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Schneck E, Reed J, Seki T, Nagata Y, Kanduč M. Experimental and simulation-based characterization of surfactant adsorption layers at fluid interfaces. Adv Colloid Interface Sci 2024; 331:103237. [PMID: 38959812 DOI: 10.1016/j.cis.2024.103237] [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: 11/07/2023] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024]
Abstract
Adsorption of surfactants to fluid interfaces occurs in numerous technological and daily-life contexts. The coverage at the interface and other properties of the formed adsorption layers determine the performance of a surfactant with regard to the desired application. Given the importance of these applications, there is a great demand for the comprehensive characterization and understanding of surfactant adsorption layers. In this review, we provide an overview of suitable experimental and simulation-based techniques and review the literature in which they were used for the investigation of surfactant adsorption layers. We come to the conclusion that, while these techniques have been successfully applied to investigate Langmuir monolayers of water-insoluble surfactants, their application to the study of Gibbs adsorption layers of water-soluble surfactants has not been fully exploited. Finally, we emphasize the great potential of these methods in providing a deeper understanding of the behavior of soluble surfactants at interfaces, which is crucial for optimizing their performance in various applications.
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Affiliation(s)
- Emanuel Schneck
- Department of Physics, Technische Universität Darmstadt, Hochschulstrasse 8, 64289 Darmstadt, Germany.
| | - Joshua Reed
- Department of Physics, Technische Universität Darmstadt, Hochschulstrasse 8, 64289 Darmstadt, Germany
| | - Takakazu Seki
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, 036-8561 Aomori, Japan
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Matej Kanduč
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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2
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Carrer M, Cezar HM, Bore SL, Ledum M, Cascella M. Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics. J Chem Inf Model 2024; 64:5510-5520. [PMID: 38963184 PMCID: PMC11267579 DOI: 10.1021/acs.jcim.4c00564] [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: 04/01/2024] [Revised: 05/15/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
We develop ∂-HylleraasMD (∂-HyMD), a fully end-to-end differentiable molecular dynamics software based on the Hamiltonian hybrid particle-field formalism, and use it to establish a protocol for automated optimization of force field parameters. ∂-HyMD is templated on the recently released HylleraaasMD software, while using the JAX autodiff framework as the main engine for the differentiable dynamics. ∂-HyMD exploits an embarrassingly parallel optimization algorithm by spawning independent simulations, whose trajectories are simultaneously processed by reverse mode automatic differentiation to calculate the gradient of the loss function, which is in turn used for iterative optimization of the force-field parameters. We show that parallel organization facilitates the convergence of the minimization procedure, avoiding the known memory and numerical stability issues of differentiable molecular dynamics approaches. We showcase the effectiveness of our implementation by producing a library of force field parameters for standard phospholipids, with either zwitterionic or anionic heads and with saturated or unsaturated tails. Compared to the all-atom reference, the force field obtained by ∂-HyMD yields better density profiles than the parameters derived from previously utilized gradient-free optimization procedures. Moreover, ∂-HyMD models can predict with good accuracy properties not included in the learning objective, such as lateral pressure profiles, and are transferable to other systems, including triglycerides.
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Affiliation(s)
- Manuel Carrer
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033, Blindern, 0315 Oslo, Norway
| | - Henrique Musseli Cezar
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033, Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033, Blindern, 0315 Oslo, Norway
| | - Morten Ledum
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033, Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033, Blindern, 0315 Oslo, Norway
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3
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Caselli L, Parra-Ortiz E, Micciulla S, Skoda MWA, Häffner SM, Nielsen EM, van der Plas MJA, Malmsten M. Boosting Membrane Interactions and Antimicrobial Effects of Photocatalytic Titanium Dioxide Nanoparticles by Peptide Coating. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309496. [PMID: 38402437 DOI: 10.1002/smll.202309496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/30/2024] [Indexed: 02/26/2024]
Abstract
Photocatalytic nanoparticles offer antimicrobial effects under illumination due to the formation of reactive oxygen species (ROS), capable of degrading bacterial membranes. ROS may, however, also degrade human cell membranes and trigger toxicity. Since antimicrobial peptides (AMPs) may display excellent selectivity between human cells and bacteria, these may offer opportunities to effectively "target" nanoparticles to bacterial membranes for increased selectivity. Investigating this, photocatalytic TiO2 nanoparticles (NPs) are coated with the AMP LL-37, and ROS generation is found by C11-BODIPY to be essentially unaffected after AMP coating. Furthermore, peptide-coated TiO2 NPs retain their positive ζ-potential also after 1-2 h of UV illumination, showing peptide degradation to be sufficiently limited to allow peptide-mediated targeting. In line with this, quartz crystal microbalance measurements show peptide coating to promote membrane binding of TiO2 NPs, particularly so for bacteria-like anionic and cholesterol-void membranes. As a result, membrane degradation during illumination is strongly promoted for such membranes, but not so for mammalian-like membranes. The mechanisms of these effects are elucidated by neutron reflectometry. Analogously, LL-37 coating promoted membrane rupture by TiO2 NPs for Gram-negative and Gram-positive bacteria, but not for human monocytes. These findings demonstrate that AMP coating may selectively boost the antimicrobial effects of photocatalytic NPs.
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Affiliation(s)
- Lucrezia Caselli
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Department of Physical Chemistry 1, Lund University, Lund, SE-22100, Sweden
| | - Elisa Parra-Ortiz
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Novonesis, Biologiens Vej 2, Lyngby, DK-2800 Kgs, Denmark
| | - Samantha Micciulla
- Institut Laue-Langevin, CS 20156, Grenoble Cedex 9, 38042, France
- Laboratoire Interdisciplinaire de Physique (LIPhy), Saint Martin d'Hères, 38402, France
- Centre National de la Recherche Scientifique (CNRS), Saint-Martin-d'Hères, Auvergne-Rhône-Alpes, France
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell, OX11 0QX, UK
| | - Sara Malekkhaiat Häffner
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- RISE Research Institutes of Sweden, Malvinas väg 3, Stockholm, 114 86, Sweden
| | | | | | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Department of Physical Chemistry 1, Lund University, Lund, SE-22100, Sweden
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4
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Shnaikat SG, Shakya AK, Bardaweel SK. Formulation, development and evaluation of hyaluronic acid-conjugated liposomal nanoparticles loaded with regorafenib and curcumin and their in vitro evaluation on colorectal cancer cell lines. Saudi Pharm J 2024; 32:102099. [PMID: 38817822 PMCID: PMC11135027 DOI: 10.1016/j.jsps.2024.102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024] Open
Abstract
Colorectal cancer is one of the major causes of global cancer, with chemotherapy and radiation therapy being effective but limited due to low specificity. Regorafenib, a multikinase inhibitor, provides hope to patients with metastatic colorectal cancer and was approved by the FDA in 2012. However, due to resistance issues and adverse events, its efficacy is compromised, necessitating further refinement. Meanwhile, curcumin, a compound of turmeric, exhibits anticancer effects through antioxidant and anti-inflammatory actions, induction of the apoptosis, arrest of cell cycle, inhibition of angiogenesis, and modulation of signaling pathways. Unfortunately, its clinical utility is limited by its poor bioavailability, pointing towards innovative drug delivery strategies for enhanced efficacy in colorectal cancer treatment. Hyaluronic acid (HA)-decorated liposomes (LIPO) have been developed to target colorectal cells through an overexpressed CD44 receptor, increasing antitumor and antimetastasis efficacy. This study investigates the possibility of loading curcumin (CUR) or regorafenib (REGO) into a liposomal formulation for passive and HA-actively targeted treatment, evaluating its critical quality attributes (CQA) (size, zeta potential, polydispersity index) and cytotoxic activity in the HT29 colorectal cancer cell line. The average particle size of the plain liposomes and those decorated with HA was 144.00 ± 0.78 nm and 140.77 ± 1.64 nm, respectively. In contrast, curcumin-loaded plain liposomes and HA-decorated liposomes had 140 ± 2.46 nm and 164.53 ± 15.13 nm, respectively. The prepared liposomes had a spherical shape with a narrow size distribution and an acceptable zeta potential of less than -30 mV. The encapsulation efficiency was 99.2 % ± 0.3 and 99.9 ± 0.2 % for HA-decorated and bare regorafenib loaded. The % EE was 98.9 ± 0.2 % and 97.5 ± 0.2 % for bare liposomal nanoparticles loaded with curcumin and coated with curcumin. The IC50 of free REGO, CUR, REGO-LIPO, CUR-LIPO, REGO-LIPO-HA and CUR-LIPO-HA were 20.17 ± 0.78, 64.4 ± 0.33, 224.8 ± 0.06, 49.66 ± 0.22, 73.66 ± 0.6, and 27.86 ± 0.49 µM, respectively. The MTT assay in HT29 cells showed significant cytotoxic activity of the HA-decorated liposomal formulation compared to the base uncoated formulation, indicating that hyaluronic acid-targeted liposomes loaded with regorafenib or curcumin could be a promising targeted formulation against colorectal cancer cells.
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Affiliation(s)
| | - Ashok K. Shakya
- Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
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Caselli L, Köhler S, Schirone D, Humphreys B, Malmsten M. Conformational control of antimicrobial peptide amphiphilicity: consequences for boosting membrane interactions and antimicrobial effects of photocatalytic TiO 2 nanoparticles. Phys Chem Chem Phys 2024; 26:16529-16539. [PMID: 38828872 DOI: 10.1039/d4cp01724b] [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: 06/05/2024]
Abstract
This study reports on the effects of conformationally controlled amphiphilicity of antimicrobial peptides (AMPs) on their ability to coat TiO2 nanoparticles (NPs) and boost the photocatalytic antimicrobial effects of such NPs. For this, TiO2 NPs were combined with AMP EFK17 (EFKRIVQRIKDFLRNLV), displaying a disordered conformation in aqueous solution but helix formation on interaction with bacterial membranes. The membrane-bound helix is amphiphilic, with all polar and charged amino acid residues located at one side and all non-polar and hydrophobic residues on the other. In contrast, the d-enantiomer variant EFK17-d (E(dF)KR(dI)VQR(dI)KD(dF)LRNLV) is unable to form the amphiphilic helix on bacterial membrane interaction, whereas the W-residues in EFK17-W (EWKRWVQRWKDFLRNLV) boost hydrophobic interactions of the amphiphilic helix. Circular dichroism results showed the effects displayed for the free peptide, to also be present for peptide-coated TiO2 NPs, causing peptide binding to decrease in the order EFK17-W > EFK17 > EFK17-d. Notably, the formation of reactive oxygen species (ROS) by the TiO2 NPs was essentially unaffected by the presence of peptide coating, for all the peptides investigated, and the coatings stabilized over hours of UV exposure. Photocatalytic membrane degradation from TiO2 NPs coated with EFK17-W and EFK17 was promoted for bacteria-like model bilayers containing anionic phosphatidylglycerol but suppressed in mammalian-like bilayers formed by zwitterionic phosphatidylcholine and cholesterol. Structural aspects of these effects were further investigated by neutron reflectometry with clear variations observed between the bacteria- and mammalian-like model bilayers for the three peptides. Mirroring these results in bacteria-like model membranes, combining TiO2 NPs with EFK17-W and EFK17, but not with non-adsorbing EFK17-d, resulted in boosted antimicrobial effects of the resulting cationic composite NPs already in darkness, effects enhanced further on UV illumination.
