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Moliner R, Girych M, Brunello CA, Kovaleva V, Biojone C, Enkavi G, Antenucci L, Kot EF, Goncharuk SA, Kaurinkoski K, Kuutti M, Fred SM, Elsilä LV, Sakson S, Cannarozzo C, Diniz CRAF, Seiffert N, Rubiolo A, Haapaniemi H, Meshi E, Nagaeva E, Öhman T, Róg T, Kankuri E, Vilar M, Varjosalo M, Korpi ER, Permi P, Mineev KS, Saarma M, Vattulainen I, Casarotto PC, Castrén E. Psychedelics promote plasticity by directly binding to BDNF receptor TrkB. Nat Neurosci 2023; 26:1032-1041. [PMID: 37280397 PMCID: PMC10244169 DOI: 10.1038/s41593-023-01316-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/21/2023] [Indexed: 06/08/2023]
Abstract
Psychedelics produce fast and persistent antidepressant effects and induce neuroplasticity resembling the effects of clinically approved antidepressants. We recently reported that pharmacologically diverse antidepressants, including fluoxetine and ketamine, act by binding to TrkB, the receptor for BDNF. Here we show that lysergic acid diethylamide (LSD) and psilocin directly bind to TrkB with affinities 1,000-fold higher than those for other antidepressants, and that psychedelics and antidepressants bind to distinct but partially overlapping sites within the transmembrane domain of TrkB dimers. The effects of psychedelics on neurotrophic signaling, plasticity and antidepressant-like behavior in mice depend on TrkB binding and promotion of endogenous BDNF signaling but are independent of serotonin 2A receptor (5-HT2A) activation, whereas LSD-induced head twitching is dependent on 5-HT2A and independent of TrkB binding. Our data confirm TrkB as a common primary target for antidepressants and suggest that high-affinity TrkB positive allosteric modulators lacking 5-HT2A activity may retain the antidepressant potential of psychedelics without hallucinogenic effects.
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Affiliation(s)
- Rafael Moliner
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mykhailo Girych
- Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Vera Kovaleva
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Caroline Biojone
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Giray Enkavi
- Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Lina Antenucci
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Erik F Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Katja Kaurinkoski
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mirjami Kuutti
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Senem M Fred
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lauri V Elsilä
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sven Sakson
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | | | - Cassiano R A F Diniz
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Nina Seiffert
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anna Rubiolo
- Neuroscience, University of Trieste, Trieste, Italy
| | - Hele Haapaniemi
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elsa Meshi
- Biomedical Sciences, Hellenic University of Thessaloniki, Thessaloniki, Greece
| | - Elina Nagaeva
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Öhman
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa R Korpi
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
- Structural and Quantitative Biology Research Program, Institute of Biotechnology, Instruct-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Mart Saarma
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Faculty of Science, University of Helsinki, Helsinki, Finland.
| | | | - Eero Castrén
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland.
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Oliveira AA, Róg T, da Silva ABF, Amaro RE, Johnson MS, Postila PA. Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations. Biomolecules 2022; 12:biom12020183. [PMID: 35204684 PMCID: PMC8961577 DOI: 10.3390/biom12020183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022] Open
Abstract
The outer mitochondrial membrane (OMM) is involved in multiple cellular functions such as apoptosis, inflammation and signaling via its membrane-associated and -embedded proteins. Despite the central role of the OMM in these vital phenomena, the structure and dynamics of the membrane have regularly been investigated in silico using simple two-component models. Accordingly, the aim was to generate the realistic multi-component model of the OMM and inspect its properties using atomistic molecular dynamics (MD) simulations. All major lipid components, phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS), were included in the probed OMM models. Because increased levels of anionic PS lipids have potential effects on schizophrenia and, more specifically, on monoamine oxidase B enzyme activity, the effect of varying the PS concentration was explored. The MD simulations indicate that the complex membrane lipid composition (MLC) behavior is notably different from the two-component PC-PE model. The MLC changes caused relatively minor effects on the membrane structural properties such as membrane thickness or area per lipid; however, notable effects could be seen with the dynamical parameters at the water-membrane interface. Increase of PS levels appears to slow down lateral diffusion of all lipids and, in general, the presence of anionic lipids reduced hydration and slowed down the PE headgroup rotation. In addition, sodium ions could neutralize the membrane surface, when PI was the main anionic component; however, a similar effect was not seen for high PS levels. Based on these results, it is advisable for future studies on the OMM and its protein or ligand partners, especially when wanting to replicate the correct properties on the water-membrane interface, to use models that are sufficiently complex, containing anionic lipid types, PI in particular.
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Affiliation(s)
- Aline A. Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland;
| | - Albérico B. F. da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Pekka A. Postila
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
- Institute of Biomedicine, Kiinamyllynkatu 10, Integrative Physiology and Pharmacy, University of Turku, FI-20520 Turku, Finland
- Aurlide Ltd., FI-21420 Lieto, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20520 Turku, Finland
- Correspondence:
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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: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Mahmoudzadeh M, Magarkar A, Koivuniemi A, Róg T, Bunker A. Mechanistic Insight into How PEGylation Reduces the Efficacy of pH-Sensitive Liposomes from Molecular Dynamics Simulations. Mol Pharm 2021; 18:2612-2621. [PMID: 34096310 PMCID: PMC8289284 DOI: 10.1021/acs.molpharmaceut.1c00122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Liposome-based drug
delivery systems composed of DOPE stabilized
with cholesteryl hemisuccinate (CHMS) have been proposed as a drug
delivery mechanism with pH-triggered release as the anionic form (CHSa)
is protonated (CHS) at reduced pH; PEGylation is known to decrease
this pH sensitivity. In this manuscript, we set out to use molecular
dynamics (MD) simulations with a model with all-atom resolution to
provide insight into why incorporation of poly(ethyleneglycol) (PEG)
into DOPE–CHMS liposomes reduces their pH sensitivity; we also
address two additional questions: (1) How CHSa stabilizes DOPE bilayers
into a lamellar conformation at a physiological pH of 7.4? and (2)
how the change from CHSa to CHS at acidic pH triggers the destabilization
of DOPE bilayers? We found that (A) CHSa stabilizes the DOPE lipid
membrane by increasing the hydrophilicity of the bilayer surface,
(B) when CHSa changes to CHS by pH reduction, DOPE bilayers are destabilized
due to a reduction in bilayer hydrophilicity and a reduction in the
area per lipid, and (C) PEG stabilizes DOPE bilayers into the lamellar
phase, thus reducing the pH sensitivity of the liposomes by increasing
the area per lipid through penetration into the bilayer, which is
our main focus.
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Affiliation(s)
- Mohammad Mahmoudzadeh
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00100 Helsinki, Finland
| | - Aniket Magarkar
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Artturi Koivuniemi
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00100 Helsinki, Finland
| | - Tomasz Róg
- Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaarie 5 E, FI-00014 Helsinki, Finland
| | - Alex Bunker
- Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaarie 5 E, FI-00014 Helsinki, Finland
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Cannarozzo C, Fred SM, Girych M, Biojone C, Enkavi G, Róg T, Vattulainen I, Casarotto PC, Castrén E. Cholesterol-recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: The case of TRKB. Eur J Neurosci 2021; 53:3311-3322. [PMID: 33825223 DOI: 10.1111/ejn.15218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 01/19/2023]
Abstract
Cholesterol is an essential constituent of cell membranes. The discovery of cholesterol-recognition amino acid consensus (CRAC) motif in proteins indicated a putative direct, non-covalent interaction between cholesterol and proteins. In the present study, we evaluated the presence of a CRAC motif and its inverted version (CARC) in the transmembrane region (TMR) of the tyrosine kinase receptor family (RTK) in several species using in silico methods. CRAC motifs were found across all species analyzed, while CARC was found only in vertebrates. The tropomyosin-related kinase B (TRKB), a member of the RTK family, through interaction with its endogenous ligand brain-derived neurotrophic factor (BDNF) is a core participant in the neuronal plasticity process and exhibits a CARC motif in its TMR. Upon identifying the conserved CARC motif in the TRKB, we performed molecular dynamics simulations of the mouse TRKB.TMR. The simulations indicated that cholesterol interaction with the TRKB CARC motif occurs mainly at the central Y433 residue. Our binding assay suggested a bell-shaped effect of cholesterol on BDNF interaction with TRKB receptors, and our results suggest that CARC/CRAC motifs may play a role in the function of the RTK family TMR.
