1
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Tharmasothirajan A, Melcr J, Linney J, Gensch T, Krumbach K, Ernst KM, Brasnett C, Poggi P, Pitt AR, Goddard AD, Chatgilialoglu A, Marrink SJ, Marienhagen J. Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis. Nat Commun 2023; 14:5619. [PMID: 37699874 PMCID: PMC10497605 DOI: 10.1038/s41467-023-40947-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/16/2023] [Indexed: 09/14/2023] Open
Abstract
Microbial synthesis of nutraceutically and pharmaceutically interesting plant polyphenols represents a more environmentally friendly alternative to chemical synthesis or plant extraction. However, most polyphenols are cytotoxic for microorganisms as they are believed to negatively affect cell integrity and transport processes. To increase the production performance of engineered cell factories, strategies have to be developed to mitigate these detrimental effects. Here, we examine the accumulation of the stilbenoid resveratrol in the cell membrane and cell wall during its production using Corynebacterium glutamicum and uncover the membrane rigidifying effect of this stilbenoid experimentally and with molecular dynamics simulations. A screen of free fatty acid supplements identifies palmitelaidic acid and linoleic acid as suitable additives to attenuate resveratrol's cytotoxic effects resulting in a three-fold higher product titer. This cost-effective approach to counteract membrane-damaging effects of product accumulation is transferable to the microbial production of other polyphenols and may represent an engineering target for other membrane-active bioproducts.
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Affiliation(s)
- Apilaasha Tharmasothirajan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - John Linney
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK
| | - Thomas Gensch
- Institute for Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Karla Marlen Ernst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Christopher Brasnett
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paola Poggi
- Remembrane Srl, via San Francesco 40, 40026, Imola, Italy
| | - Andrew R Pitt
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, UK
| | - Alan D Goddard
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK
| | | | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
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2
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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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3
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Murata M, Matsumori N, Kinoshita M, London E. Molecular substructure of the liquid-ordered phase formed by sphingomyelin and cholesterol: sphingomyelin clusters forming nano-subdomains are a characteristic feature. Biophys Rev 2022; 14:655-678. [PMID: 35791389 DOI: 10.1007/s12551-022-00967-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022] Open
Abstract
As a model of lipid rafts, the liquid-ordered (Lo) phase formed by sphingomyelin (SM) and cholesterol (Cho) in bilayer membranes has long attracted the attention of biophysics researchers. New approaches and methodologies have led to a better understanding of the molecular basis of the Lo domain structure. This review summarizes studies on model membrane systems consisting of SM/unsaturated phospholipid/Cho implying that the Lo phase contains SM-based nanodomains (or nano-subdomains). Some of the Lo phase properties may be attributed to these nanodomains. Several studies suggest that the nanodomains contain clustered SM molecules packed densely to form gel-phase-like subdomains of single-digit nanometer size at physiological temperatures. Cho and unsaturated lipids located in the Lo phase are likely to be concentrated at the boundaries between the subdomains. These subdomains are not readily detected in the Lo phase formed by saturated phosphatidylcholine (PC) molecules, suggesting that they are strongly stabilized by homophilic interactions specific to SM, e.g., between SM amide groups. This model for the Lo phase is supported by experiments using dihydro-SM, which is thought to have stronger homophilic interactions than SM, as well as by studies using the enantiomer of SM having opposite stereochemistry to SM at the 2 and 3 positions and by some molecular dynamics (MD) simulations of lipid bilayers containing Lo-lipids. Nanosized gel subdomains seem to play an important role in controlling membrane organization and function in biological membranes.
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Affiliation(s)
- Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan.,ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Masanao Kinoshita
- ERATO, Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan.,Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215 USA
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4
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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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5
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.
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6
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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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7
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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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8
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Yu Y, Klauda JB. Symmetric and Asymmetric Models for the Arabidopsis thaliana Plasma Membrane: A Simulation Study. J Phys Chem B 2021; 125:11418-11431. [PMID: 34617773 DOI: 10.1021/acs.jpcb.1c04704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Arabidopsis thaliana is an important model organism, which has attracted many biologists. While most research efforts have been on studying the genetics and proteins of this organism, a systematic study of its lipidomics is lacking. Here, we present a novel, asymmetric model of its cell membrane with its lipid composition consisting of five glycerophospholipids, two glycolipids, and sitosterol determined from multiple independent experiments. A typical lipid type in plant membranes is glycosyl inositol phosphoryl ceramide (GIPC), which accounts for about 10% of the total lipids in the outer leaflet in our model. Two symmetric models representing the inner and outer leaflets of the membrane were built and simulated until equilibrium was reached and then combined to form the asymmetric model. Our results indicate that the outer leaflet is more rigid and tightly packed compared to the inner leaflet. Pressure profiles for the two leaflets are overall similar though the outer leaflet exhibits larger oscillations. A special focus on lipid organization is discussed and the interplay between glycolipids and sitosterols is found to be important. The current model provides a baseline for future modeling of similar membranes and can be used to study partitioning of small molecules in the membrane or further developed to study the interaction between plant membrane proteins and lipids.