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Affiliation(s)
- Lucrezia Caselli
- Department of Physical Chemistry 1, Lund University, SE-22100 Lund, Sweden.
| | - Sebastian Köhler
- LINXS Institute of Advanced Neutron and X-ray Science, Scheelevagen 19, 22370 Lund, Sweden
| | - Davide Schirone
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Ben Humphreys
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - Martin Malmsten
- Department of Physical Chemistry 1, Lund University, SE-22100 Lund, Sweden.
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
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Ookubo M, Tashiro Y, Asano K, Kamei Y, Tanaka Y, Honda T, Yokoyama T, Honda M. "Rich arginine and strong positive charge" antimicrobial protein protamine: From its action on cell membranes to inhibition of bacterial vital functions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184323. [PMID: 38614236 DOI: 10.1016/j.bbamem.2024.184323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/15/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
Protamine, an antimicrobial protein derived from salmon sperm with a molecular weight of approximately 5 kDa, is composed of 60-70 % arginine and is a highly charged protein. Here, we investigated the mechanism of antimicrobial action of protamine against Cutibacterium acnes (C. acnes) focusing on its rich arginine content and strong positive charge. Especially, we focused on the attribution of dual mechanisms of antimicrobial protein, including membrane disruption or interaction with intracellular components. We first determined the dose-dependent antibacterial activity of protamine against C. acnes. In order to explore the interaction between bacterial membrane and protamine, we analyzed cell morphology, zeta potential, membrane permeability, and the composition of membrane fatty acid. In addition, the localization of protamine in bacteria was observed using fluorescent-labeled protamine. For investigation of the intracellular targets of protamine, bacterial translation was examined using a cell-free translation system. Based on our results, the mechanism of the antimicrobial action of protamine against C. acnes is as follows: 1) electrostatic interactions with the bacterial cell membrane; 2) self-internalization into the bacterial cell by changing the composition of the bacterial membrane; and 3) inhibition of bacterial growth by blocking translation inside the bacteria. However, owing to its strong electric charge, protamine can also interact with DNA, RNA, and other proteins inside the bacteria, and may inhibit various bacterial life processes beyond the translation process.
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Affiliation(s)
- Momoka Ookubo
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Yuka Tashiro
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Kosuke Asano
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Yoshiharu Kamei
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan; The advanced center for innovations in next-generation medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Takayuki Honda
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan; The advanced center for innovations in next-generation medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Michiyo Honda
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan.
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Caselli L, Conti L, De Santis I, Berti D. Small-angle X-ray and neutron scattering applied to lipid-based nanoparticles: Recent advancements across different length scales. Adv Colloid Interface Sci 2024; 327:103156. [PMID: 38643519 DOI: 10.1016/j.cis.2024.103156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
Lipid-based nanoparticles (LNPs), ranging from nanovesicles to non-lamellar assemblies, have gained significant attention in recent years, as versatile carriers for delivering drugs, vaccines, and nutrients. Small-angle scattering methods, employing X-rays (SAXS) or neutrons (SANS), represent unique tools to unveil structure, dynamics, and interactions of such particles on different length scales, spanning from the nano to the molecular scale. This review explores the state-of-the-art on scattering methods applied to unveil the structure of lipid-based nanoparticles and their interactions with drugs and bioactive molecules, to inform their rational design and formulation for medical applications. We will focus on complementary information accessible with X-rays or neutrons, ranging from insights on the structure and colloidal processes at a nanoscale level (SAXS) to details on the lipid organization and molecular interactions of LNPs (SANS). In addition, we will review new opportunities offered by Time-resolved (TR)-SAXS and -SANS for the investigation of dynamic processes involving LNPs. These span from real-time monitoring of LNPs structural evolution in response to endogenous or external stimuli (TR-SANS), to the investigation of the kinetics of lipid diffusion and exchange upon interaction with biomolecules (TR-SANS). Finally, we will spotlight novel combinations of SAXS and SANS with complementary on-line techniques, recently enabled at Large Scale Facilities for X-rays and neutrons. This emerging technology enables synchronized multi-method investigation, offering exciting opportunities for the simultaneous characterization of the structure and chemical or mechanical properties of LNPs.
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Affiliation(s)
- Lucrezia Caselli
- Physical Chemistry 1, University of Lund, S-221 00 Lund, Sweden.
| | - Laura Conti
- Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ilaria De Santis
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Debora Berti
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy; Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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8
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Královič-Kanjaková N, Asi Shirazi A, Hubčík L, Klacsová M, Keshavarzi A, Martínez JC, Combet S, Teixeira J, Uhríková D. Polymyxin B-Enriched Exogenous Lung Surfactant: Thermodynamics and Structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6847-6861. [PMID: 38501650 DOI: 10.1021/acs.langmuir.3c03746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The use of an exogenous pulmonary surfactant (EPS) to deliver other relevant drugs to the lungs is a promising strategy for combined therapy. We evaluated the interaction of polymyxin B (PxB) with a clinically used EPS, the poractant alfa Curosurf (PSUR). The effect of PxB on the protein-free model system (MS) composed of four phospholipids (diC16:0PC/16:0-18:1PC/16:0-18:2PC/16:0-18:1PG) was examined in parallel to distinguish the specificity of the composition of PSUR. We used several experimental techniques (differential scanning calorimetry, small- and wide-angle X-ray scattering, small-angle neutron scattering, fluorescence spectroscopy, and electrophoretic light scattering) to characterize the binding of PxB to both EPS. Electrostatic interactions PxB-EPS are dominant. The results obtained support the concept of cationic PxB molecules lying on the surface of the PSUR bilayer, strengthening the multilamellar structure of PSUR as derived from SAXS and SANS. A protein-free MS mimics a natural EPS well but was found to be less resistant to penetration of PxB into the lipid bilayer. PxB does not affect the gel-to-fluid phase transition temperature, Tm, of PSUR, while Tm increased by ∼+ 2 °C in MS. The decrease of the thickness of the lipid bilayer (dL) of PSUR upon PxB binding is negligible. The hydrophobic tail of the PxB molecule does not penetrate the bilayer as derived from SANS data analysis and changes in lateral pressure monitored by excimer fluorescence at two depths of the hydrophobic region of the bilayer. Changes in dL of protein-free MS show a biphasic dependence on the adsorbed amount of PxB with a minimum close to the point of electroneutrality of the mixture. Our results do not discourage the concept of a combined treatment with PxB-enriched Curosurf. However, the amount of PxB must be carefully assessed (less than 5 wt % relative to the mass of the surfactant) to avoid inversion of the surface charge of the membrane.
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Affiliation(s)
- Nina Královič-Kanjaková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia
| | - Ali Asi Shirazi
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia
| | - Lukáš Hubčík
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia
| | - Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia
| | - Atoosa Keshavarzi
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia
| | | | - Sophie Combet
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - José Teixeira
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette CEDEX, France
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia
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9
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Kiirikki AM, Antila HS, Bort LS, Buslaev P, Favela-Rosales F, Ferreira TM, Fuchs PFJ, Garcia-Fandino R, Gushchin I, Kav B, Kučerka N, Kula P, Kurki M, Kuzmin A, Lalitha A, Lolicato F, Madsen JJ, Miettinen MS, Mingham C, Monticelli L, Nencini R, Nesterenko AM, Piggot TJ, Piñeiro Á, Reuter N, Samantray S, Suárez-Lestón F, Talandashti R, Ollila OHS. Overlay databank unlocks data-driven analyses of biomolecules for all. Nat Commun 2024; 15:1136. [PMID: 38326316 PMCID: PMC10850068 DOI: 10.1038/s41467-024-45189-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.
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Affiliation(s)
- Anne M Kiirikki
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | - Hanne S Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Lara S Bort
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam-Golm, Germany
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, 99102, Zacatecas, Mexico
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Patrick F J Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), F-75005, Paris, France
- Université Paris Cité, F-75006, Paris, France
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | | | - Batuhan Kav
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
- ariadne.ai GmbH (Germany), Häusserstraße 3, 69115, Heidelberg, Germany
| | - Norbert Kučerka
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32, Bratislava, Slovakia
| | - Patrik Kula
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610, Prague, Czech Republic
| | - Milla Kurki
- School of Pharmacy, University of Eastern Finland, 70211, Kuopio, Finland
| | | | - Anusha Lalitha
- Institut Charles Gerhardt Montpellier (UMR CNRS 5253), Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, Cedex 05, France
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
| | - Jesper J Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 33612, Tampa, FL, USA
- Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, 33612, Tampa, FL, USA
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Cedric Mingham
- Hochschule Mannheim, University of Applied Sciences, 68163, Mannheim, Germany
| | - Luca Monticelli
- University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Lyon, France
| | - Ricky Nencini
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Alexey M Nesterenko
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
| | - Ángel Piñeiro
- Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Suman Samantray
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Fabián Suárez-Lestón
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
- Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
- MD.USE Innovations S.L., Edificio Emprendia, 15782, Santiago de Compostela, Spain
| | - Reza Talandashti
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - O H Samuli Ollila
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
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10
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Tian H, Chang M, Lyu Y, Dong N, Yu N, Yin T, Zhang Y, He H, Gou J, Tang X. Intramuscular injection of palmitic acid-conjugated Exendin-4 loaded multivesicular liposomes for long-acting and improving in-situ stability. Expert Opin Drug Deliv 2024; 21:169-185. [PMID: 38224039 DOI: 10.1080/17425247.2024.2305110] [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: 05/10/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
BACKGROUND Exendin-4 (Ex4) is a promising drug for diabetes mellitus with a half-life of 2.4 h in human bodies. Besides, the Ex4 formulations currently employed in the clinic or under development have problems pertaining to stability. In this study, palmitic acid-modified Ex4 (Pal-Ex4) was prepared and purified to extend the half-life of Ex4. In addition, Pal-Ex4-MVLs were further designed and optimized as a long-acting delivery system for intramuscular injection. METHODS Pal-Ex4 was encapsulated within multivesicular liposomes (MVLs) via a two-step double emulsification process. The formulated products were then assessed for their vesicle size, encapsulation efficiency, and in vitro and in vivo. RESULTS Pal-Ex4-MVLs with a notable encapsulation efficiency of 99.18% were successfully prepared. Pal-Ex4-MVLs, administered via a single intramuscular injection in Sprague-Dawley rats, sustained stable plasma concentrations for 168 h, presenting extended half-life (77.28 ± 12.919 h) and enhanced relative bioavailability (664.18%). MVLs protected Ex4 through providing stable retention and slow release. This approach considerably improved the in-situ stability of the drug for intramuscular administration. CONCLUSIONS The combination of palmitic acid modification process with MVLs provides dual protection for Ex4 and can be a promising strategy for other hydrophilic protein/polypeptide-loaded sustained-release delivery systems with high drug bioactivity.