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Affiliation(s)
| | - Senem Merve Fred
- Neuroscience Center - HiLife, University of Helsinki, Helsinki, Finland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Caroline Biojone
- Neuroscience Center - HiLife, University of Helsinki, Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | | | - Eero Castrén
- Neuroscience Center - HiLife, University of Helsinki, Helsinki, Finland
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Bunker A, Róg T. Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery. Front Mol Biosci 2020; 7:604770. [PMID: 33330633 PMCID: PMC7732618 DOI: 10.3389/fmolb.2020.604770] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
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Affiliation(s)
- Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
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Lautala S, Provenzani R, Koivuniemi A, Kulig W, Talman V, Róg T, Tuominen RK, Yli-Kauhaluoma J, Bunker A. Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators. J Chem Inf Model 2020; 60:5624-5633. [PMID: 32915560 DOI: 10.1021/acs.jcim.0c00624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but highly lipophilic (clogP = 6.46) DAG mimetic. Although a less lipophilic pyrimidine analog, PYR-1gP (clogP = 3.30), gave positive results in computational docking, it unexpectedly presented greatly diminished binding to PKC in vitro. Through more rigorous computational molecular modeling, we reveal that, unlike HMI-1a3, PYR-1gP forms an intramolecular hydrogen bond, which both obstructs binding and reorients PYR-1gP in the membrane in a fashion that prevents it from correctly accessing the PKC C1 domain. Our results highlight the great value of molecular dynamics simulations as a key component for the drug design process of ligands targeting weakly membrane-associated proteins, where simulation in the relevant membrane environment is crucial for obtaining biologically applicable results.
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Affiliation(s)
- Saara Lautala
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Riccardo Provenzani
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Artturi Koivuniemi
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P.O. Box 64, Gustaf Hällströmin katu 2, FI-00014 Helsinki, Finland
| | - Virpi Talman
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland.,National Heart and Lung Institute, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, Gustaf Hällströmin katu 2, FI-00014 Helsinki, Finland
| | - Raimo K Tuominen
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
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Kukkurainen S, Azizi L, Zhang P, Jacquier MC, Baikoghli M, von Essen M, Tuukkanen A, Laitaoja M, Liu X, Rahikainen R, Orłowski A, Jänis J, Määttä JAE, Varjosalo M, Vattulainen I, Róg T, Svergun D, Cheng RH, Wu J, Hytönen VP, Wehrle-Haller B. The F1 loop of the talin head domain acts as a gatekeeper in integrin activation and clustering. J Cell Sci 2020; 133:jcs239202. [PMID: 33046605 PMCID: PMC10679385 DOI: 10.1242/jcs.239202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
Integrin activation and clustering by talin are early steps of cell adhesion. Membrane-bound talin head domain and kindlin bind to the β integrin cytoplasmic tail, cooperating to activate the heterodimeric integrin, and the talin head domain induces integrin clustering in the presence of Mn2+ Here we show that kindlin-1 can replace Mn2+ to mediate β3 integrin clustering induced by the talin head, but not that induced by the F2-F3 fragment of talin. Integrin clustering mediated by kindlin-1 and the talin head was lost upon deletion of the flexible loop within the talin head F1 subdomain. Further mutagenesis identified hydrophobic and acidic motifs in the F1 loop responsible for β3 integrin clustering. Modeling, computational and cysteine crosslinking studies showed direct and catalytic interactions of the acidic F1 loop motif with the juxtamembrane domains of α- and β3-integrins, in order to activate the β3 integrin heterodimer, further detailing the mechanism by which the talin-kindlin complex activates and clusters integrins. Moreover, the F1 loop interaction with the β3 integrin tail required the newly identified compact FERM fold of the talin head, which positions the F1 loop next to the inner membrane clasp of the talin-bound integrin heterodimer.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sampo Kukkurainen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Latifeh Azizi
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Pingfeng Zhang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Marie-Claude Jacquier
- Department of Cell Physiology and Metabolism, University of Geneva, Centre Médical Universitaire, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Mo Baikoghli
- Department of Molecular and Cellular Biology, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Magdaléna von Essen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Anne Tuukkanen
- EMBL Hamburg c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Xiaonan Liu
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Rolle Rahikainen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Adam Orłowski
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Juha A E Määttä
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Markku Varjosalo
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, FI-33520 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Computational Physics Laboratory, Tampere University, FI-33520 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Dmitri Svergun
- EMBL Hamburg c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - R Holland Cheng
- Department of Molecular and Cellular Biology, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Jinhua Wu
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Bernhard Wehrle-Haller
- Department of Cell Physiology and Metabolism, University of Geneva, Centre Médical Universitaire, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
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9
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Kasparyan G, Poojari C, Róg T, Hub JS. Cooperative Effects of an Antifungal Moiety and DMSO on Pore Formation over Lipid Membranes Revealed by Free Energy Calculations. J Phys Chem B 2020; 124:8811-8821. [PMID: 32924486 DOI: 10.1021/acs.jpcb.0c03359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Itraconazole is a triazole drug widely used in the treatment of fungal infections, and it is in clinical trials for treatment of several cancers. However, the drug suffers from poor solubility, while experiments have shown that itraconazole delivery in liposome nanocarriers improves both circulation half-life and tissue distribution. The drug release mechanism from the nanocarrier is still unknown, and it depends on several factors including membrane stability against defect formation. In this work, we used molecular dynamics simulations and potential of mean force (PMF) calculations to quantify the influence of itraconazole on pore formation over lipid membranes, and we compared the effect by itraconazole with a pore-stabilizing effect by the organic solvent dimethyl sulfoxide (DMSO). According to the PMFs, both itraconazole and DMSO greatly reduce the free energy of pore formation, by up to ∼20 kJ mol-1. However, whereas large concentrations of itraconazole of 8 mol % (relative to lipid) were required, only small concentrations of a few mole % DMSO (relative to water) were sufficient to stabilize pores. In addition, itraconazole and DMSO facilitate pore formation by different mechanisms. Whereas itraconazole predominantly aids the formation of a partial defect with a locally thinned membrane, DMSO mainly stabilizes a transmembrane water needle by shielding it from the hydrophobic core. Notably, the two distinct mechanisms act cooperatively upon adding both itraconazole and DMSO to the membrane, as revealed by an additional reduction of the pore free energy. Overall, our simulations reveal molecular mechanisms and free energies of membrane pore formation by small molecules. We suggest that the stabilization of a locally thinned membrane as well as the shielding of a transmembrane water needle from the hydrophobic membrane core may be a general mechanism by which amphiphilic molecules facilitate pore formation over lipid membranes at sufficient concentrations.
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Affiliation(s)
- Gari Kasparyan
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Chetan Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Tomasz Róg
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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10
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Lolicato F, Juhola H, Zak A, Postila PA, Saukko A, Rissanen S, Enkavi G, Vattulainen I, Kepczynski M, Róg T. Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor. ACS Chem Neurosci 2020; 11:1914-1924. [PMID: 32538079 PMCID: PMC7735663 DOI: 10.1021/acschemneuro.9b00656] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Synaptic neurotransmission has recently been proposed to function via either a membrane-independent or a membrane-dependent mechanism, depending on the neurotransmitter type. In the membrane-dependent mechanism, amphipathic neurotransmitters first partition to the lipid headgroup region and then diffuse along the membrane plane to their membrane-buried receptors. However, to date, this mechanism has not been demonstrated for any neurotransmitter-receptor complex. Here, we combined isothermal calorimetry measurements with a diverse set of molecular dynamics simulation methods to investigate the partitioning of an amphipathic neurotransmitter (dopamine) and the mechanism of its entry into the ligand-binding site. Our results show that the binding of dopamine to its receptor is consistent with the membrane-dependent binding and entry mechanism. Both experimental and simulation results showed that dopamine favors binding to lipid membranes especially in the headgroup region. Moreover, our simulations revealed a ligand-entry pathway from the membrane to the binding site. This pathway passes through a lateral gate between transmembrane alpha-helices 5 and 6 on the membrane-facing side of the protein. All in all, our results demonstrate that dopamine binds to its receptor by a membrane-dependent mechanism, and this is complemented by the more traditional binding mechanism directly through the aqueous phase. The results suggest that the membrane-dependent mechanism is common in other synaptic receptors, too.
