1
|
Vervust W, Zhang DT, Ghysels A, Roet S, van Erp TS, Riccardi E. PyRETIS 3: Conquering rare and slow events without boundaries. J Comput Chem 2024; 45:1224-1234. [PMID: 38345082 DOI: 10.1002/jcc.27319] [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: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 04/19/2024]
Abstract
We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data.
Collapse
Affiliation(s)
- Wouter Vervust
- IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium
| | - Daniel T Zhang
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - An Ghysels
- IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium
| | - Sander Roet
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Enrico Riccardi
- Department of Energy Resources, University of Stavanger, Stavanger, Norway
| |
Collapse
|
2
|
Chiu PL, Orjuela JD, de Groot BL, Aponte-Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.16.540959. [PMID: 37292626 PMCID: PMC10245776 DOI: 10.1101/2023.05.16.540959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
Collapse
|
3
|
Ruppelt D, Trollmann MFW, Dema T, Wirtz SN, Flegel H, Mönnikes S, Grond S, Böckmann RA, Steinem C. The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes. Nat Commun 2024; 15:3521. [PMID: 38664456 PMCID: PMC11045845 DOI: 10.1038/s41467-024-47803-6] [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: 06/13/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Recently, a novel cyclo-heptapeptide composed of alternating D,L-amino acids and a unique thiazolidine heterocycle, called lugdunin, was discovered, which is produced by the nasal and skin commensal Staphylococcus lugdunensis. Lugdunin displays potent antimicrobial activity against a broad spectrum of Gram-positive bacteria, including challenging-to-treat methicillin-resistant Staphylococcus aureus (MRSA). Lugdunin specifically inhibits target bacteria by dissipating their membrane potential. However, the precise mode of action of this new class of fibupeptides remains largely elusive. Here, we disclose the mechanism by which lugdunin rapidly destabilizes the bacterial membrane potential using an in vitro approach. The peptide strongly partitions into lipid compositions resembling Gram-positive bacterial membranes but less in those harboring the eukaryotic membrane component cholesterol. Upon insertion, lugdunin forms hydrogen-bonded antiparallel β-sheets by the formation of peptide nanotubes, as demonstrated by ATR-FTIR spectroscopy and molecular dynamics simulations. These hydrophilic nanotubes filled with a water wire facilitate not only the translocation of protons but also of monovalent cations as demonstrated by voltage-clamp experiments on black lipid membranes. Collectively, our results provide evidence that the natural fibupeptide lugdunin acts as a peptidic channel that is spontaneously formed by an intricate stacking mechanism, leading to the dissipation of a bacterial cell's membrane potential.
Collapse
Affiliation(s)
- Dominik Ruppelt
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Marius F W Trollmann
- Computational Biology, Department Biologie & Erlangen National High Perfomance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Sebastian N Wirtz
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Hendrik Flegel
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Sophia Mönnikes
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department Biologie & Erlangen National High Perfomance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany.
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany.
| |
Collapse
|
4
|
Kashnik AS, Baranov DS, Dzuba SA. Spatial Arrangement of the Drug Ibuprofen in a Model Membrane in the Presence of Lipid Rafts. J Phys Chem B 2024; 128:3652-3661. [PMID: 38576273 DOI: 10.1021/acs.jpcb.4c01507] [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: 04/06/2024]
Abstract
Many pharmaceutical drugs are known to interact with lipid membranes through nonspecific molecular interactions, which affect their therapeutic effect. Ibuprofen is a nonsteroidal anti-inflammatory drug (NSAID) and one of the most commonly prescribed. In the presence of cholesterol, lipid bilayers can separate into nanoscale liquid-disordered and liquid-ordered structures, the latter known as lipid rafts. Here, we study spin-labeled ibuprofen (ibuprofen-SL) in the model membrane consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol in the molar ratio of (0.5-0.5xchol)/(0.5-0.5xchol)/xchol. Electron paramagnetic resonance (EPR) spectroscopy is employed, along with its pulsed version of double electron-electron resonance (DEER, also known as PELDOR). The data obtained indicate lateral lipid-mediated clustering of ibuprofen-SL molecules with a local surface density noticeably larger than that expected for random lateral distribution. In the absence of cholesterol, the data can be interpreted as indicating alternating clustering in two opposing leaflets of the bilayer. In the presence of cholesterol, for xchol ≥ 20 mol %, the results show that ibuprofen-SL molecules have a quasi-regular lateral distribution, with a "superlattice" parameter of ∼3.0 nm. This regularity can be explained by the entrapment of ibuprofen-SL molecules by lipid rafts known to exist in this system with the additional assumption that lipid rafts have a nanoscale substructure.
Collapse
Affiliation(s)
- Anna S Kashnik
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Denis S Baranov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| |
Collapse
|
5
|
Duché G, Sanderson JM. The Chemical Reactivity of Membrane Lipids. Chem Rev 2024; 124:3284-3330. [PMID: 38498932 PMCID: PMC10979411 DOI: 10.1021/acs.chemrev.3c00608] [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: 09/04/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024]
Abstract
It is well-known that aqueous dispersions of phospholipids spontaneously assemble into bilayer structures. These structures have numerous applications across chemistry and materials science and form the fundamental structural unit of the biological membrane. The particular environment of the lipid bilayer, with a water-poor low dielectric core surrounded by a more polar and better hydrated interfacial region, gives the membrane particular biophysical and physicochemical properties and presents a unique environment for chemical reactions to occur. Many different types of molecule spanning a range of sizes, from dissolved gases through small organics to proteins, are able to interact with membranes and promote chemical changes to lipids that subsequently affect the physicochemical properties of the bilayer. This Review describes the chemical reactivity exhibited by lipids in their membrane form, with an emphasis on conditions where the lipids are well hydrated in the form of bilayers. Key topics include the following: lytic reactions of glyceryl esters, including hydrolysis, aminolysis, and transesterification; oxidation reactions of alkenes in unsaturated fatty acids and sterols, including autoxidation and oxidation by singlet oxygen; reactivity of headgroups, particularly with reactive carbonyl species; and E/Z isomerization of alkenes. The consequences of reactivity for biological activity and biophysical properties are also discussed.
Collapse
Affiliation(s)
- Genevieve Duché
- Génie
Enzimatique et Cellulaire, Université
Technologique de Compiègne, Compiègne 60200, France
| | - John M Sanderson
- Chemistry
Department, Durham University, Durham DH1 3LE, United Kingdom
| |
Collapse
|
6
|
Kang C, Shoji A, Chipot C, Sun R. Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. J Chem Inf Model 2024; 64:933-943. [PMID: 38206804 DOI: 10.1021/acs.jcim.3c01629] [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: 01/13/2024]
Abstract
Over the last two decades, numerous molecular dynamics (MD) simulation-based investigations have attempted to predict the membrane permeability to small-molecule drugs as indicators of their bioavailability, a majority of which utilize the inhomogeneous solubility diffusion (ISD) model. However, MD-based membrane permeability is routinely 3-4 orders of magnitude larger than the values measured with the intestinal perfusion technique. There have been contentious discussions on the sources of the large discrepancies, and the two indisputable, potentially dominant ones are the fixed protonation state of the permeant and the neglect of the unstirred water layer (UWL). Employing six small-molecule drugs of different biopharmaceutical classification system classes, the current MD study relies on the ISD model but introduces the (de)protonation of the permeant by characterizing the permeation free energy of both neutral and charged states. In addition, the role of the UWL as a potential resistance against permeation is explored. The new MD protocol closely mimics the nature of small-molecule permeation and yields estimates that agree well with in vivo intestinal permeability.
Collapse
Affiliation(s)
- Christopher Kang
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Alyson Shoji
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex 54506, France
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| |
Collapse
|
7
|
Harris J, Chipot C, Roux B. How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics? J Phys Chem B 2024; 128:795-811. [PMID: 38227958 DOI: 10.1021/acs.jpcb.3c06765] [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: 01/18/2024]
Abstract
According to the pH-partition hypothesis, the aqueous solution adjacent to a membrane is a mixture of the ionization states of the permeating molecule at fixed Henderson-Hasselbalch concentrations, such that each state passes through the membrane in parallel with its own specific permeability. An alternative view, based on the assumption that the rate of switching ionization states is instantaneous, represents the permeation of ionizable molecules via an effective Boltzmann-weighted average potential (BWAP). Such an assumption is used in constant-pH molecular dynamics simulations. The inhomogeneous solubility-diffusion framework can be used to compute the pH-dependent membrane permeability for each of these two limiting treatments. With biased WTM-eABF molecular dynamics simulations, we computed the potential of mean force and diffusivity of each ionization state of two weakly basic small molecules: nicotine, an addictive drug, and varenicline, a therapeutic for treating nicotine addiction. At pH = 7, the BWAP effective permeability is greater than that determined by pH-partitioning by a factor of 2.5 for nicotine and 5 for varenicline. To assess the importance of ionization kinetics, we present a Smoluchowski master equation that includes explicitly the protonation and deprotonation processes coupled with the diffusive motion across the membrane. At pH = 7, the increase in permeability due to the explicit ionization kinetics is negligible for both nicotine and varenicline. This finding is reaffirmed by combined Brownian dynamics and Markov state model simulations for estimating the permeability of nicotine while allowing changes in its ionization state. We conclude that for these molecules the pH-partition hypothesis correctly captures the physics of the permeation process. The small free energy barriers for the permeation of nicotine and varenicline in their deprotonated neutral forms play a crucial role in establishing the validity of the pH-partitioning mechanism. Essentially, BWAP fails because ionization kinetics are too slow on the time scale of membrane crossing to affect the permeation of small ionizable molecules such as nicotine and varenicline. For the singly protonated state of nicotine, the computational results agree well with experimental measurements (P1 = 1.29 × 10-7 cm/s), but the agreement for neutral (P0 = 6.12 cm/s) and doubly protonated nicotine (P2 = 3.70 × 10-13 cm/s) is slightly worse, likely due to factors associated with the aqueous boundary layer (neutral form) or leaks through paracellular pathways (doubly protonated form).
