1
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Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
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Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
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2
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Flood JJ, Copley SD. Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum. mSystems 2018; 3:e00275-18. [PMID: 30505947 PMCID: PMC6247019 DOI: 10.1128/msystems.00275-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 11/01/2018] [Indexed: 12/02/2022] Open
Abstract
Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The alphaproteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of completely degrading PCP. This pathway produces four toxic intermediates, including a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that react with O2 to produce reactive oxygen species (ROS). RNA-seq analysis revealed that PCP causes a global stress response that resembles responses to proton motive force uncoupling and membrane disruption, while surprisingly, little of the response resembles the responses expected to be produced by the PCP degradation intermediates. Tn-seq was used to identify genes important for fitness in the presence of PCP. By comparing the genes that are important for fitness in wild-type S. chlorophenolicum and a non-PCP-degrading mutant, we identified genes that are important only when the PCP degradation intermediates are produced. These include genes encoding two enzymes that are likely to be involved in protection against ROS. In addition to these enzymes, the endogenous levels of other enzymes that protect cells from oxidative stress appear to mitigate the toxic effects of the chlorinated benzoquinone and hydroquinone metabolites of PCP. The combination of RNA-seq and Tn-seq results identify important mechanisms for defense against the toxicity of PCP. IMPORTANCE Phenolic compounds such as pentachlorophenol (PCP), triclosan, and 2,4-dichlorophenoxyacetic acid (2,4-D) represent a common class of anthropogenic biocides. Despite the novelty of these compounds, many can be degraded by microbes isolated from contaminated sites. However, degradation of this class of chemicals often generates toxic intermediates, which may contribute to their recalcitrance to biodegradation. We have addressed the stresses associated with degradation of PCP by Sphingobium chlorophenolicum by examining the transcriptional response after PCP exposure and identifying genes necessary for growth during both exposure to and degradation of PCP. This work identifies some of the mechanisms that protect cells from this toxic compound and facilitate its degradation. This information could be used to engineer strains capable of improved biodegradation of PCP or similar phenolic pollutants.
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Affiliation(s)
- Jake J. Flood
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Cooperative Institute for Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Cooperative Institute for Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, USA
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3
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Mavioso ICVC, de Andrade VCR, Palace Carvalho AJ, Martins do Canto AMT. Molecular dynamics simulations of T-2410 and T-2429 HIV fusion inhibitors interacting with model membranes: Insight into peptide behavior, structure and dynamics. Biophys Chem 2017; 228:69-80. [PMID: 28711675 DOI: 10.1016/j.bpc.2017.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/17/2022]
Abstract
T-2410 and T-2429 are HIV fusion inhibitor peptides (FI) designed to present a higher efficiency even against HIV strains that developed resistance against other FIs. Similar peptides were shown to interact with model membranes both in the liquid disordered phase and in the liquid ordered state. Those results indicated that such interaction is important to function and could be correlated with their effectiveness. Extensive molecular dynamics simulations were carried out to investigate the interactions between both T-2410 and T-2429 with bilayers of pure 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and a mixture of POPC/cholesterol (Chol) (1:1). It was observed that both peptides interact strongly with both membrane systems, especially with the POPC/Chol systems, where these peptides show the highest number of H-bonds observed so far. T-2410 and T-2429 showed higher extent of interaction with bilayers when compared to T-20 or T-1249 in previous studies. This is most notable in POPC/Chol membranes where, although able to form H-bonds with Chol, they do so to a lesser extent than T-1249 does, the latter being the only FI peptide so far that was observed to form H-bonds with Chol. This behavior suggests that interaction of FI peptides with rigid Chol rich membranes may not be as dependent from peptide/Chol H-bond formation as previous results of T-1249 behavior led to believe. As in other similar peptides, the higher ability to interact with membranes shown by T-2410 and T2429 is probably correlated with its higher inhibitory efficiency.
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Affiliation(s)
- I C V C Mavioso
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - V C R de Andrade
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - A J Palace Carvalho
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal; Centro de Química de Évora, IIFA, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - A M T Martins do Canto
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal; Centro de Química de Évora, IIFA, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal.
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4
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Bera I, Klauda JB. Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol. J Phys Chem B 2017; 121:5197-5208. [DOI: 10.1021/acs.jpcb.7b00359] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Indrani Bera
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B. Klauda
- Department
of Chemical and Biomolecular Engineering and ‡Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
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5
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Coronel JR, Aranda FJ, Teruel JA, Marqués A, Manresa Á, Ortiz A. Kinetic and Structural Aspects of the Permeabilization of Biological and Model Membranes by Lichenysin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:78-87. [PMID: 26652062 DOI: 10.1021/acs.langmuir.5b04294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The various lichenysins produced by Bacillus licheniformis are anionic surfactants with interesting properties. Here it is shown that lichenysin caused hemolysis of human erythrocytes, which varied with lichenysin concentration in a sigmoidal manner. The release of K(+) from red blood cells induced by lichenysin preceded the leakage of hemoglobin, and in addition, hemolysis could be impeded by the presence of compounds in the external medium having a size larger than that of PEG 3350, indicating a colloid-osmotic mechanism for hemolysis. Lichenysin also caused permeabilization of model phospholipid membranes, which was a slow process with an initial lag period of 10-20 s observed for all lichenysin concentrations. A high cholesterol ratio in the membrane decreased the extent of leakage as compared to that of pure POPC, whereas at lower ratios the effect of cholesterol was the opposite, enhancing the extent of leakage. POPE was found to decrease the extent of leakage at all the concentrations assayed, and inclusion of DPPC resulted in a considerable increase in CF leakage extent. From this scenario it was concluded that lipid membrane composition plays a role in the target membrane selectivity of lichenysin. Molecular dynamics simulations indicated that lichenysin is well distributed along the bilayer, and Na(+) ions can penetrate inside the bilayer through the lichenysin molecules. The presence of lichenysin in the membrane increases the permeability of the membrane to hydrophilic molecules facilitating its flux across the lipid palisade. The results presented in this work contribute to understanding the molecular mechanisms that explain the biological actions of lichenysin related to biomembranes.