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Affiliation(s)
- Fabio Lolicato
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Hanna Juhola
- Computational Physics Laboratory, Tampere University, FI-33100 Tampere, Finland
| | - Agata Zak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Pekka A. Postila
- Institute of Biomedicine, Faculty of Medicine, University of Turku, FI-20014 Turku, Finland
| | - Annina Saukko
- Department of Applied Physics, University of Eastern Finland, P.O.B. 1627, FI-70211 Kuopio, Finland
- Department of Medical Physics, Turku University Hospital, FI-20520 Turku, Finland
| | - Sami Rissanen
- Computational Physics Laboratory, Tampere University, FI-33100 Tampere, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational Physics Laboratory, Tampere University, FI-33100 Tampere, Finland
- MEMPHYS − Center for Biomembrane Physics
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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11
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Chronopoulos A, Thorpe SD, Cortes E, Lachowski D, Rice AJ, Mykuliak VV, Róg T, Lee DA, Hytönen VP, Del Río Hernández AE. Syndecan-4 tunes cell mechanics by activating the kindlin-integrin-RhoA pathway. Nat Mater 2020; 19:669-678. [PMID: 31907416 PMCID: PMC7260055 DOI: 10.1038/s41563-019-0567-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/19/2019] [Indexed: 05/24/2023]
Abstract
Extensive research over the past decades has identified integrins to be the primary transmembrane receptors that enable cells to respond to external mechanical cues. We reveal here a mechanism whereby syndecan-4 tunes cell mechanics in response to localized tension via a coordinated mechanochemical signalling response that involves activation of two other receptors: epidermal growth factor receptor and β1 integrin. Tension on syndecan-4 induces cell-wide activation of the kindlin-2/β1 integrin/RhoA axis in a PI3K-dependent manner. Furthermore, syndecan-4-mediated tension at the cell-extracellular matrix interface is required for yes-associated protein activation. Extracellular tension on syndecan-4 triggers a conformational change in the cytoplasmic domain, the variable region of which is indispensable for the mechanical adaptation to force, facilitating the assembly of a syndecan-4/α-actinin/F-actin molecular scaffold at the bead adhesion. This mechanotransduction pathway for syndecan-4 should have immediate implications for the broader field of mechanobiology.
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Affiliation(s)
- Antonios Chronopoulos
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK
| | - Stephen D Thorpe
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, UK.
| | - Ernesto Cortes
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK
| | - Dariusz Lachowski
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK
| | - Alistair J Rice
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK
| | - Vasyl V Mykuliak
- Faculty of Medicine and Health Technology and BioMediTech, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - David A Lee
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology and BioMediTech, Tampere University, Tampere, Finland.
- Fimlab Laboratories, Tampere, Finland.
| | - Armando E Del Río Hernández
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, London, UK.
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12
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Poojari C, Zak A, Dzieciuch-Rojek M, Bunker A, Kepczynski M, Róg T. Cholesterol Reduces Partitioning of Antifungal Drug Itraconazole into Lipid Bilayers. J Phys Chem B 2020; 124:2139-2148. [PMID: 32101005 PMCID: PMC7735721 DOI: 10.1021/acs.jpcb.9b11005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Cholesterol
plays a crucial role in modulating the physicochemical
properties of biomembranes, both increasing mechanical strength and
decreasing permeability. Cholesterol is also a common component of
vesicle-based delivery systems, including liposome-based drug delivery
systems (LDSs). However, its effect on the partitioning of drug molecules
to lipid membranes is very poorly recognized. Herein, we performed
a combined experimental/computational study of the potential for the
use of the LDS formulation for the delivery of the antifungal drug
itraconazole (ITZ). We consider the addition of cholesterol to the
lipid membrane. Since ITZ is only weakly soluble in water, its bioavailability
is limited. Use of an LDS has thus been proposed. We studied lipid
membranes composed of cholesterol, 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), and ITZ using a combination of
computational molecular dynamics (MD) simulations of lipid bilayers
and Brewster angle microscopy (BAM) experiments of monolayers. Both
experimental and computational results show separation of cholesterol
and ITZ. Cholesterol has a strong preference to orient parallel to
the bilayer normal. However, ITZ, a long and relatively rigid molecule
with weakly hydrophilic groups along the backbone, predominantly locates
below the interface between the hydrocarbon chain region and the polar
region of the membrane, with its backbone oriented parallel to the
membrane surface; the orthogonal orientation in the membrane could
be the cause of the observed separation. In addition, fluorescence
measurements demonstrated that the affinity of ITZ for the lipid membrane
is decreased by the presence of cholesterol, which is thus probably
not a suitable formulation component of an LDS designed for ITZ delivery.
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Affiliation(s)
- Chetan Poojari
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland.,Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Agata Zak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | | | - Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014 Helsinki, Finland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Tomasz Róg
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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13
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Augustyn B, Stepien P, Poojari C, Mobarak E, Polit A, Wisniewska-Becker A, Róg T. Cholesteryl Hemisuccinate Is Not a Good Replacement for Cholesterol in Lipid Nanodiscs. J Phys Chem B 2019; 123:9839-9845. [DOI: 10.1021/acs.jpcb.9b07853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Piotr Stepien
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Chetan Poojari
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Edouard Mobarak
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | | | | | - Tomasz Róg
- Department of Physics, Faculty of Science, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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14
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Poojari C, Wilkosz N, Lira RB, Dimova R, Jurkiewicz P, Petka R, Kepczynski M, Róg T. Behavior of the DPH fluorescence probe in membranes perturbed by drugs. Chem Phys Lipids 2019; 223:104784. [PMID: 31199906 DOI: 10.1016/j.chemphyslip.2019.104784] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/09/2019] [Accepted: 06/08/2019] [Indexed: 12/22/2022]
Abstract
1,6-Diphenyl-1,3,5-hexatriene (DPH) is one of the most commonly used fluorescent probes to study dynamical and structural properties of lipid bilayers and cellular membranes via measuring steady-state or time-resolved fluorescence anisotropy. In this study, we present a limitation in the use of DPH to predict the order of lipid acyl chains when the lipid bilayer is doped with itraconazole (ITZ), an antifungal drug. Our steady-state fluorescence anisotropy measurements showed a significant decrease in fluorescence anisotropy of DPH embedded in the ITZ-containing membrane, suggesting a substantial increase in membrane fluidity, which indirectly indicates a decrease in the order of the hydrocarbon chains. This result or its interpretation is in disagreement with the fluorescence recovery after photobleaching measurements and molecular dynamics (MD) simulation data. The results of these experiments and calculations indicate an increase in the hydrocarbon chain order. The MD simulations of the bilayer containing both ITZ and DPH provide explanations for these observations. Apparently, in the presence of the drug, the DPH molecules are pushed deeper into the hydrophobic membrane core below the lipid double bonds, and the probe predominately adopts the orientation of the ITZ molecules that is parallel to the membrane surface, instead of orienting parallel to the lipid acyl chains. For this reason, DPH anisotropy provides information related to the less ordered central region of the membrane rather than reporting the properties of the upper segments of the lipid acyl chains.
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Affiliation(s)
- Chetan Poojari
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland
| | - Natalia Wilkosz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Rafael B Lira
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424, Potsdam, Germany
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry AS CR, v.v.i, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Rafał Petka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, PO Box 64, FI-00014, Helsinki, Finland.
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15
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Kulig W, Korolainen H, Zatorska M, Kwolek U, Wydro P, Kepczynski M, Róg T. Complex Behavior of Phosphatidylcholine-Phosphatidic Acid Bilayers and Monolayers: Effect of Acyl Chain Unsaturation. Langmuir 2019; 35:5944-5956. [PMID: 30942590 DOI: 10.1021/acs.langmuir.9b00381] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phosphatidic acids (PAs) have many biological functions in biomembranes, e.g., they are involved in the proliferation, differentiation, and transformation of cells. Despite decades of research, the molecular understanding of how PAs affect the properties of biomembranes remains elusive. In this study, we explored the properties of lipid bilayers and monolayers composed of PAs and phosphatidylcholines (PCs) with various acyl chains. For this purpose, the Langmuir monolayer technique and atomistic molecular dynamics (MD) simulations were used to study the miscibility of PA and PC lipids and the molecular organization of mixed bilayers. The monolayer experiments demonstrated that the miscibility of membrane components strongly depends on the structure of the hydrocarbon chains and thus on the overall lipid shape. Interactions between PA and PC molecules vary from repulsive, for systems containing lipids with saturated and unsaturated acyl tails (strongly positive values of the excess free energy of mixing), to attractive, for systems in which all lipid tails are saturated (negative values of the excess free energy of mixing). The MD simulations provided atomistic insight into polar interactions (formation of hydrogen bonds and charge pairs) in PC-PA systems. H-bonding between PA monoanions and PCs in mixed bilayers is infrequent, and the lipid molecules interact mainly via electrostatic interactions. However, the number of charge pairs significantly decreases with the number of unsaturated lipid chains in the PA-PC system. The PA dianions weakly interact with the zwitterionic lipids, but their headgroups are more hydrated as compared to the monoanionic form. The acyl chains in all PC-PA bilayers are more ordered compared to single-component PC systems. In addition, depending on the combination of lipids, we observed a deeper location of the PA phosphate groups compared to the PC phosphate groups, which can alter the presentation of PAs for the peripheral membrane proteins, affecting their accessibility for binding.