Collapse
Affiliation(s)
- Jonathan Harris
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
8
|
Schütz GJ, Pabst G. The asymmetric plasma membrane-A composite material combining different functionalities?: Balancing Barrier Function and Fluidity for Effective Signaling. Bioessays 2023; 45:e2300116. [PMID: 37712937 DOI: 10.1002/bies.202300116] [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: 06/27/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
One persistent puzzle in the life sciences is the asymmetric lipid composition of the cellular plasma membrane: while the exoplasmic leaflet is enriched in lipids carrying predominantly saturated fatty acids, the cytoplasmic leaflet hosts preferentially lipids with (poly-)unsaturated fatty acids. Given the high energy requirements necessary for cells to maintain this asymmetry, the question naturally arises regarding its inherent benefits. In this paper, we propose asymmetry to represent a potential solution for harmonizing two conflicting requirements for the plasma membrane: first, the need to build a barrier for the uncontrolled influx or efflux of substances; and second, the need to form a fluid and dynamic two-dimensional substrate for signaling processes. We hence view here the plasma membrane as a composite material, where the exoplasmic leaflet is mainly responsible for the functional integrity of the barrier and the cytoplasmic leaflet for fluidity. We reinforce the validity of the proposed mechanism by presenting quantitative data from the literature, along with multiple examples that bolster our model.
Collapse
Affiliation(s)
| | - Georg Pabst
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth-University of Graz, Graz, Austria
| |
Collapse
|
9
|
Davoudi S, Raemdonck K, Braeckmans K, Ghysels A. Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes. J Chem Inf Model 2023; 63:6789-6806. [PMID: 37917127 DOI: 10.1021/acs.jcim.3c00936] [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: 11/03/2023]
Abstract
Liposomes are considered as advanced drug delivery systems for cancer treatment. A generation of pH-sensitive liposomes is being developed that use fatty acids (FAs) as a trigger for drug release in tumor tissues. However, FAs are also known to enhance permeability, and it is unclear whether FAs in liposomes may cause drug leakage or premature drug release. The passive permeability of the drug through the membrane of the liposome is thus a crucial factor for timely drug delivery. To investigate how the curvature and lipid composition of liposomes affect their passive permeability, coarse-grained molecular dynamics were performed. The permeability was determined with a counting method. Flat bilayers and three liposomes with varying diameters were studied, which had varying lipid compositions of dipalmitoylphosphatidylcholine, cholesterol, and deprotonated or neutral saturated FAs. The investigated permeants were water and two other small permeants, which have different free energy profiles (solubility) across the membrane. First, for the curvature effect, our results showed that curvature increases the water permeability by reducing the membrane thickness. The permeability increase for water is about a factor of 1.7 for the most curved membranes. However, a high curvature decreases permeability for permeants with free energy profiles that are a mix of wells and barriers in the headgroup region of the membrane. Importantly, the type of experimental setup is expected to play a dominant role in the permeability value, i.e., whether permeants are escaping or entering the liposomes. Second, for the composition effect, FAs decrease both the area per lipid (APL) and the membrane thickness, resulting in permeability increases of up to 55%. Cholesterol has a similar effect on the APL but has the opposite impact on membrane thickness and permeability. Therefore, FAs and cholesterol have opposing effects on permeability, with cholesterol's effect being slightly stronger in our simulated bilayers. As all permeability values were well within a factor of 2, and with liposomes usually being larger and less curved in experimental applications, it can be concluded that the passive drug release from a pH-sensitive liposome does not seem to be significantly affected by the presence of FAs.
Collapse
Affiliation(s)
- Samaneh Davoudi
- IBiTech─BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Block B-Entrance 36, 9000 Gent, Belgium
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory for General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium
| | - Kevin Braeckmans
- Bio-Photonic Imaging Group, Laboratory for General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium
| | - An Ghysels
- IBiTech─BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Block B-Entrance 36, 9000 Gent, Belgium
| |
Collapse
|
10
|
Ghorbani M, Dehghan G, Allahverdi A. Concentration-dependent mechanism of the binding behavior of ibuprofen to the cell membrane: A molecular dynamic simulation study. J Mol Graph Model 2023; 124:108581. [PMID: 37536233 DOI: 10.1016/j.jmgm.2023.108581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
Ibuprofen is a commonly used drug for treating headaches, pain, and fever. The lipid bilayer is the primary and most important interface for drugs to interact with biological systems. However, the molecular interactions between ibuprofen and the cell membrane are not well understood. Our findings suggest that the interactions between ibuprofen and the bilayer involve multiple steps and depend on the concentration of the drug. At low concentrations of ibuprofen, it can bind to the surface of the lipid bilayer. The electrostatic and vdW energies of IBU-lipid at 0 ns of the simulation were -22.5 ± 3.2 and -5.9 ± 1.2 kj.mol-1 Fig. 2. In the following, the vdW energy of the IBU-lipid was increased by around -134.6 ± 3.7 kj.mol-1 whereas the electrostatic energy of the IBU-lipid was significantly decreased. This binding is facilitated by electrostatic and vdW interactions between ibuprofen and the head group of lipids. In the second step, ibuprofen is inserted into the lipid bilayer and positioned at the interface between the bilayer and the aqueous phase. In high concentrations of ibuprofen, it moved to the central region of the lipid bilayer. At this concentration, the physical and structural properties of the cell membrane change significantly. Results from the radial distribution function analysis indicate that at low concentrations, ibuprofen molecules are situated close to the head groups of phosphate groups. However, at high concentrations of ibuprofen, these molecules move to the inner side of the lipid bilayer. In addition, our findings indicate that at low concentrations of ibuprofen, these molecules did not significantly alter the physical properties of the cell membrane. In contrast, at high concentrations of ibuprofen, the physical parameters of the hydrocarbon tails, such as thickness, fluidity, and order, changed dramatically. APL parameter for POPC membrane increased slightly to 0.60 and 0.63 nm2 in the presence of low and high concentrations of ibuprofen molecules. The three-step interaction between ibuprofen and the lipid bilayer involves several events, such as the movement of ibuprofen molecules towards the central region of the lipid bilayer and the deformation and alteration of the structural and stability properties of the cell membrane. These effects are observed only at high concentrations of ibuprofen. It appears that the side effects of ibuprofen overdose are related to changes in the properties of the cell membrane and, subsequently, the function of membrane-anchored target proteins.