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Affiliation(s)
- Jonathan R Coronel
- Laboratorio de Microbiología, Facultad de Farmacia, Universidad de Barcelona , Joan XXIII s/n, E-08028 Barcelona, Spain
| | - Francisco J Aranda
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia , E-30100 Murcia, Spain
| | - José A Teruel
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia , E-30100 Murcia, Spain
| | - Ana Marqués
- Laboratorio de Microbiología, Facultad de Farmacia, Universidad de Barcelona , Joan XXIII s/n, E-08028 Barcelona, Spain
| | - Ángeles Manresa
- Laboratorio de Microbiología, Facultad de Farmacia, Universidad de Barcelona , Joan XXIII s/n, E-08028 Barcelona, Spain
| | - Antonio Ortiz
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia , E-30100 Murcia, Spain
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6
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Lyubartsev AP, Rabinovich AL. Force Field Development for Lipid Membrane Simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2483-2497. [PMID: 26766518 DOI: 10.1016/j.bbamem.2015.12.033] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Stockholm, Sweden.
| | - Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation.
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7
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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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8
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Yoo B, Shah JK, Zhu Y, Maginn EJ. Amphiphilic interactions of ionic liquids with lipid biomembranes: a molecular simulation study. SOFT MATTER 2014; 10:8641-8651. [PMID: 25248460 DOI: 10.1039/c4sm01528b] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Current bottlenecks in the large-scale commercial use of many ionic liquids (ILs) include their high costs, low biodegradability, and often unknown toxicities. As a proactive effort to better understand the molecular mechanisms of ionic liquid toxicities, the work herein presents a comprehensive molecular simulation study on the interactions of 1-n-alkyl-3-methylimidazolium-based ILs with a phosphatidylcholine (PC) lipid bilayer. We explore the effects of increasing alkyl chain length (n = 4, 8, and 12) in the cation and anion hydrophobicity on the interactions with the lipid bilayer. Bulk atomistic molecular dynamics (MD) simulations performed at millimolar (mM) IL concentrations show spontaneous insertion of cations into the lipid bilayer regardless of the alkyl chain length and a favorable orientational preference once a cation is inserted. Cations also exhibit the ability to "flip" inside the lipid bilayer (as is common for amphiphiles) if partially inserted with an unfavorable orientation. Moreover, structural analysis of the lipid bilayer show that cationic insertion induces roughening of the bilayer surface, which may be a precursor to bilayer disruption. To overcome the limitation in the timescale of our simulations, free energies for a single IL cation and anion insertion have been determined based on potential of mean force calculations. These results show a decrease in free energy in response to both short and long alkyl chain IL cation insertion, and likewise for a single hydrophobic anion insertion, but an increase in free energy for the insertion of a hydrophilic chloride anion. Both bulk MD simulations and free energy calculations suggest that toxicity mechanisms toward biological systems are likely caused by ILs behaving as ionic surfactants. [Yoo et al., Soft Matter, 2014].
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Affiliation(s)
- Brian Yoo
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA.
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9
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Peters GH, Werge M, Elf-Lind MN, Madsen JJ, Velardez GF, Westh P. Interaction of neurotransmitters with a phospholipid bilayer: a molecular dynamics study. Chem Phys Lipids 2014; 184:7-17. [PMID: 25159594 DOI: 10.1016/j.chemphyslip.2014.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 11/15/2022]
Abstract
We have performed a series of molecular dynamics simulations to study the interactions between the neurotransmitters (NTs) γ-aminobutyrate (GABA), glycine (GLY), acetylcholine (ACH) and glutamate (GLU) as well as the amidated/acetylated γ-aminobutyrate (GABA(neu)) and the osmolyte molecule glycerol (GOL) with a dipalmitoylphosphatidylcholine (DPPC) bilayer. In agreement with previously published experimental data, we found the lowest membrane affinity for the charged molecules and a moderate affinity for zwitterionic and polar molecules. The affinity can be ranked as follows: ACH-GLU<<GABA<GLY<<GABA(neu)<<GOL. The latter three penetrated the bilayer at most with the deepest location being close to the glycerol backbone of the phospholipids. Even at that position, these solutes were noticeably hydrated and carried ∼30-80% of the bulk water along. The mobility of hydration water at the solute is also affected by the penetration into the bilayer. Two time scales of exchanging water molecules could be determined. In the bulk phase, the hydration layer contains ∼20% slow exchanging water molecules which increases 2-3 times as the solutes entered the bilayer. Our results indicate that there is no intermediate exchange of slow moving water molecules from the solutes to the lipid atoms and vice versa. Instead, the exchange relies on the reservoir of unbounded ("free") water molecules in the interfacial bilayer region. Results from the equilibrium simulations are in good agreement with the results from umbrella sampling simulations, which were conducted for the four naturally occurring NTs. Free energy profiles for ACH and GLU show a minimum of ∼2-3 kJ/mol close to the bilayer interface, while for GABA and GLY, a minimum of respectively ∼2 kJ/mol and ∼5 kJ/mol is observed when these NTs are located in the vicinity of the lipid glycerol backbone. The most important interaction of NTs with the bilayer is the charged amino group of NTs with the lipid phosphate group.
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Affiliation(s)
- Günther H Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
| | - Mikkel Werge
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | | | - Jesper J Madsen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Gustavo F Velardez
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Roskilde 4000, Denmark.