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Affiliation(s)
- Waldemar Kulig
- Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Hanna Korolainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Maria Zatorska
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Kraków , Poland
| | - Urszula Kwolek
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Kraków , Poland
| | - Paweł Wydro
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Kraków , Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Kraków , Poland
| | - Tomasz Róg
- Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
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16
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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: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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17
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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] [What about the content of this article? (0)] [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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18
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Magarkar A, Parkkila P, Viitala T, Lajunen T, Mobarak E, Licari G, Cramariuc O, Vauthey E, Róg T, Bunker A. Membrane bound COMT isoform is an interfacial enzyme: general mechanism and new drug design paradigm. Chem Commun (Camb) 2018; 54:3440-3443. [DOI: 10.1039/c8cc00221e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have determined the substrate differentiation mechanism between the membrane bound and water soluble isoforms of important drug target catechol-O-methyltransferase.
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19
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Danne R, Poojari C, Martinez-Seara H, Rissanen S, Lolicato F, Róg T, Vattulainen I. doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS. J Chem Inf Model 2017; 57:2401-2406. [PMID: 28906114 PMCID: PMC5662928 DOI: 10.1021/acs.jcim.7b00237] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Carbohydrates constitute a structurally
and functionally diverse
group of biological molecules and macromolecules. In cells they are
involved in, e.g., energy storage, signaling, and cell–cell
recognition. All of these phenomena take place in atomistic scales,
thus atomistic simulation would be the method of choice to explore
how carbohydrates function. However, the progress in the field is
limited by the lack of appropriate tools for preparing carbohydrate
structures and related topology files for the simulation models. Here
we present tools that fill this gap. Applications where the tools
discussed in this paper are particularly useful include, among others,
the preparation of structures for glycolipids, nanocellulose, and
glycans linked to glycoproteins. The molecular structures and simulation
files generated by the tools are compatible with GROMACS.
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Affiliation(s)
- Reinis Danne
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Chetan Poojari
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014 Helsinki, Finland
| | - Hector Martinez-Seara
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Sami Rissanen
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Fabio Lolicato
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014 Helsinki, Finland.,MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark , 5230 Odense, Denmark
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20
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Grabon A, Orłowski A, Tripathi A, Vuorio J, Javanainen M, Róg T, Lönnfors M, McDermott MI, Siebert G, Somerharju P, Vattulainen I, Bankaitis VA. Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle. J Biol Chem 2017; 292:14438-14455. [PMID: 28718450 DOI: 10.1074/jbc.m117.791467] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/14/2017] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling. However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability of PITPα to initiate closure around the PtdCho ligand is accompanied by loss of flexibility of two helix/loop regions, as well as of the C-terminal helix; (iii) the energy barrier of phospholipid extraction from the membrane is lowered by a network of hydrogen bonds between the lipid molecule and PITPα; (iv) the trajectory of PtdIns or PtdCho into and through the lipid-binding pocket is chaperoned by sets of PITPα residues conserved throughout the StART-like PITP family; and (v) conformational transitions in the C-terminal helix have specific functional involvements in PtdIns transfer activity. Taken together, these findings provide the first mechanistic description of key aspects of the PITPα PtdIns/PtdCho exchange cycle and offer a rationale for the high conservation of particular sets of residues across evolutionarily distant members of the metazoan StART-like PITP family.
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Affiliation(s)
- Aby Grabon
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Adam Orłowski
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland.,the Department of Physics and Energy, University of Limerick, Limerick V94 T9PX, Ireland
| | - Ashutosh Tripathi
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Joni Vuorio
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland.,the Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland
| | - Tomasz Róg
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland.,the Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland
| | - Max Lönnfors
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Mark I McDermott
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Garland Siebert
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Pentti Somerharju
- the Department of Biochemistry and Developmental Biology, University of Helsinki, P. O. Box 63, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- the Laboratory of Physics, Tampere University of Technology, FI-33720 Tampere, Finland, .,the Department of Physics, University of Helsinki, P. O. Box 64, FI-00014 Helsinki, Finland.,the Department of Physics and Chemistry, MEMPHYS, Center for Biomembrane Physics, University of Southern Denmark, DK-5230 Odense, Denmark, and
| | - Vytas A Bankaitis
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843, .,the Departments of Biochemistry and Biophysics and.,Chemistry, Texas A&M University, College Station, Texas 77843
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21
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Mokkila S, Postila PA, Rissanen S, Juhola H, Vattulainen I, Róg T. Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles. ACS Chem Neurosci 2017; 8:1242-1250. [PMID: 28165217 DOI: 10.1021/acschemneuro.6b00395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this study, the dopamine-lipid bilayer interactions were probed with three physiologically relevant ion compositions using atomistic molecular dynamics simulations and free energy calculations. The in silico results indicate that calcium is able to decrease significantly the binding of dopamine to a neutral (zwitterionic) phosphatidylcholine lipid bilayer model mimicking the inner leaflet of a presynaptic vesicle. We argue that the observed calcium-induced effect is likely in crucial role in the neurotransmitter release from the presynaptic vesicles docked in the active zone of nerve terminals. The inner leaflets of presynaptic vesicles, which are responsible for releasing neurotransmitters into the synaptic cleft, are mainly composed of neutral lipids such as phosphatidylcholine and phosphatidylethanolamine. The neutrality of the lipid head group region, enhanced by a low pH level, should limit membrane aggregation of transmitters. In addition, the simulations suggest that the high calcium levels inside presynaptic vesicles prevent even the most lipophilic transmitters such as dopamine from adhering to the inner leaflet surface, thus rendering unhindered neurotransmitter release feasible.
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Affiliation(s)
- Sini Mokkila
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Pekka A. Postila
- Structural Bioinformatics Laboratory, Biochemistry,
Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Hanna Juhola
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- MEMPHYS − Center for Biomembrane
Physics, University of Southern Denmark, 5230 Odense, Denmark
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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22
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Rissanen S, Grzybek M, Orłowski A, Róg T, Cramariuc O, Levental I, Eggeling C, Sezgin E, Vattulainen I. Phase Partitioning of GM1 and Its Bodipy-Labeled Analog Determine Their Different Binding to Cholera Toxin. Front Physiol 2017; 8:252. [PMID: 28536532 PMCID: PMC5422513 DOI: 10.3389/fphys.2017.00252] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/10/2017] [Indexed: 12/19/2022] Open
Abstract
Driven by interactions between lipids and proteins, biological membranes display lateral heterogeneity that manifests itself in a mosaic of liquid-ordered (Lo) or raft, and liquid-disordered (Ld) or non-raft domains with a wide range of different properties and compositions. In giant plasma membrane vesicles and giant unilamellar vesicles, specific binding of Cholera Toxin (CTxB) to GM1 glycolipids is a commonly used strategy to label raft domains or Lo membrane environments. However, these studies often use acyl-chain labeled bodipy-GM1 (bdGM1), whose headgroup accessibility and membrane order or phase partitioning may differ from those of GM1, rendering the interpretation of CTxB binding data quite problematic. To unravel the molecular basis of CTxB binding to GM1 and bdGM1, we explored the partitioning and the headgroup presentation of these gangliosides in the Lo and Ld phases using atomistic molecular dynamics simulations complemented by CTxB binding experiments. The conformation of both GM1 and bdGM1 was shown to be largely similar in the Lo and Ld phases. However, bdGM1 showed reduction in receptor availability when reconstituted into synthetic bilayer mixtures, highlighting that membrane phase partitioning of the gangliosides plays a considerable role in CTxB binding. Our results suggest that the CTxB binding is predominately modulated by the partitioning of the receptor to an appropriate membrane phase. Further, given that the Lo and Ld partitioning of bdGM1 differs from those of GM1, usage of bdGM1 for studying GM1 behavior in cells can lead to invalid interpretation of experimental data.