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Affiliation(s)
- Huixian Tian
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Minsi Chang
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Yanlin Lyu
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Nan Dong
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Nini Yu
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Tian Yin
- School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Yu Zhang
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Haibing He
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Jingxin Gou
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
| | - Xing Tang
- Department of Pharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, PR China
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11
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Diedrichsen RG, Vetri V, Prévost S, Foderà V, Nielsen HM. Carrier peptide interactions with liposome membranes induce reversible clustering by surface adsorption and shape deformation. J Colloid Interface Sci 2023; 650:1821-1832. [PMID: 37515972 DOI: 10.1016/j.jcis.2023.07.078] [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: 02/06/2023] [Revised: 06/27/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023]
Abstract
The cell-penetrating peptide penetratin and its analogues shuffle and penetramax have been used as carrier peptides for oral delivery of therapeutic peptides such as insulin. Their mechanism of action for this purpose is not fully understood but is believed to depend on the interactions of the peptide with the cell membrane. In the present study, peptide-liposome interactions were investigated using advanced biophysical techniques including small-angle neutron scattering and fluorescence lifetime imaging microscopy. Liposomes were used as a model system for the cell membrane. All the investigated carrier peptides induced liposome clustering at a specific peptide/lipid ratio. However, distinctively different types of membrane interactions were observed, as the liposome clustering was irreversible for penetratin, but fully or partly reversible for shuffle and penetramax, respectively. All three peptides were found to adsorb to the surface of the lipid bilayers, while only shuffle and penetramax led to shape deformation of the liposomes. Importantly, the peptide interactions did not disrupt the liposomes under any of the investigated conditions, which is advantageous for their application in drug delivery. This detailed insight on peptide-membrane interactions is important for understanding the mechanism of peptide-based excipients and the influence of peptide sequence modifications.
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Affiliation(s)
- Ragna Guldsmed Diedrichsen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Valeria Vetri
- Department of Physics and Chemistry, University of Palermo, Viale delle Scienze Ed. 18, 90128 Palermo, Italy.
| | - Sylvain Prévost
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France.
| | - Vito Foderà
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Hanne Mørck Nielsen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
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12
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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [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: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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13
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Tretiakova D, Kobanenko M, Alekseeva A, Boldyrev I, Khaidukov S, Zgoda V, Tikhonova O, Vodovozova E, Onishchenko N. Protein Corona of Anionic Fluid-Phase Liposomes Compromises Their Integrity Rather than Uptake by Cells. MEMBRANES 2023; 13:681. [PMID: 37505047 PMCID: PMC10384875 DOI: 10.3390/membranes13070681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/09/2023] [Indexed: 07/29/2023]
Abstract
Despite the undisputable role of the protein corona in the biointeractions of liposome drug carriers, the field suffers from a lack of knowledge regarding the patterns of protein deposition on lipid surfaces with different compositions. Here, we investigated the protein coronas formed on liposomes of basic compositions containing combinations of egg phosphatidylcholine (PC), palmitoyloleoyl phosphatidylglycerol (POPG), and cholesterol. Liposome-protein complexes isolated by size-exclusion chromatography were delipidated and analyzed using label-free LC-MS/MS. The addition of the anionic lipid and cholesterol both affected the relative protein abundances (and not the total bound proteins) in the coronas. Highly anionic liposomes, namely those containing 40% POPG, carried corona enriched with cationic proteins (apolipoprotein C1, beta-2-glycoprotein 1, and cathelicidins) and were the least stable in the calcein release assay. Cholesterol improved the liposome stability in the plasma. However, the differences in the corona compositions had little effect on the liposome uptake by endothelial (EA.hy926) and phagocytic cells in the culture (U937) or ex vivo (blood-derived monocytes and neutrophils). The findings emphasize that the effect of protein corona on the performance of the liposomes as drug carriers occurs through compromising particle stability rather than interfering with cellular uptake.
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Affiliation(s)
- Daria Tretiakova
- Laboratory of Lipid Chemistry, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Maria Kobanenko
- Laboratory of Lipid Chemistry, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anna Alekseeva
- Laboratory of Lipid Chemistry, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ivan Boldyrev
- Laboratory of Lipid Chemistry, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Sergey Khaidukov
- Laboratory of Carbohydrates, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Viktor Zgoda
- Institute of Biomedical Chemistry, ul. Pogodinskaya 10, 119121 Moscow, Russia
| | - Olga Tikhonova
- Institute of Biomedical Chemistry, ul. Pogodinskaya 10, 119121 Moscow, Russia
| | - Elena Vodovozova
- Laboratory of Lipid Chemistry, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Natalia Onishchenko
- Laboratory of Lipid Chemistry, Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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14
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Xu B, Li J, Zhang S, Zeb J, Chen S, Yuan Q, Gan W. The Transport of Charged Molecules across Three Lipid Membranes Investigated with Second Harmonic Generation. Molecules 2023; 28:molecules28114330. [PMID: 37298807 DOI: 10.3390/molecules28114330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Subtle variations in the structure and composition of lipid membranes can have a profound impact on their transport of functional molecules and relevant cell functions. Here, we present a comparison of the permeability of bilayers composed of three lipids: cardiolipin, DOPG (1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol), and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)). The adsorption and cross-membrane transport of a charged molecule, D289 (4-(4-diethylaminostyry)-1-methyl-pyridinium iodide), on vesicles composed of the three lipids were monitored by second harmonic generation (SHG) scattering from the vesicle surface. It is revealed that structural mismatching between the saturated and unsaturated alkane chains in POPG leads to relatively loose packing structure in the lipid bilayers, thus providing better permeability compared to unsaturated lipid bilayers (DOPG). This mismatching also weakens the efficiency of cholesterol in rigidifying the lipid bilayers. It is also revealed that the bilayer structure is somewhat disturbed by the surface curvature in small unilamellar vesicles (SUVs) composed of POPG and the conical structured cardiolipin. Such subtle information on the relationship between the lipid structure and the molecular transport capability of the bilayers may provide clues for drug development and other medical and biological studies.
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Affiliation(s)
- Baomei Xu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jianhui Li
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Shuai Zhang
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Johar Zeb
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Shunli Chen
- Key Laboratory for Preparation and Application of Ordered Structure Materials of Guangdong Province, College of Chemistry and Chemical Engineering, Shantou University, Shantou 515063, China
| | - Qunhui Yuan
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, China
| | - Wei Gan
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
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15
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Conceição CJF, Moe E, Ribeiro PA, Raposo M. Liposome Formulations for the Strategic Delivery of PARP1 Inhibitors: Development and Optimization. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13101613. [PMID: 37242030 DOI: 10.3390/nano13101613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
The development of a lipid nano-delivery system was attempted for three specific poly (ADP-ribose) polymerase 1 (PARP1) inhibitors: Veliparib, Rucaparib, and Niraparib. Simple lipid and dual lipid formulations with 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1'-glycerol) sodium salt (DPPG) and 1,2-dipalmitoyl-sn-glycero-3-phosphocoline (DPPC) were developed and tested following the thin-film method. DPPG-encapsulating inhibitors presented the best fit in terms of encapsulation efficiency (>40%, translates into concentrations as high as 100 µM), zeta potential values (below -30 mV), and population distribution (single population profile). The particle size of the main population of interest was ~130 nm in diameter. Kinetic release studies showed that DPPG-encapsulating PARP1 inhibitors present slower drug release rates than liposome control samples, and complex drug release mechanisms were identified. DPPG + Veliparib/Niraparib presented a combination of diffusion-controlled and non-Fickian diffusion, while anomalous and super case II transport was verified for DPPG + Rucaparib. Spectroscopic analysis revealed that PARP1 inhibitors interact with the DPPG lipid membrane, promoting membrane water displacement from hydration centers. A preferential membrane interaction with lipid carbonyl groups was observed through hydrogen bonding, where the inhibitors' protonated amine groups may be the major players in the PARP1 inhibitor encapsulation mode.
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Affiliation(s)
- Carlota J F Conceição
- CEFITEC, Department of Physics, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Laboratory of Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Elin Moe
- Institute of Chemical and Biological Technology (ITQB NOVA), The New University of Lisbon, 2780-157 Oeiras, Portugal
- Department of Chemistry, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Paulo A Ribeiro
- Laboratory of Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Maria Raposo
- Laboratory of Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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16
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White SH. Fifty Years of Biophysics at the Membrane Frontier. Annu Rev Biophys 2023; 52:21-67. [PMID: 36791747 DOI: 10.1146/annurev-biophys-051622-112341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The author first describes his childhood in the South and the ways in which it fostered the values he has espoused throughout his life, his development of a keen fascination with science, and the influences that supported his progress toward higher education. His experiences in ROTC as a student, followed by two years in the US Army during the Vietnam War, honed his leadership skills. The bulk of the autobiography is a chronological journey through his scientific career, beginning with arrival at the University of California, Irvine in 1972, with an emphasis on the postdoctoral students and colleagues who have contributed substantially to each phase of his lab's progress. White's fundamental findings played a key role in the development of membrane biophysics, helping establish it as fertile ground for research. A story gradually unfolds that reveals the deeply collaborative and painstakingly executed work necessary for a successful career in science.