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Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B Klauda
- Biophysics Graduate 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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9
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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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10
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Kumar N, Sastry GN. Study of lipid heterogeneity on bilayer membranes using molecular dynamics simulations. J Mol Graph Model 2021; 108:108000. [PMID: 34365255 DOI: 10.1016/j.jmgm.2021.108000] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/17/2021] [Accepted: 07/29/2021] [Indexed: 11/26/2022]
Abstract
Human cell membranes consist of various lipids that are essential for their structure and function. It typically comprises phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), sphingomyelin (PSM), and cholesterol (CHL). Several experimental and computational techniques have been employed to characterize the composition of human cell membranes, however, CHL enriched membrane is still not clearly understood through these techniques. Molecular dynamics simulation results illustrated the biophysical properties of heterogeneous membranes based on the lipid composition as well as the concentration of lipids, exclusively for CHL and PSM. Herein, we have investigated the structure-function relationships of lipids comparatively to delineate the effect of heterogeneity on the biophysical properties of different membranes. It has been observed that the significant fraction of CHL (i.e., ~33% in ternary, ~25% in quaternary, and ~16% in senary type bilayers) in combination with other lipids introduced compactness, and increased the thickness of the membrane. The analysis of lipid mass density stated that the density of lipid head group, phosphate, and glycerol-ester in presence of CHL with or without PSM is an underlying reason for membrane ordering. Results also revealed that the presence of POPI and POPS are the reasons for an adequate drop in the ordering of lipid chain, particularly on POPE chain. The self-interaction of CHL, PSM, POPE and the interaction of CHL and POPC with POPE seem to determine the structure and function of the heterogeneous membrane. Our findings provide a qualitative understanding of the effect of membrane heterogeneity on the physiological properties of membranes. The structures inspected in this study would help to select the heterogeneous bilayer model to mimic the human cell membranes to analyse or characterize the membrane-associated phenomena.
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Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, U. P., India
| | - G Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, U. P., India; Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India.
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11
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Dingjan T, Futerman AH. The role of the 'sphingoid motif' in shaping the molecular interactions of sphingolipids in biomembranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183701. [PMID: 34302797 DOI: 10.1016/j.bbamem.2021.183701] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/16/2021] [Indexed: 12/28/2022]
Abstract
Sphingolipids can be differentiated from other membrane lipids by the distinctive chemistry of the sphingoid long chain base (LCB), which is generated by the condensation of an amino acid (normally but not always serine) and a fatty acyl CoA (normally palmitoyl CoA) by the pyridoxal phosphate-dependent enzyme, serine palmitoyl transferase (SPT). The first five carbon atoms of the sphingoid LCB, herein defined as the 'sphingoid motif', are largely responsible for the unique chemical and biophysical properties of sphingolipids since they can undergo a relatively large number (compared to other lipid species) of molecular interactions with other membrane lipids, via hydrogen-bonding, charge-pairing, hydrophobic and van der Waals interactions. These interactions are responsible, for instance, for the association of sphingolipids with cholesterol in the membrane lipid bilayer. Here, we discuss some of the unique properties of this sphingoid motif, and in addition to outlining how this structural motif drives intra-bilayer interactions, discuss the atomic details of the interactions with two critical players in the biosynthetic pathway, namely SPT, and the ceramide transport protein, CERT. In the former, the selectivity of sphingolipid synthesis relies on a hydrogen bond interaction between Lys379 of SPTLC2 and the l-serine sidechain hydroxyl moiety. In the latter, the entire sphingoid motif is stereoselectively recognized by a hydrogen-bonding network involving all three sphingoid motif heteroatoms. The remarkable selectivity of these interactions, and the subtle means by which these interactions are modified and regulated in eukaryotic cells raises a number of challenging questions about the generation of these proteins, and of their interactions with the sphingoid motif in evolutionary history.