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Affiliation(s)
- Sami Rissanen
- Department of Physics, Tampere University of TechnologyTampere, Finland
| | - Michal Grzybek
- Paul Langerhans Institute Dresden of the Helmholtz Centre Munich at the University Clinic Carl Gustav Carus, TU DresdenDresden, Germany.,German Center for Diabetes ResearchNeuherberg, Germany
| | - Adam Orłowski
- Department of Physics, Tampere University of TechnologyTampere, Finland.,Department of Physics and Energy, University of LimerickLimerick, Ireland
| | - Tomasz Róg
- Department of Physics, Tampere University of TechnologyTampere, Finland.,Department of Physics, University of HelsinkiHelsinki, Finland
| | - Oana Cramariuc
- Department of Physics, Tampere University of TechnologyTampere, Finland
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science CenterHouston, TX, USA
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxford, UK
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxford, UK
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of TechnologyTampere, Finland.,Department of Physics, University of HelsinkiHelsinki, Finland.,MEMPHYS-Center for Biomembrane Physics, University of Southern DenmarkOdense, Denmark
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23
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Magarkar A, Róg T, Bunker A. A computational study suggests that replacing PEG with PMOZ may increase exposure of hydrophobic targeting moiety. Eur J Pharm Sci 2017; 103:128-135. [PMID: 28285174 DOI: 10.1016/j.ejps.2017.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 12/18/2022]
Abstract
In a previous study we showed that the cause of failure of a new, proposed, targeting ligand, the AETP moiety, when attached to a PEGylated liposome, was occlusion by the poly(ethylene glycol) (PEG) layer due to its hydrophobic nature, given that PEG is not entirely hydrophilic. At the time we proposed that possible replacement with a more hydrophilic protective polymer could alleviate this problem. In this study we have used computational molecular dynamics modelling, using a model with all atom resolution, to suggest that a specific alternative protective polymer, poly(2-methyloxazoline) (PMOZ), would perform exactly this function. Our results show that when PEG is replaced by PMOZ the relative exposure to the solvent of AETP is increased to a level even greater than that we found in previous simulations for the RGD peptide, a targeting moiety that has previously been used successfully in PEGylated liposome based therapies. While the AETP moiety itself is no longer under consideration, the results of this computational study have broader significance: the use of PMOZ as an alternative polymer coating to PEG could be efficacious in the context of more hydrophobic targeting ligands. In addition to PMOZ we studied another polyoxazoline, poly(2-ethyloxazoline) (PEOZ), that has also been mooted as a possible alternate protective polymer. It was also found that the RDG peptide occlusion was significantly greater for the case of both oxazolines as opposed to PEG and that, unlike PEG, neither oxazoline entered the membrane. As far as we are aware this is the first time that polyoxazolines have been studied using molecular dynamics simulation with all atom resolution.
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Affiliation(s)
- Aniket Magarkar
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Institute of Organic Chemistry and Biochemistry, Academy of the Sciences of the Czech Republic Prague, Czech Republic
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Alex Bunker
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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24
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Dzieciuch-Rojek M, Poojari C, Bednar J, Bunker A, Kozik B, Nowakowska M, Vattulainen I, Wydro P, Kepczynski M, Róg T. Effects of Membrane PEGylation on Entry and Location of Antifungal Drug Itraconazole and Their Pharmacological Implications. Mol Pharm 2017; 14:1057-1070. [PMID: 28234487 DOI: 10.1021/acs.molpharmaceut.6b00969] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Itraconazole (ITZ) is an antifungal agent used clinically to treat mycotic infections. However, its therapeutic effects are limited by low solubility in aqueous media. Liposome-based delivery systems (LDS) have been proposed as a delivery mechanism for ITZ to alleviate this problem. Furthermore, PEGylation, the inclusion in the formulation of a protective "stealth sheath" of poly(ethylene glycol) around carrier particles, is widely used to increase circulation time in the bloodstream and hence efficacy. Together, these themes highlight the importance of mechanistic and structural understanding of ITZ incorporation into liposomes both with and without PEGylation because it can provide a potential foundation for the rational design of LDS-based systems for delivery of ITZ, using alternate protective polymers or formulations. Here we have combined atomistic simulations, cryo-TEM, Langmuir film balance, and fluorescence quenching experiments to explore how ITZ interacts with both pristine and PEGylated liposomes. We found that the drug can be incorporated into conventional and PEGylated liposomes for drug concentrations up to 15 mol % without phase separation. We observed that, in addition to its protective properties, PEGylation significantly increases the stability of liposomes that host ITZ. In a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer without PEGylation, ITZ was found to reside inside the lipid bilayer between the glycerol and the double-bond regions of POPC, adopting a largely parallel orientation along the membrane surface. In a PEGylated liposome, ITZ partitions mainly to the PEG layer. The results provide a solid basis for further development of liposome-based delivery systems.
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Affiliation(s)
| | - Chetan Poojari
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Jan Bednar
- Université de Grenoble Alpes/CNRS, Institut Albert Bonniot , UMR 5309, 38042 CEDEX 9 Grenoble, France.,First Faculty of Medicine, Laboratory of Biology and Pathology of the Eye, Institute of Inherited Metabolic Disorders, Charles University in Prague , KeKarlovu 2, 12800 Prague 2, Czech Republic
| | - Alex Bunker
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Bartłomiej Kozik
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Maria Nowakowska
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014 Helsinki, Finland.,MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark , Odense, Denmark
| | - Paweł Wydro
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014 Helsinki, Finland
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25
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Bilkova E, Pleskot R, Rissanen S, Sun S, Czogalla A, Cwiklik L, Róg T, Vattulainen I, Cremer PS, Jungwirth P, Coskun Ü. Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition. J Am Chem Soc 2017; 139:4019-4024. [PMID: 28177616 PMCID: PMC5364432 DOI: 10.1021/jacs.6b11760] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The orchestrated recognition of phosphoinositides and concomitant intracellular release of Ca2+ is pivotal to almost every aspect of cellular processes, including membrane homeostasis, cell division and growth, vesicle trafficking, as well as secretion. Although Ca2+ is known to directly impact phosphoinositide clustering, little is known about the molecular basis for this or its significance in cellular signaling. Here, we study the direct interaction of Ca2+ with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), the main lipid marker of the plasma membrane. Electrokinetic potential measurements of PI(4,5)P2 containing liposomes reveal that Ca2+ as well as Mg2+ reduce the zeta potential of liposomes to nearly background levels of pure phosphatidylcholine membranes. Strikingly, lipid recognition by the default PI(4,5)P2 lipid sensor, phospholipase C delta 1 pleckstrin homology domain (PLC δ1-PH), is completely inhibited in the presence of Ca2+, while Mg2+ has no effect with 100 nm liposomes and modest effect with giant unilamellar vesicles. Consistent with biochemical data, vibrational sum frequency spectroscopy and atomistic molecular dynamics simulations reveal how Ca2+ binding to the PI(4,5)P2 headgroup and carbonyl regions leads to confined lipid headgroup tilting and conformational rearrangements. We rationalize these findings by the ability of calcium to block a highly specific interaction between PLC δ1-PH and PI(4,5)P2, encoded within the conformational properties of the lipid itself. Our studies demonstrate the possibility that switchable phosphoinositide conformational states can serve as lipid recognition and controlled cell signaling mechanisms.
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Affiliation(s)
- Eva Bilkova
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research (DZD e.V.) , Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Roman Pleskot
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,Institute of Experimental Botany, Academy of Sciences of the Czech Republic , v.v.i., Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | | | - Aleksander Czogalla
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław , Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Lukasz Cwiklik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014, Helsinki, Finland.,MEMPHYS- Center for Biomembrane Physics, University of Southern Denmark , DK-5230 Odense, Denmark
| | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research (DZD e.V.) , Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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26
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Euro L, Haapanen O, Róg T, Vattulainen I, Suomalainen A, Sharma V. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis. Biochemistry 2017; 56:1227-1238. [PMID: 28206745 DOI: 10.1021/acs.biochem.6b00934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.
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Affiliation(s)
- Liliya Euro
- Research Programs Unit, Molecular Neurology, University of Helsinki , 00290 Helsinki, Finland
| | - Outi Haapanen
- Department of Physics, Tampere University of Technology , Tampere, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology , Tampere, Finland.,Department of Physics, University of Helsinki , Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , Tampere, Finland.,Department of Physics, University of Helsinki , Helsinki, Finland.,MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark , Odense, Denmark
| | - Anu Suomalainen
- Research Programs Unit, Molecular Neurology, University of Helsinki , 00290 Helsinki, Finland.,Department of Neurology, Helsinki University Hospital , Helsinki, Finland.,Neuroscience Center, University of Helsinki , 00790 Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, Tampere University of Technology , Tampere, Finland.,Department of Physics, University of Helsinki , Helsinki, Finland.,Institute of Biotechnology, University of Helsinki , Helsinki, Finland
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27
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Polley A, Orłowski A, Danne R, Gurtovenko AA, Bernardino de la Serna J, Eggeling C, Davis SJ, Róg T, Vattulainen I. Glycosylation and Lipids Working in Concert Direct CD2 Ectodomain Orientation and Presentation. J Phys Chem Lett 2017; 8:1060-1066. [PMID: 28191954 PMCID: PMC5445502 DOI: 10.1021/acs.jpclett.6b02824] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/13/2017] [Indexed: 05/30/2023]
Abstract
Proteins embedded in the plasma membrane mediate interactions with the cell environment and play decisive roles in many signaling events. For cell-cell recognition molecules, it is highly likely that their structures and behavior have been optimized in ways that overcome the limitations of membrane tethering. In particular, the ligand binding regions of these proteins likely need to be maximally exposed. Here we show by means of atomistic simulations of membrane-bound CD2, a small cell adhesion receptor expressed by human T-cells and natural killer cells, that the presentation of its ectodomain is highly dependent on membrane lipids and receptor glycosylation acting in apparent unison. Detailed analysis shows that the underlying mechanism is based on electrostatic interactions complemented by steric interactions between glycans in the protein and the membrane surface. The findings are significant for understanding the factors that render membrane receptors accessible for binding and signaling.