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Affiliation(s)
- Stephen H White
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California, USA;
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17
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He J, Zhang H, Liu Y, Ju Y, He Y, Jiang Y, Jiang J. Interfacial Extraction to Trap and Characterize the Criegee Intermediates from Phospholipid Ozonolysis. Anal Chem 2023; 95:5018-5023. [PMID: 36840931 DOI: 10.1021/acs.analchem.2c05472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Criegee intermediates (CIs) play a significant role in cell membrane peroxidation, but their identification remains elusive at the molecular level. Herein, we combined interfacial extraction and sonic spray ionization mass spectrometry to study the oxidation reaction of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) mediated by ozone (O3) at/near the surface of a hung water droplet. On-line interfacial extraction and ionization provided a snapshot of the short-lived CIs. Experiments in which the content of water was varied provided evidence for the formation of CIs, which has not been previously observed. Capture experiments using 5,5-dimethyl-pyrroline N-oxide (DMPO) indicated that CIs could be selectively characterized, and the extracted ion current (EICs) of CIs vs DMPO-CI adducts further confirmed the successful observation of CIs. Theoretical calculation suggested that surface ozonolysis of POPG was mainly mediated by anti-CI. These results open a new route for aqueous surface reactive species identification, and benefit toward the understanding of disease development associated with cell oxidative stress mediated by CIs.
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Affiliation(s)
- Jing He
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
| | - Yaqi Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
| | - Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
| | - Yuwei He
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, Shandong, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150090, Heilongjiang, China
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18
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Lanrezac A, Baaden M. UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. MEMBRANES 2023; 13:362. [PMID: 36984749 PMCID: PMC10054542 DOI: 10.3390/membranes13030362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
The insertion of proteins into membranes is crucial for understanding their function in many biological processes. In this work, we present UNILIPID, a universal implicit lipid-protein description as a methodology for dealing with implicit membranes. UNILIPID is independent of the scale of representation and can be applied at the level of all atoms, coarse-grained particles down to the level of a single bead per amino acid. We provide example implementations for these scales and demonstrate the versatility of our approach by accurately reflecting the free energy of transfer for each amino acid. In addition to single membranes, we describe the analytical implementation of double membranes and show that UNILIPID is well suited for modeling at multiple scales. We generalize to membranes of arbitrary shape. With UNILIPID, we provide a methodological framework for a simple and general parameterization tuned to reproduce a selected reference hydrophobicity scale. The software we provide along with the methodological description is optimized for specific user features such as real-time response, live visual analysis, and virtual reality experiences.
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19
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Bjørnestad VA, Soto-Bustamante F, Tria G, Laurati M, Lund R. Beyond the standard model of solubilization: Non-ionic surfactants induce collapse of lipid vesicles into rippled bilamellar nanodiscs. J Colloid Interface Sci 2023; 641:553-567. [PMID: 36958276 DOI: 10.1016/j.jcis.2023.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/21/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
HYPOTHESIS Although solubilization of lipid membranes has been studied extensively, questions remain regarding the structural pathways and metastable structures involved. This study investigated whether the non-ionic detergent Triton X-100 follows the classical solubilization pathway or if intermediate nanostructures are formed. EXPERIMENTS Small angle X-ray and neutron scattering (SAXS/SANS) was used in combination with transmission electron cryo-microscopy and cryo-tomography to deduce the structure of mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles and Triton X-100. Time-resolved SAXS and dynamic light scattering were used to investigate the kinetics of the process. FINDINGS Upon addition of moderate detergent amounts at low temperatures, the lipid vesicles implode into ordered rippled bilamellar disc structures. The bilayers arrange in a ripple phase to accommodate packing constraints caused by inserted TX-100 molecules. The collapse is suggested to occur through a combination of water structure destabilization by detergents flipping across the membrane and osmotic pressure causing interbilayer attraction internally. The subsequently induced ripples then stabilize the aggregates and prevent solubilization, supported by the observation that negatively charged vesicles undergo a different pathway upon TX-100 addition, forming large bicelles. The findings demonstrate the richness in assembly pathways of simple lipids and detergents and stimulate considerations for the use of certain detergents in membrane solubilization.
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Affiliation(s)
| | | | - Giancarlo Tria
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Italy
| | - Marco Laurati
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Italy
| | - Reidar Lund
- Department of Chemistry, University of Oslo, Sem Sælandsvei 26, 0371 Oslo, Norway.
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20
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Ayscough SE, Clifton LA, Skoda MWA, Titmuss S. Suspended phospholipid bilayers: A new biological membrane mimetic. J Colloid Interface Sci 2023; 633:1002-1011. [PMID: 36516676 DOI: 10.1016/j.jcis.2022.11.148] [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: 08/15/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
HYPOTHESIS The attractive interaction between a cationic surfactant monolayer at the air-water interface and vesicles, incorporating anionic lipids, is sufficient to drive the adsorption and deformation of the vesicles. Osmotic rupture of the vesicles produces a continuous lipid bilayer beneath the monolayer. EXPERIMENTAL Specular neutron reflectivity has been measured from the surface of a purpose-built laminar flow trough, which allows for rapid adsorption of vesicles, the changes in salt concentration required for osmotic rupture of the adsorbed vesicles into a bilayer, and for neutron contrast variation of the sub-phase without disturbing the monolayer. FINDINGS The neutron reflectivity profiles measured after vesicle addition are consistent with the adsorption and flattening of the vesicles beneath the monolayer. An increase in the buffer salt concentration results in further flattening and fusion of the adsorbed vesicles, which are ruptured by a subsequent decrease in the salt concentration. This process results in a continuous, high coverage, bilayer suspended 11 Åbeneath the monolayer. As the bilayer is not constrained by a solid substrate, this new mimetic is well-suited to studying the structure of lipid bilayers that include transmembrane proteins.
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Affiliation(s)
- Sophie E Ayscough
- School of Physics & Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Luke A Clifton
- ISIS Neutron & Muon Source, Rutherford Appleton Laboratory, Harwell, Oxford OX11 0XX, UK
| | - Maximilian W A Skoda
- ISIS Neutron & Muon Source, Rutherford Appleton Laboratory, Harwell, Oxford OX11 0XX, UK
| | - Simon Titmuss
- School of Physics & Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
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21
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Moloney C, Roy Chaudhuri T, Spernyak JA, Straubinger RM, Brougham DF. Long-circulating magnetoliposomes as surrogates for assessing pancreatic tumour permeability and nanoparticle deposition. Acta Biomater 2023; 158:611-624. [PMID: 36603732 PMCID: PMC10022638 DOI: 10.1016/j.actbio.2022.12.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/29/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023]
Abstract
Nanocarriers are candidates for cancer chemotherapy delivery, with growing numbers of clinically-approved nano-liposomal formulations such as Doxil® and Onivyde® (liposomal doxorubicin and irinotecan) providing proof-of-concept. However, their complex biodistribution and the varying susceptibility of individual patient tumours to nanoparticle deposition remains a clinical challenge. Here we describe the preparation, characterisation, and biological evaluation of phospholipidic structures containing solid magnetic cores (SMLs) as an MRI-trackable surrogate that could aid in the clinical development and deployment of nano-liposomal formulations. Through the sequential assembly of size-defined iron oxide nanoparticle clusters with a stabilizing anionic phospholipid inner monolayer and an outer monolayer of independently-selectable composition, SMLs can mimic physiologically a wide range of nano-liposomal carrier compositions. In patient-derived xenograft models of pancreatic adenocarcinoma, similar tumour deposition of SML and their nano-liposomal counterparts of identical bilayer composition was observed in vivo, both at the tissue level (fluorescence intensities of 1.5 × 108 ± 1.8 × 107 and 1.2 × 108 ± 6.3 × 107, respectively; ns, 99% confidence interval) and non-invasively using MR imaging. We observed superior capabilities of SML as a surrogate for nano-liposomal formulations as compared to other clinically-approved iron oxide nano-formulations (ferumoxytol). In combination with diagnostic and therapeutic imaging tools, SMLs have high clinical translational potential to predict nano-liposomal drug carrier deposition and could assist in stratifying patients into treatment regimens that promote optimal tumour deposition of nanoparticulate chemotherapy carriers. STATEMENT OF SIGNIFICANCE: Solid magnetoliposomes (SMLs) with compositions resembling that of FDA-approved agents such as Doxil® and Onivyde® offer potential application as non-invasive MRI stratification agents to assess extent of tumour deposition of nano-liposomal therapeutics prior to administration. In animals with pancreatic adenocarcinoma (PDAC), SML-PEG exhibited (i) tumour deposition comparable to liposomes of the same composition; (ii) extended circulation times, with continued tumour deposition up to 24 hours post-injection; and (iii) MRI capabilities to determine tumour deposition up to 1 week post-injection, and confirmation of patient-to-patient variation in nanoparticulate deposition in tumours. Hence SMLs with controlled formulation are a step towards non-invasive MRI stratification approaches for patients, enabled by evaluation of the extent of deposition in tumours prior to administration of nano-liposomal therapeutics.
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Affiliation(s)
- Cara Moloney
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Tista Roy Chaudhuri
- Dept. of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Joseph A Spernyak
- Department of Cell Stress Biology Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Robert M Straubinger
- Dept. of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA; Department of Cell Stress Biology Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Dermot F Brougham
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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22
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Effects of a Semisynthetic Catechin on Phosphatidylglycerol Membranes: A Mixed Experimental and Simulation Study. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010422. [PMID: 36615630 PMCID: PMC9824143 DOI: 10.3390/molecules28010422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023]
Abstract
Catechins have been shown to display a great variety of biological activities, prominent among them are their chemo preventive and chemotherapeutic properties against several types of cancer. The amphiphilic nature of catechins points to the membrane as a potential target for their actions. 3,4,5-Trimethoxybenzoate of catechin (TMBC) is a modified structural analog of catechin that shows significant antiproliferative activity against melanoma and breast cancer cells. Phosphatidylglycerol is an anionic membrane phospholipid with important physical and biochemical characteristics that make it biologically relevant. In addition, phosphatidylglycerol is a preeminent component of bacterial membranes. Using biomimetic membranes, we examined the effects of TMBC on the structural and dynamic properties of phosphatidylglycerol bilayers by means of biophysical techniques such as differential scanning calorimetry, X-ray diffraction and infrared spectroscopy, together with an analysis through molecular dynamics simulation. We found that TMBC perturbs the thermotropic gel to liquid-crystalline phase transition and promotes immiscibility in both phospholipid phases. The modified catechin decreases the thickness of the bilayer and is able to form hydrogen bonds with the carbonyl groups of the phospholipid. Experimental data support the simulated data that locate TMBC as mostly forming clusters in the middle region of each monolayer approaching the carbonyl moiety of the phospholipid. The presence of TMBC modifies the structural and dynamic properties of the phosphatidylglycerol bilayer. The decrease in membrane thickness and the change of the hydrogen bonding pattern in the interfacial region of the bilayer elicited by the catechin might contribute to the alteration of the events taking place in the membrane and might help to understand the mechanism of action of the diverse effects displayed by catechins.