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Affiliation(s)
- Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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12
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Lipid interactions of an actinoporin pore-forming oligomer. Biophys J 2021; 120:1357-1366. [PMID: 33617834 DOI: 10.1016/j.bpj.2021.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/16/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Abstract
The actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multi-microsecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation, we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.
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13
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Yee SM, Gillams RJ, McLain SE, Lorenz CD. Effects of lipid heterogeneity on model human brain lipid membranes. SOFT MATTER 2021; 17:126-135. [PMID: 33155582 DOI: 10.1039/d0sm01766c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.
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Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Richard J Gillams
- School of Electronics and Computer Science, and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sylvia E McLain
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
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14
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Hanashima S, Fukuda N, Malabed R, Murata M, Kinoshita M, Greimel P, Hirabayashi Y. β-Glucosylation of cholesterol reduces sterol-sphingomyelin interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183496. [PMID: 33130096 DOI: 10.1016/j.bbamem.2020.183496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022]
Abstract
Cholesteryl-β-D-glucoside (ChoGlc) is a mammalian glycolipid that is expressed in brain tissue. The effects of glucosylation on the ordering and lipid interactions of cholesterol (Cho) were examined in membranes composed of N-stearoyl sphingomyelin (SSM), which is abundant in the brain, and to investigate the possible molecular mechanism involved in these interactions. Differential scanning calorimetry revealed that ChoGlc was miscible with SSM in a similar extent of Cho. Solid-state 2H NMR of deuterated SSM and fluorescent anisotropy using 1,6-diphenylhexatriene demonstrated that the glucosylation of Cho significantly reduced the effect of the sterol tetracyclic core on the ordering of SSM chains. The orientation of the sterol core was further examined by solid-state NMR analysis of deuterated and fluorinated ChoGlc analogues. ChoGlc had a smaller tilt angle between the long molecular axis (C3-C17) and the membrane normal than Cho in SSM bilayers, and the fluctuations in the tilt angle were largely unaffected by temperature-dependent mobility changes of SSM acyl chains. This orientation of the sterol core of ChoGlc leads to reduce sterol-SSM interactions. The MD simulation results suggested that the Glc moiety perturbs the SSM-sterol interactions, which reduces the umbrella effect of the phosphocholine headgroup because the hydrophilic glucose moiety resides at the same depth as an SSM amide group. These differences between ChoGlc and Cho also weaken the SSM-ChoGlc interactions. Thus, the distribution and localization of Cho and ChoGlc possibly control the stability of sphingomyelin-based domains that transiently occur at specific locations in biological membranes.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Nanami Fukuda
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Raymond Malabed
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Msanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Peter Greimel
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Institute, Wako, Saitama 351-0198, Japan
| | - Yoshio Hirabayashi
- RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan; Institute for Environmental and Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Urayasu, Chiba 279-0021, Japan
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15
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Smith P, Quinn PJ, Lorenz CD. Two Coexisting Membrane Structures Are Defined by Lateral and Transbilayer Interactions between Sphingomyelin and Cholesterol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9786-9799. [PMID: 32701297 DOI: 10.1021/acs.langmuir.0c01237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure of fully hydrated bilayers composed of equimolar proportions of palmitoylsphingomyelin (PSM) and cholesterol has been examined by synchrotron X-ray powder diffraction and atomistic molecular dynamics (MD) simulations. Two coexisting bilayer structures, which are distinguished by the transbilayer phosphate-phosphate distance of coupled PSM molecules, are observed by diffraction at 37 °C. The MD simulations reveal that PSM molecules in the thicker membrane are characterized by more ordered, more extended, and less interdigitated hydrocarbon tails compared to those in the thinner membrane. Intermolecular hydrogen bonds further distinguish the two bilayer structures, and we observe the disruption of a sphingomyelin intermolecular hydrogen bond network induced by the proximity of cholesterol. Through an unsupervised clustering of interatomic distances, we show for the first time that the asymmetry of phospholipids is important in driving their interactions with cholesterol. We identify four distinct modes of interaction, two of which lead to the dehydration of cholesterol. These two modes of interaction provide the first description of precise physical mechanisms underlying the umbrella model, which itself explains how phospholipids may shield cholesterol from water. The most dehydrating mode of interaction is particular to the N-acylated fatty acid moiety of PSM and thus may explain the long-held observation that cholesterol preferentially mixes with sphingomyelins over glycerophospholipids.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London, WC2R 2LS, U.K