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Affiliation(s)
- Anirban Polley
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 10, P.O. Box 692, FI-33101 Tampere, Finland
| | - Adam Orłowski
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 10, P.O. Box 692, FI-33101 Tampere, Finland
- Department
of Physics and Energy, University of Limerick, Limerick V94 T9PX, Ireland
| | - Reinis Danne
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 10, P.O. Box 692, FI-33101 Tampere, Finland
| | - Andrey A. Gurtovenko
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg, 199004 Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya Strasse 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Jorge Bernardino de la Serna
- Science
and Technology Facilities Council, Rutherford Appleton Laboratory, Central Laser Facility, Research
Complex at Harwell, Harwell−Oxford
Campus, OX11 0FA Didcot, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology
Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | - Simon J. Davis
- MRC Human Immunology
Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 10, P.O. Box 692, FI-33101 Tampere, Finland
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 10, P.O. Box 692, FI-33101 Tampere, Finland
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Department
of Physics and Chemistry, MEMPHYS−Center for Biomembrane
Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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28
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Wilkosz N, Rissanen S, Cyza M, Szybka R, Nowakowska M, Bunker A, Róg T, Kepczynski M. Effect of piroxicam on lipid membranes: Drug encapsulation and gastric toxicity aspects. Eur J Pharm Sci 2017; 100:116-125. [DOI: 10.1016/j.ejps.2017.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 01/11/2023]
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29
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Poojari CS, Roodhuizen J, Lolicato F, Róg T, Vattulainen I. Molecular Basis of GLUT4 in Glucose Transport: Atomistic Molecular Dynamics Study. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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30
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Kuleta P, Sarewicz M, Postila P, Róg T, Osyczka A. Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1. Biochim Biophys Acta 2016; 1857:1661-8. [PMID: 27421232 PMCID: PMC5001787 DOI: 10.1016/j.bbabio.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/22/2016] [Accepted: 07/10/2016] [Indexed: 11/23/2022]
Abstract
Describing dynamics of proton transfers in proteins is challenging, but crucial for understanding processes which use them for biological functions. In cytochrome bc1, one of the key enzymes of respiration or photosynthesis, proton transfers engage in oxidation of quinol (QH2) and reduction of quinone (Q) taking place at two distinct catalytic sites. Here we evaluated by site-directed mutagenesis the contribution of Lys251/Asp252 pair (bacterial numbering) in electron transfers and associated with it proton uptake to the quinone reduction site (Qi site). We showed that the absence of protonable group at position 251 or 252 significantly changes the equilibrium levels of electronic reactions including the Qi-site mediated oxidation of heme bH, reverse reduction of heme bH by quinol and heme bH/Qi semiquinone equilibrium. This implicates the role of H-bonding network in binding of quinone/semiquinone and defining thermodynamic properties of Q/SQ/QH2 triad. The Lys251/Asp252 proton path is disabled only when both protonable groups are removed. With just one protonable residue from this pair, the entrance of protons to the catalytic site is sustained, albeit at lower rates, indicating that protons can travel through parallel routes, possibly involving water molecules. This shows that proton paths display engineering tolerance for change as long as all the elements available for functional cooperation secure efficient proton delivery to the catalytic site.
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Affiliation(s)
- Patryk Kuleta
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Kraków, Poland
| | - Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Kraków, Poland
| | - Pekka Postila
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Kraków, Poland.
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Kaurola P, Sharma V, Vonk A, Vattulainen I, Róg T. Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria. Biochim Biophys Acta 2016; 1858:2116-2122. [PMID: 27342376 DOI: 10.1016/j.bbamem.2016.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/11/2016] [Accepted: 06/17/2016] [Indexed: 01/24/2023]
Abstract
Quinone and its analogues (Q) constitute an important class of compounds that perform key electron transfer reactions in oxidative- and photo-phosphorylation. In the inner membrane of mitochondria, ubiquinone molecules undergo continuous redox transitions enabling electron transfer between the respiratory complexes. In such a dynamic system undergoing continuous turnover for ATP synthesis, an uninterrupted supply of substrate molecules is absolutely necessary. In the current work, we have performed atomistic molecular dynamics simulations and free energy calculations to assess the structure, dynamics, and localization of quinone and its analogues in a lipid bilayer, whose composition mimics the one in the inner mitochondrial membrane. The results show that there is a strong tendency of both quinone and quinol molecules to localize in the vicinity of the lipids' acyl groups, right under the lipid head group region. Additionally, we observe a second location in the middle of the bilayer where quinone molecules tend to stabilize. Translocation of quinone through a lipid bilayer is very fast and occurs in 10-100ns time scale, whereas the translocation of quinol is at least an order of magnitude slower. We suggest that this has important mechanistic implications given that the localization of Q ensures maximal occupancy of the Q-binding sites or Q-entry points in electron transport chain complexes, thereby maintaining an optimal turnover rate for ATP synthesis.
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Affiliation(s)
- Petri Kaurola
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Vivek Sharma
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Amanda Vonk
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland.
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Affiliation(s)
- Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland
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Pathak P, Dhawan V, Magarkar A, Danne R, Govindarajan S, Ghosh S, Steiniger F, Chaudhari P, Gopal V, Bunker A, Róg T, Fahr A, Nagarsenker M. Design of cholesterol arabinogalactan anchored liposomes for asialoglycoprotein receptor mediated targeting to hepatocellular carcinoma: In silico modeling, in vitro and in vivo evaluation. Int J Pharm 2016; 509:149-158. [PMID: 27231122 DOI: 10.1016/j.ijpharm.2016.05.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/14/2016] [Accepted: 05/21/2016] [Indexed: 02/06/2023]
Abstract
We have developed active targeting liposomes to deliver anticancer agents to ASGPR which will contribute to effective treatment of hepatocellular carcinoma. Active targeting is achieved through polymeric ligands on the liposome surface. The liposomes were prepared using reverse phase evaporation method and doxorubicin hydrocholoride, a model drug, was loaded using the ammonium sulphate gradient method. Liposomes loaded with DOX were found to have a particle size of 200nm with more than 90% entrapment efficiency. Systems were observed to release the drug in a sustained manner in acidic pH in vitro. Liposomes containing targeting ligands possessed greater and selective toxicity to ASGPR positive HepG2 cell lines due to specific ligand receptor interaction. Bio-distribution studies revealed that liposomes were concentrated in the liver even after 3h of administration, thus providing conclusive evidence of targeting potential for formulated nanosystems. Tumor regression studies indicated greater tumor suppression with targeted liposomes thereby establishing superiority of the liposomal system. In this work, we used a novel methodology to guide the determination of the optimal composition of the targeting liposomes: molecular dynamics (MD) simulation that aided our understanding of the behaviour of the ligand within the bilayer. This can be seen as a demonstration of the utility of this methodology as a rational design tool for active targeting liposome formulation.
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Affiliation(s)
- Pankaj Pathak
- Bombay College of Pharmacy, University of Mumbai, Mumbai 400098, India
| | - Vivek Dhawan
- Bombay College of Pharmacy, University of Mumbai, Mumbai 400098, India
| | - Aniket Magarkar
- Academy of the Sciences of the Czech Republic, Prague, Czech Republic; Centre for Drug Research, Division of Pharmaceutical Bioscience, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland
| | - Reinis Danne
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland
| | - Srinath Govindarajan
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India
| | - Sandipto Ghosh
- Small Animal Imaging Facility (SAIF), Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Kharghar, Mumbai 410210, India
| | - Frank Steiniger
- Center for Electron Microscopy of the Medical Faculty, Friedrich-Schiller-University Jena, Ziegelmühlenweg 1, D-07740 Jena, Germany
| | - Pradip Chaudhari
- Small Animal Imaging Facility (SAIF), Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Kharghar, Mumbai 410210, India
| | - Vijaya Gopal
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India
| | - Alex Bunker
- Centre for Drug Research, Division of Pharmaceutical Bioscience, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101 Tampere, Finland
| | - Alfred Fahr
- Department of Pharmaceutical Technology, Friedrich-Schiller-University Jena, Lessing-str. 8, D-07743 Jena, Germany
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Lajunen T, Kontturi LS, Viitala L, Manna M, Cramariuc O, Róg T, Bunker A, Laaksonen T, Viitala T, Murtomäki L, Urtti A. Indocyanine Green-Loaded Liposomes for Light-Triggered Drug Release. Mol Pharm 2016; 13:2095-107. [DOI: 10.1021/acs.molpharmaceut.6b00207] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tatu Lajunen
- Centre
for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Leena-Stiina Kontturi
- Centre
for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department
of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Lauri Viitala
- Department
of Chemistry, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Moutusi Manna
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Oana Cramariuc
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Alex Bunker
- Centre
for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Timo Laaksonen
- Centre
for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Tapani Viitala
- Centre
for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Lasse Murtomäki
- Department
of Chemistry, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Arto Urtti
- Centre
for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- School
of
Pharmacy, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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Róg T, Orłowski A, Llorente A, Skotland T, Sylvänne T, Kauhanen D, Ekroos K, Sandvig K, Vattulainen I. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters. Data Brief 2016; 7:1171-1174. [PMID: 27761499 PMCID: PMC5063793 DOI: 10.1016/j.dib.2016.03.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/06/2016] [Accepted: 03/18/2016] [Indexed: 12/01/2022] Open
Abstract
In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers׳ compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids׳ topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article “Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner” (Róg et al., 2016) [3].
