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Rózsa ZB, Hantal G, Szőri M, Fábián B, Jedlovszky P. Understanding the Molecular Mechanism of Anesthesia: Effect of General Anesthetics and Structurally Similar Non-Anesthetics on the Properties of Lipid Membranes. J Phys Chem B 2023; 127:6078-6090. [PMID: 37368412 PMCID: PMC11404830 DOI: 10.1021/acs.jpcb.3c02976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
General anesthesia can be caused by various, chemically very different molecules, while several other molecules, many of which are structurally rather similar to them, do not exhibit anesthetic effects at all. To understand the origin of this difference and shed some light on the molecular mechanism of general anesthesia, we report here molecular dynamics simulations of the neat dipalmitoylphosphatidylcholine (DPPC) membrane as well as DPPC membranes containing the anesthetics diethyl ether and chloroform and the structurally similar non-anesthetics n-pentane and carbon tetrachloride, respectively. To also account for the pressure reversal of anesthesia, these simulations are performed both at 1 bar and at 600 bar. Our results indicate that all solutes considered prefer to stay both in the middle of the membrane and close to the boundary of the hydrocarbon domain, at the vicinity of the crowded region of the polar headgroups. However, this latter preference is considerably stronger for the (weakly polar) anesthetics than for the (apolar) non-anesthetics. Anesthetics staying in this outer preferred position increase the lateral separation between the lipid molecules, giving rise to a decrease of the lateral density. The lower lateral density leads to an increased mobility of the DPPC molecules, a decreased order of their tails, an increase of the free volume around this outer preferred position, and a decrease of the lateral pressure at the hydrocarbon side of the apolar/polar interface, a change that might well be in a causal relation with the occurrence of the anesthetic effect. All these changes are clearly reverted by the increase of pressure. Furthermore, non-anesthetics occur in this outer preferred position in a considerably smaller concentration and hence either induce such changes in a much weaker form or do not induce them at all.
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Affiliation(s)
- Zsófia B Rózsa
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - György Hantal
- Institute of Physics and Materials Science, University of Natural Resources and Life Sciences, Peter Jordan Straße 82, A-1190 Vienna, Austria
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly Catholic University, Leányka utca 6, H-3300 Eger, Hungary
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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3
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Grage SL, Culetto A, Ulrich AS, Weinschenk S. Membrane-Mediated Activity of Local Anesthetics. Mol Pharmacol 2021; 100:502-512. [PMID: 34475108 DOI: 10.1124/molpharm.121.000252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/19/2021] [Indexed: 01/06/2023] Open
Abstract
The activity of local anesthetics (LAs) has been attributed to the inhibition of ion channels, causing anesthesia. However, there is a growing body of research showing that LAs act on a wide range of receptors and channel proteins far beyond simple analgesia. The current concept of ligand recognition may no longer explain the multitude of protein targets influenced by LAs. We hypothesize that LAs can cause anesthesia without directly binding to the receptor proteins just by changing the physical properties of the lipid bilayer surrounding these proteins and ion channels based on LAs' amphiphilicity. It is possible that LAs act in one of the following ways: They 1) dissolve raft-like membrane microdomains, 2) impede nerve impulse propagation by lowering the lipid phase transition temperature, or 3) modulate the lateral pressure profile of the lipid bilayer. This could also explain the numerous additional effects of LAs besides anesthesia. Furthermore, the concepts of membrane-mediated activity and binding to ion channels do not have to exclude each other. If we were to consider LA as the middle part of a continuum between unspecific membrane-mediated activity on one end and highly specific ligand binding on the other end, we could describe LA as the link between the unspecific action of general anesthetics and toxins with their highly specific receptor binding. This comprehensive membrane-mediated model offers a fresh perspective to clinical and pharmaceutical research and therapeutic applications of local anesthetics. SIGNIFICANCE STATEMENT: Local anesthetics, according to the World Health Organization, belong to the most important drugs available to mankind. Their rediscovery as therapeutics and not only anesthetics marks a milestone in global pain therapy. The membrane-mediated mechanism of action proposed in this review can explain their puzzling variety of target proteins and their thus far inexplicable therapeutic effects. The new concept presented here places LAs on a continuum of structures and molecular mechanisms in between small general anesthetics and the more complex molecular toxins.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
| | - Anke Culetto
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
| | - Stefan Weinschenk
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany (S.L.G., A.C., A.S.U.); Institute of Organic Chemistry, KIT, Karlsruhe, Germany (A.C., A.S.U.); Women's Hospital, Department of Gynecological Endocrinology and Fertility Disorders, Heidelberg, Germany (S.W.); and The HUNTER Group, Heidelberg University, Women's Hospital, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany, Heidelberg University, Women's Hospital, Neural Therapy Education & Research Group (S.W.)
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Himbert S, Zhang L, Alsop RJ, Cristiglio V, Fragneto G, Rheinstädter MC. Anesthetics significantly increase the amount of intramembrane water in lipid membranes. SOFT MATTER 2020; 16:9674-9682. [PMID: 32869047 DOI: 10.1039/d0sm01271h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The potency of anesthesia was directly linked to the partitioning of the drug molecules in cell membranes by Meyer and Overton. Many molecules interact with lipid bilayers and lead to structural and functional changes. It remains an open question which change in membrane properties is responsible for a potential anesthetic effect or if anesthetics act by binding to direct targets. We studied the effect of ethanol, diethyl ether and isoflurane on the water distribution in lipid bilayers by combining all-atom molecular dynamics simulations and neutron diffraction experiments. The simulations show strong membrane-drug interactions with partitioning coefficients of 38%, 92% and 100% for ethanol, diethyl ether and isoflurane, respectively, and provide evidence for an increased water partitioning in the membrane core. The amount of intramembrane water molecules was experimentally determined by selectively deuterium labeling lipids, anesthetic drug and water molecules in neutron diffraction experiments. Four additional water molecules per lipid were observed in the presence of ethanol. Diethyl ether and isoflurane were found to significantly increase the amount of intramembrane water by 25% (8 water molecules). This increase in intramembrane water may contribute to the non-specific interactions between anesthetics and lipid membranes.
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Affiliation(s)
- Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, ABB-241, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada.
