1
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Lucker J, Kio M, Klauda JB. Expanding the CHARMM36 United Atom Chain Model for the Inclusion of Sphingolipids. J Phys Chem B 2024. [PMID: 38688001 DOI: 10.1021/acs.jpcb.4c01404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The inclusion of accurate yet computationally inexpensive lipid force fields (FF) is pertinent for the study of lipids and lipid-containing systems using molecular dynamics (MD). Within the past decade, the implementation and further expansion of a united atom (UA) FF for lipids have been developed in the CHARMM family of FFs. The most recent version of the UA presented more accurate descriptions of lipid properties for several phospholipids with saturated and monounsaturated chains, termed C36UAr. However, the original C36UAr model lacks parameters for an important class of lipids, such as sphingolipids. The focus of this article is to broaden the scope of the C36UAr chain model to incorporate these lipids. In this study, two common sphingolipids, N-palmitoyl sphingomyelin and N-stearoyl sphingomyelin are converted to a UA-chain representation and simulated to investigate the accuracy and speed over the all-atom FF model for sphingolipids. Improvements were found among multiple parameters, for example, in the surface area per lipid (SA/lip) and hydrogen order parameters, over the all-atom simulations of these sphingomyelins in C36, while as much as halving the simulation time for simulations of the same setup otherwise. Thus, the accuracy and efficiency found in this study are consistent with those found in the C36UAr model for phospholipids and expand the application of C36UAr to a wider array of membrane models to better match that in vivo.
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Affiliation(s)
- Joshua Lucker
- Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Michael Kio
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B Klauda
- Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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2
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Mistry J, Notman R. Mechanisms of the Drug Penetration Enhancer Propylene Glycol Interacting with Skin Lipid Membranes. J Phys Chem B 2024; 128:3885-3897. [PMID: 38622775 PMCID: PMC11056976 DOI: 10.1021/acs.jpcb.3c06784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024]
Abstract
Very few drugs have the necessary physicochemical properties to cross the skin's main permeability barrier, the stratum corneum (SC), in sufficient amounts. Propylene glycol (PG) is a chemical penetration enhancer that could be included in topical formulations in order to overcome the barrier properties of the skin and facilitate the transport of drugs across it. Experiments have demonstrated that PG increases the mobility and disorder of SC lipids and may extract cholesterol from the SC, but little is known about the molecular mechanisms of drug permeation enhancement by PG. In this work, we have performed molecular dynamics (MD) simulations to investigate the molecular-level effects of PG on the structure and properties of model SC lipid bilayers. The model bilayers were simulated in the presence of PG concentrations over the range of 0-100% w/w PG, using both an all-atom and a united atom force field. PG was found to localize in the hydrophilic headgroup regions at the bilayer interface, to occupy the lipid-water hydrogen-bonding sites, and to slightly increase lipid tail disorder in a concentration-dependent manner. We showed with MD simulation that PG enhances the permeation of small molecules such as water by interacting with the bilayer interface; the results of our study may be used to guide the design of formulations for transdermal drug delivery with enhanced skin permeation, as well as topical formulations and cosmetic products.
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Affiliation(s)
- Jade Mistry
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
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3
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Hesamzadeh P, Seif A, Mahmoudzadeh K, Ganjali Koli M, Mostafazadeh A, Nayeri K, Mirjafary Z, Saeidian H. De novo antioxidant peptide design via machine learning and DFT studies. Sci Rep 2024; 14:6473. [PMID: 38499731 PMCID: PMC10948870 DOI: 10.1038/s41598-024-57247-z] [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: 12/29/2023] [Accepted: 03/15/2024] [Indexed: 03/20/2024] Open
Abstract
Antioxidant peptides (AOPs) are highly valued in food and pharmaceutical industries due to their significant role in human function. This study introduces a novel approach to identifying robust AOPs using a deep generative model based on sequence representation. Through filtration with a deep-learning classification model and subsequent clustering via the Butina cluster algorithm, twelve peptides (GP1-GP12) with potential antioxidant capacity were predicted. Density functional theory (DFT) calculations guided the selection of six peptides for synthesis and biological experiments. Molecular orbital representations revealed that the HOMO for these peptides is primarily localized on the indole segment, underscoring its pivotal role in antioxidant activity. All six synthesized peptides exhibited antioxidant activity in the DPPH assay, while the hydroxyl radical test showed suboptimal results. A hemolysis assay confirmed the non-hemolytic nature of the generated peptides. Additionally, an in silico investigation explored the potential inhibitory interaction between the peptides and the Keap1 protein. Analysis revealed that ligands GP3, GP4, and GP12 induced significant structural changes in proteins, affecting their stability and flexibility. These findings highlight the capability of machine learning approaches in generating novel antioxidant peptides.
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Affiliation(s)
- Parsa Hesamzadeh
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abdolvahab Seif
- Dipartimento di Fisica, Universita' di Padova, Via Marzolo 8, 35131, Padua, Italy
- Department of Chemistry, University of Turin, Via Pietro Giuria 7, 10125, Turin, Italy
| | - Kazem Mahmoudzadeh
- Department of Organic Chemistry and Oil, Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
| | | | - Amrollah Mostafazadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Kosar Nayeri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Zohreh Mirjafary
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Saeidian
- Department of Science, Payame Noor University (PNU), PO Box: 19395-4697, Tehran, Iran.
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4
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Kang C, Bernaldez M, Stamatis SD, Rose JP, Sun R. Interaction between Permeation Enhancers and Lipid Bilayers. J Phys Chem B 2024; 128:1668-1679. [PMID: 38232311 DOI: 10.1021/acs.jpcb.3c06448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Permeation enhancers (PEs) are a class of molecules that interact with the epithelial membrane and transiently increase its transcellular permeability. Although there have been few clinical trials of PE coformulated drugs, the mechanism of action of PEs remains elusive. In this paper, the interaction between two archetypes of PEs [salcaprozate sodium (SNAC) and sodium caprate (C10)] and membranes is investigated with extensive all-atom molecular dynamics simulations. The simulations show that (1) the association between the neutral PEs and membranes is favored in free energy, (2) the propensity of neutral PE aggregation is larger in aqueous solution than in lipid bilayers, (3) the equilibrium distribution of neutral PEs in membranes is fast, e.g., accessible with unbiased MD simulations, and (4) the micelle of neutral PEs formed in aqueous solution does not rupture the membranes (e.g., not forming pores or breaking up the membrane) under simulation conditions. All results combined, this study indicates that PEs insert into the membranes in an equilibrium or near equilibrium process. This study lays the foundation for future investigations of how PEs impact the free energy of permeation for small molecules.
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Affiliation(s)
- Christopher Kang
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Mabel Bernaldez
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Stephen D Stamatis
- Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - John P Rose
- Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rui Sun
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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5
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Zamani Zakaria A, Malde AK, Gould T. Permeability of Dermatological Solutes through the Short Periodicity Phase of Human Stratum Corneum Lipid Bilayers. J Chem Inf Model 2024; 64:276-288. [PMID: 38147827 DOI: 10.1021/acs.jcim.3c01362] [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: 12/28/2023]
Abstract
Determining the permeability of drug-like solutes through the densely packed and heterogeneous stratum corneum lipid layer presents a significant challenge. In this study, we employed umbrella sampling with a periodic weighing function applied to the center of mass of the lipid bilayers. Precise umbrella sampling was conducted with an interframe distance of 0.5 Å, spanning from the bilayer center to the water phase, and each frame was simulated for at least 20 ns. Autocorrelation functions, potential of mean force (PMF), and diffusivity profiles were analyzed for six solutes (testosterone, benzene, caffeine, ethanol, mannitol, and histidine). The results revealed that autocorrelations were dependent solely on the medium, whether water or lipid phase. Diffusivity and PMF profiles along the reaction coordinate were influenced by the hydrophilicity of the solute rather than its size. For hydrophobic solutes, the PMF curves exhibited a minimum at the bilayer center, while for hydrophilic solutes, the PMFs peaked at the bilayer center and lipid tails (where the lipid tails are not interacting with the cholesterol). Diffusivity curves were low at the bilayer center and water phase, with peaks observed at the headgroup or the boundary between fatty acid and cholesterol (1 nm from the bilayer center). The quantitative findings presented in this work hold significance for pharmacists and drug designers.