| | - Peter J Quinn
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
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16
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Licari G, Strakova K, Matile S, Tajkhorshid E. Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. Chem Sci 2020; 11:5637-5649. [PMID: 32864081 PMCID: PMC7433777 DOI: 10.1039/d0sc02175j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/29/2020] [Indexed: 12/29/2022] Open
Abstract
Lateral forces in biological membranes affect a variety of dynamic cellular processes. Recent synthetic efforts have introduced fluorescent "flippers" as environment-sensitive planarizable push-pull probes that can detect lipid packing and membrane tension, and respond to lipid-induced mechanical forces by a shift in their spectroscopic properties. Herein, we investigate the molecular origin of the mechanosensitivity of the best known flipper, Flipper-TR, by an extended set of molecular dynamics (MD) simulations in membranes of increasing complexity and under different physicochemical conditions, revealing unprecedented details of the sensing process. Simulations enabled by accurate refinement of Flipper-TR force field using quantum mechanical calculations allowed us to unambiguously correlate the planarization of the two fluorescent flippers to spectroscopic response. In particular, Flipper-TR conformation exhibits bimodal distribution in disordered membranes and a unimodal distribution in highly ordered membranes. Such dramatic change was associated with a shift in Flipper-TR excitation spectra, as supported both by our simulated and experimentally-measured spectra. Flipper-TR sensitivity to phase-transition is confirmed by a temperature-jump protocol that alters the lipid phase of an ordered membrane, triggering an instantaneous mechanical twisting of the probe. Simulations show that the probe is also sensitive to surface tension, since even in a naturally disordered membrane, the unimodal distribution of coplanar flippers can be achieved if a sufficiently negative surface tension is applied to the membrane. MD simulations in ternary mixtures containing raft-like nanodomains show that the probe can discriminate lipid domains in phase-separated complex bilayers. A histogram-based approach, called DOB-phase classification, is introduced that can differentiate regions of disordered and ordered lipid phases by comparing dihedral distributions of Flipper-TR. Moreover, a new sensing mechanism involving the orientation of Flipper-TR is elucidated, corroborating experimental evidence that the probe tilt angle is strongly dependent on lipid ordering. The obtained atomic-resolution description of Flipper-TR mechanosensitivity is key to the interpretation of experimental data and to the design of novel mechanosensors with improved spectroscopic properties.
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Affiliation(s)
- Giuseppe Licari
- NIH Center for Macromolecular Modeling and Bioinformatics , Beckman Institute for Advanced Science and Technology , Department of Biochemistry , Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA . ; Tel: +1-217-244-6914
| | - Karolina Strakova
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics , Beckman Institute for Advanced Science and Technology , Department of Biochemistry , Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA . ; Tel: +1-217-244-6914
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17
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Gu RX, Baoukina S, Tieleman DP. Phase Separation in Atomistic Simulations of Model Membranes. J Am Chem Soc 2020; 142:2844-2856. [DOI: 10.1021/jacs.9b11057] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ruo-Xu Gu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - Svetlana Baoukina
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
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18
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Smith AK, Khayat E, Lockhart C, Klimov DK. Do Cholesterol and Sphingomyelin Change the Mechanism of Aβ 25-35 Peptide Binding to Zwitterionic Bilayer? J Chem Inf Model 2019; 59:5207-5217. [PMID: 31738555 DOI: 10.1021/acs.jcim.9b00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using replica exchange with solute tempering all-atom molecular dynamics, we studied the equilibrium binding of Aβ25-35 peptide to the ternary bilayer composed of an equimolar mixture of dimyristoylphosphatidylcholine (DMPC), N-palmitoylsphingomyelin (PSM), and cholesterol. Binding of the same peptide to the pure DMPC bilayer served as a control. Due to significant C-terminal hydrophobic moment, binding to the ternary and DMPC bilayers promotes helical structure in the peptide. For both bilayers a polarized binding profile is observed, in which the N-terminus anchors to the bilayer surface, whereas the C-terminus alternates between unbound and inserted states. Both ternary and DMPC bilayers feature two Aβ25-35 bound states, surface bound, S, and inserted, I, separated by modest free energy barriers. Experimental data are in agreement with our results but indicate that cholesterol impact is Aβ fragment dependent. For Aβ25-35, we predict that its binding mechanism is independent of the inclusion of PSM and cholesterol into the bilayer.