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland
| | - Adam Orłowski
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | | | | | - Kim Ekroos
- Zora Biosciences Oy, 02150 Espoo, Finland
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway; Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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Kepczynski M, Róg T. Functionalized lipids and surfactants for specific applications. Biochim Biophys Acta 2016; 1858:2362-2379. [PMID: 26946243 DOI: 10.1016/j.bbamem.2016.02.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/17/2022]
Abstract
Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101, Tampere, Finland; Department of Physics, Helsinki University, P.O. Box 64, FI 00014 Helsinki, Finland.
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Róg T, Orłowski A, Llorente A, Skotland T, Sylvänne T, Kauhanen D, Ekroos K, Sandvig K, Vattulainen I. Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner. Biochimica et Biophysica Acta (BBA) - Biomembranes 2016; 1858:281-8. [DOI: 10.1016/j.bbamem.2015.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 11/16/2015] [Accepted: 12/01/2015] [Indexed: 12/15/2022]
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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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Dhawan V, Magarkar A, Joshi G, Makhija D, Jain A, Shah J, Reddy BVV, Krishnapriya M, Róg T, Bunker A, Jagtap A, Nagarsenker M. Stearylated cycloarginine nanosystems for intracellular delivery – simulations, formulation and proof of concept. RSC Adv 2016. [DOI: 10.1039/c6ra16432c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Novel cationic agent liposomes performed better in silico translating in higher cellular uptake with reduced toxicity.
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40
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Botan A, Favela-Rosales F, Fuchs PFJ, Javanainen M, Kanduč M, Kulig W, Lamberg A, Loison C, Lyubartsev A, Miettinen MS, Monticelli L, Määttä J, Ollila OHS, Retegan M, Róg T, Santuz H, Tynkkynen J. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. J Phys Chem B 2015; 119:15075-88. [PMID: 26509669 PMCID: PMC4677354 DOI: 10.1021/acs.jpcb.5b04878] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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Affiliation(s)
- Alexandru Botan
- Institut
Lumière Matière, UMR5306 Université
Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Fernando Favela-Rosales
- Departamento
de Física, Centro de Investigación
y de Estudios Avanzados del IPN, Apartado, Postal 14-740, Mexico City, 07000 México
D.F., México
| | - Patrick F. J. Fuchs
- Institut
Jacques Monod, UMR 7592 CNRS, Université Paris
Diderot, Sorbonne, Paris Cité, F-75205 Paris, France
| | - Matti Javanainen
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Matej Kanduč
- Fachbereich
Physik, Freie Universität Berlin, Berlin, 14195 Germany
| | - Waldemar Kulig
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Antti Lamberg
- Department
of Chemical Engineering, Kyoto University, 615-8510 Kyoto, Japan
| | - Claire Loison
- Institut
Lumière Matière, UMR5306 Université
Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France
| | - Alexander Lyubartsev
- Division
of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, S-106 91 Stockholm, Sweden
| | | | - Luca Monticelli
- Institut
de Biologie et Chimie des Protéines (IBCP), CNRS UMR 5086, Lyon 69 367, France
| | - Jukka Määttä
- Department of Chemistry, Aalto University, 00076 Aalto, Finland
| | - O. H. Samuli Ollila
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Marius Retegan
- Max Planck Institute
for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
| | - Hubert Santuz
- INSERM, UMR_S 1134, DSIMB, Paris 75739, France
- Université
Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France
- Institut
National de la Transfusion Sanguine (INTS), Paris 75739, France
- Laboratoire d’Excellence GR-Ex, Paris 75015, France
| | - Joona Tynkkynen
- Department
of Physics, Tampere University of Technology, Tampere, 33101 Finland
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Abstract
Integrins are major players in cell adhesion and migration, and malfunctions in controlling their activity are associated with various diseases. Nevertheless, the details of integrin activation are not completely understood, and the role of lipids in the process is largely unknown. Herein, we show using atomistic molecular dynamics simulations that the interplay of phosphatidylinositol 4,5-bisphosphate (PIP2) and talin may directly alter the conformation of integrin αIIbβ3. Our results provide a new perspective on the role of PIP2 in integrin activation and indicate that the charged PIP2 lipid headgroup can perturb a clasp at the cytoplasmic face of the integrin heterodimer.
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Affiliation(s)
- Adam Orłowski
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Sampo Kukkurainen
- BioMediTech, University of Tampere , FI-33520 Tampere, Finland
- Fimlab Laboratories Ltd. , FI-33520 Tampere, Finland
| | - Annika Pöyry
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
- Department of Physics and Chemistry, MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
| | - Vesa P Hytönen
- BioMediTech, University of Tampere , FI-33520 Tampere, Finland
- Fimlab Laboratories Ltd. , FI-33520 Tampere, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
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Róg T, Pöyry S, Vattulainen I. Building Synthetic Sterols Computationally - Unlocking the Secrets of Evolution? Front Bioeng Biotechnol 2015; 3:121. [PMID: 26347865 PMCID: PMC4543873 DOI: 10.3389/fbioe.2015.00121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/07/2015] [Indexed: 01/28/2023] Open
Abstract
Cholesterol is vital in regulating the physical properties of animal cell membranes. While it remains unclear what renders cholesterol so unique, it is known that other sterols are less capable in modulating membrane properties, and there are membrane proteins whose function is dependent on cholesterol. Practical applications of cholesterol include its use in liposomes in drug delivery and cosmetics, cholesterol-based detergents in membrane protein crystallography, its fluorescent analogs in studies of cholesterol transport in cells and tissues, etc. Clearly, in spite of their difficult synthesis, producing the synthetic analogs of cholesterol is of great commercial and scientific interest. In this article, we discuss how synthetic sterols non-existent in nature can be used to elucidate the roles of cholesterol’s structural elements. To this end, we discuss recent atomistic molecular dynamics simulation studies that have predicted new synthetic sterols with properties comparable to those of cholesterol. We also discuss more recent experimental studies that have vindicated these predictions. The paper highlights the strength of computational simulations in making predictions for synthetic biology, thereby guiding experiments.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology , Tampere , Finland
| | - Sanja Pöyry
- 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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43
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Kwolek U, Kulig W, Wydro P, Nowakowska M, Róg T, Kepczynski M. Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study. J Phys Chem B 2015; 119:10042-51. [DOI: 10.1021/acs.jpcb.5b03604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Urszula Kwolek
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Waldemar Kulig
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Paweł Wydro
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Maria Nowakowska
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Mariusz Kepczynski
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
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44
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Dzieciuch M, Rissanen S, Szydłowska N, Bunker A, Kumorek M, Jamróz D, Vattulainen I, Nowakowska M, Róg T, Kepczynski M. PEGylated Liposomes as Carriers of Hydrophobic Porphyrins. J Phys Chem B 2015; 119:6646-57. [DOI: 10.1021/acs.jpcb.5b01351] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monika Dzieciuch
- Faculty
of Chemistry, Jagiellonian University, Krakow 31-007, Poland
| | - Sami Rissanen
- Department
of Physics, Tampere University of Technology, Tampere 33720, Finland
| | | | - Alex Bunker
- Centre
for Drug Research, Faculty of Pharmacy, University of Helsinki, Helsinki 00100, Finland
| | - Marta Kumorek
- Faculty
of Chemistry, Jagiellonian University, Krakow 31-007, Poland
| | - Dorota Jamróz
- Faculty
of Chemistry, Jagiellonian University, Krakow 31-007, Poland
| | - Ilpo Vattulainen
- Department
of Physics, Tampere University of Technology, Tampere 33720, Finland
- MEMPHYS-Center
for Biomembrane Physics, University of Southern Denmark, Odense 5230, Denmark
| | - Maria Nowakowska
- Faculty
of Chemistry, Jagiellonian University, Krakow 31-007, Poland
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Tampere 33720, Finland
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45
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Sharma V, Ala-Vannesluoma P, Vattulainen I, Wikström M, Róg T. Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase. Biochim Biophys Acta 2015; 1847:690-7. [PMID: 25896562 DOI: 10.1016/j.bbabio.2015.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 12/31/2022]
Abstract
The terminal respiratory enzyme cytochrome c oxidase (CcO) reduces molecular oxygen to water, and pumps protons across the inner mitochondrial membrane, or the plasma membrane of bacteria. A two-subunit CcO harbors all the elements necessary for oxygen reduction and proton pumping. However, it rapidly undergoes turnover-induced irreversible damage, which is effectively prevented by the presence of subunit III and its tightly bound lipids. We have performed classical atomistic molecular dynamics (MD) simulations on a three-subunit CcO, which show the formation of water wires between the polar head groups of lipid molecules bound to subunit III and the proton uptake site Asp91 (Bos taurus enzyme numbering). Continuum electrostatic calculations suggest that these lipids directly influence the proton affinity of Asp91 by 1-2pK units. We surmise that lipids bound to subunit III influence the rate of proton uptake through the D-pathway, and therefore play a key role in preventing turnover-induced inactivation. Atomistic MD simulations show that subunit III is rapidly hydrated in the absence of internally bound lipids, which is likely to affect the rate of O2 diffusion into the active-site. The role of subunit III with its indigenous lipids in the molecular mechanism of CcO is discussed.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.
| | | | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; MEMPHYS, Center for Biomembrane Physics, Department of Physics, University of Southern Denmark, Odense, Denmark
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Programme for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
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46
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Ghosh R, de Campos MKF, Huang J, Huh SK, Orlowski A, Yang Y, Tripathi A, Nile A, Lee HC, Dynowski M, Schäfer H, Róg T, Lete MG, Ahyayauch H, Alonso A, Vattulainen I, Igumenova TI, Schaaf G, Bankaitis VA. Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis. Mol Biol Cell 2015; 26:1764-81. [PMID: 25739452 PMCID: PMC4436786 DOI: 10.1091/mbc.e14-10-1475] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/26/2015] [Indexed: 12/12/2022] Open
Abstract
A Sec14-nodulin protein model is used to identify the nodulin domain as a novel phosphoinositide effector module with a role in controlling lateral organization of phosphoinositide. The domain organization of Sec14-nodulin proteins suggests a versatile principle for the bit mapping of membrane surfaces into high-definition lipid-signaling screens. Polarized membrane morphogenesis is a fundamental activity of eukaryotic cells. This process is essential for the biology of cells and tissues, and its execution demands exquisite temporal coordination of functionally diverse membrane signaling reactions with high spatial resolution. Moreover, mechanisms must exist to establish and preserve such organization in the face of randomizing forces that would diffuse it. Here we identify the conserved AtSfh1 Sec14-nodulin protein as a novel effector of phosphoinositide signaling in the extreme polarized membrane growth program exhibited by growing Arabidopsis root hairs. The data are consistent with Sec14-nodulin proteins controlling the lateral organization of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) landmarks for polarized membrane morphogenesis in plants. This patterning activity requires both the PtdIns(4,5)P2 binding and homo-oligomerization activities of the AtSfh1 nodulin domain and is an essential aspect of the polarity signaling program in root hairs. Finally, the data suggest a general principle for how the phosphoinositide signaling landscape is physically bit mapped so that eukaryotic cells are able to convert a membrane surface into a high-definition lipid-signaling screen.
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Affiliation(s)
- Ratna Ghosh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Marília K F de Campos
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Jin Huang
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Seong K Huh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Adam Orlowski
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Aaron Nile
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Hsin-Chieh Lee
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Marek Dynowski
- Zentrum für Datenverarbeitung, Universität Tübingen, 72074 Tübingen, Germany
| | - Helen Schäfer
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Marta G Lete
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Hasna Ahyayauch
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain Institut de Formation aux Carrieres de Sante de Rabat, 10000 Rabat, Morocco
| | - Alicia Alonso
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Gabriel Schaaf
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843 Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 Department of Chemistry, Texas A&M University, College Station, TX 77843
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47
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Lehto M, Karilainen T, Róg T, Cramariuc O, Vanhala E, Tornaeus J, Taberman H, Jänis J, Alenius H, Vattulainen I, Laine O. Co-exposure with fullerene may strengthen health effects of organic industrial chemicals. PLoS One 2014; 9:e114490. [PMID: 25473947 PMCID: PMC4256445 DOI: 10.1371/journal.pone.0114490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/10/2014] [Indexed: 12/17/2022] Open
Abstract
In vitro toxicological studies together with atomistic molecular dynamics simulations show that occupational co-exposure with C60 fullerene may strengthen the health effects of organic industrial chemicals. The chemicals studied are acetophenone, benzaldehyde, benzyl alcohol, m-cresol, and toluene which can be used with fullerene as reagents or solvents in industrial processes. Potential co-exposure scenarios include a fullerene dust and organic chemical vapor, or a fullerene solution aerosolized in workplace air. Unfiltered and filtered mixtures of C60 and organic chemicals represent different co-exposure scenarios in in vitro studies where acute cytotoxicity and immunotoxicity of C60 and organic chemicals are tested together and alone by using human THP-1-derived macrophages. Statistically significant co-effects are observed for an unfiltered mixture of benzaldehyde and C60 that is more cytotoxic than benzaldehyde alone, and for a filtered mixture of m-cresol and C60 that is slightly less cytotoxic than m-cresol. Hydrophobicity of chemicals correlates with co-effects when secretion of pro-inflammatory cytokines IL-1β and TNF-α is considered. Complementary atomistic molecular dynamics simulations reveal that C60 co-aggregates with all chemicals in aqueous environment. Stable aggregates have a fullerene-rich core and a chemical-rich surface layer, and while essentially all C60 molecules aggregate together, a portion of organic molecules remains in water.
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Affiliation(s)
- Maili Lehto
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Topi Karilainen
- Tampere University of Technology, Department of Physics, Tampere, Finland
| | - Tomasz Róg
- Tampere University of Technology, Department of Physics, Tampere, Finland
| | - Oana Cramariuc
- Tampere University of Technology, Department of Physics, Tampere, Finland
| | - Esa Vanhala
- Finnish Institute of Occupational Health, Helsinki, Finland
| | | | - Helena Taberman
- University of Eastern Finland, Department of Chemistry, Joensuu, Finland
| | - Janne Jänis
- University of Eastern Finland, Department of Chemistry, Joensuu, Finland
| | - Harri Alenius
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Ilpo Vattulainen
- Tampere University of Technology, Department of Physics, Tampere, Finland
- University of Southern Denmark, MEMPHYS – Center for Biomembrane Physics, Odense, Denmark
| | - Olli Laine
- Finnish Institute of Occupational Health, Helsinki, Finland
- * E-mail:
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48
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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49
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Pourmousa M, Róg T, Mikkeli R, Vattulainen L, Solanko LM, Wüstner D, List NH, Kongsted J, Karttunen M. Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well—or Does It? J Phys Chem B 2014; 118:7345-57. [DOI: 10.1021/jp406883k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mohsen Pourmousa
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere, Finland
| | - Tomasz Róg
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere, Finland
| | - Risto Mikkeli
- Department
of Applied Physics, Aalto University, P.O. Box 11100, FI-00076 Aalto, Finland
| | - llpo Vattulainen
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, 33720 Tampere, Finland
- MEMPHYS−Center
of Biomembrane Physics, Physics Department, University of Southern Denmark, Odense, Denmark
| | | | | | | | | | - Mikko Karttunen
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
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50
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Magarkar A, Dhawan V, Kallinteri P, Viitala T, Elmowafy M, Róg T, Bunker A. Cholesterol level affects surface charge of lipid membranes in saline solution. Sci Rep 2014; 4:5005. [PMID: 24845659 PMCID: PMC4028897 DOI: 10.1038/srep05005] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/01/2014] [Indexed: 12/19/2022] Open
Abstract
Cholesterol is an important component of all biological membranes as well as drug delivery liposomes. We show here that increasing the level of cholesterol in a phospholipid membrane decreases surface charge in the physiological environment. Through molecular dynamics simulation we have shown that increasing the level of cholesterol decreases Na+ ion binding. Complementary experimental ζ--potential measurements have shown a decreased ζ--potential with increasing cholesterol content, indicative of reduced surface charge. Both experiments and simulations have been carried out on both saturated 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and monounsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. This result is particularly important because membrane surface charge plays an important role in the interactions of biomembranes with peripheral membrane proteins and drug delivery liposomes with the immune system.
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Affiliation(s)
- Aniket Magarkar
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Vivek Dhawan
- Bombay College of Pharmacy, University of Mumbai, Mumbai, India
| | - Paraskevi Kallinteri
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tapani Viitala
- Division of Biopharmaceutics and Pharmacokinetics, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Mohammed Elmowafy
- Division of Biopharmaceutics and Pharmacokinetics, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Alex Bunker
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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