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Affiliation(s)
- Afshin Zamani Zakaria
- School of Environment and Science, Griffith University, Nathan, Brisbane, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Alpeshkumar K Malde
- School of Environment and Science, Griffith University, Nathan, Brisbane, QLD 4111, Australia
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Tim Gould
- School of Environment and Science, Griffith University, Nathan, Brisbane, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre, Griffith University, Nathan, Brisbane, QLD 4111, Australia
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6
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Niu Y, Chen SJ, Klauda JB. Simulations of naïve and KLA-activated macrophage plasma membrane models. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184242. [PMID: 37866689 DOI: 10.1016/j.bbamem.2023.184242] [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: 03/27/2023] [Revised: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Macrophages (MAs), which play vital roles in human immune responses and lipid metabolisms, are implicated in the development and progression of atherosclerosis, a major contributor to cardiovascular diseases. Specifically, the abnormal lipid metabolism of oxidized low-density lipids (oxLDLs) in MAs is believed to be a crucial factor. However, the precise mechanism by which the MA membrane contributes to this altered lipid metabolism remains unclear. Lipidomic studies have revealed significant differences in membrane composition between various MA phenotypes. This study serves to provide and characterize complex realistic computational models for naïve (M0) and Kdo2-lipid A-activated (M1) state MA. Analyses of surface area per lipid (SA/lip), area compressibility modulus (KA), carbon‑hydrogen order parameter (SCH), electron density profile (EDP), tilt angles, two-dimension radial distribution functions (2D RDFs), mean squared displacement (MSD), hydrogen bonds (H-bonds), lipid clustering, and lipid wobble were conducted for both models. Results indicate that the M1 state MA membrane is more tightly packed, with increased chain order across lipid species, and forms PSM-DOPG-CHOL and PSM-SLPC-CHOL clusters. Importantly, the bilayer thicknesses reported for the models are in good agreement with experimental data for the thicknesses of transmembrane regions for MA integral proteins. These findings validate the described models as physiologically accurate for future computational studies of MA membranes and their residing proteins.
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Affiliation(s)
- Yueqi Niu
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Si Jia Chen
- Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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7
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Islam MM, Nawagamuwage SU, Parshin IV, Richard MC, Burin AL, Rubtsov IV. Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy. J Am Chem Soc 2023; 145:26363-26373. [PMID: 37982703 DOI: 10.1021/jacs.3c10178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an azido moiety and a cyano or carboxylic acid moiety, connected by an alkyl chain of different lengths, was synthesized. FTIR data and molecular dynamics calculations indicated that the test compounds in a bilayer are oriented so that the cyano or carboxylic acid moiety is located in the lipid head-group region, while the azido group stays inside the bilayer at the depth determined by its alkyl chain length. We found that the asymmetric stretching mode of the azido group (νN3) can serve as a reporter of the membrane interior dynamics. FTIR and two-dimensional infrared (2DIR) studies were performed at different temperatures, ranging from 22 to 45 °C, covering the Lβ-Lα phase transition temperature of dipalmitoylphosphatidylcholine (∼41 °C). The width of the νN3 peak was found to be very sensitive to the phase transition and to the temperature in general. We introduced an order parameter, SN3, which characterizes restrictions to motion inside the bilayer. 2DIR spectra of νN3 showed different extents of inhomogeneity at different depths in the bilayer, with the smallest inhomogeneity in the middle of the leaflet. The spectral diffusion dynamics of the N3 peak was found to be dependent on the depth of the N3 group location in the bilayer. The obtained results enhance our understanding of the bilayer dynamics and can be extended to investigate membranes with more complex compositions.
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Affiliation(s)
- Md Muhaiminul Islam
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - Igor V Parshin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Margaret C Richard
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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8
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Tian GL, Hsieh CJ, Taylor M, Lee JY, Riad AA, Luedtke RR, Mach RH. Synthesis of bitopic ligands based on fallypride and evaluation of their affinity and selectivity towards dopamine D 2 and D 3 receptors. Eur J Med Chem 2023; 261:115751. [PMID: 37688938 PMCID: PMC10841072 DOI: 10.1016/j.ejmech.2023.115751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
The difference in the secondary binding site (SBS) between the dopamine 2 receptor (D2R) and dopamine 3 receptor (D3R) has been used in the design of compounds displaying selectivity for the D3R versus D2R. In the current study, a series of bitopic ligands based on Fallypride were prepared with various secondary binding fragments (SBFs) as a means of improving the selectivity of this benzamide analog for D3R versus D2R. We observed that compounds having a small alkyl group with a heteroatom led to an improvement in D3R versus D2R selectivity. Increasing the steric bulk in the SBF increase the distance between the pyrrolidine N and Asp110, thereby reducing D3R affinity. The best-in-series compound was (2S,4R)-trans-27 which had a modest selectivity for D3R versus D2R and a high potency in the β-arrestin competition assay which provides a measure of the ability of the compound to compete with endogenous dopamine for binding to the D3R. The results of this study identified factors one should consider when designing bitopic ligands based on Fallypride displaying an improved affinity for D3R versus D2R.
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Affiliation(s)
- Gui-Long Tian
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chia-Ju Hsieh
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michelle Taylor
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center-Fort Worth, Texas, TX, 76107, USA
| | - Ji Youn Lee
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aladdin A Riad
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert R Luedtke
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center-Fort Worth, Texas, TX, 76107, USA
| | - Robert H Mach
- Division of Nuclear Medicine and Clinical Molecular Imaging, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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9
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Stroh KS, Souza PCT, Monticelli L, Risselada HJ. CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization. J Chem Theory Comput 2023; 19:8384-8400. [PMID: 37971301 PMCID: PMC10688431 DOI: 10.1021/acs.jctc.3c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
Abstract
Coarse-grained force fields (CG FFs) such as the Martini model entail a predefined, fixed set of Lennard-Jones parameters (building blocks) to model virtually all possible nonbonded interactions between chemically relevant molecules. Owing to its universality and transferability, the building-block coarse-grained approach has gained tremendous popularity over the past decade. The parametrization of molecules can be highly complex and often involves the selection and fine-tuning of a large number of parameters (e.g., bead types and bond lengths) to optimally match multiple relevant targets simultaneously. The parametrization of a molecule within the building-block CG approach is a mixed-variable optimization problem: the nonbonded interactions are discrete variables, whereas the bonded interactions are continuous variables. Here, we pioneer the utility of mixed-variable particle swarm optimization in automatically parametrizing molecules within the Martini 3 coarse-grained force field by matching both structural (e.g., RDFs) as well as thermodynamic data (phase-transition temperatures). For the sake of demonstration, we parametrize the linker of the lipid sphingomyelin. The important advantage of our approach is that both bonded and nonbonded interactions are simultaneously optimized while conserving the search efficiency of vector guided particle swarm optimization (PSO) methods over other metaheuristic search methods such as genetic algorithms. In addition, we explore noise-mitigation strategies in matching the phase-transition temperatures of lipid membranes, where nucleation and concomitant hysteresis introduce a dominant noise term within the objective function. We propose that noise-resistant mixed-variable PSO methods can both improve and automate parametrization of molecules within building-block CG FFs, such as Martini.
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Affiliation(s)
- Kai Steffen Stroh
- Department
of Physics, Technische Universität
Dortmund, 44227 Dortmund, Germany
- Institute
for Theoretical Physics, Georg-August University
Göttingen, 37077 Göttingen, Germany
| | - Paulo C. T. Souza
- Molecular
Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS and University of Lyon, 69367 Lyon, France
| | - Luca Monticelli
- Molecular
Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS and University of Lyon, 69367 Lyon, France
| | - Herre Jelger Risselada
- Department
of Physics, Technische Universität
Dortmund, 44227 Dortmund, Germany
- Institute
for Theoretical Physics, Georg-August University
Göttingen, 37077 Göttingen, Germany
- Leiden
Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
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10
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Rempfert KR, Kraus EA, Nothaft DB, Dildar N, Spear JR, Sepúlveda J, Templeton AS. Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids. Front Microbiol 2023; 14:1198786. [PMID: 38029177 PMCID: PMC10667739 DOI: 10.3389/fmicb.2023.1198786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.
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Affiliation(s)
- Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Daniel B. Nothaft
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Nadia Dildar
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Department of Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, CO, United States
| | - Julio Sepúlveda
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
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11
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Gupta S, Soni J, Kumar A, Mandal T. Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures. J Chem Phys 2023; 159:165102. [PMID: 37873964 DOI: 10.1063/5.0167144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023] Open
Abstract
Structural and mechanical properties of membranes such as thickness, tail order, bending modulus and curvature energetics play crucial role in controlling various cellular functions that depend on the local lipid organization and membrane reshaping. While behavior of these biophysical properties are well understood in single component membranes, very little is known about how do they change in the mixed lipid membranes. Often various properties of the mixed lipid bilayers are assumed to change linearly with the mole fractions of the constituent lipids which, however, is true for "ideal" mixing only. In this study, using molecular dynamics simulations, we show that structural and mechanical properties of binary lipid mixture change nonlinearly with the lipid mole fractions, and the strength of the nonlinearity depends on two factors - spontaneous curvature difference and locally inhomogeneous interactions between the lipid components.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jatin Soni
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Awneesh Kumar
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
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12
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Wennberg C, Lundborg M, Lindahl E, Norlén L. Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:4900-4911. [PMID: 37462219 PMCID: PMC10428223 DOI: 10.1021/acs.jcim.3c00625] [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: 04/24/2023] [Indexed: 08/15/2023]
Abstract
Our skin constitutes an effective permeability barrier that protects the body from exogenous substances but concomitantly severely limits the number of pharmaceutical drugs that can be delivered transdermally. In topical formulation design, chemical permeation enhancers (PEs) are used to increase drug skin permeability. In vitro skin permeability experiments can measure net effects of PEs on transdermal drug transport, but they cannot explain the molecular mechanisms of interactions between drugs, permeation enhancers, and skin structure, which limits the possibility to rationally design better new drug formulations. Here we investigate the effect of the PEs water, lauric acid, geraniol, stearic acid, thymol, ethanol, oleic acid, and eucalyptol on the transdermal transport of metronidazole, caffeine, and naproxen. We use atomistic molecular dynamics (MD) simulations in combination with developed molecular models to calculate the free energy difference between 11 PE-containing formulations and the skin's barrier structure. We then utilize the results to calculate the final concentration of PEs in skin. We obtain an RMSE of 0.58 log units for calculated partition coefficients from water into the barrier structure. We then use the modified PE-containing barrier structure to calculate the PEs' permeability enhancement ratios (ERs) on transdermal metronidazole, caffeine, and naproxen transport and compare with the results obtained from in vitro experiments. We show that MD simulations are able to reproduce rankings based on ERs. However, strict quantitative correlation with experimental data needs further refinement, which is complicated by significant deviations between different measurements. Finally, we propose a model for how to use calculations of the potential of mean force of drugs across the skin's barrier structure in a topical formulation design.