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Engberg O, Bochicchio A, Brandner AF, Gupta A, Dey S, Böckmann RA, Maiti S, Huster D. Serotonin Alters the Phase Equilibrium of a Ternary Mixture of Phospholipids and Cholesterol. Front Physiol 2020; 11:578868. [PMID: 33192582 PMCID: PMC7645218 DOI: 10.3389/fphys.2020.578868] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Unsaturated and saturated phospholipids tend to laterally segregate, especially in the presence of cholesterol. Small molecules such as neurotransmitters, toxins, drugs etc. possibly modulate this lateral segregation. The small aromatic neurotransmitter serotonin (5-HT) has been found to bind to membranes. We studied the lipid structure and packing of a ternary membrane mixture consisting of palmitoyl-oleoyl-phosphatidylcholine, palmitoyl-sphingomyelin, and cholesterol at a molar ratio of 4/4/2 in the absence and in the presence of 5-HT, using a combination of solid-state 2H NMR, atomic force microscopy, and atomistic molecular dynamics (MD) simulations. Both NMR and MD report formation of a liquid ordered (L o ) and a liquid disordered (L d ) phase coexistence with small domains. Lipid exchange between the domains was fast such that single component 2H NMR spectra are detected over a wide temperature range. A drastic restructuring of the domains was induced when 5-HT is added to the membranes at a 9 mol% concentration relative to the lipids. 2H NMR spectra of all components of the mixture showed two prominent contributions indicative of molecules of the same kind residing both in the disordered and the ordered phase. Compared to the data in the absence of 5-HT, the lipid chain order in the disordered phase was further decreased in the presence of 5-HT. Likewise, addition of serotonin increased lipid chain order within the ordered phase. These characteristic lipid chain order changes were confirmed by MD simulations. The 5-HT-induced larger difference in lipid chain order results in more pronounced differences in the hydrophobic thickness of the individual membrane domains. The correspondingly enlarged hydrophobic mismatch between ordered and disordered phases is assumed to increase the line tension at the domain boundary, which drives the system into formation of larger size domains. These results not only demonstrate that small membrane binding molecules such as neurotransmitters have a profound impact on essential membrane properties. It also suggests a mechanism by which the interaction of small molecules with membranes can influence the function of membrane proteins and non-cognate receptors. Altered membrane properties may modify lateral sorting of membrane protein, membrane protein conformation, and thus influence their function as suspected for neurotransmitters, local anesthetics, and other small drug molecules.
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Affiliation(s)
- Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Anna Bochicchio
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Astrid F. Brandner
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Ankur Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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6
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NMDAR-independent, cAMP-dependent antidepressant actions of ketamine. Mol Psychiatry 2019; 24:1833-1843. [PMID: 29895894 PMCID: PMC8011999 DOI: 10.1038/s41380-018-0083-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/15/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023]
Abstract
Ketamine produces rapid and robust antidepressant effects in depressed patients within hours of administration, often when traditional antidepressant compounds have failed to alleviate symptoms. We hypothesized that ketamine would translocate Gαs from lipid rafts to non-raft microdomains, similarly to other antidepressants but with a distinct, abbreviated treatment duration. C6 glioma cells were treated with 10 µM ketamine for 15 min, which translocated Gαs from lipid raft domains to non-raft domains. Other NMDA antagonist did not translocate Gαs from lipid raft to non-raft domains. The ketamine-induced Gαs plasma membrane redistribution allows increased functional coupling of Gαs and adenylyl cyclase to increase intracellular cyclic adenosine monophosphate (cAMP). Moreover, increased intracellular cAMP increased phosphorylation of cAMP response element-binding protein (CREB), which, in turn, increased BDNF expression. The ketamine-induced increase in intracellular cAMP persisted after knocking out the NMDA receptor indicating an NMDA receptor-independent effect. Furthermore, 10 µM of the ketamine metabolite (2R,6R)-hydroxynorketamine (HNK) also induced Gαs redistribution and increased cAMP. These results reveal a novel antidepressant mechanism mediated by acute ketamine treatment that may contribute to ketamine's powerful antidepressant effect. They also suggest that the translocation of Gαs from lipid rafts is a reliable hallmark of antidepressant action that might be exploited for diagnosis or drug development.
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7
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Wu X, Chantemargue B, Di Meo F, Bourgaux C, Chapron D, Trouillas P, Rosilio V. Deciphering the Peculiar Behavior of β-Lapachone in Lipid Monolayers and Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14603-14615. [PMID: 31619039 DOI: 10.1021/acs.langmuir.9b02886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
β-Lapachone (β-Lap) is a promising anticancer drug whose applications have been limited so far because of its poor solubility and stability. Its encapsulation in liposomes has been proposed to overcome these issues. However, surface pressure measurements show that β-Lap exhibits atypical interfacial behavior when mixed with lipids. Although the drug does not seem to be retained in lipid monolayers as deduced from the π-A isotherms, small changes in compressibility moduli suggest that β-Lap actually interacts with lipids, either disorganizing or rigidifying their monolayers. Thermal and structural analyses of lipid bilayers confirm the existence of β-Lap/lipid interactions and show that the drug inserts between hydrophobic chains, close to the polar headgroup in DPPC bilayers and deeper in the acyl chains in POPC bilayers. Molecular dynamics simulations allow a comprehensive description of the drug position and orientation in DOPC and POPC bilayers in the presence or absence of cholesterol.