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10
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Balupuri A, Sobhia ME. Exploring a model of human chemokine receptor CCR2 in presence of TAK779: A membrane based molecular dynamics study. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Neale C, Madill C, Rauscher S, Pomès R. Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. J Chem Theory Comput 2013; 9:3686-703. [DOI: 10.1021/ct301005b] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chris Neale
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Chris Madill
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Sarah Rauscher
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
| | - Régis Pomès
- Molecular Structure
and Function,
The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario,
M5G 1X8, Canada
- Department
of Biochemistry,
University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7,
Canada
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12
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Robalo JR, do Canto AMTM, Carvalho AJP, Ramalho JPP, Loura LMS. Behavior of Fluorescent Cholesterol Analogues Dehydroergosterol and Cholestatrienol in Lipid Bilayers: A Molecular Dynamics Study. J Phys Chem B 2013; 117:5806-19. [DOI: 10.1021/jp312026u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Luís M. S. Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências
da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra,
Portugal
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13
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Sensing hydration and behavior of pyrene in POPC and POPC/cholesterol bilayers: A molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1094-101. [DOI: 10.1016/j.bbamem.2012.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 01/24/2023]
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14
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Karlsson BCG, Olsson GD, Friedman R, Rosengren AM, Henschel H, Nicholls IA. How Warfarin’s Structural Diversity Influences Its Phospholipid Bilayer Membrane Permeation. J Phys Chem B 2013; 117:2384-95. [DOI: 10.1021/jp400264x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Björn C. G. Karlsson
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Gustaf D. Olsson
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and
Biochemistry Group, Linnæus University Centre for Biomaterials
Chemistry, Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Annika M. Rosengren
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
| | - Henning Henschel
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
- Division of Atmospheric Sciences,
Department of Physics, University of Helsinki, P.O. Box 64, Helsinki, Finland
| | - Ian A. Nicholls
- Bioorganic and Biophysical Chemistry
Laboratory, Linnæus University Centre for Biomaterials Chemistry,
Department of Chemistry and Biomedical Sciences, Linnæus University, SE-391 82 Kalmar, Sweden
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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15
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Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interaction. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012; 2012:151854. [PMID: 22675399 PMCID: PMC3364549 DOI: 10.1155/2012/151854] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 03/08/2012] [Accepted: 03/20/2012] [Indexed: 12/19/2022]
Abstract
T-1249 is a peptide that inhibits the fusion of HIV envelope with the target cell membrane. Recent results indicate that T-1249, as in the case of related inhibitor peptide T-20 (enfuvirtide), interacts with membranes, more extensively in the bilayer liquid disordered phase than in the liquid ordered state, which could be linked to its effectiveness. Extensive molecular dynamics simulations (100 ns) were carried out to investigate the interaction between T-1249 and bilayers of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and POPC/cholesterol (1 : 1). It was observed that T-1249 interacts to different extents with both membrane systems and that peptide interaction with the bilayer surface has a local effect on membrane structure. Formation of hydrogen bonding between certain peptide residues and several acceptor and donor groups in the bilayer molecules was observed. T-1249 showed higher extent of interaction with bilayers when compared to T-20. This is most notable in POPC/Chol membranes, owing to more peptide residues acting as H bond donors and acceptors between the peptide and the bilayer lipids, including H-bonds formed with cholesterol. This behavior is at variance with that of T-20, which forms no H bonds with cholesterol. This higher ability to interact with membranes is probably correlated with its higher inhibitory efficiency.
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16
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do Canto AM, Carvalho AP, Ramalho JP, Loura LM. Molecular dynamics simulations of T-20 HIV fusion inhibitor interacting with model membranes. Biophys Chem 2011; 159:275-86. [DOI: 10.1016/j.bpc.2011.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/31/2011] [Accepted: 08/01/2011] [Indexed: 10/17/2022]
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17
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Yacoub TJ, Reddy AS, Szleifer I. Structural effects and translocation of doxorubicin in a DPPC/Chol bilayer: the role of cholesterol. Biophys J 2011; 101:378-85. [PMID: 21767490 DOI: 10.1016/j.bpj.2011.06.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 05/31/2011] [Accepted: 06/08/2011] [Indexed: 11/28/2022] Open
Abstract
We use molecular dynamics simulations to characterize the influence of cholesterol (Chol) on the interaction between the anticancer drug doxorubicin (DOX) and a dipalmitoyl phosphatidylcholine/Chol lipid bilayer. We calculate the potential of mean force, which gives us an estimate of the free energy barrier for DOX translocation across the membrane. We find free energy barriers of 23.1 ± 3.1 k(B)T, 36.8 ± 5.1 k(B)T, and 54.5 ± 4.7 k(B)T for systems composed of 0%, 15%, and 30% Chol, respectively. Our predictions agree with Arrhenius activation energies from experiments using phospholipid membranes, including 20 k(B)T for 0% Chol and 37.2 k(B)T for 20% Chol. The location of the free energy barrier for translocation across the bilayer is dependent on composition. As Chol concentration increases, this barrier changes from the release of DOX into the water to flip-flop over the membrane center. The drug greatly affects local membrane structure by attracting dipalmitoyl phosphatidylcholine headgroups, curving the membrane, and allowing water penetration. Despite its hydrophobicity, DOX facilitates water transport via its polar groups.
