1
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Chng CP, Gupta S, Huang C. Protonation State of a Bioactive Compound Regulates Its Release from Lamellar Gel-Phase Bilayers. J Phys Chem B 2024; 128:7180-7187. [PMID: 38993042 DOI: 10.1021/acs.jpcb.4c02442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Lamellar gel networks (LGNs) in personal care or pharmaceutical lotions and creams provide an opaque cream appearance and a creamy texture to these products. Within the LGNs, the lamellar gel (Lβ) phase composed of regularly spaced bilayers of surfactants and long-chain fatty alcohols is predominately responsible for the unique rheological properties of the LGNs. To extend the shelf life of LGN-containing products, bioactive compounds with antimicrobial properties are often incorporated into the formulation. However, how the protonation state of the bioactive compounds regulates their release from the Lβ-phase bilayers is currently unknown. Using molecular dynamics simulations, we found that the protonated (neutral) form of cinnamic acid, a common antimicrobial food additive, has a retention ratio higher than that of its deprotonated (charged) counterpart in the Lβ-phase bilayer. From free energy calculations, we determined that not only is the protonated molecule more stable in the hydrophobic interior of the bilayer but also the formation of hydrogen-bonded dimers significantly enhances its stability within the bilayer. Thus, the protonation state has a profound impact on bioavailability of the compounds. Our results also highlight the importance of considering possible oligomeric states of molecules when performing calculations to estimate the permeability of molecules within various bilayers.
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Affiliation(s)
- Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Shikhar Gupta
- P&G Singapore Innovation Center (SgIC), 70 Biopolis Street, Singapore 138547, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
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2
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Filipe HAL, Loura LMS, Moreno MJ. Permeation of a Homologous Series of NBD-Labeled Fatty Amines through Lipid Bilayers: A Molecular Dynamics Study. MEMBRANES 2023; 13:551. [PMID: 37367755 DOI: 10.3390/membranes13060551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/28/2023]
Abstract
Permeation through biomembranes is ubiquitous for drugs to reach their active sites. Asymmetry of the cell plasma membrane (PM) has been described as having an important role in this process. Here we describe the interaction of a homologous series of 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-labeled amphiphiles (NBD-Cn, n = 4 to 16) with lipid bilayers of different compositions (1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC):cholesterol (1:1) and palmitoylated sphingomyelin (SpM):cholesterol (6:4)), including an asymmetric bilayer. Both unrestrained and umbrella sampling (US) simulations (at varying distances to the bilayer center) were carried out. The free energy profile of NBD-Cn at different depths in the membrane was obtained from the US simulations. The behavior of the amphiphiles during the permeation process was described regarding their orientation, chain elongation, and H-bonding to lipid and water molecules. Permeability coefficients were also calculated for the different amphiphiles of the series, using the inhomogeneous solubility-diffusion model (ISDM). Quantitative agreement with values obtained from kinetic modeling of the permeation process could not be obtained. However, for the longer, and more hydrophobic amphiphiles, the variation trend along the homologous series was qualitatively better matched by the ISDM when the equilibrium location of each amphiphile was taken as reference (ΔG = 0), compared to the usual choice of bulk water.
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Affiliation(s)
- Hugo A L Filipe
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- CPIRN-IPG-Center of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - Luís M S Loura
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria João Moreno
- Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
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3
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Benetis NP, Paloncýová M, Knippenberg S. Multiscale Modeling Unravels the Influence of Biomembranes on the Photochemical Properties of Embedded Anti-Oxidative Polyphenolic and Phenanthroline Chelating Dyes. J Phys Chem B 2023; 127:212-227. [PMID: 36563093 DOI: 10.1021/acs.jpcb.2c07072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The embedding of caffeate methyl ester, the flavonoids luteolin and quercetin, and the o-phenanthroline and neocuproine in a liquid disordered lipid bilayer has been studied through extensive atomistic calculations. The location and the orientation of these bio-active antioxidants are explained and analyzed. While the two phenanthrolines strongly associate with the lipid tail region, the other three compounds are rather found among the head groups. The simulations showcase conformational changes of the flavonoids. Through the use of a hybrid quantum mechanics-molecular mechanics scheme and supported by a profound benchmarking of the electronic excited-state method for these compounds, the influence of the anisotropic environment on the compounds' optical properties is analyzed. Influences of surrounding water molecules and of the polar parts of the lipids on the transition dipole moments and excited-state dipole moments are weighted with respect to a change in conformation. The current study highlights the importance of the mapping of molecular interactions in model membranes and pinpoints properties, which can be biomedically used to discriminate and detect different lipid environments.
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Affiliation(s)
| | - Markéta Paloncýová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technologies and Research Institute, Palacký University Olomouc, Křížkovského 8, Olomouc779 00, Czech Republic
| | - Stefan Knippenberg
- Hasselt University, Theory Lab, Agoralaan Building D, 3590Diepenbeek, Belgium.,Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), Université Libre de Bruxelles, 50 Avenue F. Roosevelt, C.P. 160/09, B-1050Brussels, Belgium
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4
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5
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Foreseeing the future of green Technology. Molecular dynamic investigation on passive membrane penetration by the products of the CO2 and 1,3-butadiene reaction. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Magalhães N, Simões GM, Ramos C, Samelo J, Oliveira AC, Filipe HAL, Ramalho JPP, Moreno MJ, Loura LMS. Interactions between Rhodamine Dyes and Model Membrane Systems—Insights from Molecular Dynamics Simulations. Molecules 2022; 27:molecules27041420. [PMID: 35209208 PMCID: PMC8876248 DOI: 10.3390/molecules27041420] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
Background: rhodamines are dyes widely used as fluorescent tags in cell imaging, probing of mitochondrial membrane potential, and as P-glycoprotein model substrates. In all these applications, detailed understanding of the interaction between rhodamines and biomembranes is fundamental. Methods: we combined atomistic molecular dynamics (MD) simulations and fluorescence spectroscopy to characterize the interaction between rhodamines 123 and B (Rh123 and RhB, respectively) and POPC bilayers. Results: while the xanthene moiety orients roughly parallel to the membrane plane in unrestrained MD simulations, variations on the relative position of the benzoic ring (below the xanthene for Rh123, above it for RhB) were observed, and related to the structure of the two dyes and their interactions with water and lipids. Subtle distinctions were found among different ionization forms of the probes. Experimentally, RhB displayed a lipid/water partition coefficient more than two orders of magnitude higher than Rh123, in agreement with free energy profiles obtained from umbrella sampling MD. Conclusions: this work provided detailed insights on the similarities and differences in the behavior of bilayer-inserted Rh123 and RhB, related to the structure of the probes. The much higher affinity of RhB for the membranes increases the local concentration and explains its higher apparent affinity for P-glycoprotein reconstituted in model membranes.