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Affiliation(s)
| | - Magnus Lundborg
- Science
for Life Laboratory, ERCO Pharma AB, 171 65 Solna, Sweden
| | - Erik Lindahl
- Department
of Biophysics and Biochemistry, Stockholm
University, 106 91 Stockholm, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Lars Norlén
- Department
of Cell and Molecular Biology (CMB), Karolinska
Institutet, 171 77 Solna, Sweden
- Dermatology
Clinic. Karolinska University Hospital, 171 77 Solna, Sweden
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13
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Anishkin A, Adepu KK, Bhandari D, Adams SH, Chintapalli SV. Computational Analysis Reveals Unique Binding Patterns of Oxygenated and Deoxygenated Myoglobin to the Outer Mitochondrial Membrane. Biomolecules 2023; 13:1138. [PMID: 37509174 PMCID: PMC10377724 DOI: 10.3390/biom13071138] [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: 05/25/2023] [Revised: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Myoglobin (Mb) interaction with the outer mitochondrial membrane (OMM) promotes oxygen (O2) release. However, comprehensive molecular details on specific contact regions of the OMM with oxygenated (oxy-) and deoxygenated (deoxy-)Mb are missing. We used molecular dynamics (MD) simulations to explore the interaction of oxy- and deoxy-Mb with the membrane lipids of the OMM in two lipid compositions: (a) a typical whole membrane on average, and (b) specifically the cardiolipin-enriched cristae region (contact site). Unrestrained relaxations showed that on average, both the oxy- and deoxy-Mb established more stable contacts with the lipids typical of the cristae contact site, then with those of the average OMM. However, in steered detachment simulations, deoxy-Mb clung more tightly to the average OMM, and oxy-Mb strongly preferred the contact sites of the OMM. The MD simulation analysis further indicated that a non-specific binding, mediated by local electrostatic interactions, existed between charged or polar groups of Mb and the membrane, for stable interaction. To the best of our knowledge, this is the first computational study providing the molecular details of the direct Mb-mitochondria interaction that assisted in distinguishing the preferred localization of oxy- and deoxy-Mb on the OMM. Our findings support the existing experimental evidence on Mb-mitochondrial association and shed more insights on Mb-mediated O2 transport for cellular bioenergetics.
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Affiliation(s)
- Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Kiran Kumar Adepu
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - Sean H Adams
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, CA 95616, USA
- Center for Alimentary and Metabolic Science, University of California Davis, Sacramento, CA 95616, USA
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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14
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Beaven AH, Sapp K, Sodt AJ. Simulated dynamic cholesterol redistribution favors membrane fusion pore constriction. Biophys J 2023; 122:2162-2175. [PMID: 36588341 PMCID: PMC10257089 DOI: 10.1016/j.bpj.2022.12.024] [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: 02/08/2022] [Revised: 06/17/2022] [Accepted: 12/16/2022] [Indexed: 01/01/2023] Open
Abstract
Endo- and exocytosis proceed through a highly strained membrane fusion pore topology regardless of the aiding protein machinery. The membrane's lipid components bias fusion pores toward expansion or closure, modifying the necessary work done by proteins. Cholesterol, a key component of plasma membranes, promotes both inverted lipid phases with concave leaflets (i.e., negative total curvature, which thins the leaflet) and flat bilayer phases with thick, ordered hydrophobic interiors. We demonstrate by theory and simulation that both leaflets of nascent catenoidal fusion pores have negative total curvature. Furthermore, the hydrophobic core of bilayers with strong negative Gaussian curvature is thinned. Therefore, it is an open question whether cholesterol will be enriched in these regions because of the negative total curvature or depleted because of the membrane thinning. Here, we compare all-atom molecular dynamics simulations (built using a procedure to create specific fusion pore geometries) and theory to understand the underlying reasons for lipid redistribution on fusion pores. Our all-atom molecular dynamics simulations resolve this question by showing that cholesterol is strongly excluded from the thinned neck of fusion and fission pores, revealing that thickness (and/or lipid order) influences cholesterol distributions more than curvature. The results imply that cholesterol exclusion can drive fusion pore closure by creating a small, cholesterol-depleted zone in the neck. This model agrees with literature evidence that membrane reshaping is connected to cholesterol-dependent lateral phase separation.
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Affiliation(s)
- Andrew H Beaven
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland
| | - Kayla Sapp
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alexander J Sodt
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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15
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Ledum M, Sen S, Li X, Carrer M, Feng Y, Cascella M, Bore SL. HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter. J Chem Theory Comput 2023; 19:2939-2952. [PMID: 37130290 DOI: 10.1021/acs.jctc.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics. The methodology is based on a tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating nonphysical force aliasing. Separating the time integration of fast modes associated with internal molecular motion from slow modes associated with their density fields, we enable the first time-reversible, energy-conserving hybrid particle-field simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in particle-mesh Ewald. We demonstrate the ability of HyMD to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse-grain length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multimicrosecond regime observed with comparable coarse-grained models.
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Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Samiran Sen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Xinmeng Li
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Yu Feng
- Berkeley Center for Cosmological Physics and Department of Physics, University of California, Berkeley, California 94720, United States
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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16
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Rogers JR, Geissler PL. Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts. PLoS Comput Biol 2023; 19:e1010992. [PMID: 37036851 PMCID: PMC10085062 DOI: 10.1371/journal.pcbi.1010992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Cellular distributions of the sphingolipid ceramide-1-phosphate (C1P) impact essential biological processes. C1P levels are spatiotemporally regulated by ceramide-1-phosphate transfer protein (CPTP), which efficiently shuttles C1P between organelle membranes. Yet, how CPTP rapidly extracts and inserts C1P into a membrane remains unknown. Here, we devise a multiscale simulation approach to elucidate biophysical details of CPTP-mediated C1P transport. We find that CPTP binds a membrane poised to extract and insert C1P and that membrane binding promotes conformational changes in CPTP that facilitate C1P uptake and release. By significantly disrupting a lipid's local hydrophobic environment in the membrane, CPTP lowers the activation free energy barrier for passive C1P desorption and enhances C1P extraction from the membrane. Upon uptake of C1P, further conformational changes may aid membrane unbinding in a manner reminiscent of the electrostatic switching mechanism used by other lipid transfer proteins. Insertion of C1P into an acceptor membrane, eased by a decrease in membrane order by CPTP, restarts the transfer cycle. Most notably, we provide molecular evidence for CPTP's ability to catalyze C1P extraction by breaking hydrophobic C1P-membrane contacts with compensatory hydrophobic lipid-protein contacts. Our work, thus, provides biophysical insights into how CPTP efficiently traffics C1P between membranes to maintain sphingolipid homeostasis and, additionally, presents a simulation method aptly suited for uncovering the catalytic mechanisms of other lipid transfer proteins.
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Affiliation(s)
- Julia R Rogers
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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17
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Sen S, Ledum M, Bore SL, Cascella M. Soft Matter under Pressure: Pushing Particle–Field Molecular Dynamics to the Isobaric Ensemble. J Chem Inf Model 2023; 63:2207-2217. [PMID: 36976890 PMCID: PMC10091448 DOI: 10.1021/acs.jcim.3c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Hamiltonian hybrid particle-field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer.
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18
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Fitzgerald JE, Venable RM, Pastor RW, Lyman ER. Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations. Biophys J 2023; 122:1094-1104. [PMID: 36739477 PMCID: PMC10111272 DOI: 10.1016/j.bpj.2023.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Lipid membrane viscosity is critical to biological function. Bacterial cells grown in different environments alter their lipid composition in order to maintain a specific viscosity, and membrane viscosity has been linked to the rate of cellular respiration. To understand the factors that determine the viscosity of a membrane, we ran equilibrium all-atom simulations of single component lipid bilayers and calculated their viscosities. The viscosity was calculated via a Green-Kubo relation, with the stress-tensor autocorrelation function modeled by a stretched exponential function. By simulating a series of lipids at different temperatures, we establish the dependence of viscosity on several aspects of lipid chemistry, including hydrocarbon chain length, unsaturation, and backbone structure. Sphingomyelin is found to have a remarkably high viscosity, roughly 20 times that of DPPC. Furthermore, we find that inclusion of the entire range of the dispersion interaction increases viscosity by up to 140%. The simulated viscosities are similar to experimental values obtained from the rotational dynamics of small chromophores and from the diffusion of integral membrane proteins but significantly lower than recent measurements based on the deformation of giant vesicles.