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Affiliation(s)
- Tyrone J Yacoub
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
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Tejwani RW, Davis ME, Anderson BD, Stouch TR. An Atomic and Molecular View of the Depth Dependence of the Free Energies of Solute Transfer from Water into Lipid Bilayers. Mol Pharm 2011; 8:2204-15. [DOI: 10.1021/mp2000204] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Ravindra W. Tejwani
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Malcolm E. Davis
- Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bradley D. Anderson
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Terry R. Stouch
- Science For Solutions, LLC, 6211 Kaitlyn Court West, Windsor, New Jersey 08550,
United States
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19
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Filipe HAL, Moreno MJ, Loura LMS. Interaction of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-labeled fatty amines with 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine bilayers: a molecular dynamics study. J Phys Chem B 2011; 115:10109-19. [PMID: 21749140 DOI: 10.1021/jp203532c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complete homologous series of fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-labeled fatty amines of varying alkyl chain length, NBD-C(n), inserted in 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers, was studied using atomistic molecular dynamics (MD) simulations. For all amphiphiles, the NBD fluorophore locates near the glycerol backbone/carbonyl region of POPC and establishes stable hydrogen bonding with POPC ester oxygen atoms. Small differences observed in the transverse location of the fluorophore correlate with other calculated parameters and with small discrepancies recently measured in the photophysical properties of the molecules. The longer-chained NBD-C(n) amphiphiles show significant mass density near the bilayer midplane, and the chains of these derivatives interdigitate to some extent the opposite bilayer leaflet. This phenomenon leads to a slower lateral diffusion for the longer-chained derivatives (n > 12). Effects of these amphiphiles on the structure and dynamics of the host lipid were found to be relatively mild, in comparison with acyl-chain-labeled NBD probes. The molecular details obtained by this work allow the rationalization of the nonmonotonic behavior, recently obtained experimentally, for the photophysical parameters of the amphiphiles and the kinetic and thermodynamic parameters for their interaction with the POPC membranes.
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Affiliation(s)
- Hugo A L Filipe
- Centro de Química de Coimbra, Universidade de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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20
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Shintani M, Yoshida K, Sakuraba S, Nakahara M, Matubayasi N. NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics. J Phys Chem B 2011; 115:9106-15. [PMID: 21728286 DOI: 10.1021/jp204051f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motional correlation times between the hydrophilic and hydrophobic terminal groups in lipid membranes are studied over a wide range of curvatures using the solution-state (1)H NMR-nuclear Overhauser effect (NOE) and molecular dynamics (MD) simulation. To enable (1)H NMR-NOE measurements for large vesicles, the transient NOE method is combined with the spin-echo method, and is successfully applied to a micelle of 1-palmitoyl-lysophosphatidylcholine (PaLPC) with diameter of 5 nm and to vesicles of dipalmitoylphosphatidylcholine (DPPC) with diameters ranging from 30 to 800 nm. It is found that the NOE intensity increases with the diameter up to ∼100 nm, and the model membrane is considered planar on the molecular level beyond ∼100 nm. While the NOE between the hydrophilic terminal and hydrophobic terminal methyl groups is absent for the micelle, its intensity is comparable to that for the neighboring group for vesicles with larger diameters. The origin of NOE signals between distant sites is analyzed by MD simulations of PaLPC micelles and DPPC planar bilayers. The slow relaxation is shown to yield an observable NOE signal even for the hydrophilic and hydrophobic terminal sites. Since the information on distance and dynamics cannot be separated in the experimental NOE alone, the correlation time in large vesicles is determined by combining the experimental NOE intensity and MD-based distance distribution. For large vesicles, the correlation time is found to vary by 2 orders of magnitude over the proton sites. This study shows that NOE provides dynamic information on large vesicles when combined with MD, which provides structural information.
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Affiliation(s)
- Megumi Shintani
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Tejwani RW, Davis ME, Anderson BD, Stouch TR. DRUG DISCOVERY INTERFACE: Functional Group Dependence of Solute Partitioning to Various Locations within a DOPC Bilayer: A Comparison of Molecular Dynamics Simulations with Experiment. J Pharm Sci 2011; 100:2136-46. [DOI: 10.1002/jps.22441] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/20/2010] [Indexed: 11/08/2022]
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22
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dos Santos DJVA, Saenz-Méndez P, Eriksson LA, Guedes RC. Properties and behaviour of tetracyclic allopsoralen derivatives inside a DPPC lipid bilayer model. Phys Chem Chem Phys 2011; 13:10174-82. [DOI: 10.1039/c0cp02245d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Fiedler SL, Violi A. Simulation of nanoparticle permeation through a lipid membrane. Biophys J 2010; 99:144-52. [PMID: 20655842 DOI: 10.1016/j.bpj.2010.03.039] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/05/2010] [Accepted: 03/10/2010] [Indexed: 11/30/2022] Open
Abstract
A metric of nanoparticle toxicity is the passive permeability rate through cellular membranes. To assess the influence of nanoparticle morphology on this process, the permeability of buckyball-sized molecules through a representative lipid bilayer was investigated by molecular-dynamics simulation. When C(60) was compared with a prototypical opened C(60) molecule and a representative combustion-generated particle, C(68)H(29), the calculated free-energy profiles along the permeation coordinate revealed a sizable variation in form and depth. The orientation of the anisotropic molecules was determined by monitoring the principal axis corresponding to the largest moment of inertia, and free rotation was shown to be hindered in the bilayer interior. Diffusion constant values of the permeant molecules were calculated from a statistical average of seven to 10 trajectories at five locations along the permeation coordinate. A relatively minor variation of the values was observed in the bilayer interior; however, local resistance values spanned up to 24 orders of magnitude from the water layer to the bilayer center, due primarily to its exponential dependence on free energy. The permeability coefficient values calculated for the three similarly sized but structurally distinct nanoparticles showed a significant variance. The use of C(60) to represent similarly sized carbonaceous nanoparticles for assessments of toxicity is questioned.