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Affiliation(s)
- Xiao Wu
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
| | - Benjamin Chantemargue
- INSERM U1248, Faculty of Pharmacy , Université de Limoges , 2 rue du Docteur Marcland , 87025 Limoges, Cedex France
- Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacký University , tr. 17 listopadu 12 , 771 46 Olomouc , Czech Republic
| | - Florent Di Meo
- INSERM U1248, Faculty of Pharmacy , Université de Limoges , 2 rue du Docteur Marcland , 87025 Limoges, Cedex France
| | - Claudie Bourgaux
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
| | - David Chapron
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
| | - Patrick Trouillas
- INSERM U1248, Faculty of Pharmacy , Université de Limoges , 2 rue du Docteur Marcland , 87025 Limoges, Cedex France
- Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacký University , tr. 17 listopadu 12 , 771 46 Olomouc , Czech Republic
| | - Véronique Rosilio
- Institut Galien Paris Sud , Univ Paris-Sud, CNRS, Université Paris-Saclay , 92296 Châtenay-Malabry , France
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8
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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: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [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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9
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Bianchi F, Malboubi M, George JH, Jerusalem A, Thompson MS, Ye H. Ion current and action potential alterations in peripheral neurons subject to uniaxial strain. J Neurosci Res 2019; 97:744-751. [PMID: 30927386 PMCID: PMC6519351 DOI: 10.1002/jnr.24408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/26/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022]
Abstract
Peripheral nerves, subject to continuous elongation and compression during everyday movement, contain neuron fibers vital for movement and sensation. At supraphysiological strains resulting from trauma, chronic conditions, aberrant limb positioning, or surgery, conduction blocks occur which may result in chronic or temporary loss of function. Previous in vitro stretch models, mainly focused on traumatic brain injury modelling, have demonstrated altered electrophysiological behavior during localized deformation applied by pipette suction. Our aim was to evaluate the changes in voltage‐activated ion channel function during uniaxial straining of neurons applied by whole‐cell deformation, more physiologically relevant model of peripheral nerve trauma. Here, we quantified experimentally the changes in inwards and outwards ion currents and action potential (AP) firing in dorsal root ganglion‐derived neurons subject to uniaxial strains, using a custom‐built device allowing simultaneous cell deformation and patch clamp recording. Peak inwards sodium currents and rectifying potassium current magnitudes were found to decrease in cells under stretch, channel reversal potentials were found to be left‐shifted, and half‐maximum activation potentials right‐shifted. The threshold for AP firing was increased in stretched cells, although neurons retained the ability to fire induced APs. Overall, these results point to ion channels being damaged directly and immediately by uniaxial strain, affecting cell electrophysiological activity, and can help develop prevention and treatment strategies for peripheral neuropathies caused by mechanical trauma.
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Affiliation(s)
- Fabio Bianchi
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Majid Malboubi
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Julian H George
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Antoine Jerusalem
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Mark S Thompson
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Hua Ye
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
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Membrane Mechanical Properties Regulate the Effect of Strain on Spontaneous Electrophysiology in Human iPSC-Derived Neurons. Neuroscience 2019; 404:165-174. [PMID: 30817953 DOI: 10.1016/j.neuroscience.2019.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
Peripheral nerves contain neuron fibers vital for movement and sensation and are subject to continuous elongation and compression during everyday movement. At supraphysiological strains conduction blocks occur, resulting in permanent or temporary loss of function. The mechanisms underpinning these alterations in electrophysiological activity remain unclear; however, there is evidence that both ion channels and network synapses may be affected through cell membrane transmitted strain. The aim of this work was to quantify the changes in spontaneous activity resulting from application of uniaxial strain in a human iPS-derived motor neuron culture model, and to investigate the role of cell membrane mechanical properties during cell straining. Increasing strain in a custom-built cell-stretching device caused a linear decrease in spontaneous activity, and no immediate recovery of activity was observed after strain release. Imaging neuronal membranes with c-Laurdan showed changes to the lipid order in neural membranes during deformation with a decrease in lipid packing. Neural cell membrane stiffness can be modulated by increasing cholesterol content, resulting in reduced stretch-induced decrease of membrane lipid packing and in a reduced decrease in spontaneous activity caused by mechanical strain. Together these results indicate that the mechanism whereby cell injury causes impaired transmission of neural impulses may be governed by the mechanical state of the cell membrane, and contribute to establishing a direct relationship between neural uniaxial straining and loss of spontaneous neural activity.
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11
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Affiliation(s)
- Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, Biophysics Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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12
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Rao BD, Shrivastava S, Pal S, Chattopadhyay A. Effect of Local Anesthetics on the Organization and Dynamics of Hippocampal Membranes: A Fluorescence Approach. J Phys Chem B 2018; 123:639-647. [DOI: 10.1021/acs.jpcb.8b10232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bhagyashree D. Rao
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
| | - Sandeep Shrivastava
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Sreetama Pal
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
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13
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Hantal G, Fábián B, Sega M, Jójárt B, Jedlovszky P. Effect of general anesthetics on the properties of lipid membranes of various compositions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:594-609. [PMID: 30571949 DOI: 10.1016/j.bbamem.2018.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 10/27/2022]
Abstract
Computer simulations of four lipid membranes of different compositions, namely neat DPPC and PSM, and equimolar DPPC-cholesterol and PSM-cholesterol mixtures, are performed in the presence and absence of the general anesthetics diethylether and sevoflurane both at 1 and 600 bar. The results are analyzed in order to identify membrane properties that are potentially related to the molecular mechanism of anesthesia, namely that change in the same way in any membrane with any anesthetics, and change oppositely with increasing pressure. We find that the lateral lipid density satisfies both criteria: it is decreased by anesthetics and increased by pressure. This anesthetic-induced swelling is attributed to only those anesthetic molecules that are located close to the boundary of the apolar phase. This lateral expansion is found to lead to increased lateral mobility of the lipids, an effect often thought to be related to general anesthesia; to an increased fraction of the free volume around the outer preferred position of anesthetics; and to the decrease of the lateral pressure in the nearby range of the ester and amide groups, a region into which anesthetic molecules already cannot penetrate. All these changes are reverted by the increase of pressure. Another important finding of this study is that cholesterol has an opposite effect on the membrane properties than anesthetics, and, correspondingly, these changes are less marked in the presence of cholesterol. Therefore, changes in the membrane that can lead to general anesthesia are expected to occur in the membrane domains of low cholesterol content.
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Affiliation(s)
- György Hantal
- Faculty of Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Balázs Fábián
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, H-1111 Budapest, Hungary; Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon, France
| | - Marcello Sega
- Faculty of Physics, University of Vienna, Sensengasse 8/9, A-1090 Vienna, Austria
| | - Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Moszkvai krt 5-7, H-6725 Szeged, Hungary
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University, Leányka utca 6, H-3300 Eger, Hungary.