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Affiliation(s)
- James E Fitzgerald
- Department of Physics & Astronomy, University of Delaware, Newark, Delaware
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Edward R Lyman
- Department of Physics & Astronomy, University of Delaware, Newark, Delaware; Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware.
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19
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Piasentin N, Lian G, Cai Q. In Silico Prediction of Stratum Corneum Partition Coefficients via COSMOmic and Molecular Dynamics Simulations. J Phys Chem B 2023; 127:2719-2728. [PMID: 36930176 PMCID: PMC10068742 DOI: 10.1021/acs.jpcb.2c08566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Stratum corneum (SC) is the main barrier of human skin where the inter-corneocytes lipids provide the main pathway for transdermal permeation of functional actives of skin care and health. Molecular dynamics (MD) has been increasingly used to simulate the SC lipid bilayer structure so that the barrier property and its affecting factors can be elucidated. Among reported MD simulation studies, solute partition in the SC lipids, an important parameter affecting SC permeability, has received limited attention. In this work, we combine MD simulation with COSMOmic to predict the partition coefficients of dermatologically relevant solutes in SC lipid bilayer. Firstly, we run MD simulations to obtain equilibrated SC lipid bilayers with different lipid types, compositions, and structures. Then, the simulated SC lipid bilayer structures are fed to COSMOmic to calculate the partition coefficients of the solutes. The results show that lipid types and bilayer geometries play a minor role in the predicted partition coefficients. For the more lipophilic solutes, the predicted results of solute partition in SC lipid bilayers agree well with reported experimental values of solute partition in extracted SC lipids. For the more hydrophilic molecules, there is a systematical underprediction. Nevertheless, the MD/COSMOmic approach correctly reproduces the phenomenological correlation between the SC lipid/water partition coefficients and the octanol/water partition coefficients. Overall, the results show that the MD/COSMOmic approach is a fast and valid method for predicting solute partitioning into SC lipids and hence supporting the assessment of percutaneous absorption of skin care ingredients, dermatological drugs as well as environmental pollutants.
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Affiliation(s)
- Nicola Piasentin
- Department of Chemical and Process Engineering, University of Surrey, Guildford GU27XH, U.K.,Unilever R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K
| | - Guoping Lian
- Department of Chemical and Process Engineering, University of Surrey, Guildford GU27XH, U.K.,Unilever R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K
| | - Qiong Cai
- Department of Chemical and Process Engineering, University of Surrey, Guildford GU27XH, U.K
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20
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Kurihara Y, Ekimoto T, Gordon CT, Uchijima Y, Sugiyama R, Kitazawa T, Iwase A, Kotani R, Asai R, Pingault V, Ikeguchi M, Amiel J, Kurihara H. Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding. J Clin Invest 2023; 133:151536. [PMID: 36637912 PMCID: PMC9927936 DOI: 10.1172/jci151536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
Mutations of G protein-coupled receptors (GPCRs) cause various human diseases, but the mechanistic details are limited. Here, we establish p.E303K in the gene encoding the endothelin receptor type A (ETAR/EDNRA) as a recurrent mutation causing mandibulofacial dysostosis with alopecia (MFDA), with craniofacial changes similar to those caused by p.Y129F. Mouse models carrying either of these missense mutations exhibited a partial maxillary-to-mandibular transformation, which was rescued by deleting the ligand endothelin 3 (ET3/EDN3). Pharmacological experiments confirmed the causative ETAR mutations as gain of function, dependent on ET3. To elucidate how an amino acid substitution far from the ligand binding site can increase ligand affinity, we used molecular dynamics (MD) simulations. E303 is located at the intracellular end of transmembrane domain 6, and its replacement by a lysine increased flexibility of this portion of the helix, thus favoring G protein binding and leading to G protein-mediated enhancement of agonist affinity. The Y129F mutation located under the ligand binding pocket reduced the sodium-water network, thereby affecting the extracellular portion of helices in favor of ET3 binding. These findings provide insight into the pathogenesis of MFDA and into allosteric mechanisms regulating GPCR function, which may provide the basis for drug design targeting GPCRs.
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Affiliation(s)
- Yukiko Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Yasunobu Uchijima
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Sugiyama
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taro Kitazawa
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akiyasu Iwase
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Risa Kotani
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Medical Science, Graduate School of Medicine, University of Hiroshima, Hiroshima, Japan
| | - Rieko Asai
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Véronique Pingault
- Department of Genomic Medicine for Rare Diseases, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.,Center for Computational Science, RIKEN, Yokohama, Japan
| | - Jeanne Amiel
- INSERM UMR 1163, Institut Imagine and Université Paris-Cité, Paris, France.,Department of Genomic Medicine for Rare Diseases, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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21
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Sengottiyan S, Mikolajczyk A, Puzyn T. How Does the Study MD of pH-Dependent Exposure of Nanoparticles Affect Cellular Uptake of Anticancer Drugs? Int J Mol Sci 2023; 24:ijms24043479. [PMID: 36834890 PMCID: PMC9958846 DOI: 10.3390/ijms24043479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
The lack of knowledge about the uptake of NPs by biological cells poses a significant problem for drug delivery. For this reason, designing an appropriate model is the main challenge for modelers. To address this problem, molecular modeling studies that can describe the mechanism of cellular uptake of drug-loaded nanoparticles have been conducted in recent decades. In this context, we developed three different models for the amphipathic nature of drug-loaded nanoparticles (MTX-SS-γ-PGA), whose cellular uptake mechanism was predicted by molecular dynamics studies. Many factors affect nanoparticle uptake, including nanoparticle physicochemical properties, protein-particle interactions, and subsequent agglomeration, diffusion, and sedimentation. Therefore, the scientific community needs to understand how these factors can be controlled and the NP uptake of nanoparticles. Based on these considerations, in this study, we investigated for the first time the effects of the selected physicochemical properties of the anticancer drug methotrexate (MTX) grafted with hydrophilic-γ-polyglutamic acid (MTX-SS-γ-PGA) on its cellular uptake at different pH values. To answer this question, we developed three theoretical models describing drug-loaded nanoparticles (MTX-SS-γ-PGA) at three different pH values, such as (1) pH 7.0 (the so-called neutral pH model), (2) pH 6.4 (the so-called tumor pH model), and (3) pH 2.0 (the so-called stomach pH model). Exceptionally, the electron density profile shows that the tumor model interacts more strongly with the head groups of the lipid bilayer than the other models due to charge fluctuations. Hydrogen bonding and RDF analyses provide information about the solution of the NPs with water and their interaction with the lipid bilayer. Finally, dipole moment and HOMO-LUMO analysis showed the free energy of the solution in the water phase and chemical reactivity, which are particularly useful for determining the cellular uptake of the NPs. The proposed study provides fundamental insights into molecular dynamics (MD) that will allow researchers to determine the influence of pH, structure, charge, and energetics of NPs on the cellular uptake of anticancer drugs. We believe that our current study will be useful in developing a new model for drug delivery to cancer cells with a much more efficient and less time-consuming model.
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22
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Encapsulation of Testosterone and Dihydrotestosterone into Chiral Carbon Nanotubes: A Molecular Dynamics study. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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23
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Kim HY, Lee JY, Hsieh CJ, Taylor M, Luedtke RR, Mach RH. Design and Synthesis of Conformationally Flexible Scaffold as Bitopic Ligands for Potent D 3-Selective Antagonists. Int J Mol Sci 2022; 24:ijms24010432. [PMID: 36613875 PMCID: PMC9820167 DOI: 10.3390/ijms24010432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Previous studies have confirmed that the binding of D3 receptor antagonists is competitively inhibited by endogenous dopamine despite excellent binding affinity for D3 receptors. This result urges the development of an alternative scaffold that is capable of competing with dopamine for binding to the D3 receptor. Herein, an SAR study was conducted on metoclopramide that incorporated a flexible scaffold for interaction with the secondary binding site of the D3 receptor. The alteration of benzamide substituents and secondary binding fragments with aryl carboxamides resulted in excellent D3 receptor affinities (Ki = 0.8-13.2 nM) with subtype selectivity to the D2 receptor ranging from 22- to 180-fold. The β-arrestin recruitment assay revealed that 21c with 4-(pyridine-4-yl)benzamide can compete well against dopamine with the highest potency (IC50 = 1.3 nM). Computational studies demonstrated that the high potency of 21c and its analogs was the result of interactions with the secondary binding site of the D3 receptor. These compounds also displayed minimal effects for other GPCRs except moderate affinity for 5-HT3 receptors and TSPO. The results of this study revealed that a new class of selective D3 receptor antagonists should be useful in behavioral pharmacology studies and as lead compounds for PET radiotracer development.
