1
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Laudadio E, Minnelli C, Mobbili G, Sabbatini G, Stipa P, Rusciano D, Galeazzi R. Salt effects on mixed composition membranes containing an antioxidant lipophilic edaravone derivative: a computational-experimental study. Org Biomol Chem 2022; 20:5784-5795. [PMID: 35822625 DOI: 10.1039/d2ob01143c] [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
The protection of lipid membranes against oxidation avoids diseases associated with oxidative stress. As a strategy to contrast it, functionalized lipids with antioxidant activity are used to become part of membranes thus protecting them. For this purpose, a lipophilic edaravone derivative has been synthesized, adding a C18 saturated chain to the original structure. The antioxidant activity of C18-Edv has been demonstrated in our previous work. In this study, molecular dynamics simulations have been performed to define the effects of NaCl, MgCl2, KCl, and CaCl2 salts on a palmitoyl-oleoyl-sn-glycero-phosphocholine (POPC) lipid bilayer encapsulating C18-Edv. The results showed how different salts influence POPC lateral diffusion, and the movements of C18-Edv heads, which are antioxidant moieties, were correlated to the ability of C18-Edv molecules to protect membranes. MgCl2 showed a negative impact leading to C18-Edv clusterization and membrane stretching, while KCl and NaCl showed a moderate influence on the mixed lipid membrane structure. CaCl2 increased the exposure of the C18-Edv heads to the lipid-water interface, resulting in the salt with a higher propensity to guarantee protection against radicals in the aqueous phase. Finally, C18-Edv-POPC liposomes have been prepared following the simulation conditions, and then an experimental Oxygen Radical Absorbance Capacity (ORAC) assay has been performed to confirm the in silico predicted results.
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Affiliation(s)
- Emiliano Laudadio
- Department SIMAU, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Cristina Minnelli
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Giovanna Mobbili
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Giulia Sabbatini
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Pierluigi Stipa
- Department SIMAU, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Dario Rusciano
- Research Center, Sooft Italia SpA, 95100, Catania, Italy
| | - Roberta Galeazzi
- Department DISVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
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2
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Minnelli C, Laudadio E, Fiorini R, Galeazzi R, Armeni T, Stipa P, Rusciano D, Mobbili G. Influence of a lipophilic edaravone on physical state and activity of antioxidant liposomes: An experimental and in silico study. Colloids Surf B Biointerfaces 2021; 210:112217. [PMID: 34836703 DOI: 10.1016/j.colsurfb.2021.112217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022]
Abstract
The influence of a lipophilic derivative of Edaravone (C18Edv) on a POPC liposomal bilayer has been investigated by a combined computational-experimental approach. The order and hydration degree of three different systems composed by 10%, 20% and 40% in w/w percentage of C18Edv respect to POPC were investigated through Molecular Dynamics (MD) simulations and fluorescence spectroscopy experiments. Dynamic Light Scattering measurements showed how the presence of different amounts of C18EdV determines differences on liposome size and stability. The survey revealed that the content of lipophilic antioxidant tunes liposome rigidity and influences cellular uptake and antioxidant activity which are maximized for formulation containing 20% of C18Edv.
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Affiliation(s)
- Cristina Minnelli
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Emiliano Laudadio
- Dipartimento di Scienze e Ingegneria della Materia, dell'Ambiente e Urbanistica (SIMAU), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Rosamaria Fiorini
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Tatiana Armeni
- Dipartimento Scienze Cliniche Specialistiche ed Odontostomatologiche, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Pierluigi Stipa
- Dipartimento di Scienze e Ingegneria della Materia, dell'Ambiente e Urbanistica (SIMAU), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | | | - Giovanna Mobbili
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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3
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Agmon E, Solon J, Bassereau P, Stockwell BR. Modeling the effects of lipid peroxidation during ferroptosis on membrane properties. Sci Rep 2018; 8:5155. [PMID: 29581451 PMCID: PMC5979948 DOI: 10.1038/s41598-018-23408-0] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/12/2018] [Indexed: 01/20/2023] Open
Abstract
Ferroptosis is a form of regulated cell death characterized by the accumulation of lipid hydroperoxides. There has been significant research on the pathways leading to the accumulation of oxidized lipids, but the downstream effects and how lipid peroxides cause cell death during ferroptosis remain a major puzzle. We evaluated key features of ferroptosis in newly developed molecular dynamics models of lipid membranes to investigate the biophysical consequences of lipid peroxidation, and generated hypotheses about how lipid peroxides contribute to cell death during ferroptosis.