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Affiliation(s)
- Nisa Magalhães
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Guilherme M. Simões
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Cristiana Ramos
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Jaime Samelo
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Alexandre C. Oliveira
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hugo A. L. Filipe
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- CPIRN-IPG—Center of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - João P. Prates Ramalho
- Hercules Laboratory, LAQV, REQUIMTE, Department of Chemistry, School of Science and Technology, University of Évora, 7000-671 Evora, Portugal;
| | - Maria João Moreno
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
| | - Luís M. S. Loura
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal; (N.M.); (G.M.S.); (C.R.); (J.S.); (A.C.O.); (H.A.L.F.); (M.J.M.)
- CNC—Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- Correspondence:
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7
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Ahmad S, Strunk CH, Schott-Verdugo SN, Jaeger KE, Kovacic F, Gohlke H. Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. J Chem Inf Model 2021; 61:5626-5643. [PMID: 34748335 DOI: 10.1021/acs.jcim.1c00973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates have remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free-energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid (FA) products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by FA-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
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Affiliation(s)
- Sabahuddin Ahmad
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan N Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering, University of Talca, 3460000 Talca, Chile.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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8
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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9
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Rózsa ZB, Szőri-Dorogházi E, Viskolcz B, Szőri M. Transmembrane penetration mechanism of cyclic pollutants inspected by molecular dynamics and metadynamics: the case of morpholine, phenol, 1,4-dioxane and oxane. Phys Chem Chem Phys 2021; 23:15338-15351. [PMID: 34254082 DOI: 10.1039/d1cp01521d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of industrially produced chemicals in water is often not monitored, while their passive transport and accumulation can cause serious damage in living cells. Molecular dynamics simulations are an effective way to understand the mechanism of the action of these pollutants. In this paper, the passive membrane transport of 1,4-dioxane, phenol, oxane and morpholine was investigated and analyzed thoroughly from structural and energetic points of view. Free energy profiles for pollutant and water penetration into the bilayer were obtained from well-tempered metadynamics (WT-MD) simulations and a mass density-based approach. It was found that all four investigated compounds can penetrate biological membranes and affect the free energy profile of water penetration. Out of the investigated species, oxane has the thermodynamically most preferred position in the bilayer center, leading to a lower free energy barrier of water molecules by 3 kJ mol-1, resulting in 5 times more water molecules in the bilayer center. The concentration dependence of free energy was tested at two different phenol concentrations using WT-MD, and it was found that the higher phenol concentration lowers the main barrier by 3 kJ mol-1. Density-based free energy calculations were found to reproduce the results of WT-MD within the limits of chemical accuracy.
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Affiliation(s)
- Zsófia Borbála Rózsa
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary.
| | - Emma Szőri-Dorogházi
- Centre for Higher Education and Industrial Cooperation, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary.
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary.
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10
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Jacob G, Pramod RT, Katti H, Arun SP. Qualitative similarities and differences in visual object representations between brains and deep networks. Nat Commun 2021; 12:1872. [PMID: 33767141 PMCID: PMC7994307 DOI: 10.1038/s41467-021-22078-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Deep neural networks have revolutionized computer vision, and their object representations across layers match coarsely with visual cortical areas in the brain. However, whether these representations exhibit qualitative patterns seen in human perception or brain representations remains unresolved. Here, we recast well-known perceptual and neural phenomena in terms of distance comparisons, and ask whether they are present in feedforward deep neural networks trained for object recognition. Some phenomena were present in randomly initialized networks, such as the global advantage effect, sparseness, and relative size. Many others were present after object recognition training, such as the Thatcher effect, mirror confusion, Weber’s law, relative size, multiple object normalization and correlated sparseness. Yet other phenomena were absent in trained networks, such as 3D shape processing, surface invariance, occlusion, natural parts and the global advantage. These findings indicate sufficient conditions for the emergence of these phenomena in brains and deep networks, and offer clues to the properties that could be incorporated to improve deep networks. Deep neural networks are widely considered as good models for biological vision. Here, we describe several qualitative similarities and differences in object representations between brains and deep networks that elucidate when deep networks can be considered good models for biological vision and how they can be improved.
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Affiliation(s)
- Georgin Jacob
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India.,Department of Electrical Communication Engineering, Indian Institute of Science, Bangalore, India
| | - R T Pramod
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India.,Department of Electrical Communication Engineering, Indian Institute of Science, Bangalore, India
| | - Harish Katti
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India
| | - S P Arun
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India.
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11
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Kabelka I, Brožek R, Vácha R. Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes. J Chem Inf Model 2021; 61:819-830. [PMID: 33566605 DOI: 10.1021/acs.jcim.0c01312] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selective permeability of cellular membranes is a crucial property for controlled transport into and out of cells. Molecules that can bypass the cellular machinery and spontaneously translocate across membranes could be used as therapeutics or drug carriers. Peptides are a prominent class of such molecules, which include natural and man-developed antimicrobial and cell-penetrating peptides. However, the necessary peptide properties for translocation remain elusive. Computer simulations could uncover these properties once we have a good collective variable (CV) that accurately describes the translocation process. Here, we developed a new CV, which includes a description of peptide insertion, local membrane deformation, and peptide internal degrees of freedom related to its charged groups. By comparison of CVs, we demonstrated that all these components are necessary for an accurate description of peptide translocation. Moreover, the advantages and disadvantages of three common methods for free-energy calculations with our CV were evaluated using the MARTINI coarse-grained model: umbrella sampling, umbrella sampling with replica exchange, and metadynamics. The developed CV leads to the reliable and effective calculation of the free energy of peptide translocation, and thus, it could be useful in the design of spontaneously translocating peptides.