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23
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Greenfield ML, Martin LM, Joodaki F. Computing Individual Area per Head Group Reveals Lipid Bilayer Dynamics. J Phys Chem B 2022; 126:10697-10711. [PMID: 36475708 DOI: 10.1021/acs.jpcb.2c04633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lipid bilayers express a range of phases from solid-like to gel-like to liquid-like as a function of temperature and lipid surface concentration. The area occupied per lipid head group serves as one useful indicator of the bilayer phase, in conjunction with the two-dimensional radial distribution function (i.e., structure factor) within the bilayer. Typically, the area per head group is determined by dividing the bilayer area equally among all head groups. Such an approach is less satisfactory for a multicomponent set of diverse lipids. In this work, area determination is performed on a lipid-by-lipid basis by attributing to a lipid the volume that surrounds each atom. Voronoi tessellation provides this division of the interfacial region on a per-atom basis. The method is applied to a multicomponent system of water, NaCl, and 19 phospholipid types that was devised recently [Langmuir2022, 38, 9481-9499] as a computational representation of the Gram-positive Staphylococcus aureus phospholipid bilayer. Results demonstrate that lipids and water molecules occupy similar extents of area within the interfacial region; ascribing area only to head groups implicitly incorporates assumptions about head group hydration. Results further show that lipid tails provide non-negligible contributions to area on the membrane side of the bilayer-water interface. Results for minimum and maximum area of individual lipids reveal that spontaneous fluctuations displace head groups more than 10 Å from the interfacial region during an NPT simulation at 310 K, leading to a zero contribution to total area at some times. Total area fluctuations and fluctuations per individual lipid relax with a correlation time of ∼10 ns. The method complements density profile as an approach to quantify the structure and dynamics of computational lipid bilayers.
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Affiliation(s)
- Michael L Greenfield
- Department of Chemical Engineering, 360 Fascitelli Center for Advanced Engineering, University of Rhode Island, Kingston, Rhode Island02881, United States
| | - Lenore M Martin
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island02881, United States
| | - Faramarz Joodaki
- Department of Chemical Engineering, 360 Fascitelli Center for Advanced Engineering, University of Rhode Island, Kingston, Rhode Island02881, United States
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24
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Bespalova M, Öz R, Westerlund F, Krishnan M. Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13923-13934. [PMID: 36326814 PMCID: PMC9671048 DOI: 10.1021/acs.langmuir.2c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The repulsive electrostatic force between a biomolecule and a like-charged surface can be geometrically tailored to create spatial traps for charged molecules in solution. Using a parallel-plate system composed of silicon dioxide surfaces, we recently demonstrated single-molecule trapping and high precision molecular charge measurements in a nanostructured free energy landscape. Here we show that surfaces coated with charged lipid bilayers provide a system with tunable surface properties for molecular electrometry experiments. Working with molecular species whose effective charge and geometry are well-defined, we demonstrate the ability to quantitatively probe the electrical charge density of a supported lipid bilayer. Our findings indicate that the fraction of charged lipids in nanoslit lipid bilayers can be significantly different from that in the precursor lipid mixtures used to generate them. We also explore the temporal stability of bilayer properties in nanofluidic systems. Beyond their relevance in molecular measurement, such experimental systems offer the opportunity to examine lipid bilayer formation and wetting dynamics on nanostructured surfaces.
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Affiliation(s)
- Maria Bespalova
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
| | - Robin Öz
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, Sherrington Road, OxfordOX1 3QU, United Kingdom
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25
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Heller WT. Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes. Biomolecules 2022; 12:1591. [PMID: 36358941 PMCID: PMC9687511 DOI: 10.3390/biom12111591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 09/23/2023] Open
Abstract
Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.
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Affiliation(s)
- William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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26
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Maleš M, Zoranić L. Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes. MEMBRANES 2022; 12:891. [PMID: 36135911 PMCID: PMC9502835 DOI: 10.3390/membranes12090891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Antimicrobial peptides (AMPs) can be directed to specific membranes based on differences in lipid composition. In this study, we performed atomistic and coarse-grained simulations of different numbers of the designed AMP adepantin-1 with a eukaryotic membrane, cytoplasmic Gram-positive and Gram-negative membranes, and an outer Gram-negative membrane. At the core of adepantin-1's behavior is its amphipathic α-helical structure, which was implemented in its design. The amphipathic structure promotes rapid self-association of peptide in water or upon binding to bacterial membranes. Aggregates initially make contact with the membrane via positively charged residues, but with insertion, the hydrophobic residues are exposed to the membrane's hydrophobic core. This adaptation alters the aggregate's stability, causing the peptides to diffuse in the polar region of the membrane, mostly remaining as a single peptide or pairing up to form an antiparallel dimer. Thus, the aggregate's proposed role is to aid in positioning the peptide into a favorable conformation for insertion. Simulations revealed the molecular basics of adepantin-1 binding to various membranes, and highlighted peptide aggregation as an important factor. These findings contribute to the development of novel anti-infective agents to combat the rapidly growing problem of bacterial resistance to antibiotics.
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Affiliation(s)
- Matko Maleš
- Faculty of Maritime Studies, University of Split, 21000 Split, Croatia
| | - Larisa Zoranić
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
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27
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Parra-Ortiz E, Caselli L, Agnoletti M, Skoda MWA, Li X, Zhao D, Malmsten M. Mesoporous silica as a matrix for photocatalytic titanium dioxide nanoparticles: lipid membrane interactions. NANOSCALE 2022; 14:12297-12312. [PMID: 35960150 DOI: 10.1039/d2nr01958b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the present study, we investigate the combined interaction of mesoporous silica (SiO2) and photocatalytic titanium dioxide (TiO2) nanoparticles with lipid membranes, using neutron reflectometry (NR), cryo-transmission electron microscopy (cryo-TEM), fluorescence oxidation assays, dynamic light scattering (DLS), and ζ-potential measurements. Based on DLS, TiO2 nanoparticles were found to display strongly improved colloidal stability at physiological pH of skin (pH 5.4) after incorporation into either smooth or spiky ("virus-like") mesoporous silica nanoparticles at low pH, the latter demonstrated by cryo-TEM. At the same time, such matrix-bound TiO2 nanoparticles retain their ability to destabilize anionic bacteria-mimicking lipid membranes under UV-illumination. Quenching experiments indicated both hydroxyl and superoxide radicals to contribute to this, while NR showed that free TiO2 nanoparticles and TiO2 loaded into mesoporous silica nanoparticles induced comparable effects on supported lipid membranes, including membrane thinning, lipid removal, and formation of a partially disordered outer membrane leaflet. By comparing effects for smooth and virus-like mesoporous nanoparticles as matrices for TiO2 nanoparticles, the interplay between photocatalytic and direct membrane binding effects were elucidated. Taken together, the study outlines how photocatalytic nanoparticles can be readily incorporated into mesoporous silica nanoparticles for increased colloidal stability and yet retain most of their capacity for photocatalytic destabilization of lipid membranes, and with maintained mechanisms for oxidative membrane destabilization. As such, the study provides new mechanistic information to the widely employed, but poorly understood, practice of loading photocatalytic nanomaterials onto/into matrix materials for increased performance.
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Affiliation(s)
- Elisa Parra-Ortiz
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Lucrezia Caselli
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Monica Agnoletti
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, OX11 0QX Harwell, Oxfordshire, UK
| | - Xiaomin Li
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, 200433 Shanghai, P. R. China
| | - Dongyuan Zhao
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, 200433 Shanghai, P. R. China
| | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.
- Department of Physical Chemistry 1, University of Lund, SE-22100 Lund, Sweden
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28
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DiPasquale M, Nguyen MHL, Pabst G, Marquardt D. Partial Volumes of Phosphatidylcholines and Vitamin E: α-Tocopherol Prefers Disordered Membranes. J Phys Chem B 2022; 126:6691-6699. [PMID: 36027485 DOI: 10.1021/acs.jpcb.2c04209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite its discovery over 95 years ago, the biological and nutritional roles of vitamin E remain subjects of much controversy. Though it is known to possess antioxidant properties, recent assertions have implied that vitamin E may not be limited to this function in living systems. Through densitometry measurements and small-angle X-ray scattering we observe favorable interactions between α-tocopherol and unsaturated phospholipids, with more favorable interactions correlating to an increase in lipid chain unsaturation. Our data provide evidence that vitamin E may preferentially associate with oxygen sensitive lipids─an association that is considered innate for a viable membrane antioxidant.
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Affiliation(s)
- Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria.,BioTechMed-Graz, Graz 8010, Austria
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada.,Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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29
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Membranolytic Mechanism of Amphiphilic Antimicrobial β-Stranded [KL]n Peptides. Biomedicines 2022; 10:biomedicines10092071. [PMID: 36140173 PMCID: PMC9495826 DOI: 10.3390/biomedicines10092071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Amphipathic peptides can act as antibiotics due to membrane permeabilization. KL peptides with the repetitive sequence [Lys-Leu]n-NH2 form amphipathic β-strands in the presence of lipid bilayers. As they are known to kill bacteria in a peculiar length-dependent manner, we suggest here several different functional models, all of which seem plausible, including a carpet mechanism, a β-barrel pore, a toroidal wormhole, and a β-helix. To resolve their genuine mechanism, the activity of KL peptides with lengths from 6–26 amino acids (plus some inverted LK analogues) was systematically tested against bacteria and erythrocytes. Vesicle leakage assays served to correlate bilayer thickness and peptide length and to examine the role of membrane curvature and putative pore diameter. KL peptides with 10–12 amino acids showed the best therapeutic potential, i.e., high antimicrobial activity and low hemolytic side effects. Mechanistically, this particular window of an optimum β-strand length around 4 nm (11 amino acids × 3.7 Å) would match the typical thickness of a lipid bilayer, implying the formation of a transmembrane pore. Solid-state 15N- and 19F-NMR structure analysis, however, showed that the KL backbone lies flat on the membrane surface under all conditions. We can thus refute any of the pore models and conclude that the KL peptides rather disrupt membranes by a carpet mechanism. The intriguing length-dependent optimum in activity can be fully explained by two counteracting effects, i.e., membrane binding versus amyloid formation. Very short KL peptides are inactive, because they are unable to bind to the lipid bilayer as flexible β-strands, whereas very long peptides are inactive due to vigorous pre-aggregation into β-sheets in solution.