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Affiliation(s)
- Ho Young Kim
- Vagelos Laboratories, Department of Radiology, University of Pennsylvania, 1012, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Ji Youn Lee
- Vagelos Laboratories, Department of Radiology, University of Pennsylvania, 1012, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Chia-Ju Hsieh
- Vagelos Laboratories, Department of Radiology, University of Pennsylvania, 1012, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Michelle Taylor
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Robert R. Luedtke
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Robert H. Mach
- Vagelos Laboratories, Department of Radiology, University of Pennsylvania, 1012, 231 S. 34th Street, Philadelphia, PA 19104, USA
- Correspondence:
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24
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Jemmett P, Milan DC, Nichols RJ, Howitt T, Martin AL, Arnold T, Rawle JL, Nicklin CL, Dafforn TR, Cox LR, Horswell SL. Influence of the Lipid Backbone on Electrochemical Phase Behavior. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14290-14301. [PMID: 36354380 PMCID: PMC9686133 DOI: 10.1021/acs.langmuir.2c02370] [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: 08/30/2022] [Revised: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Sphingolipids are an important class of lipids found in mammalian cell membranes with important structural and signaling roles. They differ from another major group of lipids, the glycerophospholipids, in the connection of their hydrocarbon chains to their headgroups. In this study, a combination of electrochemical and structural methods has been used to elucidate the effect of this difference on sphingolipid behavior in an applied electric field. N-Palmitoyl sphingomyelin forms bilayers of similar coverage and thickness to its close analogue di-palmitoyl phosphatidylcholine. Grazing incidence diffraction data show slightly closer packing and a smaller chain tilt angle from the surface normal. Electrochemical IR results at low charge density show that the difference in tilt angle is retained on deposition to form bilayers. The bilayers respond differently to increasing electric field strength: chain tilt angles increase for both molecules, but sphingomyelin chains remain tilted as field strength is further increased. This behavior is correlated with disruption of the hydrogen-bonding network of small groups of sphingomyelin molecules, which may have significance for the behavior of molecules in lipid rafts in the presence of strong fields induced by ion gradients or asymmetric distribution of charged lipids.
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Affiliation(s)
- Philip
N. Jemmett
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - David C. Milan
- Department
of Chemistry, University of Liverpool, Crown Street, LiverpoolL69 7ZD, UK
| | - Richard J. Nichols
- Department
of Chemistry, University of Liverpool, Crown Street, LiverpoolL69 7ZD, UK
| | - Thomas Howitt
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Alexandra L. Martin
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Thomas Arnold
- Diamond
Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OxfordshireOX11
0DE, UK
- European
Spallation Source ERICPO Box 176, LundSE-221
00, Sweden
- ISIS
Pulsed Neutron and Muon Source, Science and Technology Facilities
Council, Rutherford Appleton Laboratory, Harwell, OxfordshireOX11 0QX, UK
- Department
of Chemistry, University of Bath, Claverton Down, BathBA2 7AY, UK
| | - Jonathan L. Rawle
- Diamond
Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OxfordshireOX11
0DE, UK
| | - Christopher L. Nicklin
- Diamond
Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OxfordshireOX11
0DE, UK
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Liam R. Cox
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
| | - Sarah L. Horswell
- School
of Chemistry, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK
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25
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Gul G, Faller R, Ileri-Ercan N. Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery. Biophys J 2022; 121:4271-4279. [PMID: 36230001 PMCID: PMC9703093 DOI: 10.1016/j.bpj.2022.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/28/2022] [Accepted: 10/11/2022] [Indexed: 12/14/2022] Open
Abstract
To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.
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Affiliation(s)
- Gulsah Gul
- Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey; Department of Chemical Engineering, University of California, Davis, Davis, California
| | - Roland Faller
- Department of Chemical Engineering, University of California, Davis, Davis, California
| | - Nazar Ileri-Ercan
- Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey.
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26
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Vogel K, Bläske T, Nagel MK, Globisch C, Maguire S, Mattes L, Gude C, Kovermann M, Hauser K, Peter C, Isono E. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat Commun 2022; 13:6897. [PMID: 36371501 PMCID: PMC9653390 DOI: 10.1038/s41467-022-34637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
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Affiliation(s)
- Karin Vogel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Tobias Bläske
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Marie-Kristin Nagel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Christoph Globisch
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Shane Maguire
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Lorenz Mattes
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christian Gude
- grid.6936.a0000000123222966School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Kovermann
- grid.9811.10000 0001 0658 7699NMR, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Karin Hauser
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christine Peter
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Erika Isono
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
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27
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Fernandes JB, Yu Y, Klauda JB. Molecular dynamics simulations of the human ocular lens with age and cataract. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184025. [PMID: 35944665 DOI: 10.1016/j.bbamem.2022.184025] [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: 03/22/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The human ocular lens consists primarily of elongated, static fibers characterized by high stability and low turnover, which differ dramatically in their composition and properties from other biological membranes. Cholesterol (Chol) and sphingolipids (SL) are present at high concentrations, including saturated SLs, such as dihyrosphingomyelin (DHSM). Past molecular dynamics simulations demonstrated that the presence of DHSM and high Chol concentration contributes to higher order in lipid membranes. This current study simulated more complex models of human lens membranes. Models were developed representing physiological compositions in cataractous lenses aged 74 ± 6 years and in healthy lenses aged 22 ± 4, 41 ± 6, and 69 ± 3 years. With older age, Chol and ceramide concentrations increase and glycerophospholipid concentration decreases. With cataract, ceramide concentration increases and Chol and glycerophospholipid concentrations decrease. Surface area per lipid, deuterium order parameters (SCD), sterol tilt angle, electron density profiles, bilayer thickness, chain interdigitation, two-dimensional radial distribution functions (2D-RDF), lipid clustering, and hydrogen bonding were calculated for all simulations. All systems exhibited low surface area per lipid and high bilayer thickness, indicative of strong vertical packing. SCD parameters suggest similarly, with saturated tails in the hydrophobic core of the membrane having elevated order. Vertical packing and acyl tail order increased with both age and cataract condition. Lateral diffusion decreased with age and cataracts, with the older and cataractous models demonstrating increased long-range structure by the 2D-RDF analysis. In future work examining the membrane proteins of the lens, these models can serve as a physiologically accurate representation of the lens lipidome.
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Affiliation(s)
- Joshua B Fernandes
- Department of Chemical and Biomolecular Engineering, College Park, MD 20742, USA
| | - Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, College Park, MD 20742, USA; Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
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28
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Lundborg M, Wennberg C, Lidmar J, Hess B, Lindahl E, Norlén L. Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophys J 2022; 121:3837-3849. [PMID: 36104960 PMCID: PMC9674988 DOI: 10.1016/j.bpj.2022.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/22/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022] Open
Abstract
A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics and skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skin's barrier structure to predict skin permeability and the effects of chemical penetration enhancers. In particular, we introduce a new approach to use two-dimensional reaction coordinates in the accelerated weight histogram method, where we combine sampling along spatial coordinates with an alchemical perturbation virtual coordinate. We present predicted properties for 20 permeants, and demonstrate how our approach improves correlation with ex vivo/in vitro skin permeation data. For the compounds included in this study, the obtained log KPexp-calc mean square difference was 0.9 cm2 h-2.
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Affiliation(s)
| | | | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Erik Lindahl
- Department of Biophysics and Biochemistry, Science for Life Laboratory, Stockholm University, Solna, Sweden; Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden.
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29
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Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys J 2022; 121:3630-3650. [PMID: 35778842 PMCID: PMC9617161 DOI: 10.1016/j.bpj.2022.06.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Francesco Di Natale
- Applications, Simulations, and Quality, Lawrence Livermore National Laboratory, Livermore, California
| | | | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Albert H Chan
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Harsh Bhatia
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Gulcin Gulten
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tyler Reddy
- CCS-7, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Violetta Burns
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Nick Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Peer-Timo Bremer
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - De Chen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Rebika Shrestha
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thomas Turbyville
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
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30
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Umegawa Y, Shimonishi T, Tsuchikawa H, Murata M. LnDOTA-d 8 , a versatile chemical-shift thermometer for 2 H solid-state NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:1005-1013. [PMID: 35938541 DOI: 10.1002/mrc.5303] [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: 05/30/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
2 H solid-state nuclear magnetic resonance (NMR) is a method for examining the mobility and orientation of molecules in the field of biophysics. In studies on lipid bilayer membranes, 2 H NMR is often adopted to detect a phase transition from the gel to the liquid-crystal phase, which is observed as a change in spectral shape, and to evaluate the ordering of lipid alkyl chains using quadrupole coupling values. Because the mobility of membrane lipids is highly temperature dependent, precise temperature control is a prerequisite for evaluating the physical properties of membranes. Generally, NMR instruments monitor the temperature of the variable temperature (VT) gas. The temperature inside the sample tube and the VT gas match only when the heat generated by the radio frequency (rf) pulse emitted from the coil or magic angle spinning is significantly lower than the cooling capacity of the VT gas. In other words, the sample temperature inside the tube depends on the measurement method. Therefore, in this study, we took advantage of temperature-dependent changes in the chemical shift of a paramagnetic metal-ligand complex. We designed and synthesized a deuterated ligand complex and evaluated its temperature dependence as a thermometer for 2 H solid-state NMR spectroscopy. We chose Tb, Dy, Ho, and Er as the paramagnetic central metals. We then measured the 2 H NMR spectrum of each metal complex and confirmed the 2 H chemical shift to be temperature dependent. Furthermore, with the use of the thermometer molecule with Er, we succeeded in accurately evaluating the segmental melting of an alkyl chain in lipid bilayers with 0.1°C accuracy.