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Affiliation(s)
- Amy K Smith
- School of Systems Biology , George Mason University , Manassas , Virginia 20110 , United States
| | - Elias Khayat
- School of Systems Biology , George Mason University , Manassas , Virginia 20110 , United States
| | - Christopher Lockhart
- School of Systems Biology , George Mason University , Manassas , Virginia 20110 , United States
| | - Dmitri K Klimov
- School of Systems Biology , George Mason University , Manassas , Virginia 20110 , United States
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19
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Kumari P, Kashyap HK. DMSO induced dehydration of heterogeneous lipid bilayers and its impact on their structures. J Chem Phys 2019; 151:215103. [DOI: 10.1063/1.5127852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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20
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Kumari P, Kumari M, Kashyap HK. Counter-effects of Ethanol and Cholesterol on the Heterogeneous PSM–POPC Lipid Membrane: A Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:9616-9628. [DOI: 10.1021/acs.jpcb.9b07107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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21
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Hanashima S, Murakami K, Yura M, Yano Y, Umegawa Y, Tsuchikawa H, Matsumori N, Seo S, Shinoda W, Murata M. Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup. Biophys J 2019; 117:307-318. [PMID: 31303249 DOI: 10.1016/j.bpj.2019.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
Sphingomyelin (SM) and cholesterol (Cho) are the important lipids for the formation of biologically functional membrane domains, lipid rafts. However, the interaction between Cho and the headgroup of SM remains unclear. In this study, we performed solid-state NMR experiments to reveal the Cho effects on the headgroup conformation using 2H-labeled stearoyl-SM (SSM). Deuterated SSMs at the Cα, Cβ, and Cγ positions of a choline moiety were separately prepared and subjected to NMR measurements to determine the quadrupolar splitting of 2H signals in hydrated SSM unitary and SSM/Cho (1:1) bilayers. Using 2H NMR and 13C-31P REDOR data, the conformation and orientation of the choline moiety were deduced and compared with those derived from molecular dynamics simulations. In SSM unitary bilayers, three torsional angles in the phosphocholine moiety, P-O-Cα-Cβ, were found to be consecutive +gauche(g)/+g/+g or -g/-g/-g. The orientation and conformation of the SSM headgroup were consistent with the results of our molecular dynamics simulations and the previous results on phosphatidylcholines. The quadrupolar coupling at the α methylene group slightly increased in the presence of Cho, and those at the Cβ and Cγ decreased more significantly, thus suggesting that Cho reduced the gauche conformation at the Cα-Cβ torsion. The conformational ensemble in the presence of Cho may enhance the so-called umbrella effect of the SSM headgroup, resulting in the stabilization of Cho near the SM molecules by concealing the hydrophobic Cho core from interfacial water. We also examined the effect of the chiral centers at the sphingosine chain to the headgroup conformation by determining the enantiomeric excess between the diastereomeric +g/+g/+g and -g/-g/-g conformers using (S)-Cα-deuterated and (R)-Cα-deuterated SSMs. Their 2H NMR measurements showed that the chiral centers induced the slight diastereomeric excess in the SM headgroup conformation.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Kazuhiro Murakami
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Michihiro Yura
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan.
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22
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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23
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Wang E, Klauda JB. Structure and Permeability of Ceramide Bilayers and Multilayers. J Phys Chem B 2019; 123:2525-2535. [DOI: 10.1021/acs.jpcb.9b00037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Almeida PF. How to Determine Lipid Interactions in Membranes from Experiment Through the Ising Model. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:21-40. [PMID: 30589556 DOI: 10.1021/acs.langmuir.8b03054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The determination and the meaning of interactions in lipid bilayers are discussed and interpreted through the Ising model. Originally developed to understand phase transitions in ferromagnetic systems, the Ising model applies equally well to lipid bilayers. In the case of a membrane, the essence of the Ising model is that each lipid is represented by a site on a lattice and that the interaction of each site with its nearest neighbors is represented by an energy parameter ω. To calculate the thermodynamic properties of the system, such as the enthalpy, the Gibbs energy, and the heat capacity, the partition function is derived. The calculation of the configurational entropy factor in the partition function, however, requires approximations or the use of Monte Carlo (MC) simulations. Those approximations are described. Ultimately, MC simulations are used in combination with experiment to determine the interaction parameters ω in lipid bilayers. Several experimental approaches are described, which can be used to obtain interaction parameters. They include nearest-neighbor recognition, differential scanning calorimetry, and Förster resonance energy transfer. Those approaches are most powerful when used in combination of MC simulations of Ising models. Lipid membranes of different compositions are discussed, which have been studied with these approaches. They include mixtures of cholesterol, saturated (ordered) phospholipids, and unsaturated (disordered) phospholipids. The interactions between those lipid species are examined as a function of molecular properties such as the degree of unsaturation and the acyl chain length. The general rule that emerges is that interactions between different lipids are usually unfavorable. The exception is that cholesterol interacts favorably with saturated (ordered) phospholipids. However, the interaction of cholesterol with unsaturated phospholipids becomes extremely unfavorable as the degree of unsaturation increases.