Collapse
Affiliation(s)
| | | | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran.
| |
Collapse
|
11
|
Yanagisawa H, Kita Y, Oda T, Kikkawa M. Cryo-EM elucidates the uroplakin complex structure within liquid-crystalline lipids in the porcine urothelial membrane. Commun Biol 2023; 6:1018. [PMID: 37805589 PMCID: PMC10560298 DOI: 10.1038/s42003-023-05393-x] [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: 06/19/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023] Open
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
Collapse
Affiliation(s)
- Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
12
|
Aceves-Luna H, Glossman-Mitnik D, Flores-Holguín N. Permeability of antioxidants through a lipid bilayer model with coarse-grained simulations. J Biomol Struct Dyn 2023:1-19. [PMID: 37768552 DOI: 10.1080/07391102.2023.2262044] [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: 06/30/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Oxidative stress caused by pollution and lifestyle changes causes an excess of free radicals that react chemically with cell constituents leading to irreversible damage. There are molecules known as antioxidants that reduce the levels of free radicals. Some pigments of fruits and vegetables known as anthocyanins have antioxidant properties. Their interaction with the cell membrane becomes a crucial step in studying these substances. In this research, molecular dynamics simulations, particularly, coarse-grained molecular dynamics (CGMD) were used. This technique aims to replace functional groups with corresponding beads that represent their level of polarity and affinities to other chemical groups. Also, umbrella sampling was carried out to obtain free energy profiles that describe well the orientation and location of antioxidants in a membrane considering Trolox, Cyanidin, Gallic Acid, and Resveratrol molecules to study the structural effects they cause on it. It was concluded in this study that an antioxidant when crossing the membrane does not cause either damage to the structural properties or the loss of packing and stratification of phospholipids. it was also observed that the most reactive part of the molecules could easily approach area A prone to lipid oxidation, which can describe the antioxidant capacity of these molecules.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hugo Aceves-Luna
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| |
Collapse
|
13
|
Pandey P, MacKerell AD. Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. J Chem Inf Model 2023; 63:5903-5915. [PMID: 37682640 PMCID: PMC10603762 DOI: 10.1021/acs.jcim.3c00514] [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] [Indexed: 09/10/2023]
Abstract
Membrane permeability of drug molecules plays a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based site identification by ligand competitive saturation (SILCS) method and data-driven artificial intelligence (AI) to create a high-throughput predictive model for the passive permeability of druglike molecules. In this study, we present a comparative analysis of four regression models to predict membrane permeabilities of small druglike molecules; of the tested models, Random Forest was the most predictive yielding an R2 of 0.81 for the independent data set. The input feature vector used to train the developed prediction model includes absolute free energy profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. The use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability, while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design.
Collapse
Affiliation(s)
- Poonam Pandey
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
| |
Collapse
|
14
|
Nandakumar A, Ito Y, Ueda M. Peptide-lipid hybrid vesicles with stimuli-responsive phase separation for controlled membrane functions. Chem Commun (Camb) 2023; 59:10644-10647. [PMID: 37580993 DOI: 10.1039/d3cc02954a] [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: 08/16/2023]
Abstract
A disulfide-tethered peptide-lipid conjugate self-assembled into a homogeneously distributed peptide-lipid hybrid vesicle. Upon dithiothreitol treatment, the homogeneous peptide-lipid membrane spontaneously divided into lipid-rich and peptide-rich domains, while the vesicle retained its size and shape. Membrane phase separation enhanced temperature-dependent cargo release.
Collapse
Affiliation(s)
- Avanashiappan Nandakumar
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Motoki Ueda
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| |
Collapse
|
15
|
Chipot C. Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice? J Chem Inf Model 2023; 63:4533-4544. [PMID: 37449868 DOI: 10.1021/acs.jcim.3c00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Predicting from first-principles the rate of passive permeation of small molecules across the biological membrane represents a promising strategy for screening lead compounds upstream in the drug-discovery and development pipeline. One popular avenue for the estimation of permeation rates rests on computer simulations in conjunction with the inhomogeneous solubility-diffusion model, which requires the determination of the free-energy change and position-dependent diffusivity of the substrate along the translocation pathway through the lipid bilayer. In this Perspective, we will clarify the physical meaning of the membrane permeability inferred from such computer simulations, and how theoretical predictions actually relate to what is commonly measured experimentally. We will also examine why these calculations remain both technically challenging and overly computationally expensive, which has hitherto precluded their routine use in nonacademic settings. We finally synopsize possible research directions to meet these challenges, increase the predictive power of physics-based rates of passive permeation, and, by ricochet, improve their practical usefulness.
Collapse
Affiliation(s)
- Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦7019, Université de Lorraine, 54500 Vandœuvre-lès-Nancy cedex, France
- Beckman Institute for Advanced Science and Technology, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
16
|
Park S, Levental I, Pastor RW, Im W. Unsaturated Lipids Facilitate Partitioning of Transmembrane Peptides into the Liquid Ordered Phase. J Chem Theory Comput 2023; 19:5303-5314. [PMID: 37417947 PMCID: PMC10413867 DOI: 10.1021/acs.jctc.3c00398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Indexed: 07/08/2023]
Abstract
The affinity of single-pass transmembrane (TM) proteins for ordered membrane phases has been reported to depend on their lipidation, TM length, and lipid accessible surface area. In this work, the raft affinities of the TM domain of the linker for activation of T cells and its depalmitoylated variant are assessed using free energy simulations in a binary bilayer system composed of two laterally patched bilayers of ternary liquid ordered (Lo) and liquid disordered (Ld) phases. These phases are modeled by distinct compositions of distearoylphosphatidylcholine, palmitoyloleoylphosphatidylcholine (POPC), and cholesterol, and the simulations were carried out for 4.5 μs/window. Both peptides are shown to preferentially partition into the Ld phase in agreement with model membrane experiments and previous simulations on ternary lipid mixtures but not with measurements on giant plasma membrane vesicles where the Lo is slightly preferred. However, the 500 ns average relaxation time of lipid rearrangement around the peptide precluded a quantitative analysis of free energy differences arising from peptide palmitoylation and two different lipid compositions. When in the Lo phase, peptides reside in regions rich in POPC and interact preferentially with its unsaturated tail. Hence, the detailed substructure of the Lo phase is an important modulator of peptide partitioning, in addition to the inherent properties of the peptide.
Collapse
Affiliation(s)
- Soohyung Park
- Departments
of Biological Sciences and Chemistry, Lehigh
University, Bethlehem, Pennsylvania 18015, United States
| | - Ilya Levental
- Department
of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903-1738, United States
| | - Richard W. Pastor
- Laboratory
of Computational Biology, National Heart,
Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wonpil Im
- Departments
of Biological Sciences and Chemistry, Lehigh
University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
17
|
Yanagisawa H, Kita Y, Oda T, Kikkawa M. Unveiling Liquid-Crystalline Lipids in the Urothelial Membrane through Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542358. [PMID: 37398191 PMCID: PMC10312457 DOI: 10.1101/2023.05.29.542358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
Collapse
Affiliation(s)
- Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| |
Collapse
|
18
|
Oda T, Yanagisawa H, Kikkawa M, Kita Y. Unveiling Liquid-Crystalline Lipids in the Urothelial Membrane through Cryo-EM. RESEARCH SQUARE 2023:rs.3.rs-3080731. [PMID: 37503277 PMCID: PMC10371089 DOI: 10.21203/rs.3.rs-3080731/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this investigation, we employed cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex embedded within the porcine AUM at a resolution of 3.5 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
Collapse
|
19
|
Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
Collapse
Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
20
|
Doktorova M, Khelashvili G, Ashkar R, Brown MF. Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics. Biophys J 2023; 122:984-1002. [PMID: 36474442 PMCID: PMC10111610 DOI: 10.1016/j.bpj.2022.12.007] [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: 09/03/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent κC modulus for bilayer bending. Our results show a strong correlation with κC values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.
Collapse
Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona; Program in Applied Mathematics, University of Arizona, Tucson, Arizona.
| |
Collapse
|
21
|
Jin H, Cui J, Zhan W. Enzymatic Janus Liposome Micromotors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4198-4206. [PMID: 36893357 DOI: 10.1021/acs.langmuir.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A liposome-based micromotor system that utilizes regional enzymatic conversion and gas generation to achieve directional motion in water is presented. Constituted mainly of a low-melting lipid and a high-melting lipid together with cholesterol, these liposomes maintain stable Janus configuration at room temperature as a result of lipid liquid-liquid phase separation. Local placement of enzymes such as horseradish peroxidase is realized via affinity binding between avidin and biotin, the latter as a lipid conjugate sorted specifically into one domain of these Janus liposomes as a minor component. In the presence of the substrate, hydrogen peroxide, these enzyme-decorated Janus liposomes undergo directional motion, yielding velocities exceeding thermal diffusion by three folds in some cases. Experimental details on liposome size control, motor assembly, and substrate distribution are presented; effects of key experimental factors on liposome motion, such as substrate concentration and liposome Janus ratio, are also examined. This work thus provides a viable approach to building asymmetrical lipid-assembled, enzyme-attached colloids and, in addition, stresses the importance of asymmetry in achieving particle directional motion.
Collapse
Affiliation(s)
- Hui Jin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jinyan Cui
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Wei Zhan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| |
Collapse
|
22
|
Zimmerberg J, Soubias O, Pastor RW. Special issue for Klaus Gawrisch. Biophys J 2023; 122:E1-E8. [PMID: 36921597 PMCID: PMC10111273 DOI: 10.1016/j.bpj.2023.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/17/2023] Open
Affiliation(s)
- Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Olivier Soubias
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
23
|
Vervust W, Zhang DT, van Erp TS, Ghysels A. Path sampling with memory reduction and replica exchange to reach long permeation timescales. Biophys J 2023:S0006-3495(23)00127-3. [PMID: 36809877 PMCID: PMC10398259 DOI: 10.1016/j.bpj.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. Next, recent and current developments in three RETIS aspects are discussed: several new Monte Carlo moves in the path-sampling algorithm, memory reduction by reducing pathlengths, and exploitation of parallel computing with CPU-imbalanced replicas. Finally, the memory reduction presenting a new replica exchange implementation, coined REPPTIS, is showcased with a permeant needing to pass a membrane with two permeation channels, either representing an entropic or energetic barrier. The REPPTIS results showed clearly that inclusion of some memory and enhancing ergodic sampling via replica exchange moves are both necessary to obtain correct permeability estimates. In an additional example, ibuprofen permeation through a dipalmitoylphosphatidylcholine membrane was modeled. REPPTIS succeeded in estimating the permeability of this amphiphilic drug molecule with metastable states along the permeation pathway. In conclusion, the presented methodological advances allow for deeper insight into membrane biophysics even if the pathways are slow, as RETIS and REPPTIS push the permeability calculations to longer timescales.