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14
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Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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15
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Juhola H, Postila PA, Rissanen S, Lolicato F, Vattulainen I, Róg T. Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters. Neuroscience 2018; 384:214-223. [DOI: 10.1016/j.neuroscience.2018.05.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 01/09/2023]
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16
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Chantemargue B, Di Meo F, Berka K, Picard N, Arnion H, Essig M, Marquet P, Otyepka M, Trouillas P. Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms. Pharmacol Res 2018. [DOI: 10.1016/j.phrs.2018.02.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Exploring the biophysical properties of phytosterols in the plasma membrane for novel cancer prevention strategies. Biochimie 2018; 153:150-161. [PMID: 29730298 DOI: 10.1016/j.biochi.2018.04.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 02/08/2023]
Abstract
Cancer is a global problem with no sign that incidences are reducing. The great costs associated with curing cancer, through developing novel treatments and applying patented therapies, is an increasing burden to developed and developing nations alike. These financial and societal problems will be alleviated by research efforts into prevention, or treatments that utilise off-patent or repurposed agents. Phytosterols are natural components of the diet found in an array of seeds, nuts and vegetables and have been added to several consumer food products for the management of cardio-vascular disease through their ability to lower LDL-cholesterol levels. In this review, we provide a connected view between the fields of structural biophysics and cellular and molecular biology to evaluate the growing evidence that phytosterols impair oncogenic pathways in a range of cancer types. The current state of understanding of how phytosterols alter the biophysical properties of plasma membrane is described, and the potential for phytosterols to be repurposed from cardio-vascular to oncology therapeutics. Through an overview of the types of biophysical and molecular biology experiments that have been performed to date, this review informs the reader of the molecular and biophysical mechanisms through which phytosterols could have anti-cancer properties via their interactions with the plasma cell membrane. We also outline emerging and under-explored areas such as computational modelling, improved biomimetic membranes and ex vivo tissue evaluation. Focus of future research in these areas should improve understanding, not just of phytosterols in cancer cell biology but also to give insights into the interaction between the plasma membrane and the genome. These fields are increasingly providing meaningful biological and clinical data but iterative experiments between molecular biology assays, biosynthetic membrane studies and computational membrane modelling improve and refine our understanding of the role of different sterol components of the plasma membrane.
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18
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Cheung AS, Zhang DK, Koshy ST, Mooney DJ. Scaffolds that mimic antigen-presenting cells enable ex vivo expansion of primary T cells. Nat Biotechnol 2018; 36:160-169. [PMID: 29334370 PMCID: PMC5801009 DOI: 10.1038/nbt.4047] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 12/01/2017] [Indexed: 12/22/2022]
Abstract
Therapeutic ex vivo T-cell expansion is limited by low rates and T-cell products of limited functionality. Here we describe a system that mimics natural antigen-presenting cells (APCs) and consists of a fluid lipid bilayer supported by mesoporous silica micro-rods. The lipid bilayer presents membrane-bound cues for T-cell receptor stimulation and costimulation, while the micro-rods enable sustained release of soluble paracrine cues. Using anti-CD3, anti-CD28, and interleukin-2, we show that the APC-mimetic scaffolds (APC-ms) promote two- to tenfold greater polyclonal expansion of primary mouse and human T cells compared with commercial expansion beads (Dynabeads). The efficiency of expansion depends on the density of stimulatory cues and the amount of material in the starting culture. Following a single stimulation, APC-ms enables antigen-specific expansion of rare cytotoxic T-cell subpopulations at a greater magnitude than autologous monocyte-derived dendritic cells after 2 weeks. APC-ms support over fivefold greater expansion of restimulated CD19 CAR-T cells than Dynabeads, with similar efficacy in a xenograft lymphoma model.
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Affiliation(s)
- Alexander S. Cheung
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Cambridge, Massachusetts, USA
| | - David K.Y. Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Cambridge, Massachusetts, USA
| | - Sandeep T. Koshy
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - David J. Mooney
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering Harvard University, Cambridge, Massachusetts, USA
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Szöllősi D, Rose-Sperling D, Hellmich UA, Stockner T. Comparison of mechanistic transport cycle models of ABC exporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:818-832. [PMID: 29097275 PMCID: PMC7610611 DOI: 10.1016/j.bbamem.2017.10.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. “This article is part of a Special Issue entitled: Beyond the Structure Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.”
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Affiliation(s)
- Dániel Szöllősi
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria
| | - Dania Rose-Sperling
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Ute A Hellmich
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Stockner
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria.
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20
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Rabinovich AL, Lyubartsev AP, Zhurkin DV. Unperturbed hydrocarbon chains and liquid phase bilayer lipid chains: a computer simulation study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:109-130. [PMID: 28698919 PMCID: PMC5834621 DOI: 10.1007/s00249-017-1231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/13/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022]
Abstract
In this work, the properties of saturated and unsaturated fatty acid acyl chains 16:0, 18:0, 18:1(n-9)cis, 18:2(n-6)cis, 18:3(n-3)cis, 18:4(n-3)cis, 18:5(n-3)cis, 20:4(n-6)cis, 20:5(n-3)cis and 22:6(n-3)cis in a bilayer liquid crystalline state and similar hydrocarbon chains (with CH[Formula: see text] terminal groups instead of C=O groups) in the unperturbed state characterised by a lack of long-range interaction were investigated. The unperturbed hydrocarbon chains were modelled by Monte Carlo simulations at temperature [Formula: see text] K; sixteen fully hydrated homogeneous liquid crystalline phosphatidylcholine bilayers containing these chains were studied by molecular dynamics simulations at the same temperature. To eliminate effects of the simulation parameters, the molecular dynamics and Monte Carlo simulations were carried out using the same structural data and force field coefficients. From these computer simulations, the average distances between terminal carbon atoms of the chains (end-to-end distances) were calculated and compared. The trends in the end-to-end distances obtained for the unperturbed chains were found to be qualitatively similar to those obtained for the same lipid chains in the bilayers. So, for understanding of a number of processes in biological membranes (e.g., changes in fatty acid composition caused by environmental changes such as temperature and pressure), it is possible to use, at least as a first approximation, the relationships between the structure and properties for unperturbed or isolated hydrocarbon chains.