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Affiliation(s)
- Paulo F Almeida
- Department of Chemistry and Biochemistry , University of North Carolina Wilmington , Wilmington , North Carolina 28403 , United States
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26
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Hanashima S, Ibata Y, Watanabe H, Yasuda T, Tsuchikawa H, Murata M. Side-chain deuterated cholesterol as a molecular probe to determine membrane order and cholesterol partitioning. Org Biomol Chem 2019; 17:8601-8610. [DOI: 10.1039/c9ob01342c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
24dCho, which perfectly retains the cholesterol's membrane properties, was developed to examine cholesterol's interactions and membrane partitions using solid state 2H NMR.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Yuki Ibata
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hirofumi Watanabe
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Tomokazu Yasuda
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Michio Murata
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
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27
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Seo S, Shinoda W. SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol. J Chem Theory Comput 2018; 15:762-774. [PMID: 30514078 DOI: 10.1021/acs.jctc.8b00987] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heterogeneity is essential for multicomponent lipid membranes. Especially, sterol-induced domain formation in membranes has recently attracted attention because of its biological importance. To investigate such membrane domains at the molecular level, coarse-grained molecular dynamics (CG-MD) simulations are a promising approach since they allow one to consider the temporal and spatial scales involved in domain formation. In this work, we present a new CG force field, named SPICA, which can accurately predict domain formation within various lipids in membranes. The SPICA force field was developed as an extension of a previous CG model, known as SDK (Shinoda-DeVane-Klein), in which membrane properties such as tension, elasticity, and structure are well reproduced. By examining domain formation in a series of ternary lipid bilayers, we observed a separation into liquid-ordered and liquid-disordered phases fully consistent with experimental observations. Importantly, it is shown that the SPICA force field can detect the different phase behavior that results from subtle differences in the lipid composition of the bilayer.
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Affiliation(s)
- Sangjae Seo
- Department of Materials Chemistry , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Wataru Shinoda
- Department of Materials Chemistry , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
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28
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Klauda JB. Perspective: Computational modeling of accurate cellular membranes with molecular resolution. J Chem Phys 2018; 149:220901. [DOI: 10.1063/1.5055007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
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29
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Wang E, Klauda JB. Models for the Stratum Corneum Lipid Matrix: Effects of Ceramide Concentration, Ceramide Hydroxylation, and Free Fatty Acid Protonation. J Phys Chem B 2018; 122:11996-12008. [DOI: 10.1021/acs.jpcb.8b06188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Smith AK, Klimov DK. Molecular Dynamics Investigation of the Ternary Bilayer Formed by Saturated Phosphotidylcholine, Sphingomyelin, and Cholesterol. J Phys Chem B 2018; 122:11311-11325. [DOI: 10.1021/acs.jpcb.8b07256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Amy K. Smith
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K. Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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31
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Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E. Microscopic view of lipids and their diverse biological functions. Curr Opin Struct Biol 2018; 51:177-186. [PMID: 30048836 DOI: 10.1016/j.sbi.2018.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 12/21/2022]
Abstract
Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.
