sodium binding to SERT, which is the first step in the transport cycle that leads to serotonin uptake. Comparing data from 51 independent simulations, we find a remarkably well-defined path for sodium entry and could identify two transient binding sites, while observing binding kinetics that are comparable to experimental data. Importantly, the structure and dynamics of the sodium binding sites indicate that sodium binding is accompanied by an induced-fit mechanism that leads to new conformations and reduces local dynamics.
Collapse
Affiliation(s)
- Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
45
|
Sousa CF, Coimbra JTS, Ferreira M, Pereira-Leite C, Reis S, Ramos MJ, Fernandes PA, Gameiro P. Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study. J Mol Biol 2021; 433:166911. [PMID: 33676927 DOI: 10.1016/j.jmb.2021.166911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 11/17/2022]
Abstract
Fluoroquinolones (FQ) are antibiotics widely used in clinical practise, but the development of bacterial resistance to these drugs is currently a critical public health problem. In this context, ternary copper complexes of FQ (CuFQPhen) have been studied as a potential alternative. In this study, we compared the passive diffusion across the lipid bilayer of one of the most used FQ, ciprofloxacin (Cpx), and its ternary copper complex, CuCpxPhen, that has shown previous promising results regarding antibacterial activity and membrane partition. A combination of spectroscopic studies and molecular dynamics simulations were used and two different model membranes tested: one composed of anionic phospholipids, and the other composed of zwitterionic phospholipids. The obtained results showed a significantly higher membrane permeabilization activity, larger partition, and a more favourable free energy landscape for the permeation of CuCpxPhen across the membrane, when compared to Cpx. Furthermore, the computational results indicated a more favourable translocation of CuCpxPhen across the anionic membrane, when compared to the zwitterionic one, suggesting a higher specificity towards the former. These findings are important to decipher the influx mechanism of CuFQPhen in bacterial cells, which is crucial for the ultimate use of CuFQPhen complexes as an alternative to FQ to tackle multidrug-resistant bacteria.
Collapse
Affiliation(s)
- Carla F Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| | - João T S Coimbra
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| | - Mariana Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| | - Catarina Pereira-Leite
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Salette Reis
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| | - Paula Gameiro
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| |
Collapse
|
46
|
Antila HS, M. Ferreira T, Ollila OHS, Miettinen MS. Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. J Chem Inf Model 2021; 61:938-949. [PMID: 33496579 PMCID: PMC7903423 DOI: 10.1021/acs.jcim.0c01299] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.
Collapse
Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Tiago M. Ferreira
- NMR
Group−Institute for Physics, Martin-Luther
University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| |
Collapse
|
47
|
Kundu S, Malik S, Ghosh M, Nandi S, Pyne A, Debnath A, Sarkar N. A Comparative Study on DMSO-Induced Modulation of the Structural and Dynamical Properties of Model Bilayer Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:2065-2078. [PMID: 33529530 DOI: 10.1021/acs.langmuir.0c03037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Modulating the structures and properties of biomembranes via permeation of small amphiphilic molecules is immensely important, having diverse applications in cell biology, biotechnology, and pharmaceuticals, because their physiochemical and biological interactions lead to new pathways for transdermal drug delivery and administration. In this work, we have elucidated the role of dimethyl sulfoxide (DMSO), broadly used as a penetration-enhancing agent and cryoprotective agent on model lipid membranes, using a combination of fluorescence microscopy and time-resolved fluorescence spectroscopy. Spatially resolved fluorescence lifetime imaging microscopy (FLIM) has been employed to unravel how the fluidity of the DMSO-induced bilayer regulates the structural alteration of the vesicles. Moreover, we have also shown that the dehydration effect of DMSO leads to weakening of the hydrogen bond between lipid headgroups and water molecules and results in faster solvation dynamics as demonstrated by femtosecond time-resolved fluorescence spectroscopy. It has been gleaned that the water dynamics becomes faster because bilayer rigidity decreases in the presence of DMSO, which is also supported by time-resolved rotational anisotropy measurements. The enhanced diffusivity and increased membrane fluidity in the presence of DMSO are further ratified at the single-molecule level through fluorescence correlation spectroscopy (FCS) measurements. Our results indicate that while the presence of DMSO significantly affects the 1,2-dimyristoyl-rac-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-rac-glycero-3-phosphatidylcholine (DPPC) bilayers, it has a weak effect on 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG) vesicles, which might explain the preferential interaction of DMSO with the positively charged choline group present in DMPC and DPPC vesicles. The experimental findings have also been further verified with molecular dynamics simulation studies. Moreover, it has been observed that DMSO is likely to have a differential effect on heterogeneous bilayer membranes depending on the structure and composition of their headgroups. Our results illuminate the importance of probing the lipid structure and composition of cellular membranes in determining the effects of cryoprotective agents.
Collapse
Affiliation(s)
- Sangita Kundu
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Meghna Ghosh
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sourav Nandi
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Arghajit Pyne
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| |
Collapse
|
48
|
Dämgen MA, Biggin PC. State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane. PLoS Comput Biol 2021; 17:e1007856. [PMID: 33571182 PMCID: PMC7904231 DOI: 10.1371/journal.pcbi.1007856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/24/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are receptor proteins that are sensitive to their membrane environment, but the mechanism for how lipids modulate function under physiological conditions in a state dependent manner is not known. The glycine receptor is a pLGIC whose structure has been resolved in different functional states. Using a realistic model of a neuronal membrane coupled with coarse-grained molecular dynamics simulations, we demonstrate that some key lipid-protein interactions are dependent on the receptor state, suggesting that lipids may regulate the receptor's conformational dynamics. Comparison with existing structural data confirms known lipid binding sites, but we also predict further protein-lipid interactions including a site at the communication interface between the extracellular and transmembrane domain. Moreover, in the active state, cholesterol can bind to the binding site of the positive allosteric modulator ivermectin. These protein-lipid interaction sites could in future be exploited for the rational design of lipid-like allosteric drugs.
Collapse
Affiliation(s)
- Marc A. Dämgen
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
49
|
Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
Collapse
|
50
|
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.
Collapse
Affiliation(s)
- Inna Ermilova
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | | |
Collapse
|