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Affiliation(s)
- Ivo Kabelka
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Radim Brožek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
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12
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Aloi E, Rizzuti B, Guzzi R, Bartucci R. Binding of warfarin differently affects the thermal behavior and chain packing of anionic, zwitterionic and cationic lipid membranes. Arch Biochem Biophys 2020; 694:108599. [PMID: 32979389 DOI: 10.1016/j.abb.2020.108599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/06/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022]
Abstract
Warfarin is a coumarin derivative drug widely used for its anticoagulant properties. The interaction of warfarin with fully hydrated lipid bilayers has been studied by combining differential scanning calorimetry, spectrophotometry, electron spin resonance of chain-labelled lipids and molecular docking. Bilayers formed by lipids with different chemico-physical properties were considered, namely dimyristoyl-phosphatidylcholine (DMPC), dimyristoyl-phosphatidylglycerol (DMPG), and dioleoyltrimethyl-ammoniumpropane (DOTAP). We observed in all cases the binding of warfarin in proximity of the surface of the bilayers, leading to a variety of distinct effects on key molecular properties of the membranes. The drug associates with the lipid bilayers in the deprotonated open chain form, with an association constant similar for DMPC and DMPG (1.27·104 and 2.82·104 M-1, respectively) and lower for DOTAP (0.46·104 M-1). In DMPC bilayers, which are zwitterionic and with saturated symmetrical chains, warfarin at 10 mol% suppresses the pre-transition, slightly stabilizes the fluid state and reduces the cooperativity of the main transition. Moreover, it alters the lateral packing density of the chain segments close to the polar/apolar interface at any temperature through the gel phase. In anionic DMPG bilayers, the drug slightly perturbs the thermotropic phase behavior, and at 10 mol% markedly loosens the compact gel phase packing of the first chain segments. In cationic DOTAP bilayers, possessing unsaturated acyl chains, the drug induces a slightly higher degree of order and motional restriction in the outer hydrocarbon region in the frozen state. In all cases, as a surface adsorbed molecule, warfarin does not affect the segmental chain order and dynamics for temperatures in the fluid phase. The overall results provide an outline of the action of warfarin on membranes formed by lipids of different types.
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Affiliation(s)
- Erika Aloi
- Department of Physics and Molecular Biophysics Laboratory, University of Calabria, 87036, Rende, Italy
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Rende, 87036, Italy
| | - Rita Guzzi
- Department of Physics and Molecular Biophysics Laboratory, University of Calabria, 87036, Rende, Italy; CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Rende, 87036, Italy
| | - Rosa Bartucci
- Department of Chemistry and Chemical Technologies and Molecular Biophysics Laboratory, University of Calabria, 87036, Rende, Italy.
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13
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Osella S, Knippenberg S. The influence of lipid membranes on fluorescent probes' optical properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183494. [PMID: 33129783 DOI: 10.1016/j.bbamem.2020.183494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Organic fluorophores embedded in lipid bilayers can nowadays be described by a multiscale computational approach. Combining different length and time scales, a full characterization of the probe localization and optical properties led to novel insight into the effect of the environments. SCOPE OF REVIEW Following an introduction on computational advancements, three relevant probes are reviewed that delineate how a multiscale approach can lead to novel insight into the probes' (non) linear optical properties. Attention is paid to the quality of the theoretical description of the optical techniques. MAJOR CONCLUSIONS Computation can assess a priori novel probes' optical properties and guide the analysis and interpretation of experimental data in novel studies. The properties can be used to gain information on the phase and condition of the surrounding biological environment. GENERAL SIGNIFICANCE Computation showed that a canonical view on some of the probes should be revisited and adapted.
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Affiliation(s)
- Silvio Osella
- Biological Systems Simulation Lab, Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland.
| | - Stefan Knippenberg
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic; Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden; Theoretical Physics, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
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14
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Zapata-Morin PA, Sierra-Valdez FJ, Ruiz-Suárez JC. The cut-off effect of n-alcohols in lipid rafts: A lipid-dependent phenomenon ☆. J Mol Graph Model 2020; 101:107732. [PMID: 32920240 DOI: 10.1016/j.jmgm.2020.107732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
n-Aliphatic alcohols act as anesthetics only up to a certain chain length, beyond which its biological activity disappears. This is known as the 'cut-off' phenomenon. Although the most accepted explanation is based on action sites in membrane proteins, it is not well understood why alcohols alter their functions. The structural dependence of these protein receptors to lipid domains known as 'lipid rafts', suggests a new approach to tackle the puzzling phenomenon. In this work, by performing molecular dynamic simulations (MDS) to explore the lipid role, we provide relevant molecular details about the membrane-alcohol interaction at the cut-off point regime. Since the high variability of the cut-off points found on protein receptors in neurons may be a consequence of differences in the lipid composition surrounding such proteins, our results could have a clear-cut importance.
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Affiliation(s)
- Patricio A Zapata-Morin
- Facultad de Ciencias Biológicas, Laboratorio de Micología y Fitopatología, Universidad Autónoma de Nuevo León, San Nicolás de Los Garza, Nuevo León, 66455, Mexico
| | - F J Sierra-Valdez
- Centro de Investigación Biomédica, Hospital Zambrano Hellion, TecSalud, Ave. Batallón de San Patricio 112, San Pedro Garza García, 66278, Nuevo León, Mexico; Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo León, 64849, Mexico
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15
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Filipe HAL, Moreno MJ, Loura LMS. The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations. Molecules 2020; 25:E3424. [PMID: 32731549 PMCID: PMC7435664 DOI: 10.3390/molecules25153424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022] Open
Abstract
Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.
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Affiliation(s)
- Hugo A. L. Filipe
- Chemistry Department, Coimbra Chemistry Center, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Maria João Moreno
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal;
| | - Luís M. S. Loura
- Coimbra Chemistry Center and CNC—Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
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16
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Filipe HAL, Esteves MIM, Henriques CA, Antunes FE. Effect of Protein Flexibility from Coarse-Grained Elastic Network Parameterizations on the Calculation of Free Energy Profiles of Ligand Binding. J Chem Theory Comput 2020; 16:4734-4743. [PMID: 32496775 DOI: 10.1021/acs.jctc.0c00418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The characterization of the affinity and binding mechanism of specific molecules to a protein active site is scientifically and industrially relevant for many applications. In principle, this information can be obtained using molecular dynamics (MD) simulations by calculating the free energy profile of the process. However, this is a computationally demanding calculation. Currently, coarse-grained (CG) force fields are very well implemented for MD simulations of biomolecular systems. These computationally efficient force fields are a major advantage to the study of large model systems and/or those requiring long simulation times. The Martini model is currently one of the most popular CG force fields for these systems. For the specific case of protein simulations, to correctly maintain the macromolecular three-dimensional structure, the Martini model needs to include an elastic network (EN). In this work, the effect of protein flexibility, as induced by three EN models compatible with the Martini force field, was tested on the calculation of free energy profiles for protein-ligand binding. The EN models used were ElNeDyn, GoMartini, and GEN. The binding of triolein (TOG) and triacetin (TAG) to a lipase protein (thermomyces lanuginosa lipase-TLL) was used as a case study. The results show that inclusion of greater flexibility in the CG parameterization of proteins is of high importance in the calculation of the free energy profiles of protein-ligand systems. However, care must be taken in order to avoid unjustified large protein deformations. In addition, due to molecular flexibility there may be no absolute need for the center of the ligand to reach the center of the protein-binding site. The calculation of the energy profile to a distance of about 0.5 nm from the active site center can be sufficient to differentiate the affinity of different ligands to a protein.