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Affiliation(s)
- Eran Agmon
- Department of Biological Sciences, MC4846, Columbia University, 550 West 120th Street, New York, NY, 10027, USA
| | - Jérôme Solon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.,Sorbonne Université, 75005, Paris, France.,Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.,Sorbonne Université, 75005, Paris, France
| | - Brent R Stockwell
- Department of Biological Sciences, MC4846, Columbia University, 550 West 120th Street, New York, NY, 10027, USA. .,Department of Chemistry, MC4846, Columbia University, 550 West 120th Street, New York, NY, 10027, USA.
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4
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Laudadio E, Minnelli C, Amici A, Massaccesi L, Mobbili G, Galeazzi R. Liposomal Formulations for an Efficient Encapsulation of Epigallocatechin-3-gallate: An in- Silico/Experimental Approach. Molecules 2018; 23:molecules23020441. [PMID: 29462955 PMCID: PMC6017453 DOI: 10.3390/molecules23020441] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 01/29/2023] Open
Abstract
As a part of research project aimed to optimize antioxidant delivery, here we studied the influence of both salts and lipid matrix composition on the interaction of epigallocatechin-3-gallate (EGCG) with bilayer leaflets. Thus, we combined in silico and experimental methods to study the ability of neutral and anionic vesicles to encapsulate EGCG in the presence of Ca2+ and Mg2+ divalent salts. Experimental and in silico results show a very high correlation, thus confirming the efficiency of the developed methodology. In particular, we found out that the presence of calcium ions hinders the insertion of EGCG in the liposome bilayer in both neutral and anionic systems. On the contrary, the presence of MgCl2 improves the insertion degree of EGCG molecules respect to the liposomes without divalent salts. The best and most efficient salt concentration is that corresponding to a 5:1 molar ratio between Mg2+ and EGCG, in both neutral and anionic vesicles. Concerning the lipid matrix composition, the anionic one results in better promotion of the catechin insertion within the bilayer since experimentally we achieved 100% EGCG encapsulation in the lipid carrier in the presence of a 5:1 molar ratio of magnesium. Thus, the combination of this anionic liposomal formulation with magnesium chloride, avoids time-consuming separation steps of unentrapped active principle and appears particularly suitable for EGCG delivery applications.
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Affiliation(s)
- Emiliano Laudadio
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Cristina Minnelli
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Adolfo Amici
- Dipartimento Scienze Cliniche Specialistiche ed Odontostomatologiche, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Luca Massaccesi
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Giovanna Mobbili
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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5
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Laudadio E, Mobbili G, Minnelli C, Massaccesi L, Galeazzi R. Salts Influence Cathechins and Flavonoids Encapsulation in Liposomes: A Molecular Dynamics Investigation. Mol Inform 2017. [PMID: 28635075 DOI: 10.1002/minf.201700059] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cathechins and flavonoids are responsible of numerous health benefits. Two of the most representatives' compounds for their antioxidant and therapeutic effects are Epigallocatechin 3-Gallate (EGCG), from green tea extracts, and morelloflavone (MF), from Garcinia dulcis. Here we explore, by atomistic Molecular Dynamics simulations, how EGCG and MF interact with lipid bilayers and we show the salts' influence on their encapsulation degree in neutral liposomes. As a result, we found out that EGCGs naturally bind to the hydrophilic regions of phospholipids, positioning themselves mostly at the interface between water and lipid phases. The presence of a salt clearly influences the EGCG molecules' absorption and the total effect depends strongly on the salt nature and concentration. Beside, for MF, we observed a high stability of the intermolecular MFs aggregates in water that strongly penalizes the flavonoid's interaction with the lipid polar heads. However, salts can influence MF's liposomal penetration, even if they are not able to promote completely its absorption inside the bilayer. For both compounds, the increase of penetration is more marked in presence of magnesium chloride, whilst calcium chloride showed the opposite effect.