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Affiliation(s)
- Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91, Stockholm, Sweden.
| | - Dmitrii V Zhurkin
- Physics and Technology Department, Petrozavodsk State University, Universitetskaya 10, Petrozavodsk, 185910, Russian Federation
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21
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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22
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Sohail A, Jayaraman K, Venkatesan S, Gotfryd K, Daerr M, Gether U, Loland CJ, Wanner KT, Freissmuth M, Sitte HH, Sandtner W, Stockner T. The Environment Shapes the Inner Vestibule of LeuT. PLoS Comput Biol 2016; 12:e1005197. [PMID: 27835643 PMCID: PMC5105988 DOI: 10.1371/journal.pcbi.1005197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/12/2016] [Indexed: 12/27/2022] Open
Abstract
Human neurotransmitter transporters are found in the nervous system terminating synaptic signals by rapid removal of neurotransmitter molecules from the synaptic cleft. The homologous transporter LeuT, found in Aquifex aeolicus, was crystallized in different conformations. Here, we investigated the inward-open state of LeuT. We compared LeuT in membranes and micelles using molecular dynamics simulations and lanthanide-based resonance energy transfer (LRET). Simulations of micelle-solubilized LeuT revealed a stable and widely open inward-facing conformation. However, this conformation was unstable in a membrane environment. The helix dipole and the charged amino acid of the first transmembrane helix (TM1A) partitioned out of the hydrophobic membrane core. Free energy calculations showed that movement of TM1A by 0.30 nm was driven by a free energy difference of ~15 kJ/mol. Distance measurements by LRET showed TM1A movements, consistent with the simulations, confirming a substantially different inward-open conformation in lipid bilayer from that inferred from the crystal structure. Crystal structures of the bacterial small amino acid transporter LeuT provided structural evidence for the alternating access model. Thereby, these structures shaped our understanding of the mechanisms underlying substrate translocation by neurotransmitter transporters. However, it has been questioned, if the crystallized inward-open conformation of LeuT can exist in the membrane environment. Here we show that, while stable in detergent micelles, the inward-open conformation of LeuT is of high energy and undergoes structural readjustments. We use a multi-faceted approach including molecular dynamics simulations, scintillation proximity assays, free energy calculations and apply for the first time lanthanide resonance energy transfer measurements to verify the in silico predictions. In silico and in vitro approaches using the same conditions allowed us to combine the macroscopic experimental data with microscopic all atom results from simulations to identify the underlying driving forces: partitioning of charged and polar groups from the hydrophobic membrane interior to the hydrophilic environment. We propose that the inward-facing state shows a much smaller movement of TM1A, but large enough to create an access path to the S1 substrate binding site from the vestibule.
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Affiliation(s)
- Azmat Sohail
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kumaresan Jayaraman
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Santhoshkannan Venkatesan
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kamil Gotfryd
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
- University of Copenhagen, Faculty of Health Sciences Denmark, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Markus Daerr
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Ulrik Gether
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Claus J. Loland
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Klaus T. Wanner
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Michael Freissmuth
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Harald H. Sitte
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
- * E-mail:
| | - Walter Sandtner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
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23
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Wang H, Meng F. Molecular simulation study on concentration effects of rofecoxib with POPC bilayer. J Mol Graph Model 2016; 70:94-99. [DOI: 10.1016/j.jmgm.2016.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 10/21/2022]
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24
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Mayne CG, Arcario MJ, Mahinthichaichan P, Baylon JL, Vermaas JV, Navidpour L, Wen PC, Thangapandian S, Tajkhorshid E. The cellular membrane as a mediator for small molecule interaction with membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:2290-2304. [PMID: 27163493 PMCID: PMC4983535 DOI: 10.1016/j.bbamem.2016.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 01/05/2023]
Abstract
The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Mark J Arcario
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
| | - Paween Mahinthichaichan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Javier L Baylon
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Latifeh Navidpour
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Po-Chao Wen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
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25
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Reigada R. Alteration of interleaflet coupling due to compounds displaying rapid translocation in lipid membranes. Sci Rep 2016; 6:32934. [PMID: 27596355 PMCID: PMC5011781 DOI: 10.1038/srep32934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/17/2016] [Indexed: 12/02/2022] Open
Abstract
The spatial coincidence of lipid domains at both layers of the cell membrane is expected to play an important role in many cellular functions. Competition between the surface interleaflet tension and a line hydrophobic mismatch penalty are conjectured to determine the transversal behavior of laterally heterogeneous lipid membranes. Here, by a combination of molecular dynamics simulations, a continuum field theory and kinetic equations, I demonstrate that the presence of small, rapidly translocating molecules residing in the lipid bilayer may alter its transversal behavior by favoring the spatial coincidence of similar lipid phases.
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Affiliation(s)
- Ramon Reigada
- Department de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/ Martí i Franqués 1, Pta 4, 08028 Barcelona Spain
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26
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Calcium and protons affect the interaction of neurotransmitters and anesthetics with anionic lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2215-2222. [DOI: 10.1016/j.bbamem.2016.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/16/2016] [Accepted: 06/22/2016] [Indexed: 01/09/2023]
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27
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Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P. In silico pharmacology: Drug membrane partitioning and crossing. Pharmacol Res 2016; 111:471-486. [PMID: 27378566 DOI: 10.1016/j.phrs.2016.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Over the past decade, molecular dynamics (MD) simulations have become particularly powerful to rationalize drug insertion and partitioning in lipid bilayers. MD simulations efficiently support experimental evidences, with a comprehensive understanding of molecular interactions driving insertion and crossing. Prediction of drug partitioning is discussed with respect to drug families (anesthetics; β-blockers; non-steroidal anti-inflammatory drugs; antioxidants; antiviral drugs; antimicrobial peptides). To accurately evaluate passive permeation coefficients turned out to be a complex theoretical challenge; however the recent methodological developments based on biased MD simulations are particularly promising. Particular attention is paid to membrane composition (e.g., presence of cholesterol), which influences drug partitioning and permeation. Recent studies concerning in silico models of membrane proteins involved in drug transport (influx and efflux) are also reported here. These studies have allowed gaining insight in drug efflux by, e.g., ABC transporters at an atomic resolution, explicitly accounting for the mandatory forces induced by the surrounded lipid bilayer. Large-scale conformational changes were thoroughly analyzed.
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Affiliation(s)
- Florent Di Meo
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Gabin Fabre
- LCSN, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Karel Berka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Tahani Ossman
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Benjamin Chantemargue
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Pierre Marquet
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Michal Otyepka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Patrick Trouillas
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic.