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Affiliation(s)
- Hugo A L Filipe
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - Margarida I M Esteves
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
| | - César A Henriques
- EcoXperience, HIESE, Quinta Vale do Espinhal, Penela 3230-343, Portugal
| | - Filipe E Antunes
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, Coimbra 3004-535, Portugal
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17
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Faulkner C, Santos-Carballal D, Plant DF, de Leeuw NH. Atomistic Molecular Dynamics Simulations of Propofol and Fentanyl in Phosphatidylcholine Lipid Bilayers. ACS OMEGA 2020; 5:14340-14353. [PMID: 32596571 PMCID: PMC7315410 DOI: 10.1021/acsomega.0c00813] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Atomistic molecular dynamics (MD) and steered MD simulations in combination with umbrella sampling methodology were utilized to study the general anesthetic propofol and the opioid analgesic fentanyl and their interaction with lipid bilayers, which is not yet fully understood. These molecules were inserted into two different fully hydrated phospholipid bilayers, namely, dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC), to investigate the effects that these drugs have on the bilayer. We determined the role of the lipid chain length and saturation on the behavior of the two drugs. Pure, fully hydrated DOPC and DPPC bilayers were also simulated, and the results were in excellent agreement with the experimental values. Various structural and mechanical properties of each system, such as the area per lipid, area compressibility modulus, order parameter, lateral lipid diffusion, hydrogen bonds, and radial distribution functions, have been calculated to assess how the drug molecules affect the different bilayers. From the calculated results, we show that fentanyl and propofol generally follow similar trends in each bilayer but adopt different favorable positions close to the headgroup/chain interface at the carbonyl groups. Propofol was shown to selectively form hydrogen bonds at the carbonyl carbon in each bilayer, whereas fentanyl interacts with water molecules at the headgroup interface. From the calculated free-energy profiles, we determined that both molecules show a preference for the low-density, low-order acyl chain region of the bilayers and both significantly preferred the DOPC bilayer with propofol and fentanyl having energy minima at -6.66 and -43.07 kcal mol-1, respectively. This study suggests that different chain lengths and levels of saturation directly affect the properties of these two important molecules, which are seen to work together to control anesthesia in surgical applications.
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Affiliation(s)
- Christopher Faulkner
- School
of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
| | - David Santos-Carballal
- School
of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
| | | | - Nora H. de Leeuw
- School
of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
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18
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Chen H, Song Y, Li X. A deep learning framework for identifying children with ADHD using an EEG-based brain network. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2019.04.058] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Rózsa ZB, Németh LJ, Jójárt B, Nehéz K, Viskolcz B, Szőri M. Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models. J Phys Chem B 2019; 123:7869-7884. [DOI: 10.1021/acs.jpcb.9b04313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zsófia Borbála Rózsa
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Lukács József Németh
- Department of Food Engineering, Faculty of Engineering, University of Szeged, Mars tér 7, 6724 Szeged, Hungary
| | - Balázs Jójárt
- Department of Food Engineering, Faculty of Engineering, University of Szeged, Mars tér 7, 6724 Szeged, Hungary
| | - Károly Nehéz
- Department of Information Engineering, University of Miskolc, Miskolc-Egyetemváros Informatics Building, H-3515 Miskolc, Hungary
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
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20
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Hossain S, Kabedev A, Parrow A, Bergström CAS, Larsson P. Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning. Eur J Pharm Biopharm 2019; 137:46-55. [PMID: 30771454 PMCID: PMC6434319 DOI: 10.1016/j.ejpb.2019.02.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023]
Abstract
In this review we will discuss how computational methods, and in particular classical molecular dynamics simulations, can be used to calculate solubility of pharmaceutically relevant molecules and systems. To the extent possible, we focus on the non-technical details of these calculations, and try to show also the added value of a more thorough and detailed understanding of the solubilization process obtained by using computational simulations. Although the main focus is on classical molecular dynamics simulations, we also provide the reader with some insights into other computational techniques, such as the COSMO-method, and also discuss Flory-Huggins theory and solubility parameters. We hope that this review will serve as a valuable starting point for any pharmaceutical researcher, who has not yet fully explored the possibilities offered by computational approaches to solubility calculations.
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Affiliation(s)
- Shakhawath Hossain
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden
| | - Aleksei Kabedev
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Albin Parrow
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden.
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21
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Palaiokostas M, Ding W, Shahane G, Orsi M. Effects of lipid composition on membrane permeation. SOFT MATTER 2018; 14:8496-8508. [PMID: 30346462 DOI: 10.1039/c8sm01262h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Passive permeation through lipid membranes is an essential process in biology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tendency to form lamellar sheet-like structures, which are predominant in nature. Nonlamellar lipids, when isolated, instead form more geometrically complex nonlamellar phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous lamellar bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties, which in turn may alter related biological processes. This work focuses on one such process, i.e., permeation, by utilising atomistic molecular dynamics simulations in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients for a series of thirteen small molecules and drugs. Each permeant is tested on two bilayer membranes of different lipid composition, i.e., purely lamellar and mixed lamellar/nonlamellar. Our results indicate that the presence of nonlamellar lipids reduces permeation for smaller molecules (molecular weight < 100) but facilitates it for the largest ones (molecular weight > 100). This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
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Affiliation(s)
- Michail Palaiokostas
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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22
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Badaoui M, Kells A, Molteni C, Dickson CJ, Hornak V, Rosta E. Calculating Kinetic Rates and Membrane Permeability from Biased Simulations. J Phys Chem B 2018; 122:11571-11578. [DOI: 10.1021/acs.jpcb.8b07442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Adam Kells
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, WC2R 2LS London, United Kingdom
| | - Callum J. Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
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23
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Knippenberg S, Fabre G, Osella S, Di Meo F, Paloncýová M, Ameloot M, Trouillas P. Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9072-9084. [PMID: 29983063 DOI: 10.1021/acs.langmuir.8b01164] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. However, it is currently not always clear in which phase the probe resides. The well-known orange 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbo-cyanine perchlorate (DiI-C18(5)) fluorophore, for instance, and the new, blue BODIPY (4,4-difluoro-4-bora-3 a,4 a-diaza- s-indacene) derivative were experimentally seen to target and highlight identical parts of giant unilamellar vesicles of various compositions, comprising mixtures of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), sphingomyelin (SM), and cholesterol (Chol). However, it was not clear which of the coexisting membrane phases were visualized (Bacalum et al., Langmuir. 2016, 32, 3495). The present study addresses this issue by utilizing large-scale molecular dynamics simulations and the z-constraint method, which allows evaluating Gibbs free-energy profiles. The current calculations give an indication why, at room temperature, both BODIPY and DiI-C18(5) probes prefer the gel (So) phase in DOPC/DPPC (2:3 molar ratio) and the liquid-ordered (Lo) phase in DOPC/SM/Chol (1:2:1 molar ratio) mixtures. This study highlights the important differences in orientation and location and therefore in efficiency between the probes when they are used in fluorescence microscopy to screen various lipid bilayer membrane phases. Dependent on the lipid composition, the angle between the transition-state dipole moments of both probes and the normal to the membrane is found to deviate clearly from 90°. It is seen that the DiI-C18(5) probe is located in the headgroup region of the SM/Chol mixture, in close contact with water molecules. A fluorescence anisotropy study also indicates that DiI-C18(5) gives rise to a distinctive behavior in the SM/Chol membrane compared to the other considered membranes. The latter behavior has not been seen for the studied BODIPY probe, which is located deeper in the membrane.