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Affiliation(s)
- Steven L Fiedler
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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25
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Xu L, Wang X, Zhao W. Bridging the gap between molecular descriptors and mechanism: cases studies by molecular dynamics simulations. J Mol Graph Model 2009; 27:829-35. [PMID: 19195915 DOI: 10.1016/j.jmgm.2008.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 12/17/2008] [Accepted: 12/30/2008] [Indexed: 10/21/2022]
Abstract
In recent years, both classification models and quantitative structure-activity relationships (QSARs) have been developed to discriminate the acute toxicity of polar narcotics and uncouplers. One of fundamental issues is how to select and interpret the molecular descriptors used in both methods. In this work, we first employed support vector machine on a dataset containing 155 polar narcotics and 19 uncouplers to filter the predictive hydrophobic and hydrogen bonding descriptors. Molecular dynamics simulations were then conducted to investigate the behavior of salicylate and pentachlorophenol molecules in the context of a palmitoyl-oleoyl-phosphatidylcholine lipid bilayer. The results demonstrated that their equilibrium properties in the lipid bilayer were closely associated with hydrophobic and hydrogen bonding descriptors. The preferable occupations of these molecules in the lipid bilayer were discussed in terms of their modes of toxic action. The observations from molecular dynamics simulations facilitated to elucidate the mechanism of polar narcotics and uncouplers.
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Affiliation(s)
- Liang Xu
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
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26
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Gurtovenko AA, Anwar J. Interaction of Ethanol with Biological Membranes: The Formation of Non-bilayer Structures within the Membrane Interior and their Significance. J Phys Chem B 2009; 113:1983-92. [PMID: 19199697 DOI: 10.1021/jp808041z] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Computational Biophysics Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Jamshed Anwar
- Computational Biophysics Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
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Abstract
The adamantanes are a class of compounds that have found use in the treatment of influenza A and Parkinson's disease, among others. The mode of action for influenza A is based on the adamantanes' interaction with the transmembrane M2 channel, whereas the treatment of Parkinson's disease is thought to relate to a channel block of N-methyl-D-aspartate receptors. An understanding of how these compounds interact with the lipid bilayer is thus of great interest. We used molecular-dynamics simulations to calculate the potential of mean force of adamantanes in a lipid bilayer. Our results demonstrate a preference for the interfacial region of the lipid bilayer for both protonated and deprotonated species, with the protonated species proving significantly more favorable. However, the protonated species have a large free-energy barrier in the center of the membrane. In contrast, there is no barrier (compared with aqueous solution) at the center of the bilayer for deprotonated species, suggesting that the permeant species is indeed the neutral form, as commonly assumed. We discuss the results with respect to proposed mechanisms of action and implications for drug-delivery in general.
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28
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Klamt A, Huniar U, Spycher S, Keldenich J. COSMOmic: a mechanistic approach to the calculation of membrane-water partition coefficients and internal distributions within membranes and micelles. J Phys Chem B 2008; 112:12148-57. [PMID: 18754634 DOI: 10.1021/jp801736k] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new approach for the modeling of molecules in micellar systems and especially in biomembranes, COSMOmic, is presented, and its performance is validated on the example of the partitioning of molecules between water and biological membranes. Starting from quantum chemical calculations of the surfactant, solvent, and solute molecules, and being based on the COSMO-RS method for fluid-phase thermodynamic properties, COSMOmic is essentially free of additional adjustable parameters. The inclusion of an elastic energy correction into the COSMOmic model did not turn out to yield any significant improvement. The novel COSMOmic method allows for the efficient prediction of the distribution of molecules in micellar systems.
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Affiliation(s)
- Andreas Klamt
- COSMOlogic GmbH&COKG, Burscheider Strasse 515, 51381 Leverkusen, Germany.
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29
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Zhao W, Róg T, Gurtovenko AA, Vattulainen I, Karttunen M. Role of phosphatidylglycerols in the stability of bacterial membranes. Biochimie 2008; 90:930-8. [DOI: 10.1016/j.biochi.2008.02.025] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Accepted: 02/29/2008] [Indexed: 11/30/2022]
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30
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MacCallum JL, Tieleman DP. Chapter 8 Interactions between Small Molecules and Lipid Bilayers. CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00008-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Yeagle PL, Bennett M, Lemaître V, Watts A. Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:530-7. [PMID: 17223071 DOI: 10.1016/j.bbamem.2006.11.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 11/28/2006] [Accepted: 11/30/2006] [Indexed: 10/23/2022]
Abstract
A novel mechanism for membrane modulation of transmembrane protein structure, and consequently function, is suggested in which mismatch between the hydrophobic surface of the protein and the hydrophobic interior of the lipid bilayer induces a flexing or bending of a transmembrane segment of the protein. Studies on model hydrophobic transmembrane peptides predict that helices tilt to submerge the hydrophobic surface within the lipid bilayer to satisfy the hydrophobic effect if the helix length exceeds the bilayer width. The hydrophobic surface of transmembrane helix 1 (TM1) of lactose permease, LacY, is accessible to the bilayer, and too long to be accommodated in the hydrophobic portion of a typical lipid bilayer if oriented perpendicular to the membrane surface. Hence, nuclear magnetic resonance (NMR) data and molecular dynamics simulations show that TM1 from LacY may flex as well as tilt to satisfy the hydrophobic mismatch with the bilayer. In an analogous study of the hydrophobic mismatch of TM7 of bovine rhodopsin, similar flexing of the transmembrane segment near the conserved NPxxY sequence is observed. As a control, NMR data on TM5 of lacY, which is much shorter than TM1, show that TM5 is likely to tilt, but not flex, consistent with the close match between the extent of hydrophobic surface of the peptide and the hydrophobic thickness of the bilayer. These data suggest mechanisms by which the lipid bilayer in which the protein is embedded modulates conformation, and thus function, of integral membrane proteins through interactions with the hydrophobic transmembrane helices.