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Affiliation(s)
- Emiliano Laudadio
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona -, ITALY
| | - Giovanna Mobbili
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona -, ITALY
| | - Cristina Minnelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona -, ITALY
| | - Luca Massaccesi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona -, ITALY
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona -, ITALY
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6
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Membrane engineering via trans unsaturated fatty acids production improves Escherichia coli robustness and production of biorenewables. Metab Eng 2016; 35:105-113. [DOI: 10.1016/j.ymben.2016.02.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 11/23/2022]
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7
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Casciola M, Tarek M. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2278-2289. [PMID: 27018309 DOI: 10.1016/j.bbamem.2016.03.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/26/2022]
Abstract
The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Maura Casciola
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; Department of Information Engineering, Electronics and Telecommunications (D.I.E.T), Sapienza University of Rome, 00184 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Mounir Tarek
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; CNRS, UMR 7565, F-54506 Vandoeuvre les Nancy, France.
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8
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Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, Klauda JB, Im W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput 2016. [PMID: 26631602 DOI: 10.1021/acs.jctc.5b00935/asset/images/large/ct-2015-00935e0005.jpeg] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
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Affiliation(s)
- Jumin Lee
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Jason M Swails
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information , Yuseong-gu, Daejeon 305-806, Korea
| | - Peter K Eastman
- Department of Bioengineering, Stanford University , Stanford, California 94035, United States
| | - Justin A Lemkul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Shuai Wei
- Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Joshua Buckner
- Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jong Cheol Jeong
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Harvard Medical School , Boston, Massachusetts 02215, United States
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory , 9700 Cass Avenue, Building 240, Argonne, Illinois 60439, United States
| | - Vijay S Pande
- Department of Bioengineering, Stanford University , Stanford, California 94035, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Charles L Brooks
- Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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10
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Boonnoy P, Jarerattanachat V, Karttunen M, Wong-Ekkabut J. Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids. J Phys Chem Lett 2015; 6:4884-8. [PMID: 26673194 DOI: 10.1021/acs.jpclett.5b02405] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The influence of different oxidized lipids on lipid bilayers was investigated with 16 individual 1 μs atomistic molecular dynamics (MD) simulations. Binary mixtures of lipid bilayers of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) and its peroxide and aldehyde products were performed at different concentrations. In addition, an asymmetrical short chain lipid, 1-palmitoyl-2-decanoyl-sn-glycero-3-phosphatidylcholine (PDPC), was used to compare the effects of polar/apolar groups in the lipid tail on lipid bilayer. Although water defects occurred with both aldehyde and peroxide lipids, full pore formation was observed only for aldehyde lipids. At medium concentrations the pores were stable. At higher concentrations, however, the pores became unstable and micellation occurred. Data analysis shows that aldehyde lipids' propensity for pore formation is due to their shorter and highly mobile tail. The highly polar peroxide lipids are stabilized by strong hydrogen bonds with interfacial water.
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Affiliation(s)
- Phansiri Boonnoy
- Department of Physics, Faculty of Science, Kasetsart University , Bangkok, 10900, Thailand
| | - Viwan Jarerattanachat
- Department of Physics, Faculty of Science, Kasetsart University , Bangkok, 10900, Thailand
- Clarendon Laboratory, Department of Physics, University of Oxford , Oxford OX1 3PU, United Kingdom
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, MetaForum , 5600 MB Eindhoven, The Netherlands
| | - Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University , Bangkok, 10900, Thailand
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11
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Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, Klauda JB, Im W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput 2015; 12:405-13. [PMID: 26631602 PMCID: PMC4712441 DOI: 10.1021/acs.jctc.5b00935] [Citation(s) in RCA: 2146] [Impact Index Per Article: 238.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Proper treatment of nonbonded interactions
is essential for the
accuracy of molecular dynamics (MD) simulations, especially in studies
of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in
different MD simulation programs can result in disagreements with
published simulations performed with CHARMM due to differences in
the protocols used to treat the long-range and 1-4 nonbonded interactions.