Collapse
Affiliation(s)
- Wouter Vervust
- IBiTech - Biommeda Research Group, Faculty of Engineering and Architecture, Ghent University, Gent, Belgium
| | - Daniel T Zhang
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - An Ghysels
- IBiTech - Biommeda Research Group, Faculty of Engineering and Architecture, Ghent University, Gent, Belgium.
| |
Collapse
|
24
|
Structural Analyses of the Glycolipids in Lipid Rafts. Methods Mol Biol 2023; 2613:145-152. [PMID: 36587077 DOI: 10.1007/978-1-0716-2910-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Lipid rafts are usually isolated from cells or tissues using sucrose gradient ultracentrifugation in the presence of detergents such as Triton X-100 at 4 °C. Although detergents should be removed for further structural characterization following fractionation, these compounds are often difficult to completely remove, especially from the glycolipids. In this chapter, we describe a novel method for the fast and convenient removal of detergents from lipid raft glycolipids following fraction and describe the application of this method.
Collapse
|
25
|
Carvajal-Barriga EJ, Putaux JL, Martín-Ramos P, Simbaña J, Portero-Barahona P, Martín-Gil J. Opportunities for Ivory Nut Residue Valorization as a Source of Nanocellulose Colloidal Suspensions. Gels 2022; 9:32. [PMID: 36661799 PMCID: PMC9857895 DOI: 10.3390/gels9010032] [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: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023] Open
Abstract
Ivory nut seeds have been traditionally exploited in Central and South America for obtaining vegetable ivory. The residues from this industry are susceptible to valorization as a source of fatty acids (by organic extraction) and mannans (by alkaline dissolution and regeneration). Nonetheless, cellulose may also be recovered at the end of this fractionation process by acid hydrolysis and functionalization, with associated advantages over other lignocellulosic sources due to the absence of lignin in the endospermic tissue. In this work, various experimental parameters (sulfuric acid concentration, temperature, and hydrolysis time) were investigated to optimize the processing conditions for preparing stable nanocellulose suspensions after ultrasonication. The most stable nanocellulose gel (1 wt% solid content) was obtained after 4-h hydrolysis at 60 °C with 8 M H2SO4 and was characterized by using complementary tech-niques, including dynamic light scattering (DLS), transmission electron microscopy (TEM), X-ray powder diffraction (XRD), nano-fibril sulfation measurements, vibrational and solid-state nuclear magnetic resonance (CP/MAS 13C-NMR) spectroscopies, and thermal analysis. This nanocellulose hydrogel is susceptible to further utilization in various applications and fields, e.g., in agricul-ture for controlling the release of agrochemicals, in pharmaceutics for developing new dosage forms, and in the treatment of wastewater from the textile and paper industries.
Collapse
Affiliation(s)
- Enrique Javier Carvajal-Barriga
- Neotropical Center for the Biomass Research, School of Biological Sciences, Pontificia Universidad Católica del Ecuador Av. 12 de Octubre 1076 y Roca, Quito 170523, Ecuador
| | - Jean-Luc Putaux
- University Grenoble Alpes, CNRS, CERMAV, F-38000 Grenoble, France
| | - Pablo Martín-Ramos
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), EPS, Universidad de Zaragoza, Carretera de Cuarte s/n, 22071 Huesca, Spain
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - Jennifer Simbaña
- Neotropical Center for the Biomass Research, School of Biological Sciences, Pontificia Universidad Católica del Ecuador Av. 12 de Octubre 1076 y Roca, Quito 170523, Ecuador
| | - Patricia Portero-Barahona
- Neotropical Center for the Biomass Research, School of Biological Sciences, Pontificia Universidad Católica del Ecuador Av. 12 de Octubre 1076 y Roca, Quito 170523, Ecuador
| | - Jesús Martín-Gil
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| |
Collapse
|
26
|
Baek JM, Jung WH, Yu ES, Ahn DJ, Ryu YS. In Vitro Membrane Platform for the Visualization of Water Impermeability across the Liquid-Ordered Phase under Hypertonic Conditions. J Am Chem Soc 2022; 144:21887-21896. [PMID: 36367984 DOI: 10.1021/jacs.2c06626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Passive water penetration across the cell membrane by osmotic diffusion is essential for the homeostasis of cell volume, in addition to the protein-assisted active transportation of water. Since membrane components can regulate water permeability, controlling compositional variation during the volume regulatory process is a prerequisite for investigating the underlying mechanisms of water permeation and related membrane dynamics. However, the lack of a viable in vitro membrane platform in hypertonic solutions impedes advanced knowledge of cell volume regulation processes, especially cholesterol-enriched lipid domains called lipid rafts. By reconstituting the liquid-ordered (Lo) domain as a likeness of lipid rafts, we verified suppressed water permeation across the Lo domains, which had yet to be confirmed with experimental demonstrations despite a simulation approach. With the help of direct transfer of the Lo domains from vesicles to supported lipid membranes, the biological roles of lipid composition in suppressed water translocation were experimentally confirmed. Additionally, the improvement in membrane stability under hypertonic conditions was demonstrated based on molecular dynamics simulations.
Collapse
Affiliation(s)
- Ji Min Baek
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woo Hyuk Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Eui-Sang Yu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Dong June Ahn
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Yong-Sang Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
27
|
Rice A, Haldar S, Wang E, Blank PS, Akimov SA, Galimzyanov TR, Pastor RW, Zimmerberg J. Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration. Nat Commun 2022; 13:7336. [PMID: 36470871 PMCID: PMC9722698 DOI: 10.1038/s41467-022-34576-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/28/2022] [Indexed: 12/07/2022] Open
Abstract
To infect, enveloped viruses employ spike protein, spearheaded by its amphipathic fusion peptide (FP), that upon activation extends out from the viral surface to embed into the target cellular membrane. Here we report that synthesized influenza virus FPs are membrane active, generating pores in giant unilamellar vesicles (GUV), and thus potentially explain both influenza virus' hemolytic activity and the liposome poration seen in cryo-electron tomography. Experimentally, FPs are heterogeneously distributed on the GUV at the time of poration. Consistent with this heterogeneous distribution, molecular dynamics (MD) simulations of asymmetric bilayers with different numbers of FPs in one leaflet show FP aggregation. At the center of FP aggregates, a profound change in the membrane structure results in thinning, higher water permeability, and curvature. Ultimately, a hybrid bilayer nanodomain forms with one lipidic leaflet and one peptidic leaflet. Membrane elastic theory predicts a reduced barrier to water pore formation when even a dimer of FPs thins the membrane as above, and the FPs of that dimer tilt, to continue the leaflet bending initiated by the hydrophobic mismatch between the FP dimer and the surrounding lipid.
Collapse
Affiliation(s)
- Amy Rice
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Sourav Haldar
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA ,grid.418363.b0000 0004 0506 6543Present Address: Division of Virus Research and Therapeutics, CSIR-Central Drug Research Institute, Lucknow, UP India
| | - Eric Wang
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Paul S. Blank
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Sergey A. Akimov
- grid.4886.20000 0001 2192 9124A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Timur R. Galimzyanov
- grid.4886.20000 0001 2192 9124A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia ,grid.35043.310000 0001 0010 3972National University of Science and Technology “MISiS”, 4 Leninskiy Prospect, Moscow, Russia
| | - Richard W. Pastor
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Joshua Zimmerberg
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| |
Collapse
|
28
|
Kordyum EL, Artemenko OA, Hasenstein KH. Lipid Rafts and Plant Gravisensitivity. Life (Basel) 2022; 12:1809. [PMID: 36362962 PMCID: PMC9695138 DOI: 10.3390/life12111809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 07/24/2023] Open
Abstract
The necessity to include plants as a component of a Bioregenerative Life Support System leads to investigations to optimize plant growth facilities as well as a better understanding of the plant cell membrane and its numerous activities in the signaling, transport, and sensing of gravity, drought, and other stressors. The cell membrane participates in numerous processes, including endo- and exocytosis and cell division, and is involved in the response to external stimuli. Variable but stabilized microdomains form in membranes that include specific lipids and proteins that became known as (detergent-resistant) membrane microdomains, or lipid rafts with various subclassifications. The composition, especially the sterol-dependent recruitment of specific proteins affects endo- and exo-membrane domains as well as plasmodesmata. The enhanced saturated fatty acid content in lipid rafts after clinorotation suggests increased rigidity and reduced membrane permeability as a primary response to abiotic and mechanical stress. These results can also be obtained with lipid-sensitive stains. The linkage of the CM to the cytoskeleton via rafts is part of the complex interactions between lipid microdomains, mechanosensitive ion channels, and the organization of the cytoskeleton. These intricately linked structures and functions provide multiple future research directions to elucidate the role of lipid rafts in physiological processes.