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Affiliation(s)
- Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- JST ERATO, Lipid Active Structure Project and Project Research Center for Fundamental Science, Osaka University, Osaka, Japan
| | - Takeshi Shimonishi
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- JST ERATO, Lipid Active Structure Project and Project Research Center for Fundamental Science, Osaka University, Osaka, Japan
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31
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Braun RJ, Swanson JMJ. Capturing the Liquid-Crystalline Phase Transformation: Implications for Protein Targeting to Sterol Ester-Rich Lipid Droplets. MEMBRANES 2022; 12:949. [PMID: 36295707 PMCID: PMC9607156 DOI: 10.3390/membranes12100949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Lipid droplets are essential organelles that store and traffic neutral lipids. The phospholipid monolayer surrounding their neutral lipid core engages with a highly dynamic proteome that changes according to cellular and metabolic conditions. Recent work has demonstrated that when the abundance of sterol esters increases above a critical concentration, such as under conditions of starvation or high LDL exposure, the lipid droplet core can undergo an amorphous to liquid-crystalline phase transformation. Herein, we study the consequences of this transformation on the physical properties of lipid droplets that are thought to regulate protein association. Using simulations of different sterol-ester concentrations, we have captured the liquid-crystalline phase transformation at the molecular level, highlighting the alignment of sterol esters in alternating orientations to form concentric layers. We demonstrate how ordering in the core permeates into the neutral lipid/phospholipid interface, changing the magnitude and nature of neutral lipid intercalation and inducing ordering in the phospholipid monolayer. Increased phospholipid packing is concomitant with altered surface properties, including smaller area per phospholipid and substantially reduced packing defects. Additionally, the ordering of sterol esters in the core causes less hydration in more ordered regions. We discuss these findings in the context of their expected consequences for preferential protein recruitment to lipid droplets under different metabolic conditions.
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32
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Wei X, Liu N, Song J, Ren C, Tang X, Jiang W. Effect of silica nanoparticles on cell membrane fluidity: The role of temperature and membrane composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156552. [PMID: 35688239 DOI: 10.1016/j.scitotenv.2022.156552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
The increasing production and application of silica nanoparticles (SiO2 NPs) raise public concern regarding their environmental and health risks. The fluidity of the cell membrane is essential for supporting membrane proteins and regulating membrane transport. Changes in membrane fluidity inevitably influence the physiological activities of cells and even cause biological effects. In this study, the effect of SiO2 NPs on membrane fluidity was studied at 25 °C and 37 °C, and the role of membrane components in SiO2 NP-membrane interactions was investigated using giant plasma membrane vesicles (GPMVs) isolated from RBL-2H3 cells. SiO2 NPs cause a more serious membrane fluidity decrease at 37 °C than at 25 °C, which is revealed by the shift of Laurdan fluorescence emission and further quantified via forster resonance energy transfer (FRET) experiments. In addition, after the removal of 75 % cholesterol from the membrane, SiO2 NPs caused a greater extent of membrane gelation. These results indicate that SiO2 NPs prefer to interact with membranes that are more dynamic and less densely packed. Moreover, fluorescent experiments confirmed that the existence of phosphatidyl ethanolamine (PE) and phosphoinositide (PI) can mitigate NP-induced membrane gelation. Molecular dynamics simulation further demonstrated that SiO2 NPs form hydrogen bonds with the terminal of PE or PI but with the -PO4-- group in the middle of phosphatidylcholine (PC). The bonding that occurs in the terminal gives less restriction of phospholipid movement and a weaker effect on membrane fluidity. This research provides both evidence and mechanisms of SiO2 NP-induced membrane fluidity changes, which are helpful for understanding cell membrane damage and the biological effects of NPs.
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Affiliation(s)
- Xiaoran Wei
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China; Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Nan Liu
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Jian Song
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Chao Ren
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaowen Tang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266071, China
| | - Wei Jiang
- Environment Research Institute, Shandong University, Qingdao 266237, China.
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33
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Chen LY. Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183975. [PMID: 35654150 DOI: 10.1016/j.bbamem.2022.183975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37 °C.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, The University of Texas at San Antonio, San Antonio, TX 78249, USA.
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34
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Shamaprasad P, Frame CO, Moore TC, Yang A, Iacovella CR, Bouwstra JA, Bunge AL, McCabe C. Using molecular simulation to understand the skin barrier. Prog Lipid Res 2022; 88:101184. [PMID: 35988796 PMCID: PMC10116345 DOI: 10.1016/j.plipres.2022.101184] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022]
Abstract
Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.
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Affiliation(s)
- Parashara Shamaprasad
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Chloe O Frame
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Alexander Yang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Joke A Bouwstra
- Division of BioTherapeutics, LACDR, Leiden University, 2333 CC Leiden, the Netherlands
| | - Annette L Bunge
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, United States of America
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America; School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, United Kingdom.
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35
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Exploration of Diazaspiro Cores as Piperazine Bioisosteres in the Development of σ2 Receptor Ligands. Int J Mol Sci 2022; 23:ijms23158259. [PMID: 35897835 PMCID: PMC9332756 DOI: 10.3390/ijms23158259] [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: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023] Open
Abstract
A series of σ2R compounds containing benzimidazolone and diazacycloalkane cores was synthesized and evaluated in radioligand binding assays. Replacing the piperazine moiety in a lead compound with diazaspiroalkanes and the fused octahydropyrrolo[3,4-b] pyrrole ring system resulted in a loss in affinity for the σ2R. On the other hand, the bridged 2,5-diazabicyclo[2.2.1]heptane, 1,4-diazepine, and a 3-aminoazetidine analog possessed nanomolar affinities for the σ2R. Computational chemistry studies were also conducted with the recently published crystal structure of the σ2R/TMEM97 and revealed that hydrogen bond interactions with ASP29 and π-stacking interactions with TYR150 were largely responsible for the high binding affinity of small molecules to this protein.
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36
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Caro-Gómez LA, Rosas-Trigueros JL, Mixcoha E, Zamorano-Carrillo A, Martínez-Martínez J, Benítez-Cardoza CG. Anti-apoptotic Bcl-2 protein in apo and holo conformation anchored to the membrane: comparative molecular dynamics simulations. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, SEPI de la ESCOM del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Edgar Mixcoha
- Catedrático-CONACYT Instituto Nacional de Psiquiatría Ramon de la Fuente Muñiz, Mexico City, Mexico
| | - Absalom Zamorano-Carrillo
- Laboratorio de Bioquímica y Biofísica Computacional, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
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37
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Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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Santos AL, Liu D, Reed AK, Wyderka AM, van Venrooy A, Li JT, Li VD, Misiura M, Samoylova O, Beckham JL, Ayala-Orozco C, Kolomeisky AB, Alemany LB, Oliver A, Tegos GP, Tour JM. Light-activated molecular machines are fast-acting broad-spectrum antibacterials that target the membrane. SCIENCE ADVANCES 2022; 8:eabm2055. [PMID: 35648847 PMCID: PMC9159576 DOI: 10.1126/sciadv.abm2055] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/14/2022] [Indexed: 06/01/2023]
Abstract
The increasing occurrence of antibiotic-resistant bacteria and the dwindling antibiotic research and development pipeline have created a pressing global health crisis. Here, we report the discovery of a distinctive antibacterial therapy that uses visible (405 nanometers) light-activated synthetic molecular machines (MMs) to kill Gram-negative and Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus, in minutes, vastly outpacing conventional antibiotics. MMs also rapidly eliminate persister cells and established bacterial biofilms. The antibacterial mode of action of MMs involves physical disruption of the membrane. In addition, by permeabilizing the membrane, MMs at sublethal doses potentiate the action of conventional antibiotics. Repeated exposure to antibacterial MMs is not accompanied by resistance development. Finally, therapeutic doses of MMs mitigate mortality associated with bacterial infection in an in vivo model of burn wound infection. Visible light-activated MMs represent an unconventional antibacterial mode of action by mechanical disruption at the molecular scale, not existent in nature and to which resistance development is unlikely.