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Affiliation(s)
- Philip L Yeagle
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269, USA.
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32
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Alessandrini A, Valdrè G, Valdrè U, Muscatello U. Defects in ordered aggregates of cardiolipin visualized by atomic force microscopy. Chem Phys Lipids 2007; 146:111-24. [PMID: 17274972 DOI: 10.1016/j.chemphyslip.2007.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 01/01/2007] [Accepted: 01/09/2007] [Indexed: 11/23/2022]
Abstract
The formation and the nature of defects in ordered aggregates of cardiolipin (tetra acyl diphosphatidylglycerol) supported on solid substrates have been investigated by atomic force microscopy (AFM). The experiments were performed on two model systems, i.e. three-dimensional liquid crystals dispersed in water and partially de-hydrated on a hydrophilic surface, and two-dimensional films of molecules self-assembled onto an isotropic hydrophobic surface. Defects were induced both by varying the preparation temperature and by treatment with specific chemicals known to modify the order parameters in natural and artificial membranes, specifically: 2,4-dinitro-phenol (DNP) and pentachloro-phenol (PCP). The effect of lipid oxidation on the nanocrystalline order was also investigated. The images obtained by AFM allow to characterize the type of defects and their local density at nanoscale level. They also provide additional information to differentiate the specific role of acyl chains and polar heads in the process of lipid self-organization.
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Affiliation(s)
- Andrea Alessandrini
- CNR-INFM-S3 NanoStructures and BioSystems at Surfaces, Via Campi 213/A, I-41100, Modena, Italy.
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33
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Xiang TX, Anderson BD. Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. Adv Drug Deliv Rev 2006; 58:1357-78. [PMID: 17092601 DOI: 10.1016/j.addr.2006.09.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 09/04/2006] [Indexed: 11/21/2022]
Abstract
Computational methods to predict drug permeability across biomembranes prior to synthesis are increasingly desirable to minimize the investment in drug design and development. Significant progress in molecular dynamics (MD) simulation methodologies applied to lipid bilayer membranes, for example, is making it possible to move beyond characterization of the membranes themselves to explore various thermodynamic and kinetic processes governing membrane binding and transport. Such methods are also likely to be directly applicable to the design and optimization of liposomal delivery systems. MD simulations are particularly valuable in addressing issues that are difficult to explore in laboratory experiments due to the heterogeneity of lipid bilayer membranes at the molecular level. Insights emerging from MD simulations are contributing to an understanding of which regions within bilayers are most and least favored by solutes at equilibrium as the solute structure is varied, local diffusivities of permeants, and the origin of the amplified selectivity to permeant size imposed by lipid bilayer membranes, particularly as changes in composition increase acyl chain ordering.
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Affiliation(s)
- Tian-Xiang Xiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
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Abstract
Molecular dynamics simulations have been performed to explore the distribution and translocation of a set of furocoumarins (psoralen derivatives) inside saturated and partially unsaturated lipid membranes. Within the simulations, strong accumulation of the photodynamic drugs is observed near the polar headgroup region, although the populations also extend out into the membrane/water interface as well as to the membrane center. The computed transverse (Dz) diffusion coefficients are in the range 0.01-0.03 x 10(-5) cm2 s(-1)-significantly slower than those reported for small molecules like water, ethane, and ammonia-and are related to the low mobility inside the polar headgroup region. Trimethylpsoralen (TMP) has a very low free energy barrier to transversion, only approximately 10 kJ/mol, whereas 5- and 8-methoxy psoralens (5-MOP, 8-MOP) have the largest barriers of the compounds studied-between 25 and 40 kJ/mol. Upper bounds to the permeation coefficients, obtained by integrating the resistance profiles across the bilayers, range from 5.2 x 10(-8) cm s(-1) for TMP to 4.1 x 10(-12) cm s(-1) for 5-MOP. The current simulations explain the high level of furocoumarin-lipid membrane complexes found in experimental studies of albino Wistar rats exposed to topical application of 8-MOP, and points to the possibility of membrane photodamage as a viable mechanism in psoralen ultraviolet-A treatment.
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Affiliation(s)
- Daniel J V A dos Santos
- Orebro Life Science Center and Department of Natural Sciences, Orebro University, 701 82 Orebro, Sweden
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Aliste MP, Tieleman DP. Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces. BMC BIOCHEMISTRY 2005; 6:30. [PMID: 16368010 PMCID: PMC1351180 DOI: 10.1186/1471-2091-6-30] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Accepted: 12/20/2005] [Indexed: 11/23/2022]
Abstract
BACKGROUND Peptide-membrane interactions play a key role in the binding, partitioning and folding of membrane proteins, the activity of antimicrobial and fusion peptides, and a number of other processes. To gain a better understanding of the thermodynamics of such interactions, White and Wimley created an interfacial hydrophobicity scale based of the transfer free energy from water to octanol or lipid bilayers of a series of synthetic peptapeptides (Ace-WLXLL, with X being any of the twenty natural amino acids) (White and Wimley (1996) Nat. Struct. Biol. 3, 842-848). In this study, we performed molecular dynamics simulations of a representative set of ten of these peptides (X = D, K, R, N, A, T, S, I, F and W) in two membrane mimetic interfaces: water-cyclohexane (10 ns) and a fully solvated dioleoylphosphatidylcholine (DOPC) bilayer (50 ns) using both constant pressure and constant area ensembles. We focus on partitioning of the ten peptides at the cyclohexane/water and lipid/water interfaces. RESULTS The peptides rapidly equilibrate (< 2 ns) and partition at the cyclohexane/water interface. The X3 guest residue assumes average orientations that depend on the nature of the side chain. At the DOPC/water interface, dynamics is much slower and convergence is difficult to achieve on a 50 ns timescale. Nonetheless, all peptides partition to the lipid/water interface with distributions with widths of 1-2 nm. The peptides assume a broad range of side chain and backbone orientations and have only a small effect on the area of the unit cell. On average, hydrophobic guest residues partition deeper into the hydrophobic core than hydrophilic residues. In some cases the peptides penetrate sufficiently deep to somewhat affect the distribution of the C=C double bond in DOPC. The relative distribution of the X3 guest residue compared to W1 and L5 is similar in the water/cyclohexane and water/lipid simulations. Snapshots show mostly extended backbone conformations in both environments. There is little difference between simulations at a constant area of 0.66 nm2 and simulations at constant pressure that approximately yield the same average area of 0.66 nm2. CONCLUSION These peptides were designed to assume extended conformations, which is confirmed by the simulations. The distribution of the X3 side chain depends on its nature, and can be determined from molecular dynamics simulations. The time scale of peptide motion at a phospholipids-water interface is too long to directly calculate the experimentally measured hydrophobicity scale to test and improve the simulation parameters. This should be possible at the water/cyclohexane interface and likely will become feasible in the future for the phospholipids/water case.