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28
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Postila PA, Vattulainen I, Róg T. Selective effect of cell membrane on synaptic neurotransmission. Sci Rep 2016; 6:19345. [PMID: 26782980 PMCID: PMC4725992 DOI: 10.1038/srep19345] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/07/2015] [Indexed: 12/25/2022] Open
Abstract
Atomistic molecular dynamics simulations were performed with 13 non-peptidic neurotransmitters (NTs) in three different membrane environments. The results provide compelling evidence that NTs are divided into membrane-binding and membrane-nonbinding molecules. NTs adhere to the postsynaptic membrane surface whenever the ligand-binding sites of their synaptic receptors are buried in the lipid bilayer. In contrast, NTs that have extracellular ligand-binding sites do not have a similar tendency to adhere to the membrane surface. This finding is a seemingly simple yet important addition to the paradigm of neurotransmission, essentially dividing it into membrane-independent and membrane-dependent mechanisms. Moreover, the simulations also indicate that the lipid composition especially in terms of charged lipids can affect the membrane partitioning of NTs. The revised paradigm, highlighting the importance of cell membrane and specific lipids for neurotransmission, should to be of interest to neuroscientists, drug industry and the general public alike.
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Affiliation(s)
- Pekka A. Postila
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Chemistry and Biochemistry, University of California San Diego, 92093-0340 San Diego, CA, USA
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- MEMPHYS– Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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Lyubartsev AP, Rabinovich AL. Force Field Development for Lipid Membrane Simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2483-2497. [PMID: 26766518 DOI: 10.1016/j.bbamem.2015.12.033] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Stockholm, Sweden.
| | - Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation.
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30
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Membrane Interactions of Phytochemicals as Their Molecular Mechanism Applicable to the Discovery of Drug Leads from Plants. Molecules 2015; 20:18923-66. [PMID: 26501254 PMCID: PMC6332185 DOI: 10.3390/molecules201018923] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 02/02/2023] Open
Abstract
In addition to interacting with functional proteins such as receptors, ion channels, and enzymes, a variety of drugs mechanistically act on membrane lipids to change the physicochemical properties of biomembranes as reported for anesthetic, adrenergic, cholinergic, non-steroidal anti-inflammatory, analgesic, antitumor, antiplatelet, antimicrobial, and antioxidant drugs. As well as these membrane-acting drugs, bioactive plant components, phytochemicals, with amphiphilic or hydrophobic structures, are presumed to interact with biological membranes and biomimetic membranes prepared with phospholipids and cholesterol, resulting in the modification of membrane fluidity, microviscosity, order, elasticity, and permeability with the potencies being consistent with their pharmacological effects. A novel mechanistic point of view of phytochemicals would lead to a better understanding of their bioactivities, an insight into their medicinal benefits, and a strategic implication for discovering drug leads from plants. This article reviews the membrane interactions of different classes of phytochemicals by highlighting their induced changes in membrane property. The phytochemicals to be reviewed include membrane-interactive flavonoids, terpenoids, stilbenoids, capsaicinoids, phloroglucinols, naphthodianthrones, organosulfur compounds, alkaloids, anthraquinonoids, ginsenosides, pentacyclic triterpene acids, and curcuminoids. The membrane interaction’s applicability to the discovery of phytochemical drug leads is also discussed while referring to previous screening and isolating studies.
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31
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Svane S, Kuntsche J, Steiniger F, Eich A, Duelund L, McKee V, McKenzie C. Dimetallic functionalities in liposome bilayers. Supramol Chem 2015. [DOI: 10.1080/10610278.2015.1067316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- S. Svane
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
| | - J. Kuntsche
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
| | - F. Steiniger
- Center for Electron Microscopy of the Medical Faculty, Friedrich Schiller University, Jena 07740, Germany
| | - A. Eich
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
- Department of Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53012 Bonn, Germany
| | - L. Duelund
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
| | - V. McKee
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
| | - C.J. McKenzie
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
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32
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Drasler B, Drobne D, Sadeghpour A, Rappolt M. Fullerene up-take alters bilayer structure and elasticity: A small angle X-ray study. Chem Phys Lipids 2015; 188:46-53. [DOI: 10.1016/j.chemphyslip.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/27/2015] [Accepted: 04/03/2015] [Indexed: 12/21/2022]
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33
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Angelova A, Angelov B, Mutafchieva R, Lesieur S. Biocompatible Mesoporous and Soft Nanoarchitectures. J Inorg Organomet Polym Mater 2014. [DOI: 10.1007/s10904-014-0143-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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34
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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35
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Arcario MJ, Mayne CG, Tajkhorshid E. Atomistic models of general anesthetics for use in in silico biological studies. J Phys Chem B 2014; 118:12075-86. [PMID: 25303275 PMCID: PMC4207551 DOI: 10.1021/jp502716m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
While small molecules have been used
to induce anesthesia in a
clinical setting for well over a century, a detailed understanding
of the molecular mechanism remains elusive. In this study, we utilize
ab initio calculations to develop a novel set of CHARMM-compatible
parameters for the ubiquitous modern anesthetics desflurane, isoflurane,
sevoflurane, and propofol for use in molecular dynamics (MD) simulations.
The parameters generated were rigorously tested against known experimental
physicochemical properties including dipole moment, density, enthalpy
of vaporization, and free energy of solvation. In all cases, the anesthetic
parameters were able to reproduce experimental measurements, signifying
the robustness and accuracy of the atomistic models developed. The
models were then used to study the interaction of anesthetics with
the membrane. Calculation of the potential of mean force for inserting
the molecules into a POPC bilayer revealed a distinct energetic minimum
of 4–5 kcal/mol relative to aqueous solution at the level of
the glycerol backbone in the membrane. The location of this minimum
within the membrane suggests that anesthetics partition to the membrane
prior to binding their ion channel targets, giving context to the
Meyer–Overton correlation. Moreover, MD simulations of these
drugs in the membrane give rise to computed membrane structural parameters,
including atomic distribution, deuterium order parameters, dipole
potential, and lateral stress profile, that indicate partitioning
of anesthetics into the membrane at the concentration range studied
here, which does not appear to perturb the structural integrity of
the lipid bilayer. These results signify that an indirect, membrane-mediated
mechanism of channel modulation is unlikely.