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30
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Dolder N, Müller P, von Ballmoos C. Experimental platform for the functional investigation of membrane proteins in giant unilamellar vesicles. SOFT MATTER 2022; 18:5877-5893. [PMID: 35916307 PMCID: PMC9364335 DOI: 10.1039/d2sm00551d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Giant unilamellar vesicles (GUVs) are micrometer-sized model membrane systems that can be viewed directly under the microscope. They serve as scaffolds for the bottom-up creation of synthetic cells, targeted drug delivery and have been widely used to study membrane related phenomena in vitro. GUVs are also of interest for the functional investigation of membrane proteins that carry out many key cellular functions. A major hurdle to a wider application of GUVs in this field is the diversity of existing protocols that are optimized for individual proteins. Here, we compare PVA assisted and electroformation techniques for GUV formation under physiologically relevant conditions, and analyze the effect of immobilization on vesicle structure and membrane tightness towards small substrates and protons. There, differences in terms of yield, size, and leakage of GUVs produced by PVA assisted swelling and electroformation were found, dependent on salt and buffer composition. Using fusion of oppositely charged membranes to reconstitute a model membrane protein, we find that empty vesicles and proteoliposomes show similar fusion behavior, which allows for a rapid estimation of protein incorporation using fluorescent lipids.
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Affiliation(s)
- Nicolas Dolder
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Philipp Müller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Christoph von Ballmoos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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31
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Joodaki F, Martin LM, Greenfield ML. Generation and Computational Characterization of a Complex Staphylococcus aureus Lipid Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9481-9499. [PMID: 35901279 DOI: 10.1021/acs.langmuir.2c00483] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Studies indicate a crucial cell membrane role in the antibiotic resistance of Staphylococcus aureus. To simulate its membrane structure and dynamics, a complex molecular-scale computational representation of the S. aureus lipid bilayer was developed. Phospholipid types and their amounts were optimized by reverse Monte Carlo to represent characterization data from the literature, leading to 19 different phospholipid types that combine three headgroups [phosphatidylglycerol, lysyl-phosphatidylglycerol (LPG), and cardiolipin] and 10 tails, including iso- and anteiso-branched saturated chains. The averaged lipid bilayer thickness was 36.7 Å, and area per headgroup was 67.8 Å2. Phosphorus and nitrogen density profiles showed that LPG headgroups tended to be bent and oriented more parallel to the bilayer plane. The water density profile showed that small amounts reached the membrane center. Carbon density profiles indicated hydrophobic interactions for all lipids in the middle of the bilayer. Bond vector order parameters along each tail demonstrated different C-H ordering even within distinct lipids of the same type; however, all tails followed similar trends in average order parameter. These complex simulations further revealed bilayer insights beyond those attainable with monodisperse, unbranched lipids. Longer tails often extended into the opposite leaflet. Carbon at and beyond a branch showed significantly decreased ordering compared to carbon in unbranched tails; this feature arose in every branched lipid. Diverse tail lengths distributed these disordered methyl groups throughout the middle third of the bilayer. Distributions in mobility and ordering reveal diverse properties that cannot be obtained with monodisperse lipids.
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Affiliation(s)
- Faramarz Joodaki
- Department of Chemical Engineering, University of Rhode Island, 360 Fascitelli Center for Advanced Engineering, Kingston, Rhode Island 02881, United States
| | - Lenore M Martin
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Michael L Greenfield
- Department of Chemical Engineering, University of Rhode Island, 360 Fascitelli Center for Advanced Engineering, Kingston, Rhode Island 02881, United States
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32
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Thermodynamics and In-Plane Viscoelasticity of Anionic Phospholipid Membranes Modulated by an Ionic Liquid. Pharm Res 2022; 39:2447-2458. [PMID: 35902532 DOI: 10.1007/s11095-022-03348-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022]
Abstract
This article presents the effects of an imidazolium-based ionic liquid (IL) on the thermodynamics and in-plane viscoelastic properties of model membranes of anionic phospholipids. The negative Zeta potential of multilamellar vesicles of 14 carbon lipid 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) is observed to reduce due to the presence of few mole % of an IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). The effect was found to be stronger on enhancing the chain length of the lipid. The surface pressure-area isotherms of lipid monolayer formed at air-water interface are modified by the IL reducing the effective area per molecule. Further, the equilibrium elasticity of the film is altered depending upon the thermodynamic phase of the lipids. While the presence of the IL in the DMPG lipid makes it ordered in the gel phase by reducing the entropy, the effect is opposite in the fluid phase. The in-plane viscoelastic parameters of the lipid film is quantified by dilation rheology using the oscillatory barriers of a Langmuir trough. Even though the low chain lipid DMPG does not show any effect of IL on its storage and loss moduli, the longer chain lipids exhibit a prominent effect in the liquid extended (LE) phase. Further, the dynamic response of the lipid film is found to be distinctly different in the liquid condensed (LC) phase from that of the LE phase.
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33
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Sutherland M, Tran N, Hong M. Clustering of tetrameric influenza M2 peptides in lipid bilayers investigated by 19F solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183909. [PMID: 35276226 DOI: 10.1016/j.bbamem.2022.183909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/19/2022]
Abstract
The influenza M2 protein forms a drug-targeted tetrameric proton channel to mediate virus uncoating, and carries out membrane scission to enable virus release. While the proton channel function of M2 has been extensively studied, the mechanism by which M2 catalyzes membrane scission is still not well understood. Previous fluorescence and electron microscopy studies indicated that M2 tetramers concentrate at the neck of the budding virus in the host plasma membrane. However, molecular evidence for this clustering is scarce. Here, we use 19F solid-state NMR to investigate M2 clustering in phospholipid bilayers. By mixing equimolar amounts of 4F-Phe47 labeled M2 peptide and CF3-Phe47 labeled M2 peptide and measuring F-CF3 cross peaks in 2D 19F19F correlation spectra, we show that M2 tetramers form nanometer-scale clusters in lipid bilayers. This clustering is stronger in cholesterol-containing membranes and phosphatidylethanolamine (PE) membranes than in cholesterol-free phosphatidylcholine and phosphatidylglycerol membranes. The observed correlation peaks indicate that Phe47 sidechains from different tetramers are less than ~2 nm apart. 1H19F correlation peaks between lipid chain protons and fluorinated Phe47 indicate that Phe47 is more deeply inserted into the lipid bilayer in the presence of cholesterol than in its absence, suggesting that Phe47 preferentially interacts with cholesterol. Static 31P NMR spectra indicate that M2 induces negative Gaussian curvature in the PE membrane. These results suggest that M2 tetramers cluster at cholesterol- and PE-rich regions of cell membranes to cause membrane curvature, which in turn can facilitate membrane scission in the last step of virus budding and release.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
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34
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Marquardt D, van Oosten B, Dziura M, Long JR, Harroun TA. The interaction and orientation of Peptide KL 4 in model membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183893. [PMID: 35219719 DOI: 10.1016/j.bbamem.2022.183893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/18/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
We report on the orientation and location of synthetic pulmonary surfactant peptide KL4, (KLLLL)4K, in model lipid membranes. The partitioning depths of selectively deuterated leucine residues within KL4 were determined in DPPC:POPG (4:1) and POPC:POPG (4:1) bilayers by oriented neutron diffraction. These measurements were combined with an NMR-generated model of the peptide structure to determine the orientation and partitioning of the peptide at the lipid-water interface. The results demonstrate KL4 adopting an orientation that interacts with a single membrane leaflet. These observations are consistent with past 2H NMR and EPR studies (Antharam et al., 2009; Turner et al., 2014).
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Affiliation(s)
- Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada; Department of Physics, University of Windsor, Windsor, Ontario, Canada.
| | - Brad van Oosten
- Department of Physics, Brock University, St. Catharines, Ontario, Canada
| | - Maksymilian Dziura
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, Ontario, Canada.
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35
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Rath SL, Tripathy M, Mandal N. How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations. J Membr Biol 2022; 255:341-356. [PMID: 35552785 PMCID: PMC9101995 DOI: 10.1007/s00232-022-00244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unraveling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane-embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature-induced fluctuations are expected to be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low-temperature behavior. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature-dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~ 30-40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.
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Affiliation(s)
- Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India.
| | - Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
| | - Nabanita Mandal
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India
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36
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Moreno-Pescador GS, Aswad DS, Florentsen CD, Bahadori A, Arastoo MR, Danielsen HMD, Heitmann ASB, Boye TL, Nylandsted J, Oddershede LB, Bendix PM. Thermoplasmonic nano-rupture of cells reveals annexin V function in plasma membrane repair. NANOSCALE 2022; 14:7778-7787. [PMID: 35510386 DOI: 10.1039/d1nr08274d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Maintaining the integrity of the cell plasma membrane (PM) is critical for the survival of cells. While an efficient PM repair machinery can aid survival of healthy cells by preventing influx of extracellular calcium, it can also constitute an obstacle in drug delivery and photothermal therapy. We show how nanoscopic holes can be created in a controlled fashion to the cell's plasma membrane, thus allowing identification of molecular components which have a pivotal role in PM repair. Cells are punctured by laser induced local heating of gold nanostructures at the cell surface which causes nano-ruptures in cellular PMs. Recruitment of annexin V near the hole is found to locally reshape the ruptured plasma membrane. Experiments using model membranes, containing recombinant annexin V, provide further biophysical insight into the ability of annexin V to reshape edges surrounding a membrane hole. The thermoplasmonic method provides a general strategy to monitor the response to nanoscopic injuries to the cell surface which offer new insight into how cells respond to photothermal treatment.
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Affiliation(s)
| | - Dunya S Aswad
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark.
| | | | - Azra Bahadori
- Center for Chromosome Stability, University of Copenhagen, Blegdamsvej 3B, 2200 København N, Denmark
| | - Mohammad R Arastoo
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark.
| | | | - Anne Sofie B Heitmann
- Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Theresa L Boye
- Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Jesper Nylandsted
- Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Lene B Oddershede
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark.
| | - Poul Martin Bendix
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, Denmark.