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Affiliation(s)
- Marcela P Aliste
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
- School of Biology, Georgia Institute of Technology, 310 Ferst Dr NW, Atlanta, Georgia, 30332, USA
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
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Kim EB, Lockwood N, Chopra M, Guzmán O, Abbott NL, de Pablo JJ. Interactions of liquid crystal-forming molecules with phospholipid bilayers studied by molecular dynamics simulations. Biophys J 2005; 89:3141-58. [PMID: 16113112 PMCID: PMC1366811 DOI: 10.1529/biophysj.105.065193] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 06/13/2005] [Indexed: 11/18/2022] Open
Abstract
Recent experiments have shown that liquid crystals can be used to image mammalian cell membranes and to amplify structural reorganization in phospholipid-laden liquid crystal-aqueous interfaces. In this work, molecular dynamics simulations were employed to explore the interactions between commonly used liquid crystal-forming molecules and phospholipid bilayers. In particular, umbrella sampling was used to obtain the potential of mean force of 4-cyano-4'-pentylbiphenyl (5CB) and 4'-(3,4-difluor-phenyl)-4-pentyl-bicylohexyl (5CF) molecules partitioning into a dipalmitoylphosphatidylcholine bilayer. In addition, results of simulations are presented for systems consisting of a fully hydrated bilayer with 5CB or 5CF molecules at the lowest (4.5 mol %) and highest (20 mol %) concentrations used in recent laboratory experiments. It is found that mesogens preferentially partition from the aqueous phase into the membrane; the potential of mean force exhibits highly favorable free energy differences for partitioning (-18 k(B)T for 5CB and -26 k(B)T for 5CF). The location and orientation of mesogens associated with the most stable free energies in umbrella sampling simulations of dilute systems were found to be consistent with those observed in liquid-crystal-rich bilayers. It is found that the presence of mesogens in the bilayer enhances the order of lipid acyl tails, and changes the spatial and orientational arrangement of lipid headgroup atoms. These effects are more pronounced at higher liquid-crystal concentrations. In comparing the behavior of 5CB and 5CF, a stronger spatial correlation (i.e., possibly leading to aggregation) is observed between 5CB molecules within a bilayer than between 5CF molecules. Also, the range of molecular orientations and positions along the bilayer normal is larger for 5CB molecules. At the same time, 5CF molecules were found to bind more strongly to lipid headgroups, thereby slowing the lateral motion of lipid molecules.
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Affiliation(s)
- Evelina B Kim
- Department of Chemical Engineering, University of Wisconsin, Madison, WI 53706, USA
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Bemporad D, Luttmann C, Essex JW. Behaviour of small solutes and large drugs in a lipid bilayer from computer simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1718:1-21. [PMID: 16321606 DOI: 10.1016/j.bbamem.2005.07.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 07/14/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
To reach their biological target, drugs have to cross cell membranes, and understanding passive membrane permeation is therefore crucial for rational drug design. Molecular dynamics simulations offer a powerful way of studying permeation at the single molecule level. Starting from a computer model proven to be able to reproduce the physical properties of a biological membrane, the behaviour of small solutes and large drugs in a lipid bilayer has been studied. Analysis of dihedral angles shows that a few nano seconds are sufficient for the simulations to converge towards common values for those angles, even if the starting structures belong to different conformations. Results clearly show that, despite their difference in size, small solutes and large drugs tend to lie parallel to the bilayer normal and that, when moving from water solution into biomembranes, permeants lose degrees of freedom. This explains the experimental observation that partitioning and permeation are highly affected by entropic effects and are size-dependent. Tilted orientations, however, occur when they make possible the formation of hydrogen bonds. This helps to understand the reason why hydrogen bonding possibilities are an important parameter in cruder approaches which predict drug absorption after administration. Interestingly, hydration is found to occur even in the membrane core, which is usually considered an almost hydrophobic region. Simulations suggest the possibility for highly polar compounds like acetic acid to cross biological membranes while hydrated. These simulations prove useful for drug design in rationalising experimental observations and predicting solute behaviour in biomembranes.