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Affiliation(s)
- Ana L. Santos
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- IdISBA–Fundación de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Dongdong Liu
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Anna K. Reed
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Aaron M. Wyderka
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | | | - John T. Li
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Victor D. Li
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Mikita Misiura
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Olga Samoylova
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Jacob L. Beckham
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | | | | | - Lawrence B. Alemany
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Shared Equipment Authority, Rice University, Houston, TX 77005, USA
| | - Antonio Oliver
- IdISBA–Fundación de Investigación Sanitaria de las Islas Baleares, Palma, Spain
- Servicio de Microbiologia, Hospital Universitari Son Espases, Palma, Spain
| | - George P. Tegos
- Office of Research, Reading Hospital, Tower Health, 420 S. Fifth Avenue, West Reading, PA 19611, USA
| | - James M. Tour
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, Houston, TX 77005, USA
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005, USA
- NanoCarbon Center and the Welch Institute for Advanced Materials, Rice University, Houston, TX 77005, USA
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Winslow M, Robinson D. Computational development of a phase-sensitive membrane raft probe. Phys Chem Chem Phys 2022; 24:8260-8268. [PMID: 35319559 DOI: 10.1039/d2cp00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Derivatives of the widely used 1,6-diphenyl-1,3,5-hexatriene molecular probe have been considered using a multiscale approach involving spin-flip time-dependent density functional theory, classical molecular dynamics and hybrid quantum mechanics/molecular mechanics. We identify a potential probe of membrane phase (i.e. to preferentially detect liquid-ordered regions of lipid bilayers), which exhibits restricted access to a conical intersection in the liquid-ordered phase but is freely accessible in less ordered molecular environments. The characteristics of this probe also mark it as a candidate for an aggregation induced emission fluorophore.
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Affiliation(s)
- Max Winslow
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - David Robinson
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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Hsieh MK, Yu Y, Klauda JB. All-Atom Modeling of Complex Cellular Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3-17. [PMID: 34962814 DOI: 10.1021/acs.langmuir.1c02084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.
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Piasentin N, Lian G, Cai Q. Evaluation of Constrained and Restrained Molecular Dynamics Simulation Methods for Predicting Skin Lipid Permeability. ACS OMEGA 2021; 6:35363-35374. [PMID: 34984268 PMCID: PMC8717400 DOI: 10.1021/acsomega.1c04684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 05/05/2023]
Abstract
Recently, molecular dynamics (MD) simulations have been utilized to investigate the barrier properties of human skin stratum corneum (SC) lipid bilayers. Different MD methods and force fields have been utilized, with predicted permeabilities varying by few orders of magnitude. In this work, we compare constrained MD simulations with restrained MD simulations to obtain the potential of the mean force and the diffusion coefficient profile for the case of a water molecule permeating across an SC lipid bilayer. Corresponding permeabilities of the simulated lipid bilayer are calculated via the inhomogeneous solubility diffusion model. Results show that both methods perform similarly, but restrained MD simulations have proven to be the more robust approach for predicting the potential of the mean force profile. Critical to both methods are the sampling of the whole trans-bilayer axis and the following symmetrization process. Re-analysis of the previously reported free energy profiles showed that some of the discrepancies in the reported permeability values is due to misquotation of units, while some are due to the inaccurately obtained potential of the mean force. By using the existing microscopic geometrical models via the intercellular lipid pathway, the permeation through the whole SC is predicted from the MD simulation results, and the predicted barrier properties have been compared to experimental data from the literature with good agreement.
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Affiliation(s)
- Nicola Piasentin
- Department
of Chemical and Process Engineering, University
of Surrey, Guildford GU27XH, U.K..
- Unilever
R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K..
| | - Guoping Lian
- Department
of Chemical and Process Engineering, University
of Surrey, Guildford GU27XH, U.K..
- Unilever
R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K..
- . Phone: +44 1234 222741
| | - Qiong Cai
- Department
of Chemical and Process Engineering, University
of Surrey, Guildford GU27XH, U.K..
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42
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Gupta M, Weaver DF. Microsecond molecular dynamics studies of cholesterol-mediated myelin sheath degeneration in early Alzheimer's disease. Phys Chem Chem Phys 2021; 24:222-239. [PMID: 34878462 DOI: 10.1039/d1cp03844c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cholesterol-mediated perturbations of membrane structural integrity are key early events in the molecular pathogenesis of Alzheimer's disease (AD). In AD, protein misfolding (proteopathy) and pro-inflammatory conditions (immunopathy) culminate in neuronal death, a process enabled by altered membrane biophysical properties which render neurons more susceptible to proteopathic and immunopathic cytotoxicities. Since cholesterol is a principal neuronal membrane lipid, normal cholesterol homeostasis is central to membrane health; also, since increased cholesterol composition is especially present in neuronal myelin sheath (i.e. brain "white matter"), recent studies have not surprisingly revealed that white matter atrophy precedes the conventional biomarkers of AD (amyloid plaques, tau tangles). Employing extensive microsecond all-atom molecular dynamics simulations, we investigated biophysical and mechanical properties of myelin sheath membrane as a function of cholesterol mole fraction (χCHL). Impaired χCHL modulates multiple bilayer properties, including surface area per lipid (APL), chain order, number and mass density profiles, area compressibility and bending moduli, bilayer thickness, lipid tilt angles, H-bonding interactions and tail interdigitation. The increased orientational ordering of both palmitoyl and oleoyl chains in model healthy myelin sheath (HMS) membranes illustrates the condensing effect of cholesterol. With an increase in χCHL, number density profiles of water tend to attain bulk water number density more quickly, indicating shrinkage in the interfacial region with increasing χCHL. The average tilt value is 11.5° for the C10-C13 angle in cholesterol and 64.2° for the P-N angle in POPC lipids in HMS. These calculations provide a molecular-level understanding of myelin sheath susceptibility to pathology as an early event in the pathogenesis of AD.
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Affiliation(s)
- Mayuri Gupta
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, M5T 0S8, Canada.
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, M5T 0S8, Canada. .,Departments of Chemistry, Medicine and Pharmaceutical Sciences, University of Toronto, Toronto, ON, M55 3H6, Canada
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Canner SW, Feller SE, Wassall SR. Molecular Organization of a Raft-like Domain in a Polyunsaturated Phospholipid Bilayer: A Supervised Machine Learning Analysis of Molecular Dynamics Simulations. J Phys Chem B 2021; 125:13158-13167. [PMID: 34812629 DOI: 10.1021/acs.jpcb.1c06511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous health benefits are associated with omega-3 polyunsaturated fatty acids (n-3 PUFA) consumed in fish oils. An understanding of the mechanism remains elusive. The plasma membrane as a site of action is the focus in this study. With large-scale all-atom MD simulations run on a model membrane (1050 lipid molecules), we observed the evolution over time (6 μs) of a circular (raft-like) domain composed of N-palmitoylsphingomyelin (PSM) and cholesterol embedded into a surrounding (non-raft) patch composed of polyunsaturated 1-palmitoyl-2-docosahexaenoylphosphatylcholine (PDPC) (1:1:1 mol). A supervised machine learning algorithm was developed to characterize the migration of each lipid based on molecular conformation and the local environment. PDPC molecules were seen to infiltrate the ordered raft-like domain in a small amount, while a small concentration of PSM and cholesterol molecules was seen to migrate into the disordered non-raft region. Enclosing the raft-like domain, a narrow (∼2 nm in width) interfacial zone composed of PDPC, PSM, and cholesterol that buffers the substantial difference in order (ΔSCD ≈ 0.12) between raft-like and non-raft environments was seen to form. Our results suggest that n-3 PUFA regulate the architecture of lipid rafts enriched in sphingolipids and cholesterol with a minimal effect on order within their interior in membranes.
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Affiliation(s)
- Samuel W Canner
- Department of Physics, IUPUI, Indianapolis, Indiana 46202-3273, United States.,Department of Computer and Information Science, IUPUI, Indianapolis, Indiana 46202-5132, United States
| | - Scott E Feller
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, United States
| | - Stephen R Wassall
- Department of Physics, IUPUI, Indianapolis, Indiana 46202-3273, United States
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Kognole AA, Lee J, Park SJ, Jo S, Chatterjee P, Lemkul JA, Huang J, MacKerell AD, Im W. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. J Comput Chem 2021; 43:359-375. [PMID: 34874077 DOI: 10.1002/jcc.26795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/10/2021] [Accepted: 11/25/2021] [Indexed: 12/18/2022]
Abstract
Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. In addition, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. The capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.