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Affiliation(s)
- S Knippenberg
- Department of Theoretical Chemistry and Biology , KTH Royal Institute of Technology , Roslagstullsbacken 15 , S-106 91 Stockholm , Sweden
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
| | - G Fabre
- LCSN-EA1069, Faculty of Pharmacy , Limoges University , 2 rue du Dr. Marcland , 87025 Limoges Cedex , France
| | - S Osella
- Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
| | - F Di Meo
- Faculty of Pharmacy , INSERM UMR 1248, Limoges University , 2 rue du Docteur Marcland , 87025 Limoges Cedex , France
| | - M Paloncýová
- Department of Theoretical Chemistry and Biology , KTH Royal Institute of Technology , Roslagstullsbacken 15 , S-106 91 Stockholm , Sweden
| | - M Ameloot
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
| | - P Trouillas
- Faculty of Pharmacy , INSERM UMR 1248, Limoges University , 2 rue du Docteur Marcland , 87025 Limoges Cedex , France
- Centre of Advanced Technologies and Materials, Faculty of Science , Palacký University , tř. 17 listopadu 12 , 771 46 Olomouc , Czech Republic
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24
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Metronidazole within phosphatidylcholine lipid membranes: New insights to improve the design of imidazole derivatives. Eur J Pharm Biopharm 2018; 129:204-214. [PMID: 29859282 DOI: 10.1016/j.ejpb.2018.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Metronidazole is a imidazole derivative with antibacterial and antiprotozoal activity. Despite its therapeutic efficacy, several studies have been developing new imidazole derivatives with lower toxicity. Considering that drug-membrane interactions are key factors for drugs pharmacokinetic and pharmacodynamic properties, the aim of this work is to provide new insights into the structure-toxicity relationship of metronidazole within phosphatidylcholine membranes. For that purpose, lipid membrane models (liposomes and monolayers) composed of dipalmitoylphosphatidylcholine were used. Experimental techniques (determination of partition coefficients and Langmuir isotherm measurements) were combined with molecular dynamics simulations. Different pHs and lipid phases were evaluated to enable a better extrapolation for in vivo conditions. The partition of metronidazole depends on the pH and on the biphasic system (octanol/water or DPPC/water system). At pH 1.2, metronidazole is hydrophilic. At pH 7.4, metronidazole disturbs the order and the packing of phospholipids. For this toxic effect, the hydroxyl group of the side chain of metronidazole is crucial by interacting with the water embedded in the membrane and with the phosphate group and the apolar chains of phospholipids.
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25
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Sodeifian G, Razmimanesh F. Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen. J Biomol Struct Dyn 2018; 37:1666-1684. [PMID: 29695194 DOI: 10.1080/07391102.2018.1464956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this research, for the first time, molecular dynamics (MD) method was used to simulate aspirin and ibuprofen at various concentrations and in neutral and charged states. Effects of the concentration (dosage), charge state, and existence of an integral protein in the membrane on the diffusion rate of drug molecules into lipid bilayer membrane were investigated on 11 systems, for which the parameters indicating diffusion rate and those affecting the rate were evaluated. Considering the diffusion rate, a suitable score was assigned to each system, based on which, analysis of variance (ANOVA) was performed. By calculating the effect size of the indicative parameters and total scores, an optimum system with the highest diffusion rate was determined. Consequently, diffusion rate controlling parameters were obtained: the drug-water hydrogen bond in protein-free systems and protein-drug hydrogen bond in the systems containing protein.
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Affiliation(s)
- Gholamhossein Sodeifian
- a Faculty of Engineering, Department of Chemical Engineering, Modeling and Simulation Centre , University of Kashan , Kashan 87317-53153 , Iran
| | - Fariba Razmimanesh
- a Faculty of Engineering, Department of Chemical Engineering, Modeling and Simulation Centre , University of Kashan , Kashan 87317-53153 , Iran
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26
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Zhu Q, Lu Y, He X, Liu T, Chen H, Wang F, Zheng D, Dong H, Ma J. Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane. Sci Rep 2017; 7:17749. [PMID: 29255188 PMCID: PMC5735159 DOI: 10.1038/s41598-017-18012-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/05/2017] [Indexed: 11/09/2022] Open
Abstract
Partition and transportation of drug in the plasma membrane of a mammalian cell are the prerequisite for its function on target protein. Therefore, comprehensive understanding of the physicochemical properties and mechanism behind these complex phenomena is crucial in pharmaceutical research. By using the state-of-art molecular simulations with polarization effect implicitly or explicitly included, we studied the permeation behavior of 2-aminoethoxydiphenyl borate (2-APB), a broad-spectrum modulator for a number of membrane proteins. We showed that the protonation state and therefore the polarity of the drug is critical for its partition, and that the drug is likely to switch between different protonation states along its permeation pathway. By changing the degrees of freedom, protonation further affects the thermodynamic of the permeation pathway of 2-APB, leading to different entropic contributions. A survey on 54 analog structures with similar backbone to 2-APB showed that delicate balance between entropy and polarity plays an important role in drugs’ potency.