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Affiliation(s)
- D Bemporad
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
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Word RC, Smejtek P. Partitioning of Tetrachlorophenol into Lipid Bilayers and Sarcoplasmic Reticulum: Effect of Length of Acyl Chains, Carbonyl Group of Lipids and Biomembrane Structure. J Membr Biol 2005; 203:127-42. [PMID: 15986092 DOI: 10.1007/s00232-005-0737-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 02/04/2005] [Indexed: 10/25/2022]
Abstract
We report results of a partitioning study of 2,3,4,6-tetrachlorophenol (TeCP). In the study we explored (1) the effect of the length of acyl chains of lipids (C16:1 - C24:1) and alkanes (C6-C16), (2) the role of the carbonyl group of lipids, and (3) the effect of molecular structure of the sarcoplasmic reticulum membrane on TeCP partitioning. Mole fraction partition coefficients have been measured using equilibrium dialysis for un-ionized (HA), and ionized (A) species, Kp(x) (HA), Kp(x) (A). Their values are concentration-dependent. Partition coefficients were analyzed in terms of a model that accounts for saturation of membrane associated with the finite area of partition site, and electrostatic interactions of (A-) species with charged membrane. Limiting values of partition coefficients, corresponding to infinite dilution of solute, Kp(x0) (HA), Kp(x0) (A) were obtained. Kp(x0) (HA) and Kp(x0) (A ) measure the strength of solute-membrane interactions. Studies were done with single-layered vesicles of lipids with variable chain length: 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (C16:1), 1,2-dioleoyl-sn-glycero-3-phosphocholine (C18:1), 1,2-dierucoyl-sn-glycero-3-phosphocholine (C22:1), and 1 ,2-dinervonoyl-sn-glycero-3-phosphocholine (C24:1), and egg-PC. Kp(x0) for transfer of TeCP from water into lipid membranes was found to be independent of the length of acyl chains, whereas Kp(x0) for transfer from water into alkanes increased with the length of alkane. The effect of the carbonyl CO group of lipids on partitioning was measured using 1,2-di-o-octadecenyl-sn-glycero-3-phosphocholine (CO absent) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (CO present) liposomes. Carbonyl groups, known to change dipolar potential, had no effect on partitioning. Partition coefficients of un-ionized and ionized forms of TeCP were invariant to the presence of proteins and other membrane components of sarcoplasmic reticulum (SR) membrane.
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Affiliation(s)
- R C Word
- Department of Physics, Portland State University, OR 97207, USA
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Ash WL, Zlomislic MR, Oloo EO, Tieleman DP. Computer simulations of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:158-89. [PMID: 15519314 DOI: 10.1016/j.bbamem.2004.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.
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Affiliation(s)
- Walter L Ash
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB, Canada T2N 1N4
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Hoff B, Strandberg E, Ulrich AS, Tieleman DP, Posten C. 2H-NMR study and molecular dynamics simulation of the location, alignment, and mobility of pyrene in POPC bilayers. Biophys J 2004; 88:1818-27. [PMID: 15596514 PMCID: PMC1305236 DOI: 10.1529/biophysj.104.052399] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The alignment of pyrene in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer was investigated using two different approaches, namely solid-state (2)H-NMR spectroscopy and molecular dynamics (MD) simulations. Quadrupolar splittings from (2)H-NMR spectra of deuterated pyrene-d(10) in an oriented lipid bilayer give information about the orientation of C-D bonds with respect to the membrane normal. From MD simulations, geometric information is accessible via trajectories. By defining molecular and bond order parameters, the data from MD trajectories and NMR spectra can be compared straightforwardly. To ensure that the results from both methods are comparable, parameters of the experimental and the simulation setup were chosen to be as similar as possible. From simulations, we saw that pyrene prefers a position inside the lipid membrane near the headgroups and has no tendency to diffuse from one monolayer of the membrane to the other. The results from simulation and NMR show that the normal of the molecular plane is aligned nearly perpendicular to the bilayer normal. The long axis of pyrene lies preferentially parallel to the bilayer normal within a range of +/-30 degrees . The results from the two different methods are remarkably consistent. The good agreement can be explained by the fact that the different kind of motions of a pyrene molecule are already averaged within a few nanoseconds, which is the timescale covered by the MD simulation.
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Affiliation(s)
- Barbara Hoff
- IMVM, Bioprocess Engineering, University of Karlsruhe, 76131 Karlsruhe, Germany
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Mukhopadhyay P, Monticelli L, Tieleman DP. Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. Biophys J 2004; 86:1601-9. [PMID: 14990486 PMCID: PMC1303994 DOI: 10.1016/s0006-3495(04)74227-7] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Two 40 ns molecular dynamics simulations of a palmitoyl-oleoyl phosphatidylserine (POPS) lipid bilayer in the liquid crystalline phase with Na(+) counterions and NaCl were carried out to investigate the structure of the negatively charged lipid bilayer and the effect of salt (NaCl) on the lipid bilayer structure. Na(+) ions were found to penetrate deep into the ester region of the water/lipid interface of the bilayer. Interaction of the Na(+) ions with the lipid bilayer is accompanied by a loss of water molecules around the ion and a simultaneous increase in the number of ester carbonyl oxygen atoms binding the ion, which define an octahedral and square pyramidal geometry. The amine group of the lipid molecule is involved in the formation of inter- and intramolecular hydrogen bonds with the carboxylate and the phosphodiester groups of the lipid molecule. The area per lipid of the POPS bilayer is unaffected by the presence of 0.15M NaCl. There is a small increase in the order parameter of carbon atoms in the beginning of the alkyl chain in the presence of NaCl. This is due to a greater number of Na(+) ions being coordinated by the ester carbonyl oxygen atoms in the water/lipid interface region of the POPS bilayer.
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Affiliation(s)
- Parag Mukhopadhyay
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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de Vries AH, Mark AE, Marrink SJ. The Binary Mixing Behavior of Phospholipids in a Bilayer: A Molecular Dynamics Study. J Phys Chem B 2004. [DOI: 10.1021/jp0366926] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alex H. de Vries
- MD Group, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Alan E. Mark
- MD Group, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- MD Group, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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