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Affiliation(s)
- Po-Chao Wen
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric Shinn
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuhang Wang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chun Kit Chan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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32
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Cyclosporin A distribution in cholesterol-sphingomyelin artificial membranes modeled as Langmuir monolayers. Colloids Surf B Biointerfaces 2018; 166:286-294. [DOI: 10.1016/j.colsurfb.2018.03.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 11/18/2022]
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Kumari P, Kaur S, Sharma S, Kashyap HK. Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations. J Chem Phys 2018; 148:165102. [DOI: 10.1063/1.5021310] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Supreet Kaur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shobha Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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34
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Wang E, Klauda JB. Simulations of Pure Ceramide and Ternary Lipid Mixtures as Simple Interior Stratum Corneum Models. J Phys Chem B 2018; 122:2757-2768. [DOI: 10.1021/acs.jpcb.8b00348] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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35
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Fei Q, Kent D, Botello-Smith WM, Nur F, Nur S, Alsamarah A, Chatterjee P, Lambros M, Luo Y. Molecular Mechanism of Resveratrol's Lipid Membrane Protection. Sci Rep 2018; 8:1587. [PMID: 29371621 PMCID: PMC5785473 DOI: 10.1038/s41598-017-18943-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Resveratrol, a natural compound found in red wine and various vegetables, has drawn increasing interest due to its reported benefit in cardiovascular protection, neurodegenerative disorders, and cancer therapy. The mechanism by which resveratrol exerts such pleiotropic effects remains unclear. It remains as one of the most discussed polyphenol compounds in the debating "French Paradox". In this study, using molecular dynamics simulations of dipalmitoyl phosphatidylcholine (DPPC) bilayer with resveratrol, we generated a free energy map of resveratrol's location and orientation of inside the lipid bilayer. We found that resveratrol increases the surface area per lipid and decreases membrane thickness, which is the opposite effect of the well-studied cholesterol on liquid phase DPPC. Most importantly, based on the simulation observation that resveratrol has a high probability of forming hydrogen bonds with sn-1 and sn-2 ester groups, we discovered a new mechanism using experimental approach, in which resveratrol protects both sn-1 and sn-2 ester bonds of DPPC and distearoyl phosphatidylcholine (DSPC) from phospholipase A1 (PLA1) and phospholipase A2 (PLA2) cleavage. Our study elucidates the new molecular mechanism of potential health benefits of resveratrol and possibly other similar polyphenols and provides a new paradigm for drug design based on resveratrol and its analogs.
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Affiliation(s)
- Qinqin Fei
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA
| | - David Kent
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA
| | | | - Fariah Nur
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA
| | - Saadia Nur
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA
| | - Abdelaziz Alsamarah
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA
| | - Payal Chatterjee
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA
| | - Maria Lambros
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA.
| | - Yun Luo
- Western University of Health Sciences, College of pharmacy, Pomona, CA, 91766, USA.
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36
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Leonard AN, Simmonett AC, Pickard FC, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW. Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations. J Chem Theory Comput 2018; 14:948-958. [PMID: 29268012 DOI: 10.1021/acs.jctc.7b00948] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Long-range Lennard-Jones (LJ) interactions have a significant impact on the structural and thermodynamic properties of nonpolar systems. While several methods have been introduced for the treatment of long-range LJ interactions in molecular dynamics (MD) simulations, increased accuracy and extended applicability is required for anisotropic systems such as lipid bilayers. The recently refined Lennard-Jones particle-mesh Ewald (LJ-PME) method extends the particle-mesh Ewald (PME) method to long-range LJ interactions and is suitable for use with anisotropic systems. Implementation of LJ-PME with the CHARMM36 (C36) additive and CHARMM Drude polarizable force fields improves agreement with experiment for density, isothermal compressibility, surface tension, viscosity, translational diffusion, and 13C T1 relaxation times of pure alkanes. Trends in the temperature dependence of the density and isothermal compressibility of hexadecane are also improved. While the C36 additive force field with LJ-PME remains a useful model for liquid alkanes, the Drude polarizable force field with LJ-PME is more accurate for nearly all quantities considered. LJ-PME is also preferable to the isotropic long-range correction for hexadecane because the molecular order extends to nearly 20 Å, well beyond the usual 10-12 Å cutoffs used in most simulations.