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Affiliation(s)
- Abhishek A Kognole
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Jumin Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Sang-Jun Park
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois, USA
| | - Payal Chatterjee
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Zhejiang, Hangzhou, China
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
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45
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Park S, Im W, Pastor RW. Developing initial conditions for simulations of asymmetric membranes: a practical recommendation. Biophys J 2021; 120:5041-5059. [PMID: 34653389 DOI: 10.1016/j.bpj.2021.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/09/2021] [Accepted: 10/08/2021] [Indexed: 01/03/2023] Open
Abstract
It has been proposed that the surface tension difference between leaflets (or differential stress) in asymmetric bilayers is generally nonvanishing. This implies that there is no unique approach to generate initial conditions for simulations of asymmetric bilayers in the absence of experimentally derived constraints. Current generation methods include individual area per lipid (APL) based, leaflet surface area (SA) matching, and zero leaflet tension based (0-DS). This work adds a bilayer-based approach that aims for achieving partial chemical equilibrium by interleaflet switching of selected lipids via P21 periodic boundary conditions. Based on a recently proposed theoretical framework, we obtained expressions for tensions in asymmetric bilayers from both the bending and area strains. We also developed a quantitative measure for the energetic penalty from the differential stress. The impacts of APL-, SA-, and 0-DS-based approaches on mechanical properties are assessed for two different asymmetric bilayers. The lateral pressure profile and its moments differ significantly for each method, whereas the area compressibility modulus is relatively insensitive. Application of P21 periodic boundary conditions (APL/P21, SA/P21, and 0-DS/P21) results in better agreement in mechanical properties between asymmetric bilayers generated by APL-, SA-, and 0-DS-based approaches, in which changes are the smallest for bilayers from the SA-based method. The estimated differential stress from the theory shows good agreement with that from the simulations. These simulation results and the good agreement between the predicted and observed differential stress further support the theoretical framework in which bilayer mechanical properties are outcomes of the interplay between intrinsic bending and asymmetric lipid packing. Based on the simulation results and theoretical predictions, the SA/P21-based, or at least the SA-based (when the differential stress is small), approach is recommended as a practical method for developing initial conditions for asymmetric bilayer simulations.
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Affiliation(s)
- Sooyhung Park
- Department of Biological Sciences, Bethlehem, Pennsylvania; Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania.
| | - Wonpil Im
- Department of Biological Sciences, Bethlehem, Pennsylvania; Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Gupta M, Weaver DF. Axonal plasma membrane-mediated toxicity of cholesterol in Alzheimer's disease: A microsecond molecular dynamics study. Biophys Chem 2021; 281:106718. [PMID: 34808480 DOI: 10.1016/j.bpc.2021.106718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease is increasingly being recognized as an immune-mediated disease of brain. Since physiological brain health and brain immune function is dependent upon homeostatic neuronal membrane structure and function, alterations in membrane lipid biochemistry may predispose to disease. Brain is rich in cholesterol, and cholesterol metabolism dysfunction is a known risk factor for AD. Employing extensive microsecond all-atom molecular dynamics simulations, we investigated the properties of model neuronal membranes as a function of cholesterol concentration; phospholipid and phospholipid/cholesterol bilayers were also simulated to compare against available experimental data. Increased cholesterol concentrations compact and stiffen the lipid membrane, reducing permeability while modulating local water densities in the peri-membranous environment. Conversely, lower cholesterol mole fraction yields membranes with increased molecular disorder, enhanced fluidity, higher molecular tilting, and augmented interdigitation between bilayer leaflet lipids. Our findings provide a molecular insight on effect of cholesterol composition on various biochemical processes occurring at neuronal axon plasma membrane. These calculations also endeavor to establish a membrane-based link between cholesterol as an AD risk factor and possible AD pathology.
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Affiliation(s)
- Mayuri Gupta
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto M5T 0S8, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto M5T 0S8, Canada; Department of Chemistry, University of Toronto, Toronto M55 3H6, Canada; Department of Medicine, University of Toronto, Toronto M5G 2C4, Canada; Department of Pharmaceutical Sciences, University of Toronto, Toronto M5S 3M2, Canada.
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47
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Suga K, Matsui D, Watanabe N, Okamoto Y, Umakoshi H. Insight into the Exosomal Membrane: From Viewpoints of Membrane Fluidity and Polarity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11195-11202. [PMID: 34528800 DOI: 10.1021/acs.langmuir.1c00687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Numerous research studies have been done for exosomes, particularly focusing on membrane proteins and included nucleic acids, and the volume of the knowledge about the lipids in the exosomal membrane has been increasing. However, the dynamic property of the exosomal membrane is hardly studied. By employing milk exosome as an example, herein the exosomal membrane was characterized focusing on the membrane fluidity and polarity. The lipid composition and phase state of milk exosome (exosome from bovine milk) were estimated. The milk exosome contained enriched Chol (43.6 mol % in total lipid extracts), which made the membrane in the liquid-ordered (lo) phase by interacting with phospholipids. To suggest a model of exosomal vesicle cargo, the liposome compositions that mimic milk exosome were studied: liposomes were made of cholesterol (Chol), milk sphingomyelin (milk SM), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). By using fluorescent probes 1,6-diphenyl-1,3,5-hexatriene and 6-dodecanoyl-2-dimethylaminonaphthalene, the microenvironments of submicron-sized membranes of exosome and model liposomes were investigated. The membrane fluidity of milk exosome was slightly higher than those of Chol/milk SM/POPC liposomes with a similar content of Chol, suggesting the presence of enriched unsaturated lipids. The most purposeful membrane property was obtained by the liposome composition of Chol/milk SM/POPC = 40/15/45. From the above, it is concluded that Chol is a fundamental component of the milk exosomal membrane to construct the enriched lo phase, which could increase the membrane rigidity and contribute to the function of exosome.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
- Department of Chemical Engineering, Tohoku University, 6-6-07 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 9808579, Japan
| | - Daiki Matsui
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
| | - Nozomi Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
| | - Yukihiro Okamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 5608531, Japan
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48
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Siani P, Donadoni E, Ferraro L, Re F, Di Valentin C. Molecular dynamics simulations of doxorubicin in sphingomyelin-based lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1864:183763. [PMID: 34506799 DOI: 10.1016/j.bbamem.2021.183763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022]
Abstract
Doxorubicin (DOX) is one of the most efficient antitumor drugs employed in numerous cancer therapies. Its incorporation into lipid-based nanocarriers, such as liposomes, improves the drug targeting into tumor cells and reduces drug side effects. The carriers' lipid composition is expected to affect the interactions of DOX and its partitioning into liposomal membranes. To get a rational insight into this aspect and determine promising lipid compositions, we use numerical simulations, which provide unique information on DOX-membrane interactions at the atomic level of resolution. In particular, we combine classical molecular dynamics simulations and free energy calculations to elucidate the mechanism of penetration of a protonated Doxorubicin molecule (DOX+) into potential liposome membranes, here modeled as lipid bilayers based on mixtures of phosphatidylcholine (PC), sphingomyelin (SM) and cholesterol lipid molecules, of different compositions and lipid phases. Moreover, we analyze DOX+ partitioning into relevant regions of SM-based lipid bilayer systems using a combination of free energy methods. Our results show that DOX+ penetration and partitioning are facilitated into less tightly packed SM-based membranes and are dependent on lipid composition. This work paves the way to further investigations of optimal formulations for lipid-based carriers, such as those associated with pH-responsive membranes.
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Affiliation(s)
- Paulo Siani
- Department of Materials Science, University of Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Edoardo Donadoni
- Department of Materials Science, University of Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Lorenzo Ferraro
- Department of Materials Science, University of Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Francesca Re
- School of Medicine and Surgery, University of Milano-Bicocca, via Raoul Follereau 3, Vedano al Lambro, MB 20854, Italy; BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, Italy
| | - Cristiana Di Valentin
- Department of Materials Science, University of Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy; BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, Italy.
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Kaltenegger M, Kremser J, Frewein MPK, Ziherl P, Bonthuis DJ, Pabst G. Intrinsic lipid curvatures of mammalian plasma membrane outer leaflet lipids and ceramides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183709. [PMID: 34332987 DOI: 10.1016/j.bbamem.2021.183709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/26/2023]
Abstract
We developed a global X-ray data analysis method to determine the intrinsic curvatures of lipids hosted in inverted hexagonal phases. In particular, we combined compositional modelling with molecular shape-based arguments to account for non-linear mixing effects of guest-in-host lipids on intrinsic curvature. The technique was verified by all-atom molecular dynamics simulations and applied to sphingomyelin and a series of phosphatidylcholines and ceramides with differing composition of the hydrocarbon chains. We report positive lipid curvatures for sphingomyelin and all phosphatidylcholines with disaturated and monounsaturated hydrocarbons. Phosphatidylcholines with diunsaturated hydrocarbons in turn yielded intrinsic lipid curvatures with negative values. All ceramides, with chain lengths varying between C2:0 and C24:0, displayed significant negative lipid curvature values. Moreover, we report non-additive mixing for C2:0 ceramide and sphingomyelin. This suggests for sphingolipids that in addition to lipid headgroup and hydrocarbon chain volumes also lipid-specific interactions are important contributors to membrane curvature stress.
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Affiliation(s)
- Michael Kaltenegger
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria; BioTechMed Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Johannes Kremser
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria; BioTechMed Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Moritz P K Frewein
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria; BioTechMed Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; Institut Laue-Langevin, 38043 Grenoble, France
| | - Primož Ziherl
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia; Jožef Stefan Institute, Ljubljana, Slovenia
| | - Douwe J Bonthuis
- Graz University of Technology, Institute of Theoretical and Computational Physics, NAWI Graz, 8010 Graz, Austria
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, NAWI Graz, 8010 Graz, Austria; BioTechMed Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria.
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