Collapse
Affiliation(s)
- Elizabeth L. Kordyum
- Department of Cell Biology and Anatomy, Institute of Botany NASU, Tereschenkivska Str. 2, 01601 Kyiv, Ukraine
| | - Olga A. Artemenko
- Department of Cell Biology and Anatomy, Institute of Botany NASU, Tereschenkivska Str. 2, 01601 Kyiv, Ukraine
| | - Karl H. Hasenstein
- Biology Department, University of Louisiana at Lafayette, Lafayette, LA 70504-3602, USA
| |
Collapse
|
29
|
Boafo GF, Magar KT, Ekpo MD, Qian W, Tan S, Chen C. The Role of Cryoprotective Agents in Liposome Stabilization and Preservation. Int J Mol Sci 2022; 23:ijms232012487. [PMID: 36293340 PMCID: PMC9603853 DOI: 10.3390/ijms232012487] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 10/15/2022] [Indexed: 11/18/2022] Open
Abstract
To improve liposomes’ usage as drug delivery vehicles, cryoprotectants can be utilized to prevent constituent leakage and liposome instability. Cryoprotective agents (CPAs) or cryoprotectants can protect liposomes from the mechanical stress of ice by vitrifying at a specific temperature, which forms a glassy matrix. The majority of studies on cryoprotectants demonstrate that as the concentration of the cryoprotectant is increased, the liposomal stability improves, resulting in decreased aggregation. The effectiveness of CPAs in maintaining liposome stability in the aqueous state essentially depends on a complex interaction between protectants and bilayer composition. Furthermore, different types of CPAs have distinct effective mechanisms of action; therefore, the combination of several cryoprotectants may be beneficial and novel attributed to the synergistic actions of the CPAs. In this review, we discuss the use of liposomes as drug delivery vehicles, phospholipid–CPA interactions, their thermotropic behavior during freezing, types of CPA and their mechanism for preventing leakage of drugs from liposomes.
Collapse
Affiliation(s)
- George Frimpong Boafo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Kosheli Thapa Magar
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Marlene Davis Ekpo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Wang Qian
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Correspondence: (S.T.); (C.C.)
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Correspondence: (S.T.); (C.C.)
| |
Collapse
|
30
|
Maleš P, Pem B, Petrov D, Jurašin DD, Bakarić D. Deciphering the origin of the melting profile of unilamellar phosphatidylcholine liposomes by measuring the turbidity of its suspensions. SOFT MATTER 2022; 18:6703-6715. [PMID: 36017811 DOI: 10.1039/d2sm00878e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The elucidation of the thermal properties of phosphatidylcholine liposomes is often based on the analysis of the thermal capacity profiles of multilamellar liposomes (MLV), which may qualitatively disagree with those of unilamellar liposomes (LUV). Experiments and interpretation of LUV liposomes is further complicated by aggregation and lamellarization of lipid bilayers in a short time period, which makes it almost impossible to distinguish the signatures of the two types of bilayers. To characterize independently MLV and LUV of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the latter were prepared with the addition of small amounts of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylglycerol (DPPG) which, due to the sterical hindrance and negative charge at a given pH value, cause LUV repellence and contribute to their stability. Differential scanning calorimetry curves and temperature-dependent UV/Vis spectra of the prepared MLV and LUV were measured. Multivariate analysis of spectrophotometric data determined the phase transition temperatures (pretransition at Tp and the main phase transition at Tm), and based on the changes in turbidities, the thickness of the lipid bilayer in LUV was determined. The obtained data suggested that the curvature change is a key distinguishing factor in MLV and LUV heat capacity profiles. By combining the experimental results and those obtained by MD simulations, the interfacial water layer was characterized and its contribution to the thermal properties of LUV was discussed.
Collapse
Affiliation(s)
- Petra Maleš
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Barbara Pem
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Dražen Petrov
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Darija Domazet Jurašin
- Division for Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| |
Collapse
|
31
|
Himbert S, Rheinstädter MC. Structural and mechanical properties of the red blood cell’s cytoplasmic membrane seen through the lens of biophysics. Front Physiol 2022; 13:953257. [PMID: 36171967 PMCID: PMC9510598 DOI: 10.3389/fphys.2022.953257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
Red blood cells (RBCs) are the most abundant cell type in the human body and critical suppliers of oxygen. The cells are characterized by a simple structure with no internal organelles. Their two-layered outer shell is composed of a cytoplasmic membrane (RBCcm) tethered to a spectrin cytoskeleton allowing the cell to be both flexible yet resistant against shear stress. These mechanical properties are intrinsically linked to the molecular composition and organization of their shell. The cytoplasmic membrane is expected to dominate the elastic behavior on small, nanometer length scales, which are most relevant for cellular processes that take place between the fibrils of the cytoskeleton. Several pathologies have been linked to structural and compositional changes within the RBCcm and the cell’s mechanical properties. We review current findings in terms of RBC lipidomics, lipid organization and elastic properties with a focus on biophysical techniques, such as X-ray and neutron scattering, and Molecular Dynamics simulations, and their biological relevance. In our current understanding, the RBCcm’s structure is patchy, with nanometer sized liquid ordered and disordered lipid, and peptide domains. At the same time, it is surprisingly soft, with bending rigidities κ of 2–4 kBT. This is in strong contrast to the current belief that a high concentration of cholesterol results in stiff membranes. This extreme softness is likely the result of an interaction between polyunsaturated lipids and cholesterol, which may also occur in other biological membranes. There is strong evidence in the literature that there is no length scale dependence of κ of whole RBCs.
Collapse
Affiliation(s)
- Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
- Origins Institute, McMaster University, Hamilton, ON, Canada
- *Correspondence: Sebastian Himbert, ; Maikel C. Rheinstädter,
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
- Origins Institute, McMaster University, Hamilton, ON, Canada
- *Correspondence: Sebastian Himbert, ; Maikel C. Rheinstädter,
| |
Collapse
|
32
|
The bending rigidity of the red blood cell cytoplasmic membrane. PLoS One 2022; 17:e0269619. [PMID: 35913930 PMCID: PMC9342732 DOI: 10.1371/journal.pone.0269619] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
An important mechanical property of cells is the membrane bending modulus, κ. In the case of red blood cells (RBCs) there is a composite membrane consisting of a cytoplasmic membrane and an underlying spectrin network. Literature values of κ are puzzling, as they are reported over a wide range, from 5 kBT to 230 kBT. To disentangle the contribution of the cytoplasmic membrane from the spectrin network, we investigated the bending of red blood cell cytoplasmic membranes (RBCcm) in the absence of spectrin and adenosine triphosphate (ATP). We used a combination of X-ray diffuse scattering (XDS), neutron spin-echo (NSE) spectrometry and Molecular Dynamics (MD) simulations. Our results indicate values of κ of order 4 kBT to 6 kBT, relatively small compared to literature values for most single component lipid bilayers. We suggest two ways this relative softness might confer biological advantage.
Collapse
|
33
|
MacDermott-Opeskin HI, Panizza A, Eijkelkamp BA, O'Mara ML. Dynamics of the Acinetobacter baumannii inner membrane under exogenous polyunsaturated fatty acid stress. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183908. [PMID: 35276227 DOI: 10.1016/j.bbamem.2022.183908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/11/2022] [Accepted: 03/05/2022] [Indexed: 01/04/2023]
Abstract
Exogenous polyunsaturated fatty acids (PUFAs) are readily incorporated into the synthesis pathways of A. baumannii membrane phospholipids, where they contribute to reduced bacterial fitness and increased antimicrobial susceptibility. Here we examine the impact of PUFA membrane modification on membrane organisation and biophysical properties using coarse grained MARTINI simulations of chemically representative membrane models developed from mass-spectrometry datasets of an untreated, arachidonic acid (AA) treated and docosahexaenoic acid (DHA) treated A. baumannii membranes. Enzymatic integration of AA or DHA into phospholipids of the A. baumannii membrane resulted in modulation of membrane biophysical properties. Membrane thickness decreased slightly following PUFA treatment, concomitant with changes in the lateral area per lipid of each lipid headgroup class. PUFA treatment resulted in a decrease in membrane ordering and an increase in lipid lateral diffusion. Changes in lateral membrane organisation were observed in the PUFA treated membranes, with a concurrent increase in ordered cardiolipin domains and disordered PUFA-containing domains. Notably, separation between ordered and disordered domains was enhanced and was more pronounced for DHA relative to AA, providing a possible mechanism for greater antimicrobial action of DHA relative to AA observed experimentally. Furthermore, the membrane active antimicrobial, pentamidine, preferentially adsorbs to cardiolipin domains of the A. baumannii model membranes. This interaction, and membrane penetration of pentamidine, was enhanced following PUFA treatment. Cumulatively, this work explores the wide-ranging effects of PUFA incorporation on the A. baumannii membrane and provides a molecular basis for bacterial inner membrane disruption by PUFAs.