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37
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Formation of a Fully Anionic Supported Lipid Bilayer to Model Bacterial Inner Membrane for QCM-D Studies. MEMBRANES 2022; 12:membranes12060558. [PMID: 35736265 PMCID: PMC9229009 DOI: 10.3390/membranes12060558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 12/04/2022]
Abstract
Supported lipid bilayers (SLBs) on quartz crystals are employed as versatile model systems for studying cell membrane behavior with the use of the highly sensitive technique of quartz crystal microbalance with dissipation monitoring (QCM-D). Since the lipids constituting cell membranes vary from predominantly zwitterionic lipids in mammalian cells to predominantly anionic lipids in the inner membrane of Gram-positive bacteria, the ability to create SLBs of different lipid compositions is essential for representing different cell membranes. While methods to generate stable zwitterionic SLBs and zwitterionic-dominant mixed zwitterionic–anionic SLBs on quartz crystals have been well established, there are no reports of being able to form predominantly or fully anionic SLBs. We describe here a method for forming entirely anionic SLBs by treating the quartz crystal with cationic (3-aminopropyl) trimethoxysilane (APTMS). The formation of the anionic SLB was tracked using QCM-D by monitoring the adsorption of anionic lipid vesicles to a quartz surface and subsequent bilayer formation. Anionic egg L-α-phosphatidylglycerol (PG) vesicles adsorbed on the surface-treated quartz crystal, but did not undergo the vesicle-to-bilayer transition to create an SLB. However, when PG was mixed with 10–40 mole% 1-palmitoyl-2-hydroxy-sn-glycero-3-phospho-(1′-rac-glycerol) (LPG), the mixed vesicles led to the formation of stable SLBs. The dynamics of SLB formation monitored by QCM-D showed that while SLB formation by zwitterionic lipids followed a two-step process of vesicle adsorption followed by the breakdown of the adsorbed vesicles (which in turn is a result of multiple events) to create the SLB, the PG/LPG mixed vesicles ruptured immediately on contacting the quartz surface resulting in a one-step process of SLB formation. The QCM-D data also enabled the quantitative characterization of the SLB by allowing estimation of the lipid surface density as well as the thickness of the hydrophobic region of the SLB. These fully anionic SLBs are valuable model systems to conduct QCM-D studies of the interactions of extraneous substances such as antimicrobial peptides and nanoparticles with Gram-positive bacterial membranes.
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38
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He J, Zhang H, Ma Y, He Y, Liu Z, Liu J, Wang S, Liu Y, Yu K, Jiang J. Sea spray aerosols intervening phospholipids ozonolysis at the air-water interface. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128466. [PMID: 35739660 DOI: 10.1016/j.jhazmat.2022.128466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/22/2022] [Accepted: 02/08/2022] [Indexed: 06/15/2023]
Abstract
With more than half of the world's population lives along the coast and in its vicinity, the sea spray aerosols (SSAs) with respect to respiratory system impact has attracted increasing attention. In this paper, ozonolysis of model lung phospholipids intervened by salt cations in SSAs at air-water interface was investigated using acoustic levitation-nano-electrospray ionization-mass spectrometry (AL-nano-ESI-MS). The cation species facilitated the interfacial ozonolysis of phospholipids, and this increased ozonolysis showed a dependence on the concentration of salt cations. The charge number and ion radius of salt cations were also investigated, and the times of increased efficiency for phospholipids ozonolysis at the air-water interface were higher with more charge numbers or lower ion radius. The mechanism study revealed that the electrostatic interaction between the electronegative headgroup of phospholipids and the cations disturbed the packing of phospholipids, and resulted in oleyl chains more vulnerable with ozone. Finally, aerosolization of the salt-dominated artificial seawater and real seawater revealed a significant increase on ozonolysis of phospholipid intervened by salt cations. These results reveal SSAs intervening phospholipids interfacial reaction at the molecule level, which will be beneficial to gain the knowledge of the negative health effect concerning the components involved in SSAs.
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Affiliation(s)
- Jing He
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China.
| | - Yingxue Ma
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Yuwei He
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Zhuo Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Junyu Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Sheng Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Yaqi Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Jie Jiang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China.
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39
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Chiou PC, Hsu WW, Chang Y, Chen YF. Molecular packing of lipid membranes and action mechanisms of membrane-active peptides. Colloids Surf B Biointerfaces 2022; 213:112384. [PMID: 35151994 DOI: 10.1016/j.colsurfb.2022.112384] [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: 07/09/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 10/19/2022]
Abstract
Biomembranes are involved in diverse cellular activities. How membranes and proteins interact in the activities might hinge on the former's physical characteristics, which in turn are influenced by packing of lipid molecules. Yet, the validity of this understanding and its mechanism are unclear. By varying chain saturation of membranes, we explored correlations between lipid packing and peptide-mediated membrane disruption for the antimicrobial peptide, melittin, and amyloidogenic peptide, β-amyloid (1-42). Remarkably, reducing molecular packing flexibility enhanced the membrane disruption, possibly due to a shift from membrane perforation to micellization. A theoretical analysis suggested the energetic basis of this shift. This mechanistically shows that a peptide's mechanism might be dictated not only by its intrinsic properties but also by physical characteristics of membranes.
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Affiliation(s)
- Pin-Chiuan Chiou
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Wen-Wei Hsu
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Yung Chang
- R&D Center for Membrane Technology and Department of Chemical Engineering, Chung Yuan Christian University, Jhong-Li, Taoyuan 320, Taiwan
| | - Yi-Fan Chen
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan.
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40
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Sweeney DT, Krueger S, Sen K, Hackett JC. Structures and Dynamics of Anionic Lipoprotein Nanodiscs. J Phys Chem B 2022; 126:2850-2862. [PMID: 35393859 PMCID: PMC10061508 DOI: 10.1021/acs.jpcb.2c00758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanolipoprotein particles known as nanodiscs (NDs) have emerged as versatile and powerful tools for the stabilization of membrane proteins permitting a plethora of structural and biophysical studies. Part of their allure is their flexibility to accommodate many types of lipids and precise control of the composition. However, little is known about how variations in lipid composition impact their structures and dynamics. Herein, we investigate how the introduction of the anionic lipid POPG into POPC NDs impacts these features. Small-angle X-ray and neutron scattering (SAXS and SANS) of variable-composition NDs are complemented with molecular dynamics simulations to interrogate how increasing the concern of POPG impacts the ND shape, structure of the lipid core, and the dynamics of the popular membrane scaffold protein, MSP1D1(-). A convenient benefit of including POPG is that it eliminates D2O-induced aggregation observed in pure POPC NDs, permitting studies by SANS at multiple contrasts. SAXS and SANS data could be globally fit to a stacked elliptical cylinder model as well as an extension of the model that accounts for membrane curvature. Fitting to both models supports that the introduction of POPG results in strongly elliptical NDs; however, MD simulations predict the curvature of the membrane, thereby supporting the use of the latter model. Trends in the model-independent parameters suggest that increases in POPG reduce the conformational heterogeneity of the MSP1D1(-), which is in agreement with MD simulations that show that the incorporation of sufficient POPG suppresses disengagement of the N-terminal helix from the lipid core. These studies highlight novel structural changes in NDs in response to an anionic lipid and will inform the interpretation of future structural studies of membrane proteins embedded in NDs of mixed lipid composition.
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Affiliation(s)
- D Tyler Sweeney
- Department of Physiology and Biophysics and the Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Susan Krueger
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, Maryland 20899, United States
| | - Kakali Sen
- Scientific Computing Department, Science and Technology Facilities Council Daresbury Laboratory, Warrington, Cheshire WA4 4AD, United Kingdom
| | - John C Hackett
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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41
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Sule K, Prenner EJ. Lipid headgroup and side chain architecture determine manganese-induced dose dependent membrane rigidification and liposome size increase. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:205-223. [PMID: 35166865 DOI: 10.1007/s00249-022-01589-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/25/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Metal ion-membrane interactions have gained appreciable attention over the years resulting in increasing investigations into the mode of action of toxic and essential metals. More work has focused on essential ions like Ca or Mg and toxic metals like Cd and Pb, whereas this study investigates the effects of the abundant essential trace metal manganese with model lipid systems by screening zwitterionic and anionic glycerophospholipids. Despite its essentiality, deleterious impact towards cell survival is known under Mn stress. The fluorescent dyes Laurdan and diphenylhexatriene were used to assess changes in membrane fluidity both in the head group and hydrophobic core region of the membrane, respectively. Mn-rigidified membranes composed of the anionic phospholipids, phosphatidic acid, phosphatidylglycerol, cardiolipin, and phosphatidylserine. Strong binding resulted in large shifts of the phase transition temperature. The increase was in the order phosphatidylserine > phosphatidylglycerol > cardiolipin, and in all cases, saturated analogues > mono-unsaturated forms. Dynamic light scattering measurements revealed that Mn caused extensive aggregation of liposomes composed of saturated analogues of phosphatidic acid and phosphatidylserine, whilst the mono-unsaturated analogue had significant membrane swelling. Increased membrane rigidity may interfere with permeability of ions and small molecules, possibly disrupting cellular homeostasis. Moreover, liposome size changes could indicate fusion, which could also be detrimental to cellular transport. Overall, this study provided further understanding into the effects of Mn with biomembranes, whereby the altered membrane properties are consequential to the proper structural and signalling functions of membrane lipids.
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Affiliation(s)
- Kevin Sule
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Elmar J Prenner
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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42
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Giulimondi F, Vulpis E, Digiacomo L, Giuli MV, Mancusi A, Capriotti AL, Laganà A, Cerrato A, Zenezini Chiozzi R, Nicoletti C, Amenitsch H, Cardarelli F, Masuelli L, Bei R, Screpanti I, Pozzi D, Zingoni A, Checquolo S, Caracciolo G. Opsonin-Deficient Nucleoproteic Corona Endows UnPEGylated Liposomes with Stealth Properties In Vivo. ACS NANO 2022; 16:2088-2100. [PMID: 35040637 PMCID: PMC8867903 DOI: 10.1021/acsnano.1c07687] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/14/2022] [Indexed: 05/21/2023]
Abstract
For several decades, surface grafted polyethylene glycol (PEG) has been a go-to strategy for preserving the synthetic identity of liposomes in physiological milieu and preventing clearance by immune cells. However, the limited clinical translation of PEGylated liposomes is mainly due to the protein corona formation and the subsequent modification of liposomes' synthetic identity, which affects their interactions with immune cells and blood residency. Here we exploit the electric charge of DNA to generate unPEGylated liposome/DNA complexes that, upon exposure to human plasma, gets covered with an opsonin-deficient protein corona. The final product of the synthetic process is a biomimetic nanoparticle type covered by a proteonucleotidic corona, or "proteoDNAsome", which maintains its synthetic identity in vivo and is able to slip past the immune system more efficiently than PEGylated liposomes. Accumulation of proteoDNAsomes in the spleen and the liver was lower than that of PEGylated systems. Our work highlights the importance of generating stable biomolecular coronas in the development of stealth unPEGylated particles, thus providing a connection between the biological behavior of particles in vivo and their synthetic identity.