In this study, we systematically test the use of the C36 lipid FF
in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of
Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested
to find the optimal simulation protocol to best match bilayer properties
of six lipids with varying acyl chain saturation and head groups.
MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine
(DPPC) bilayer were used to obtain the optimal protocol for each program.
MD simulations with all programs were found to reasonably match the
DPPC bilayer properties (surface area per lipid, chain order parameters,
and area compressibility modulus) obtained using the standard protocol
used in CHARMM as well as from experiments. The optimal simulation
protocol was then applied to the other five lipid simulations and
resulted in excellent agreement between results from most simulation
programs as well as with experimental data. AMBER compared least favorably
with the expected membrane properties, which appears to be due to
its use of the hard-truncation in the LJ potential versus a force-based
switching function used to smooth the LJ potential as it approaches
the cutoff distance. The optimal simulation protocol for each program
has been implemented in CHARMM-GUI. This protocol is expected to be
applicable to the remainder of the additive C36 FF including the proteins,
nucleic acids, carbohydrates, and small molecules.
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Affiliation(s)
- Jumin Lee
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Jason M Swails
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information , Yuseong-gu, Daejeon 305-806, Korea
| | - Peter K Eastman
- Department of Bioengineering, Stanford University , Stanford, California 94035, United States
| | - Justin A Lemkul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Shuai Wei
- Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Joshua Buckner
- Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jong Cheol Jeong
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Harvard Medical School , Boston, Massachusetts 02215, United States
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
| | - Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory , 9700 Cass Avenue, Building 240, Argonne, Illinois 60439, United States
| | - Vijay S Pande
- Department of Bioengineering, Stanford University , Stanford, California 94035, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Charles L Brooks
- Department of Chemistry and the Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , Lawrence, Kansas 66047, United States
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Venable RM, Brown FLH, Pastor RW. Mechanical properties of lipid bilayers from molecular dynamics simulation. Chem Phys Lipids 2015; 192:60-74. [PMID: 26238099 PMCID: PMC4684433 DOI: 10.1016/j.chemphyslip.2015.07.014] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/11/2015] [Accepted: 07/25/2015] [Indexed: 01/21/2023]
Abstract
Lipid areas (Aℓ), bilayer area compressibilities (KA), bilayer bending constants (KC), and monolayer spontaneous curvatures (c0) from simulations using the CHARMM36 force field are reported for 12 representative homogenous lipid bilayers. Aℓ (or their surrogate, the average deuterium order parameter in the "plateau region" of the chain) agree very well with experiment, as do the KA. Simulated KC are in near quantitative agreement with vesicle flicker experiments, but are somewhat larger than KC from X-ray, pipette aspiration, and neutron spin echo for saturated lipids. Spontaneous curvatures of bilayer leaflets from the simulations are approximately 30% smaller than experimental values of monolayers in the inverse hexagonal phase.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, CA 93106, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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Galeazzi R, Bruni P, Crucianelli E, Laudadio E, Marini M, Massaccesi L, Mobbili G, Pisani M. Liposome-based gene delivery systems containing a steroid derivative: computational and small angle X-ray diffraction study. RSC Adv 2015. [DOI: 10.1039/c5ra08439c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structural properties and the phase behaviour of mixed composition liposomes containing a functionalized lipid are investigated with the aim to design neutral liposomes able to coordinate metals and to complex DNA.
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Affiliation(s)
- R. Galeazzi
- Di.S.V.A. Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - P. Bruni
- SIMAU Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - E. Crucianelli
- Di.S.V.A. Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - E. Laudadio
- Di.S.V.A. Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - M. Marini
- SIMAU Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - L. Massaccesi
- Di.S.V.A. Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - G. Mobbili
- Di.S.V.A. Department
- Polytechnic University of Marche
- Ancona
- Italy
| | - M. Pisani
- SIMAU Department
- Polytechnic University of Marche
- Ancona
- Italy
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