Collapse
Affiliation(s)
- Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Alessandra Panizza
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Bart A Eijkelkamp
- Molecular Science and Technology, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT, 2601, Australia.
| |
Collapse
|
34
|
Bronstein LG, Tóth Á, Cressey P, Rosilio V, Di Meo F, Makky A. Phospholipid-porphyrin conjugates: deciphering the driving forces behind their supramolecular assemblies. NANOSCALE 2022; 14:7387-7407. [PMID: 35536011 DOI: 10.1039/d2nr01158a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phospholipid-porphyrin conjugates (PL-Por) are nowadays considered as a unique class of building blocks that can self-assemble into supramolecular structures that possess multifunctional properties and enhanced optoelectronics characteristics compared to their disassembled counterparts. However, despite their versatile properties, little is known about the impact of the packing parameter of PL-Por conjugates on their assembling mechanism and their molecular organization inside these assemblies. To gain a better understanding on their assembling properties, we synthesized two new series of PL-Por conjugates with different alkyl sn2-chain lengths linked via an amide bond to either pheophorbide-a (PhxLPC) or pyropheophorbide-a (PyrxLPC). By combining a variety of experimental techniques with molecular dynamics (MD) simulations, we investigated both the assembling and optical properties of the PL-Por either self-assembled or when incorporated into lipid bilayers. We demonstrated that independently of the linker length, PhxLPC assembled into closed ovoid structures, whereas PyrxLPC formed rigid open sheets. Interestingly, PyrxLPC assemblies displayed a significant red shift and narrowing of the Q-band indicating the formation of ordered J-aggregates. The MD simulations highlighted the central role of the interaction between porphyrin cores rather than the length difference between the two phospholipid chains in controlling the structure of the lipid bilayer membranes and thus their optical properties. Indeed, while PhxLPC have the tendency to form inter-leaflet π-stacked dimers, PyrxLPC conjugates formed dimers within the same leaflet. Altogether, this work could be used as guidelines for the design of new PL-Por conjugates that self-assemble into bilayer-like supramolecular structures with tunable morphology and optical properties.
Collapse
Affiliation(s)
- Louis-Gabriel Bronstein
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France.
| | - Ágota Tóth
- INSERM U1248 Pharmacology & Transplantation, Univ. Limoges, 2 rue du Prof. Descottes, F-87025, Limoges, France.
| | - Paul Cressey
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France.
| | - Véronique Rosilio
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France.
| | - Florent Di Meo
- INSERM U1248 Pharmacology & Transplantation, Univ. Limoges, 2 rue du Prof. Descottes, F-87025, Limoges, France.
| | - Ali Makky
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France.
| |
Collapse
|
35
|
Winslow M, Robinson D. Computational development of a phase-sensitive membrane raft probe. Phys Chem Chem Phys 2022; 24:8260-8268. [PMID: 35319559 DOI: 10.1039/d2cp00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Derivatives of the widely used 1,6-diphenyl-1,3,5-hexatriene molecular probe have been considered using a multiscale approach involving spin-flip time-dependent density functional theory, classical molecular dynamics and hybrid quantum mechanics/molecular mechanics. We identify a potential probe of membrane phase (i.e. to preferentially detect liquid-ordered regions of lipid bilayers), which exhibits restricted access to a conical intersection in the liquid-ordered phase but is freely accessible in less ordered molecular environments. The characteristics of this probe also mark it as a candidate for an aggregation induced emission fluorophore.
Collapse
Affiliation(s)
- Max Winslow
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - David Robinson
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| |
Collapse
|
36
|
Frallicciardi J, Melcr J, Siginou P, Marrink SJ, Poolman B. Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nat Commun 2022; 13:1605. [PMID: 35338137 PMCID: PMC8956743 DOI: 10.1038/s41467-022-29272-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/02/2022] [Indexed: 12/16/2022] Open
Abstract
Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While the cytoplasmic membrane of bacterial cells is highly permeable for weak acids and glycerol, yeasts can maintain large concentration gradients. Here we show that such differences can arise from the physical state of the plasma membrane. By combining stopped-flow kinetic measurements with molecular dynamics simulations, we performed a systematic analysis of the permeability of a variety of small molecules through synthetic membranes of different lipid composition to obtain detailed molecular insight into the permeation mechanisms. While membrane thickness is an important parameter for the permeability through fluid membranes, the largest differences occur when the membranes transit from the liquid-disordered to liquid-ordered and/or to gel state, which is in agreement with previous work on passive diffusion of water. By comparing our results with in vivo measurements from yeast, we conclude that the yeast membrane exists in a highly ordered and rigid state, which is comparable to synthetic saturated DPPC-sterol membranes. Membrane permeability of small molecules depends on the composition of the lipid bilayer. Here, authors compare permeability measured on membranes in different physical states and conclude that the yeast membrane exists in a highly ordered phase.
Collapse
Affiliation(s)
- Jacopo Frallicciardi
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands
| | - Josef Melcr
- Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands
| | - Pareskevi Siginou
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands
| | - Siewert J Marrink
- Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands.
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, the Netherlands.
| |
Collapse
|
37
|
Pan X, Li L, Huang HH, Wu J, Zhou X, Yan X, Jia J, Yue T, Chu YH, Yan B. Biosafety-inspired structural optimization of triazolium ionic liquids based on structure-toxicity relationships. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127521. [PMID: 34736187 DOI: 10.1016/j.jhazmat.2021.127521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/30/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Ionic liquids (ILs), owing to their low vapor pressure and excellent solvating ability, are being increasingly applied in various industries to replace highly toxic organic solvents. They mainly pollute aquatic environment and soils, directly endangering eco-environment and human health. Therefore, it is critical to understand and optimize structural motifs of ILs with reduced toxicity. Considering human oral exposure is the major route, our investigations employed a human cell panel (modeling oral exposures) including human stomach (GES-1), intestinal (FHC), liver (HepG2) and kidney (HEK293) cells using a series of experimental and computational approaches to explore the cytotoxicity and molecular mechanism of ILs. We discovered that the cytotoxicity of triazolium and imidazolium ILs was human cell line-dependent with cytotoxicity in an order of FHC > GES-1 > HepG2 > HEK293. For this reason, a toxicity assay using a single cell line was highly inappropriate. Compared to anions (Br-, OTs-, OTMBS-) we tested, the cation of ILs played a major role in causing cytotoxicity. Ionic liquids with cations having longer hydrophobic sidechains (IL09 vs. IL01) readily insert into cell membranes with enhanced membrane and lipidomic perturbations, induce cytotoxicity by triggering cell cycle arrest and apoptosis. Reducing sidechain length and incorporating three nitrogen atoms (triazolium) instead of two (imidazolium) in the cation core alleviated cytotoxicity by reducing cell membrane perturbations and cell function interference. These findings provide important guiding principles for the design of the next-generation of "green" and safe ILs.
Collapse
Affiliation(s)
- Xiujiao Pan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lingzhi Li
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hsin-Heng Huang
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi 62102, Taiwan, ROC
| | - Jialong Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaoxia Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiliang Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jianbo Jia
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
| | - Yen-Ho Chu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi 62102, Taiwan, ROC.
| | - Bing Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Shandong University, Jinan 250100, China.
| |
Collapse
|
38
|
Truzzolillo D. Mixing-demixing transition and void formation in quasi-2D binary mixtures on a sphere. J Chem Phys 2022; 156:034904. [DOI: 10.1063/5.0080352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Truzzolillo
- Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Universitè de Montpellier, F-34095 Montpellier, France
| |
Collapse
|
39
|
Vervust W, Ghysels A. Oxygen Storage in Stacked Phospholipid Membranes Under an Oxygen Gradient as a Model for Myelin Sheaths. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1395:301-307. [PMID: 36527653 DOI: 10.1007/978-3-031-14190-4_49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Axons in the brain and peripheral nervous system are enveloped by myelin sheaths, which are composed of stacked membrane bilayers containing large fractions of cholesterol, phospholipids, and glycolipids. The oxygen availability to the nearby oxygen consuming cytochrome c oxidase in the mitochondria is essential for the well-functioning of a cell. By constructing a rate network model based on molecular dynamics simulations, and solving it for steady-state conditions, this work calculates the oxygen storage in stacked membranes under an oxygen gradient. It is found that stacking membranes increases the oxygen storage capacity, indicating that myelin can function as an oxygen reservoir. However, it is found that the storage enhancement levels out for stacks with a large number of bilayers, suggesting why myelin sheaths consist of only 10-300 membranes rather than thousands. The presence of additional water between the stacked bilayers, as seen in cancer cells, is shown to diminish myelin oxygen storage enhancement.