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Affiliation(s)
- Mark J Arcario
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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36
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Koller D, Lohner K. The role of spontaneous lipid curvature in the interaction of interfacially active peptides with membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2250-9. [PMID: 24853655 DOI: 10.1016/j.bbamem.2014.05.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 01/28/2023]
Abstract
Research on antimicrobial peptides is in part driven by urgent medical needs such as the steady increase in pathogens being resistant to antibiotics. Despite the wealth of information compelling structure-function relationships are still scarce and thus the interfacial activity model has been proposed to bridge this gap. This model also applies to other interfacially active (membrane active) peptides such as cytolytic, cell penetrating or antitumor peptides. One parameter that is strongly linked to interfacial activity is the spontaneous lipid curvature, which is experimentally directly accessible. We discuss different parameters such as H-bonding, electrostatic repulsion, changes in monolayer surface area and lateral pressure that affect induction of membrane curvature, but also vice versa how membrane curvature triggers peptide response. In addition, the impact of membrane lipid composition on the formation of curved membrane structures and its relevance for diverse mode of action of interfacially active peptides and in turn biological activity are described. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Daniel Koller
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Schmiedlstraße 6, A-8042 Graz, Austria.
| | - Karl Lohner
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Schmiedlstraße 6, A-8042 Graz, Austria.
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37
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Kopec W, Khandelia H. Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations. J Comput Aided Mol Des 2014; 28:123-34. [DOI: 10.1007/s10822-014-9737-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
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38
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Martin LJ, Chao R, Corry B. Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer. Biophys Chem 2013; 185:98-107. [PMID: 24406394 DOI: 10.1016/j.bpc.2013.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
Molecular dynamics simulations were used to examine the partitioning behaviour of the local anaesthetic benzocaine and the anti-epileptic phenytoin into lipid bilayers, a factor that is critical to their mode of action. Free energy methods are used to quantify the thermodynamics of drug movement between water and octanol as well as for permeation across a POPC membrane. Both drugs are shown to favourably partition into the lipid bilayer from water and are likely to accumulate just inside the lipid headgroups where they may alter bilayer properties or interact with target proteins. Phenytoin experiences a large barrier to cross the centre of the bilayer due to less favourable energetic interactions in this less dense region of the bilayer. Remarkably, in our simulations both drugs are able to pull water into the bilayer, creating water chains that extend back to bulk, and which may modify the local bilayer properties. We find that the choice of atomic partial charges can have a significant impact on the quantitative results, meaning that careful validation of parameters for new drugs, such as performed here, should be performed prior to their use in biomolecular simulations.
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Affiliation(s)
- Lewis J Martin
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - Rebecca Chao
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra 0200, Australia.
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39
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Zhan H, Lazaridis T. Inclusion of lateral pressure/curvature stress effects in implicit membrane models. Biophys J 2013; 104:643-54. [PMID: 23442915 DOI: 10.1016/j.bpj.2012.12.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/06/2012] [Accepted: 12/10/2012] [Indexed: 02/06/2023] Open
Abstract
Implicit membrane models usually treat the membrane as a hydrophobic slab and neglect lateral pressure/curvature stress effects. As a result, they cannot distinguish, for example, PE from PC lipids. Here, the implicit membrane model IMM1 is extended to include these effects using a combination of classical thermodynamics and membrane elasticity theory. The proposed model is tested by molecular dynamics simulation of the peptides alamethicin, melittin, cyclotide kalata B1, 18A, and KKpL15. The lateral pressure term stabilizes interfacial binding due to the negative pressure at the hydrocarbon-water interface. In agreement with experiment, increase in the peptide/lipid molar ratio shifts the equilibrium from the interfacial to the transmembrane orientation. Simulations of mixed DOPC/DOPE bilayers show that increase of the DOPE mole fraction in general stabilizes interfacial orientations and destabilizes transmembrane orientations. The extent of the stabilization or destabilization varies depending on the exact position of the peptides. The computational results are in good agreement with experiments.
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Affiliation(s)
- Huan Zhan
- Department of Chemistry, City College of New York/City University of New York, New York, New York, USA
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40
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Ibarguren M, López DJ, Encinar JA, González-Ros JM, Busquets X, Escribá PV. Partitioning of liquid-ordered/liquid-disordered membrane microdomains induced by the fluidifying effect of 2-hydroxylated fatty acid derivatives. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2553-63. [PMID: 23792066 DOI: 10.1016/j.bbamem.2013.06.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/19/2013] [Accepted: 06/10/2013] [Indexed: 01/15/2023]
Abstract
Cellular functions are usually associated with the activity of proteins and nucleic acids. Recent studies have shown that lipids modulate the localization and activity of key membrane-associated signal transduction proteins, thus regulating the cell's physiology. Membrane Lipid Therapy aims to reverse cell dysfunctions (i.e., diseases) by modulating the activity of membrane signaling proteins through regulation of the lipid bilayer structure. The present work shows the ability of a series of 2-hydroxyfatty acid (2OHFA) derivatives, varying in the acyl chain length and degree of unsaturation, to regulate the membrane lipid structure. These molecules have shown greater therapeutic potential than their natural non-hydroxylated counterparts. We demonstrated that both 2OHFA and natural FAs induced reorganization of lipid domains in model membranes of POPC:SM:PE:Cho, modulating the liquid-ordered/liquid-disordered structures ratio and the microdomain lipid composition. Fluorescence spectroscopy, confocal microscopy, Fourier transform infrared spectroscopy and differential detergent solubilization experiments showed a destabilization of the membranes upon addition of the 2OHFAs and FAs which correlated with the observed disordering effect. The changes produced by these synthetic fatty acids on the lipid structure may constitute part of their mechanism of action, leading to changes in the localization/activity of membrane proteins involved in signaling cascades, and therefore modulating cell responses.
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Affiliation(s)
- Maitane Ibarguren
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands-Lipopharma Therapeutics, S.L., Palma, Spain
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41
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Kopeć W, Telenius J, Khandelia H. Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranes. FEBS J 2013; 280:2785-805. [DOI: 10.1111/febs.12286] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/10/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Wojciech Kopeć
- MEMPHYS - Center for Biomembrane Physics; University of Southern Denmark; Odense; Denmark
| | - Jelena Telenius
- MEMPHYS - Center for Biomembrane Physics; University of Southern Denmark; Odense; Denmark
| | - Himanshu Khandelia
- MEMPHYS - Center for Biomembrane Physics; University of Southern Denmark; Odense; Denmark
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42
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Agelis G, Resvani A, Ntountaniotis D, Chatzigeorgiou P, Koukoulitsa C, Androutsou ME, Plotas P, Matsoukas J, Mavromoustakos T, Cendak T, Godec TU, Mali G. Interactions of the potent synthetic AT1 antagonist analog BV6 with membrane bilayers and mesoporous silicate matrices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1846-55. [PMID: 23506680 DOI: 10.1016/j.bbamem.2013.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 11/27/2022]
Abstract
The present work describes the drug:membrane interactions and a drug delivery system of the novel potent AT1 blocker BV6. This designed analog has most of the pharmacological segments of losartan and an additional biphenyltetrazole moiety resulting in increased lipophilicity. We found that BV6:membrane interactions lead to compact bilayers that may in part explain its higher in vitro activity compared to losartan since such environment may facilitate its approach to AT1 receptor. Its high docking score to AT1 receptor stems from more hydrophobic interactions compared to losartan. X-ray powder diffraction (XRPD) and thermogravimetric analysis (TGA) have shown that BV6 has a crystalline form that is not decomposed completely up to 600°C. These properties are desirable for a drug molecule. BV6 can also be incorporated into a mesoporous silicate drug-delivery matrix SBA-15. The properties of the obtained drug-delivery system have been inspected by XRD, (13)C CP/MAS, TGA and nitrogen sorption experiments.