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Affiliation(s)
- Alison N Leonard
- Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.,Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jeffery B Klauda
- 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
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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37
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Adams M, Wang E, Zhuang X, Klauda JB. Simulations of simple Bovine and Homo sapiens outer cortex ocular lens membrane models with a majority concentration of cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:2134-2144. [PMID: 29169746 DOI: 10.1016/j.bbamem.2017.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 12/31/2022]
Abstract
The lipid composition of bovine and human ocular lens membranes has been probed, and a variety of lipids have been found including phosphatidylcholine (PC), phosphatidylethanolamine (PE), sphingomyelin (SM), and cholesterol (CHOL) with cholesterol being present in particularly high concentrations. In this study, we use the all-atom CHARMM36 force field to simulate binary, ternary, and quaternary mixtures as models of the ocular lens. High concentration of cholesterol, in combination with different and varying diversity of phospholipids (PL) and sphingolipids (SL), affect the structure of the ocular lens lipid bilayer. The following analyses were done for each simulation: surface area per lipid, component surface area per lipid, deuterium order parameters (SCD), electron density profiles (EDP), membrane thickness, hydrogen bonding, radial distribution functions, clustering, and sterol tilt angle distribution. The SCD show significant bilayer alignment and packing in cholesterol-rich bilayers. The EDP show the transition from liquid crystalline to liquid ordered with the addition of cholesterol. Hydrogen bonds in our systems show the tendency for intramolecular interactions between cholesterol and fully saturated lipid tails for less complex bilayers. But with an increased number of components in the bilayer, the acyl chain of the lipids becomes a less important characteristic, and the headgroup of the lipid becomes more significant. Overall, cholesterol is the driving force of membrane structure of the ocular lens membrane where interactions between cholesterol, PL, and SL determine structure and function of the biomembrane. The goal of this work is to develop a baseline for further study of more physiologically realistic ocular lens lipid membranes. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Mark Adams
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Eric Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Xiaohong Zhuang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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38
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Wang E, Klauda JB. Molecular Dynamics Simulations of Ceramide and Ceramide-Phosphatidylcholine Bilayers. J Phys Chem B 2017; 121:10091-10104. [PMID: 29017324 DOI: 10.1021/acs.jpcb.7b08967] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent studies in lipid raft formation and stratum corneum permeability have focused on the role of ceramides (CER). In this study, we use the all-atom CHARMM36 (C36) force field to simulate bilayers using N-palmitoylsphingosine (CER16) or α-hydroxy-N-stearoyl phytosphingosine (CER[AP]) in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) or 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), which serve as general membrane models. Conditions are replicated from experimental studies for comparison purposes, and concentration (XCER) is varied to probe the effect of CER on these systems. Comparisons with experiment based on deuterium order parameters and bilayer thickness demonstrate good agreement, thus supporting further use of the C36 force field. CER concentration is shown to have a profound effect on nearly all membrane properties including surface area per lipid, chain order and tilt, area compressibility moduli, bilayer thickness, hydrogen bonding, and lipid clustering. Hydrogen bonding in particular can significantly affect other membrane properties and can even encourage transition to a gel phase. Despite CER's tendency to condense the membrane, an expansion of CER lipids with increasing XCER is possible depending on how the balance between various hydrogen-bond pairs and lipid clustering is perturbed. Based on gel phase transitions, support is given for phytosphingosine's role as a hydrogen-bond bridge between sphingosine ordered domains in the stratum corneum.
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Affiliation(s)
- Eric Wang
- Department of Chemical and Biomolecular Engineering and ‡Biophysics Graduate Program, University of Maryland , College Park, Maryland 20742, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and ‡Biophysics Graduate Program, University of Maryland , College Park, Maryland 20742, United States
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39
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Breidigan JM, Krzyzanowski N, Liu Y, Porcar L, Perez-Salas U. Influence of the membrane environment on cholesterol transfer. J Lipid Res 2017; 58:2255-2263. [PMID: 29046341 PMCID: PMC5711489 DOI: 10.1194/jlr.m077909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/09/2017] [Indexed: 01/28/2023] Open
Abstract
Cholesterol, an essential component in biological membranes, is highly unevenly distributed within the cell, with most localized in the plasma membrane while only a small fraction is found in the endoplasmic reticulum, where it is synthesized. Cellular membranes differ in lipid composition and protein content, and these differences can exist across their leaflets too. This thermodynamic landscape that cellular membranes impose on cholesterol is expected to modulate its transport. To uncover the role the membrane environment has on cholesterol inter- and intra-membrane movement, we used time-resolved small angle neutron scattering to study the passive movement of cholesterol between and within membranes with varying degrees of saturation content. We found that cholesterol moves systematically slower as the degree of saturation in the membranes increases, from a palmitoyl oleyl phosphotidylcholine membrane, which is unsaturated, to a dipalmitoylphosphatidylcholine (DPPC) membrane, which is fully saturated. Additionally, we found that the energetic barrier to move cholesterol in these phosphatidylcholine membranes is independent of their relative lipid composition and remains constant for both flip-flop and exchange at ∼100 kJ/mol. Further, by replacing DPPC with the saturated lipid palmitoylsphingomyelin, an abundant saturated lipid of the outer leaflet of the plasma membrane, we found the rates decreased by a factor of two. This finding is in stark contrast with recent molecular dynamic simulations that predict a dramatic slow-down of seven orders of magnitude for cholesterol flipping in membranes with a similar phosphocholine and SM lipid composition.
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Affiliation(s)
| | | | - Yangmingyue Liu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607
| | - Lionel Porcar
- Large Scale Structures Group, Institut Laue-Langevin, F-38042 Grenoble CEDEX 9, France
| | - Ursula Perez-Salas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607
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