Collapse
|
40
|
Lin X, Lin X. Designing amphiphilic Janus nanoparticles with tunable lipid raft affinity via molecular dynamics simulation. Biomater Sci 2021; 9:8249-8258. [PMID: 34757373 DOI: 10.1039/d1bm01364e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the differential interactions among lipids and proteins, the plasma membrane can segregate into a series of functional nanoscale membrane domains ("lipid rafts"), which are essential in multiple biological processes such as signaling transduction, protein trafficking and endocytosis. On the other hand, Janus nanoparticles (NPs) have shown great promise in various biomedical applications due to their asymmetric characteristics and can integrate different surface properties and thus synergetic functions. Hence, in this work, we aim to design an amphiphilic Janus NP to target and regulate lipid rafts via tuning its surface ligand amphiphilicity using coarse-grained molecular dynamics (MD) simulations. Our μs-scale free coarse-grained MD simulations as well as umbrella sampling free energy calculations indicated that the hydrophobicity of the hydrophobic surface ligands not only determined the lateral membrane partitioning thermodynamics of Janus NPs in phase-separated lipid membranes, but also the difficulty in their insertion into different membrane domains of the lipid membrane. These two factors jointly regulated the lipid raft affinity of Janus NPs. Meanwhile, the hydrophilicity of the hydrophilic surface ligands could affect the insertion ability of Janus NPs. Besides, the ultra-small size could ensure the membrane-bound behavior of Janus NPs without disrupting the overall structure and phase separation kinetics of the lipid membrane. These results may provide valuable insights into the design of functional NPs targeting and controllably regulating lipid rafts.
Collapse
Affiliation(s)
- Xiaoqian Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China. .,Shen Yuan Honors College, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
| |
Collapse
|
41
|
Himbert S, Qadri SM, Sheffield WP, Schubert P, D’Alessandro A, Rheinstädter MC. Blood bank storage of red blood cells increases RBC cytoplasmic membrane order and bending rigidity. PLoS One 2021; 16:e0259267. [PMID: 34767588 PMCID: PMC8589153 DOI: 10.1371/journal.pone.0259267] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/17/2021] [Indexed: 12/05/2022] Open
Abstract
Blood banks around the world store blood components for several weeks ensuring its availability for transfusion medicine. Red blood cells (RBCs) are known to undergo compositional changes during storage, which may impact the cells' function and eventually the recipients' health. We extracted the RBC's cytoplasmic membrane (RBCcm) to study the effect of storage on the membranes' molecular structure and bending rigidity by a combination of X-ray diffraction (XRD), X-ray diffuse scattering (XDS) and coarse grained Molecular Dynamics (MD) simulations. Blood was stored in commercial blood bags for 2 and 5 weeks, respectively and compared to freshly drawn blood. Using mass spectrometry, we measured an increase of fatty acids together with a slight shift towards shorter tail lengths. We observe an increased fraction (6%) of liquid ordered (lo) domains in the RBCcms with storage time, and an increased lipid packing in these domains, leading to an increased membrane thickness and membrane order. The size of both, lo and liquid disordered (ld) lipid domains was found to decrease with increased storage time by up to 25%. XDS experiments reveal a storage dependent increase in the RBCcm's bending modulus κ by a factor of 2.8, from 1.9 kBT to 5.3 kBT. MD simulations were conducted in the absence of proteins. The results show that the membrane composition has a small contribution to the increased bending rigidity and suggests additional protein-driven mechanisms.
Collapse
Affiliation(s)
- Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
- Origins Institute, McMaster University, Hamilton, ON, Canada
| | - Syed M. Qadri
- Faculty of Health Sciences, Ontario Tech University, Oshawa, ON, Canada
| | - William P. Sheffield
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Centre for Innovation, Canadian Blood Services, Hamilton, ON, Canada
| | - Peter Schubert
- Centre for Innovation, Canadian Blood Services, Vancouver, BC, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - Angelo D’Alessandro
- University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, United States of America
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
- Origins Institute, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
42
|
Wilson KA, Wang L, O’Mara ML. Site of Cholesterol Oxidation Impacts Its Localization and Domain Formation in the Neuronal Plasma Membrane. ACS Chem Neurosci 2021; 12:3873-3884. [PMID: 34633798 DOI: 10.1021/acschemneuro.1c00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cholesterol is integral to the structure of mammalian cell membranes. Oxidation of cholesterol alters how it behaves in the membrane and influences the membrane biophysical properties. Elevated levels of oxidized cholesterol are associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, and Huntington's disease. Previous work has investigated the impact of oxidized cholesterol in the context of simple model membrane systems. However, there is a growing body of literature that shows that complex membranes possessing physiological phospholipid distributions have different properties from those of binary or trinary model membranes. In the current work, the impact of oxidized cholesterol on the biophysical properties of a complex neuronal plasma membrane is investigated using coarse-grained Martini molecular dynamics simulations. Comparison of the native neuronal membrane to neuronal membranes containing 10% tail-oxidized or 10% head-oxidized cholesterol shows that the site of oxidization changes the behavior of the oxidized cholesterol in the membrane. Furthermore, species-specific domain formation is observed between each oxidized cholesterol and minor lipid classes. Although both tail-oxidized and head-oxidized cholesterols modulate the biophysical properties of the membrane, smaller changes are observed in the complex neuronal membrane than seen in the previous work on simple binary or trinary model membranes. This work highlights the presence of compensatory effects of lipid diversity in the complex neuronal membrane. Overall, this study improves our molecular-level understanding of the effects of oxidized cholesterol on the properties of neuronal tissue and emphasizes the importance of studying membranes with realistic lipid compositions.
Collapse
Affiliation(s)
- Katie A. Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Lily Wang
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
43
|
Subczynski WK, Widomska J, Stein N, Swartz HM. Factors determining barrier properties to oxygen transport across model and cell plasma membranes based on EPR spin-label oximetry. APPLIED MAGNETIC RESONANCE 2021; 52:1237-1260. [PMID: 36267674 PMCID: PMC9581439 DOI: 10.1007/s00723-021-01412-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/23/2021] [Accepted: 08/04/2021] [Indexed: 06/01/2023]
Abstract
This review is motivated by the exciting new area of radiation therapy using a phenomenon termed FLASH in which oxygen is thought to have a central role. Well-established principles of radiation biology and physics suggest that if oxygen has a strong role, it should be the level at the DNA. The key aspect discussed is the rate of oxygen diffusion. If oxygen freely diffuses into cells and rapidly equilibrates, then measurements in the extracellular compartment would enable FLASH to be investigated using existing methodologies that can readily measure oxygen in the extracellular compartment. EPR spin-label oximetry allows evaluation of the oxygen permeability coefficient across lipid bilayer membranes. It is established that simple fluid phase lipid bilayers are not barriers to oxygen transport. However, further investigations indicate that many physical and chemical (compositional) factor can significantly decrease this permeation. In biological cell plasma membranes, the lipid bilayer forms the matrix in which integral membrane proteins are immersed, changing organization and properties of the lipid matrix. To evaluate oxygen permeability coefficients across these complex membranes, oxygen permeation across all membrane domains and components must be considered. In this review, we consider many of the factors that affect (decrease) oxygen permeation across cell plasma membranes. Finally, we address the question, can the plasma membrane of the cell form a barrier to the free diffusion of oxygen into the cell interior? If there is a barrier then this must be considered in the investigations of the role of oxygen in FLASH.