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Affiliation(s)
- Qiang Zhu
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, P. R. China.,Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yilin Lu
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, P. R. China
| | - Xibing He
- School of Pharmacy, University of Pittsburgh, 3501 Terrace Street, Pittsburgh, PA, 15213, USA
| | - Tao Liu
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, P. R. China
| | - Hongwei Chen
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, P. R. China
| | - Fang Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, P. R. China.,College of electronic information engineering, Sanjiang University, Nanjing, 210012, P. R. China
| | - Dong Zheng
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, P. R. China.
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
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27
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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] [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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28
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Saeedi M, Lyubartsev AP, Jalili S. Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations. Biophys Chem 2017; 226:1-13. [DOI: 10.1016/j.bpc.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 12/20/2022]
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29
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Coimbra JTS, Fernandes PA, Ramos MJ. Revisiting Partition in Hydrated Bilayer Systems. J Chem Theory Comput 2017; 13:2290-2299. [PMID: 28388088 DOI: 10.1021/acs.jctc.6b01258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We discuss potential-of-mean force convergence issues involving the methods for generating starting structures of umbrella sampling simulations for the study of the water-bilayer permeation of drug-like compounds. We provide a proof of concept of the benefits of potential-energy modification methods, in particular the flooding technique, to enhance the sampling and improve the convergence of the potential-of-mean force. In addition, we also discuss how these potential modifiers could introduce the necessary bias to induce the correct description of other relevant internal degrees of freedom for the compounds, thus providing a more accurate description of the permeation process. Effective methodological approximations are taken into consideration, more specifically the inclusion of atomic polarization, and experimental data are used in the validation of computed values whenever possible. The parametrization of the atomic point charges is always a relevant issue in biomolecular simulations. We discuss the influence of a molecule's conformation-dependent atomic point charges and their impact on the predicted potential-of-mean force.
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Affiliation(s)
- João T S Coimbra
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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30
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Yousefpour A, Modarress H, Goharpey F, Amjad-Iranagh S. Combination of anti-hypertensive drugs: a molecular dynamics simulation study. J Mol Model 2017; 23:158. [DOI: 10.1007/s00894-017-3333-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/27/2017] [Indexed: 01/03/2023]
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31
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Osella S, Knippenberg S. Triggering On/Off States of Photoswitchable Probes in Biological Environments. J Am Chem Soc 2017; 139:4418-4428. [DOI: 10.1021/jacs.6b13024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Silvio Osella
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Stefan Knippenberg
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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32
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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33
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Dickson CJ, Hornak V, Pearlstein RA, Duca JS. Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling. J Am Chem Soc 2016; 139:442-452. [DOI: 10.1021/jacs.6b11215] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Callum J. Dickson
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert A. Pearlstein
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jose S. Duca
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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34
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Holmboe M, Larsson P, Anwar J, Bergström CAS. Partitioning into Colloidal Structures of Fasted State Intestinal Fluid Studied by Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12732-12740. [PMID: 27934534 PMCID: PMC5271571 DOI: 10.1021/acs.langmuir.6b03008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/04/2016] [Indexed: 06/06/2023]
Abstract
We performed molecular dynamics (MD) simulations to obtain insights into the structure and molecular interactions of colloidal structures present in fasted state intestinal fluid. Drug partitioning and interaction were studied with a mixed system of the bile salt taurocholate (TCH) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLiPC). Spontaneous aggregation of TCH and DLiPC from unconstrained MD simulations at the united-atom level using the Berger/Gromos54A7 force fields demonstrated that intermolecular hydrogen bonding between TCH molecules was an important factor in determining the overall TCH and DLiPC configuration. In bilayered systems, these intermolecular hydrogen bonds resulted in embedded transmembrane TCH clusters. Free energy simulations using the umbrella sampling technique revealed that the stability of these transmembrane TCH clusters was superior when they consisted of 3 or 4 TCH per bilayer leaflet. All-atom simulations using the Slipids/GAFF force fields showed that the TCH embedded in the bilayer decreased the energy barrier to penetrate the bilayer (ΔGpen) for water, ethanol, and carbamazepine, but not for the more lipophilic felodipine and danazol. This suggests that diffusion of hydrophilic to moderately lipophilic molecules through the bilayer is facilitated by the embedded TCH molecules. However, the effect of embedded TCH on the overall lipid/water partitioning was significant for danazol, indicating that the incorporation of TCH plays a crucial role for the partitioning of lipophilic solutes into e.g. lipidic vesicles existing in fasted state intestinal fluids. To conclude, the MD simulations revealed important intermolecular interactions in lipidic bilayers, both between the bile components themselves and with the drug molecules.
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Affiliation(s)
- Michael Holmboe
- Department
of Pharmacy, Uppsala University, Uppsala
Biomedical Centre, P.O. Box 580, SE-751 23 Uppsala, Sweden
- Department
of Chemistry, Umeå University, Umeå, Sweden
| | - Per Larsson
- Department
of Pharmacy, Uppsala University, Uppsala
Biomedical Centre, P.O. Box 580, SE-751 23 Uppsala, Sweden
| | - Jamshed Anwar
- Chemical
Theory & Computation, Department of Chemistry, University of Lancaster, Lancaster LA1 4YB, U.K.
| | - Christel A. S. Bergström
- Department
of Pharmacy, Uppsala University, Uppsala
Biomedical Centre, P.O. Box 580, SE-751 23 Uppsala, Sweden
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35
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Osella S, Murugan NA, Jena NK, Knippenberg S. Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives. J Chem Theory Comput 2016; 12:6169-6181. [DOI: 10.1021/acs.jctc.6b00906] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvio Osella
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Naresh K. Jena
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Stefan Knippenberg
- Division of Theoretical
Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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36
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Votapka LW, Lee CT, Amaro RE. Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B 2016; 120:8606-16. [PMID: 27154639 PMCID: PMC5002937 DOI: 10.1021/acs.jpcb.6b02814] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/30/2016] [Indexed: 01/17/2023]
Abstract
Prediction of passive permeation rates of solutes across lipid bilayers is important to drug design, toxicology, and other biological processes such as signaling. The inhomogeneous solubility-diffusion (ISD) equation is traditionally used to relate the position-dependent potential of mean force and diffusivity to the permeability coefficient. The ISD equation is derived via the Smoluchowski equation and assumes overdamped system dynamics. It has been suggested that the complex membrane environment may exhibit more complicated damping conditions. Here we derive a variant of the inhomogeneous solubility diffusion equation as a function of the mean first passage time (MFPT) and show how milestoning, a method that can estimate kinetic quantities of interest, can be used to estimate the MFPT of membrane crossing and, by extension, the permeability coefficient. We further describe a second scheme, agnostic to the damping condition, to estimate the permeability coefficient from milestoning results or other methods that compute a probability of membrane crossing. The derived relationships are tested using a one-dimensional Langevin dynamics toy system confirming that the presented theoretical methods can be used to estimate permeabilities given simulation and milestoning results.