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Affiliation(s)
- Francesca Giulimondi
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Elisabetta Vulpis
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Luca Digiacomo
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Maria Valeria Giuli
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Angelica Mancusi
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Anna Laura Capriotti
- Department
of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Aldo Laganà
- Department
of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Cerrato
- Department
of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Zenezini Chiozzi
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Carmine Nicoletti
- Unit
of Histology and Medical Embryology, Department of Anatomy, Histology,
Forensic Medicine and Orthopedics, Sapienza
University of Rome, Viale A. Scarpa 16, 00161 Rome, Italy
| | - Heinz Amenitsch
- Institute
of inorganic Chemistry, Graz University
of Technology, Stremayerg 6/IV, 8010 Graz, Austria
| | | | - Laura Masuelli
- Department
of Experimental Medicine, University of
Rome “Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy
| | - Roberto Bei
- Department
of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Isabella Screpanti
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Daniela Pozzi
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alessandra Zingoni
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Saula Checquolo
- Department
of Medico-Surgical Sciences and Biotechnology, Sapienza University of Rome, Corso della Repubblica 79, 04100 Latina, Italy
| | - Giulio Caracciolo
- Department
of Molecular Medicine, Sapienza University
of Rome, Viale Regina Elena 291, 00161 Rome, Italy
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43
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Abstract
![]()
We extend the modular AMBER lipid
force field to include anionic
lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin,
allowing the simulation of realistic cell membrane lipid compositions,
including raft-like domains. Head group torsion parameters are revised,
resulting in improved agreement with NMR order parameters, and hydrocarbon
chain parameters are updated, providing a better match with phase
transition temperature. Extensive validation runs (0.9 μs per
lipid type) show good agreement with experimental measurements. Furthermore,
the simulation of raft-like bilayers demonstrates the perturbing effect
of increasing PUFA concentrations on cholesterol molecules. The force
field derivation is consistent with the AMBER philosophy, meaning
it can be easily mixed with protein, small molecule, nucleic acid,
and carbohydrate force fields.
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Affiliation(s)
- Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ross C Walker
- GlaxoSmithKline PLC, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ian R Gould
- Department of Chemistry, Imperial College London, London, SW7 2AZ, U.K
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44
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Identifying Membrane Lateral Organization by Contrast-Matched Small Angle Neutron Scattering. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2402:163-177. [PMID: 34854044 DOI: 10.1007/978-1-0716-1843-1_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lipid domains in model membranes are routinely studied to provide insight into the physical interactions that drive raft formation in cellular membranes. Using small angle neutron scattering, contrast-matching techniques enable the detection of lipid domains ranging from tens to hundreds of nanometers which are not accessible to other techniques without the use of extrinsic probes. Here, we describe a probe-free experimental approach and model-free analysis to identify lipid domains in freely floating vesicles of ternary phase separating lipid mixtures.
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45
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Lewis-Laurent A, Doktorova M, Heberle FA, Marquardt D. Vesicle Viewer: Online visualization and analysis of small-angle scattering from lipid vesicles. Biophys J 2021; 120:4639-4648. [PMID: 34571013 DOI: 10.1016/j.bpj.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022] Open
Abstract
Small-angle X-ray and neutron scattering are among the most powerful experimental techniques for investigating the structure of biological membranes. Much of the critical information contained in small-angle scattering (SAS) data is not easily accessible to researchers who have limited time to analyze results by hand or to nonexperts who may lack the necessary scientific background to process such data. Easy-to-use data visualization software can allow them to take full advantage of their SAS data and maximize the use of limited resources. To this end, we developed an internet-based application called Vesicle Viewer to visualize and analyze SAS data from unilamellar lipid bilayer vesicles. Vesicle Viewer utilizes a modified scattering density profile (SDP) analysis called EZ-SDP in which key bilayer structural parameters, such as area per lipid and bilayer thickness, are easily and robustly determined. Notably, we introduce a bilayer model that is able to describe an asymmetric bilayer, whether it be chemically or isotopically asymmetric. The application primarily uses Django, a Python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project; notable examples are Matplotlib (for graphs) and NumPy (for calculations). By eliminating the barrier of downloading and installing software, this web-based application will allow scientists to analyze their own vesicle scattering data using their preferred operating system. The web-based application can be found at https://vesicleviewer.dmarquardt.ca/.
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Affiliation(s)
- Aislyn Lewis-Laurent
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | | | - Drew Marquardt
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada; Department of Physics, University of Windsor, Windsor, Ontario, Canada.
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46
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Rocha-Roa C, Orjuela JD, Leidy C, Cossio P, Aponte-Santamaría C. Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Lett 2021; 595:2701-2714. [PMID: 34633077 DOI: 10.1002/1873-3468.14206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's cardiolipin composition to resist such types of perturbations that compromise their membrane stability. Here, we used molecular dynamic simulations to quantify the role of cardiolipin on the formation of pores in simple bacterial-like membrane models composed of phosphatidylglycerol and cardiolipin mixtures. Cardiolipin modified the structure and ordering of the lipid bilayer, making it less susceptible to mechanical changes. Accordingly, the free-energy barrier for the formation of a transmembrane pore and its kinetic instability augmented by increasing the cardiolipin concentration. This is attributed to the unfavorable positioning of cardiolipin near the formed pore, due to its small polar head and bulky hydrophobic body. Overall, our study demonstrates how cardiolipin prevents membrane-pore formation and this constitutes a plausible mechanism used by bacteria to act against stress perturbations and, thereby, gain resistance to antimicrobial agents.
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Affiliation(s)
- Cristian Rocha-Roa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
| | - Juan David Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los Andes, Bogotá, Colombia
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Chad Leidy
- Biophysics Group, Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
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47
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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48
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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49
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Frampton MB, Yakoub D, Katsaras J, Zelisko PM, Marquardt D. A calorimetric, volumetric and combined SANS and SAXS study of hybrid siloxane phosphocholine bilayers. Chem Phys Lipids 2021; 241:105149. [PMID: 34627769 DOI: 10.1016/j.chemphyslip.2021.105149] [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: 06/22/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Siloxanes are molecules used extensively in commercial, industrial, and biomedical applications. The inclusion of short siloxane chains into phospholipids results in interesting physical properties, including the ability to form low polydispersity unilamellar vesicles. As such, hybrid siloxane phosphocholines (SiPCs) have been examined as a potential platform for the delivery of therapeutic agents. Using small angle X-ray and neutron scattering, vibrating tube densitometry, and differential scanning calorimetry, we studied four hybrid SiPCs bilayers. Lipid volume measurements for the different SiPCs compared well with those previously determined for polyunsaturated PCs. Furthermore, the different SiPC's membrane thicknesses increased monotonically with temperature and, for the most part, consistent with the behavior observed in unsaturated lipids such as, 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine, and the branched lipid 1,2-diphytanoyl-sn-glyerco-3-phosphocholine (DPhyPC).
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Affiliation(s)
- Mark B Frampton
- Department of Chemistry and Centre for Biotechnology, Brock University, St. Catharines, ON, Canada; Advanced Biomanufacturing Centre, Brock University, St. Catharines, ON, Canada; School of Biosciences, Loyalist College, Belleville, ON, Canada
| | - Doruntina Yakoub
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - John Katsaras
- Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; The Bredesen Center, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Physics, Brock University, St. Catharines, ON, Canada; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA
| | - Paul M Zelisko
- Department of Chemistry and Centre for Biotechnology, Brock University, St. Catharines, ON, Canada; Advanced Biomanufacturing Centre, Brock University, St. Catharines, ON, Canada
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada; Department of Physics, University of Windsor, Windsor, ON, Canada
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50
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Pal S, Koeppe RE, Chattopadhyay A. Membrane electrostatics sensed by tryptophan anchors in hydrophobic model peptides depends on non-aromatic interfacial amino acids: implications in hydrophobic mismatch. Faraday Discuss 2021; 232:330-346. [PMID: 34549729 DOI: 10.1039/d0fd00065e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
WALPs are synthetic α-helical membrane-spanning peptides that constitute a well-studied system for exploring hydrophobic mismatch. These peptides represent a simplified consensus motif for transmembrane domains of intrinsic membrane proteins due to their hydrophobic core of alternating leucine and alanine flanked by membrane-anchoring aromatic tryptophan residues. Although the modulation of mismatch responses in WALPs by tryptophan anchors has been reported earlier, there have been limited attempts to utilize the intrinsic tryptophan fluorescence of this class of peptides in mismatch sensors. We have previously shown, utilizing the red edge excitation shift (REES) approach, that interfacial WALP tryptophan residues in fluid phase bilayers experience a dynamically constrained membrane microenvironment. Interestingly, emerging reports suggest the involvement of non-aromatic interfacially localized residues in modulating local structure and dynamics in WALP analogs. In this backdrop, we have explored the effect of interfacial amino acids, such as lysine (in KWALPs) and glycine (in GWALPs), on the tryptophan microenvironment of WALP analogs in zwitterionic and negatively charged membranes. We show that interfacial tryptophans in KWALP and GWALP experience a more restricted microenvironment, as reflected in the substantial increase in magnitude of REES and apparent rotational correlation time, relative to those in WALP in zwitterionic membranes. Interestingly, in contrast to WALP, the tryptophan anchors in KWALP and GWALP appear insensitive to the presence of negatively charged lipids in the membrane. These results reveal a subtle interplay between non-aromatic flanking residues in transmembrane helices and negatively charged lipids at the membrane interface, which could modulate the membrane microenvironment experienced by interfacially localized tryptophan residues. Since interfacial tryptophans are known to influence mismatch responses in WALPs, our results highlight the possibility of utilizing the fluorescence signatures of tryptophans in membrane proteins or model peptides such as WALP as markers for assessing protein responses to hydrophobic mismatch. More importantly, these results constitute one of the first reports on the influence of lipid headgroup charge in fine-tuning hydrophobic mismatch in membrane bilayers, thereby enriching the existing framework of hydrophobic mismatch.
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Affiliation(s)
- Sreetama Pal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. .,CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India.,Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, AR 72701, USA
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India. .,Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
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