Collapse
Affiliation(s)
- Witold K. Subczynski
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Justyna Widomska
- Department of Biophysics, Medical University of Lublin, Jaczewskiego 4, Lublin, Poland
| | - Natalia Stein
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Harold M. Swartz
- Department of Radiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| |
Collapse
|
44
|
Angles G, Hail A, Dotson RJ, Pias SC. Atomistic simulations modify interpretation of spin-label oximetry data. Part 1: intensified water-lipid interfacial resistances. APPLIED MAGNETIC RESONANCE 2021; 52:1261-1289. [PMID: 37292189 PMCID: PMC10249954 DOI: 10.1007/s00723-021-01398-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 06/10/2023]
Abstract
The role of membrane cholesterol in cellular function and dysfunction has been the subject of much inquiry. A few studies have suggested that cholesterol may slow oxygen diffusive transport, altering membrane physical properties and reducing oxygen permeability. The primary experimental technique used in recent years to study membrane oxygen transport is saturation-recovery electron paramagnetic resonance (EPR) oximetry, using spin-label probes targeted to specific regions of a lipid bilayer. The technique has been used, in particular, to assess the influence of cholesterol on oxygen transport and membrane permeability. The reliability of such EPR recordings at the water-lipid interface near the phospholipid headgroups has been challenged by all-atom molecular dynamics (MD) simulation data that show substantive agreement with spin-label probe measurements throughout much of the bilayer. This work uses further MD simulations, with an updated oxygen model, to determine the location of the maximum resistance to permeation and the rate-limiting barrier to oxygen permeation in 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) and POPC/cholesterol bilayers at 25 and 35°C. The current simulations show a spike of resistance to permeation in the headgroup region that was not detected by EPR but was predicted in early theoretical work by Diamond and Katz. Published experimental nuclear magnetic resonance (NMR) oxygen measurements provide key validation of the MD models and indicate that the positions and relative magnitudes of the phosphatidylcholine resistance peaks are accurate. Consideration of the headgroup-region resistances predicts bilayer permeability coefficients lower than estimated in EPR studies, giving permeabilities lower than the permeability of unstirred water layers of the same thickness. Here, the permeability of POPC at 35°C is estimated to be 13 cm/s, compared with 10 cm/s for POPC/cholesterol and 118 cm/s for simulation water layers of similar thickness. The value for POPC is 12 times lower than estimated from EPR measurements, while the value for POPC/cholesterol is 5 times lower. These findings underscore the value of atomic resolution models for guiding the interpretation of experimental probe-based measurements.
Collapse
Affiliation(s)
| | | | | | - Sally C. Pias
- Corresponding author: , Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), 801 Leroy Place, Socorro, NM 87801, USA
| |
Collapse
|
45
|
Ghysels A. Bringing hidden variables into the open unveils a barrier for lipid insertion into membranes. Biophys J 2021; 120:3542-3543. [PMID: 34407388 DOI: 10.1016/j.bpj.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- An Ghysels
- IBiTech - Biommeda research group, Ghent University, Ghent, Belgium.
| |
Collapse
|
46
|
Dutta A, Vreeken J, Ghiringhelli LM, Bereau T. Data-driven equation for drug-membrane permeability across drugs and membranes. J Chem Phys 2021; 154:244114. [PMID: 34241352 DOI: 10.1063/5.0053931] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally consider the functional relationship between passive permeation and acidity. To discover easily interpretable equations that explain the data well, we use the recently proposed sure-independence screening and sparsifying operator (SISSO), an artificial-intelligence technique that combines symbolic regression with compressed sensing. Our study is based on a large in silico dataset of 0.4 × 106 small molecules extracted from coarse-grained simulations. We rationalize the equation suggested by SISSO via an analysis of the inhomogeneous solubility-diffusion model in several asymptotic acidity regimes. We further extend our analysis to the dependence on lipid-membrane composition. Lipid-tail unsaturation plays a key role but surprisingly contributes stepwise rather than proportionally. Our results are in line with previously observed changes in permeability, suggesting the distinction between liquid-disordered and liquid-ordered permeation. Together, compressed sensing with analytically derived asymptotes establish and validate an accurate, broadly applicable, and interpretable equation for passive permeability across both drug and lipid-tail chemistry.
Collapse
Affiliation(s)
- Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jilles Vreeken
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Luca M Ghiringhelli
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
| |
Collapse
|
47
|
Aydin F, Durumeric AEP, da Hora GCA, Nguyen JDM, Oh MI, Swanson JMJ. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables. J Chem Phys 2021; 155:045101. [PMID: 34340389 DOI: 10.1063/5.0055489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Understanding the permeation of biomolecules through cellular membranes is critical for many biotechnological applications, including targeted drug delivery, pathogen detection, and the development of new antibiotics. To this end, computer simulations are routinely used to probe the underlying mechanisms of membrane permeation. Despite great progress and continued development, permeation simulations of realistic systems (e.g., more complex drug molecules or biologics through heterogeneous membranes) remain extremely challenging if not intractable. In this work, we combine molecular dynamics simulations with transition-tempered metadynamics and techniques from the variational approach to conformational dynamics to study the permeation mechanism of a drug molecule, trimethoprim, through a multicomponent membrane. We show that collective variables (CVs) obtained from an unsupervised machine learning algorithm called time-structure based Independent Component Analysis (tICA) improve performance and substantially accelerate convergence of permeation potential of mean force (PMF) calculations. The addition of cholesterol to the lipid bilayer is shown to increase both the width and height of the free energy barrier due to a condensing effect (lower area per lipid) and increase bilayer thickness. Additionally, the tICA CVs reveal a subtle effect of cholesterol increasing the resistance to permeation in the lipid head group region, which is not observed when canonical CVs are used. We conclude that the use of tICA CVs can enable more efficient PMF calculations with additional insight into the permeation mechanism.
Collapse
Affiliation(s)
- Fikret Aydin
- Quantum Simulation Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | | | - Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Myong In Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| |
Collapse
|
48
|
Wilson KA, Fairweather SJ, MacDermott-Opeskin HI, Wang L, Morris RA, O'Mara ML. The role of plasmalogens, Forssman lipids, and sphingolipid hydroxylation in modulating the biophysical properties of the epithelial plasma membrane. J Chem Phys 2021; 154:095101. [PMID: 33685172 DOI: 10.1063/5.0040887] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A coarse-grain model of the epithelial plasma membrane was developed from high-resolution lipidomic data and simulated using the MARTINI force field to characterize its biophysical properties. Plasmalogen lipids, Forssman glycosphingolipids, and hydroxylated Forssman glycosphingolipids and sphingomyelin were systematically added to determine their structural effects. Plasmalogen lipids have a minimal effect on the overall biophysical properties of the epithelial plasma membrane. In line with the hypothesized role of Forssman lipids in the epithelial apical membrane, the introduction of Forssman lipids initiates the formation of glycosphingolipid-rich nanoscale lipid domains, which also include phosphatidylethanolamine (PE), sphingomyelin (SM), and cholesterol (CHOL). This decreases the lateral diffusion in the extracellular leaflet, as well as the area per lipid of domain forming lipids, most notably PE. Finally, hydroxylation of the Forssman glycosphingolipids and sphingomyelin further modulates the lateral organization of the membrane. Through comparison to the previously studied average and neuronal plasma membranes, the impact of membrane lipid composition on membrane properties was characterized. Overall, this study furthers our understanding of the biophysical properties of complex membranes and the impact of lipid diversity in modulating membrane properties.
Collapse
Affiliation(s)
- Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Stephen J Fairweather
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Lily Wang
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Richard A Morris
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
49
|
Davoudi S, Ghysels A. Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility-diffusion model. J Chem Phys 2021; 154:054106. [PMID: 33557559 DOI: 10.1063/5.0033476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Permeability is a key property in various fields such as membrane technology for chemical separation and transport of substances through cell membranes. At the molecular scale, the counting method uses the number of membrane crossings in a conventional unbiased molecular dynamics simulation to predict the permeability. This contribution investigates under which conditions the counting method has insufficient statistics. An equation is derived for a compartmental model based on the inhomogeneous solubility-diffusion (Smoluchowski) model, giving insight into how the flux correlates with the solubility of permeants. This equation shows that a membrane crossing is a rare event not only when the membrane forms a large free energy barrier but also when the membrane forms a deep free energy well that traps permeants. Such a permeant trap has a high permeability; yet, the counting method suffers from poor statistics. To illustrate this, coarse-grained MD was run for 16 systems of dipalmitoylphosphatidylcholine bilayer membranes with different permeant types. The composition rule for permeability is shown to also hold for fluxes, and it is highlighted that the considered thickness of the membrane causes uncertainty in the permeability calculation of highly permeable membranes. In conclusion, a high permeability in itself is not an effective indicator of the sampling efficiency of the counting method, and caution should be taken for permeants whose solubility varies greatly over the simulation box. A practical consequence relevant in, e.g., drug design is that a drug with high membrane permeability might get trapped by membranes thus reducing its efficacy.
Collapse
Affiliation(s)
- Samaneh Davoudi
- IBiTech-BioMMeda Group, Ghent University, Corneel Heymanslaan 10, Block B-entrance 36, 9000 Gent, Belgium
| | - An Ghysels
- IBiTech-BioMMeda Group, Ghent University, Corneel Heymanslaan 10, Block B-entrance 36, 9000 Gent, Belgium
| |
Collapse
|
50
|
Oliveira MC, Yusupov M, Bogaerts A, Cordeiro RM. Lipid Oxidation: Role of Membrane Phase-Separated Domains. J Chem Inf Model 2021; 61:2857-2868. [PMID: 34080860 DOI: 10.1021/acs.jcim.1c00104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are "hot spots" for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.
Collapse
Affiliation(s)
- Maria C Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil.,Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil
| |
Collapse
|