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Affiliation(s)
- Lane W. Votapka
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Christopher T. Lee
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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37
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Chun BJ, Lu J, Weck M, Jang SS. Characterization of molecular association of poly(2-oxazoline)s-based micelles with various epoxides and diols via the Flory-Huggins theory: a molecular dynamics simulation approach. Phys Chem Chem Phys 2016; 17:29161-70. [PMID: 26463559 DOI: 10.1039/c5cp03854e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrolytic kinetic resolution (HKR) of epoxides has been performed in a shell-crosslinked micellar (SCM) nanoreactor consisting of amphiphilic triblock copolymers based on poly(2-oxazline)s polymer derivatives with attached Co(iii)-salens to the micelle core. To investigate the effect of the molecular interaction of reactant/product molecules with the SCM nanoreactor on the rate of HKR, we calculated the Flory-Huggins interaction parameters (χ) using the molecular dynamics simulation method. For this, the blend systems were constructed with various compositions such as 15, 45, and 70 wt% of the reactant/product molecules with respect to the polymers such as poly(2-methyl-2-oxazoline) (PMOX), poly(2-(3-butinyl)2-oxazoline) (PBOX), and poly(methyl-3-oxazol-2-yl)pentanoate with Co(iii)-salen (PSCoX). From the χ parameters, we demonstrate that the miscibility of reactants/products with polymers has a strong correlation with the experimental reaction rate of the HKR: phenyl glycidyl ether (Reac-OPh) > epoxyhexane (Reac-C4) > styrene oxide (Reac-Ph) > epichlorohydrin (Reac-Cl). To validate this finding, we also conducted the potential of mean force analysis using steered molecular dynamics simulation for the molecular displacement of Reac-Cl and Reac-OPh through PMOX and PSCoX, revealing that the free energy reduction was greater when Reac-OPh molecule enters the polymer phase compared to Reac-Cl, which agrees with the findings from the χ parameters calculations.
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Affiliation(s)
- Byeong Jae Chun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, USA and Computational NanoBio Technology Laboratory, School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, USA.
| | - Jie Lu
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
| | - Marcus Weck
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
| | - Seung Soon Jang
- Computational NanoBio Technology Laboratory, School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, USA. and Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
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38
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Ayee MAA, Roth CW, Akpa BS. Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study. J Colloid Interface Sci 2016; 468:227-237. [PMID: 26852346 PMCID: PMC4762473 DOI: 10.1016/j.jcis.2016.01.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/24/2016] [Accepted: 01/26/2016] [Indexed: 12/26/2022]
Abstract
Compounds with nominally similar biological activity may exhibit differential toxicity due to differences in their interactions with cell membranes. Many pharmaceutical compounds are amphiphilic and can be taken up by phospholipid bilayers, interacting strongly with the lipid-aqueous interface whether or not subsequent permeation through the bilayer is possible. Bolaamphiphilic compounds, which possess two hydrophilic ends and a hydrophobic linker, can likewise undergo spontaneous uptake by bilayers. While membrane-spanning bolaamphiphiles can stabilize membranes, small molecules with this characteristic have the potential to create membrane defects via disruption of bilayer structure and dynamics. When compared to the amphiphilic therapeutic anticoagulant, warfarin, the bolaamphiphilic analogue, brodifacoum, exhibits heightened toxicity that goes beyond superior inhibition of the pharmacological target enzyme. We explore, herein, the consequences of anticoagulant accumulation in a dipalmitoylphosphatidylcholine (DPPC) bilayer. Coarse-grained molecular dynamics simulations reveal that permeation of phospholipid bilayers by brodifacoum causes a disruption of membrane barrier function that is driven by the bolaamphiphilic nature and size of this molecule. We find that brodifacoum partitioning into bilayers causes membrane thinning and permeabilization and promotes lipid flip-flop - phenomena that are suspected to play a role in triggering cell death. These phenomena are either absent or less pronounced in the case of the less toxic, amphiphilic compound, warfarin.
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Affiliation(s)
- Manuela Aseye Ayele Ayee
- Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St., Chicago, IL 60607, USA; Department of Medicine, University of Illinois at Chicago, 909 S. Wolcott Ave., Chicago, IL 60612, USA.
| | - Charles William Roth
- Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St., Chicago, IL 60607, USA.
| | - Belinda Sena Akpa
- Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St., Chicago, IL 60607, USA; Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr., Raleigh, NC 27607, USA.
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39
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Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model 2016; 56:721-33. [PMID: 27043429 DOI: 10.1021/acs.jcim.6b00022] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient Pm was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized Langevin method, both being sensitive to chosen parameters and the slow relaxation of membrane defects. Agreement within 1.5 log units of the computed Pm with experiment is found for all permeants and methods. Remaining discrepancies can likely be attributed to limitations of the force field as well as slowly relaxing collective movements within the lipid environment. Numerical calculations based on model profiles show that Pm can be reliably estimated from only a few data points, leading to recommendations for calculating Pm from simulations.
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Affiliation(s)
- Christopher T Lee
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University , P-213 Mosier Hall, Manhattan, Kansas 66506, United States
| | - Conner Herndon
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Nelson Leung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Robert V Swift
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chris Tung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland , St. John's, NL A1B 3X7 Canada
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy, France.,Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
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40
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Permeability across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2254-2265. [PMID: 27085977 DOI: 10.1016/j.bbamem.2016.03.032] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 11/22/2022]
Abstract
Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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41
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Bacalum M, Wang L, Boodts S, Yuan P, Leen V, Smisdom N, Fron E, Knippenberg S, Fabre G, Trouillas P, Beljonne D, Dehaen W, Boens N, Ameloot M. A Blue-Light-Emitting BODIPY Probe for Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3495-3505. [PMID: 27003513 DOI: 10.1021/acs.langmuir.6b00478] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C18, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5-positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single-exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C18. The directions of the absorption and emission transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70°, which is comparable with the value reported for DiI-C18.