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Affiliation(s)
- G Agelis
- Eldrug S.A., Patras Science Park, Stadiou, Platani, Rio Patras, Greece
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43
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Abstract
All cells are influenced by mechanical forces. In the brain, force-generating and load-bearing proteins twist, turn, ratchet, flex, compress, expand and bend to mediate neuronal signalling and plasticity. Although the functions of mechanosensitive proteins have been thoroughly described in classical sensory systems, the effects of endogenous mechanical energy on cellular function in the brain have received less attention, and many working models in neuroscience do not currently integrate principles of cellular mechanics. An understanding of cellular-mechanical concepts is essential to allow the integration of mechanobiology into ongoing studies of brain structure and function.
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44
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Reigada R. Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia. PLoS One 2013; 8:e52631. [PMID: 23300982 PMCID: PMC3534722 DOI: 10.1371/journal.pone.0052631] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/20/2012] [Indexed: 01/29/2023] Open
Abstract
The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic) and carbon tetrachloride (non-anesthetic). Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.
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Affiliation(s)
- Ramon Reigada
- Departament de Química Física and Institut de Química Teòrica i Computacional, Universitat de Barcelona, Barcelona, Spain.
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45
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Coupling Membrane Elasticity and Structure to Protein Function. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/b978-0-12-411515-6.00004-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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46
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Boulgaropoulos B, Rappolt M, Sartori B, Amenitsch H, Pabst G. Lipid sorting by ceramide and the consequences for membrane proteins. Biophys J 2012; 102:2031-8. [PMID: 22824266 DOI: 10.1016/j.bpj.2012.03.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/08/2012] [Accepted: 03/23/2012] [Indexed: 01/09/2023] Open
Abstract
We mimicked the effect of sphingomyelinase activity on lipid mixtures of palmitoyl-oleoyl-phosphatidylcholine, sphingomyelin, ceramide, and 10 mol % cholesterol. Using x-ray diffraction experiments in combination with osmotic stress we found, in agreement with previous studies, that ceramide induces a coexistence of L(α) and L(β) domains. A detailed structural analysis of the coexisting domains demonstrated an increase of lipid packing density and membrane thickness in the L(α) domains upon increasing overall ceramide levels. This provides evidence for a ceramide-driven accumulation of cholesterol in the L(α) domains, in support of previous reports. We further determined the bending rigidities of the coexisting domains and found that the accumulation of cholesterol in the L(α) domains stabilizes their bending rigidity, which experiences a dramatic drop in the absence of cholesterol. Deriving experimental estimates for the spontaneous curvature and Gaussian modulus of curvature, we show, using a simple geometric model for ion channels, that in this way changes in the conformational equilibrium of membrane proteins can be kept small.
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Affiliation(s)
- Beate Boulgaropoulos
- Institute of Biophysics and Nanosystems Research, Austrian Academy of Sciences, Graz, Austria
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47
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Fotakis C, Megariotis G, Christodouleas D, Kritsi E, Zoumpoulakis P, Ntountaniotis D, Zervou M, Potamitis C, Hodzic A, Pabst G, Rappolt M, Mali G, Baldus J, Glaubitz C, Papadopoulos MG, Afantitis A, Melagraki G, Mavromoustakos T. Comparative study of the AT1 receptor prodrug antagonist candesartan cilexetil with other sartans on the interactions with membrane bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:3107-20. [DOI: 10.1016/j.bbamem.2012.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/26/2012] [Accepted: 08/13/2012] [Indexed: 11/28/2022]
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48
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Orłowski A, Grzybek M, Bunker A, Pasenkiewicz-Gierula M, Vattulainen I, Männistö PT, Róg T. Strong preferences of dopamine and l-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism. J Neurochem 2012; 122:681-90. [DOI: 10.1111/j.1471-4159.2012.07813.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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49
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Bernardi RC, Pascutti PG. Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction. J Chem Theory Comput 2012; 8:2197-203. [PMID: 26588952 DOI: 10.1021/ct300213u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biomolecular dynamics studies using a QM/MM approach have been largely used especially to study enzymatic reactions. However, to the best of our knowledge, the very same approach has not been used to study the water/membrane interface using a quantum mechanical treatment for the lipids. Since a plethora of biochemical processes take place in this region, we believe that it is of primary importance to understand, at the level of molecular orbitals, the behavior of a drug in such an odd environment. In this work, we take advantage of an integration of the CPMD and the GROMACS code, using the Car-Parrinello method, to treat the benzocaine local anesthetic as well as two of the membrane lipids and the GROMOS force field to treat the remaining lipids and the water molecules.
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Affiliation(s)
- Rafael C Bernardi
- Laboratório de Biotecnologia, Diretoria de Programa (DIPRO), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO) , Av. Nossa Sra das Graças, 50, Prédio 6, Xerém, Duque de Caxias, Rio de Janeiro, 25250-020, Brazil
| | - Pedro G Pascutti
- Laboratório de Biotecnologia, Diretoria de Programa (DIPRO), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO) , Av. Nossa Sra das Graças, 50, Prédio 6, Xerém, Duque de Caxias, Rio de Janeiro, 25250-020, Brazil.,Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ) , Av. Carlos Chagas Filho, 373, Bl. D Sl. 30, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, 21941-902, Brazil
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Use of X-ray scattering to aid the design and delivery of membrane-active drugs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:915-29. [DOI: 10.1007/s00249-012-0821-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/30/2012] [Accepted: 05/05/2012] [Indexed: 10/28/2022]
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