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Affiliation(s)
- Mihaela Bacalum
- Biomedical Research Institute, Hasselt University , Agoralaan Building C, 3590, Diepenbeek, Belgium
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering , Reactorului 30, Măgurele, 077125, Romania
| | - Lina Wang
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Stijn Boodts
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Peijia Yuan
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Volker Leen
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Nick Smisdom
- Biomedical Research Institute, Hasselt University , Agoralaan Building C, 3590, Diepenbeek, Belgium
| | - Eduard Fron
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Stefan Knippenberg
- Biomedical Research Institute, Hasselt University , Agoralaan Building C, 3590, Diepenbeek, Belgium
- Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, School of Biotechnology , Roslagstullsbacken 15, S-106 91 Stockholm, Sweden
| | - Gabin Fabre
- LCSN-EA1069, Faculté de Pharmacie, Université de Limoges , 2, rue du Dr. Marcland, 87025 Limoges Cedex, France
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Patrick Trouillas
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- INSERM UMR-S850, Faculté de Pharmacie, Université de Limoges , 2 rue du Docteur Marcland, 87025 Limoges Cedex, France
- Service de Chimie des Matériaux Nouveaux, Université de Mons , Place du Parc 20, B-7000 Mons, Belgium
| | - David Beljonne
- Service de Chimie des Matériaux Nouveaux, Université de Mons , Place du Parc 20, B-7000 Mons, Belgium
| | - Wim Dehaen
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Noël Boens
- Department of Chemistry, Katholieke Universiteit Leuven (KU Leuven) , Celestijnenlaan 200f - bus 02404, 3001 Leuven, Belgium
| | - Marcel Ameloot
- Biomedical Research Institute, Hasselt University , Agoralaan Building C, 3590, Diepenbeek, Belgium
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Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2539-2548. [PMID: 26952019 DOI: 10.1016/j.bbamem.2016.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180-3590, USA
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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43
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Molecular dynamics simulations of Oxprenolol and Propranolol in a DPPC lipid bilayer. J Mol Graph Model 2016; 64:153-164. [DOI: 10.1016/j.jmgm.2016.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 11/18/2022]
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Fabre G, Bayach I, Berka K, Paloncýová M, Starok M, Rossi C, Duroux JL, Otyepka M, Trouillas P. Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes. Chem Commun (Camb) 2016; 51:7713-6. [PMID: 25851839 DOI: 10.1039/c5cc00636h] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vitamins E, C and polyphenols (flavonoids and non-flavonoids) are major natural antioxidants capable of preventing damage generated by oxidative stress. Here we show the capacity of these antioxidants to form non-covalent association within lipid bilayers close to the membrane/cytosol interface. Antioxidant regeneration is significantly enhanced in these complexes.
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Affiliation(s)
- Gabin Fabre
- LCSN EA1069, Univ. Limoges, Faculté de Pharmacie, 2 rue du Docteur Marcland, 87025 Limoges Cedex, France
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45
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Benay G, Wipff G. Liquid–liquid extraction of alkali cations by 18-crown-6: complexation and interface crossing studied by MD and PMF simulations. NEW J CHEM 2016. [DOI: 10.1039/c5nj02609a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 18C6/M+Pic−complexes form and adsorb “right at the nano-interface” where 18C6 prefers the K+guest.
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Affiliation(s)
- Gael Benay
- Laboratoire MSM
- UMR 7140
- Institut de Chimie
- 67000 Strasbourg
- France
| | - Georges Wipff
- Laboratoire MSM
- UMR 7140
- Institut de Chimie
- 67000 Strasbourg
- France
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46
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Casalegno M, Raos G, Sello G. From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations. Phys Chem Chem Phys 2016; 18:17731-9. [DOI: 10.1039/c6cp01728b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamics simulations indicate that dioxin likely accumulates in cell membranes more than its congeners (anthracene, tetrahydrodioxin, 3,3′,5,5′-tetrachlorobiphenyl, and 1,2-dihydroxytetrahydrodibenzo-p-dioxin).
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Affiliation(s)
- Mosé Casalegno
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Raos
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Sello
- Dipartimento di Chimica
- Università degli Studi di Milano
- I-20133 Milano
- Italy
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47
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Awoonor-Williams E, Rowley CN. Molecular simulation of nonfacilitated membrane permeation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1672-87. [PMID: 26706099 DOI: 10.1016/j.bbamem.2015.12.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 12/29/2022]
Abstract
This is a review. Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada.
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48
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Abstract
Work done by Bennett et al. [ Nature 2002 , 420 , 398 - 401 ] demonstrated that Ca(2+) ions can be actively transported through a lipid bilayer membrane by an artificial photosynthetic machine. However, details of the pump process, such as the oxidation state of the shuttle molecule and stoichiometry of the shuttle-ion complex, are not fully understood, which hinders the development of ion pumps of this type with higher efficiency. In this study, we combine all atom molecular dynamics simulations and quantum mechanics calculations to estimate the time scale of the shuttle-ion complex diffusion process and charge transfer step. We find that the process of shuttle-ion complex diffusion across the lipid bilayer membrane is the rate-limiting step, with a time scale of seconds to minutes. Other processes such as charge transfer between the redox reaction center and the shuttle molecule have picoseconds time scales. We also show that a shuttle-ion complex with 2:1 stoichiometry ratio has a lower energy barrier across the lipid membrane than other choices of complexes. The calculations show that the Ca(2+) ion is likely to be shuttled by a semiquinone type of shuttle molecule as this has the lowest free energy barrier across the lipid bilayer membrane, the fewest electrons transferred in the redox cycle, and it does not generate (or require) proton flow. Estimates of ion flow rates are consistent with measured values.
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Affiliation(s)
- Cheng-Tsung Lai
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Yu Zhang
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Center for Bioinspired Energy Science, Northwestern University , Chicago, Illinois 60611, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Center for Bioinspired Energy Science, Northwestern University , Chicago, Illinois 60611, United States
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Fabre G, Hänchen A, Calliste CA, Berka K, Banala S, Otyepka M, Süssmuth RD, Trouillas P. Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane. Bioorg Med Chem 2015; 23:4866-4870. [DOI: 10.1016/j.bmc.2015.05.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/13/2015] [Accepted: 05/15/2015] [Indexed: 11/27/2022]
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50
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Yousefpour A, Modarress H, Goharpey F, Amjad-Iranagh S. Interaction of PEGylated anti-hypertensive drugs, amlodipine, atenolol and lisinopril with lipid bilayer membrane: A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1687-98. [DOI: 10.1016/j.bbamem.2015.04.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 04/10/2015] [Indexed: 12/12/2022]
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