1
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Bouquiaux C, Castet F, Champagne B. Unravelling the Effects of Cholesterol on the Second-Order Nonlinear Optical Responses of Di-8-ANEPPS Dye Embedded in Phosphatidylcholine Lipid Bilayers. J Phys Chem B 2021; 125:10195-10212. [PMID: 34491062 DOI: 10.1021/acs.jpcb.1c05630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cholesterol is known for its role in maintaining the correct fluidity and rigidity of the animals cell membranes and thus their functions. Assessing the content and the role of cholesterol in lipid bilayers is therefore of crucial importance for a deeper understanding and control of membrane functioning. In this computational work, we investigate bilayers built from three types of glycerophospholipid phosphatidylcholine (PC) lipids, namely dipalmitoylphosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and dioleoylphosphatidylcholine (DOPC), and containing different amounts of cholesterol by analyzing the second-harmonic generation (SHG) nonlinear optical (NLO) response of a probe molecule, di-8-ANEPPS, inserted into the membranes. This molecular property presents the advantage to be specific to interfacial regions such as lipid bilayers. To unravel these effects, Molecular Dynamics (MD) simulations have been performed on both DPPC and DOPC lipids by varying the cholesterol mole fraction (from 0 to 0.66), while POPC was only considered as a pure bilayer. In the case of the structural properties of the bilayers, all the analyses converge toward the same conclusion: as the mole fraction of cholesterol increases, the systems become more rigid, confirming the condensing effect of cholesterol. In addition, the chromophore is progressively more aligned with respect to the normal to the bilayer. On the contrary, addition of unsaturation disorders the lipid bilayers, with barely no impact on the alignment of the chromophore. Then, using the frames obtained from the MD simulations, the first hyperpolarizability β of the dye in its environment has been computed at the TDDFT level. On the one hand, the addition of cholesterol induces a progressive increase of the diagonal component the β tensor parallel to the bilayer normal. On the other hand, larger β values have been calculated for the unsaturated than for the saturated lipid systems. In summary, this study illustrates the relationship between the composition and structure of the bilayers and the NLO responses of the embedded dye.
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Affiliation(s)
- Charlotte Bouquiaux
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Frédéric Castet
- , Institut des Sciences Moléculaires, UMR 5255 CNRS, University of Bordeaux, cours de la Libération 351, F-33405 Talence Cedex, France
| | - Benoît Champagne
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
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2
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Martelli F, Crain J, Franzese G. Network Topology in Water Nanoconfined between Phospholipid Membranes. ACS NANO 2020; 14:8616-8623. [PMID: 32578978 DOI: 10.1021/acsnano.0c02984] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Water provides the driving force for the assembly and stability of many cellular components. Despite its impact on biological functions, a nanoscale understanding of the relationship between its structure and dynamics under soft confinement has remained elusive. As expected, water in contact with biological membranes recovers its bulk density and dynamics at ∼1 nm from phospholipid headgroups but surprisingly enhances its intermediate range order (IRO) over a distance, at least, twice as large. Here, we explore how the IRO is related to the water's hydrogen-bond network (HBN) and its coordination defects. We characterize the increased IRO by an alteration of the HBN up to more than eight coordination shells of hydration water. The HBN analysis emphasizes the existence of a bound-unbound water interface at ∼0.8 nm from the membrane. The unbound water has a distribution of defects intermediate between bound and bulk water, but with density and dynamics similar to bulk, while bound water has reduced thermal energy and many more HBN defects than low-temperature water. This observation could be fundamental for developing nanoscale models of biological interactions and for understanding how alteration of the water structure and topology, for example, due to changes in extracellular ions concentration, could affect diseases and signaling. More generally, it gives us a different perspective to study nanoconfined water.
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Affiliation(s)
- Fausto Martelli
- Hartree Centre, IBM Research Europe, Daresbury WA4 4AD, United Kingdom
| | - Jason Crain
- Hartree Centre, IBM Research Europe, Daresbury WA4 4AD, United Kingdom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària, Departament de Física de la Matèria Condensada, and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028 Barcelona, Spain
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3
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Azalomycin F5a, a polyhydroxy macrolide binding to the polar head of phospholipid and targeting to lipoteichoic acid to kill methicillin-resistant Staphylococcus aureus. Biomed Pharmacother 2019; 109:1940-1950. [DOI: 10.1016/j.biopha.2018.11.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 11/22/2022] Open
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4
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Patra MC, Kwon HK, Batool M, Choi S. Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer. Front Immunol 2018; 9:489. [PMID: 29593733 PMCID: PMC5857566 DOI: 10.3389/fimmu.2018.00489] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/26/2018] [Indexed: 01/07/2023] Open
Abstract
Toll-like receptors (TLRs) are a unique category of pattern recognition receptors that recognize distinct pathogenic components, often utilizing the same set of downstream adaptors. Specific molecular features of extracellular, transmembrane (TM), and cytoplasmic domains of TLRs are crucial for coordinating the complex, innate immune signaling pathway. Here, we constructed a full-length structural model of TLR4-a widely studied member of the interleukin-1 receptor/TLR superfamily-using homology modeling, protein-protein docking, and molecular dynamics simulations to understand the differential domain organization of TLR4 in a membrane-aqueous environment. Results showed that each functional domain of the membrane-bound TLR4 displayed several structural transitions that are biophysically essential for plasma membrane integration. Specifically, the extracellular and cytoplasmic domains were partially immersed in the upper and lower leaflets of the membrane bilayer. Meanwhile, TM domains tilted considerably to overcome the hydrophobic mismatch with the bilayer core. Our analysis indicates an alternate dimerization or a potential oligomerization interface of TLR4-TM. Moreover, the helical properties of an isolated TM dimer partly agree with that of the full-length receptor. Furthermore, membrane-absorbed or solvent-exposed surfaces of the toll/interleukin-1 receptor domain are consistent with previous X-ray crystallography and biochemical studies. Collectively, we provided a complete structural model of membrane-bound TLR4 that strengthens our current understanding of the complex mechanism of receptor activation and adaptor recruitment in the innate immune signaling pathway.
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Affiliation(s)
- Mahesh Chandra Patra
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Hyuk-Kwon Kwon
- Department of Orthopaedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
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5
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Hien Nguyen T, C. Moore C, B. Moore P, Liu Z. Molecular dynamics study of homo-oligomeric ion channels: Structures of the surrounding lipids and dynamics of water movement. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.1.50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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6
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Sandoval-Perez A, Pluhackova K, Böckmann RA. Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface. J Chem Theory Comput 2017; 13:2310-2321. [PMID: 28388089 DOI: 10.1021/acs.jctc.7b00001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.
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Affiliation(s)
- Angelica Sandoval-Perez
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
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7
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Atomistic determinants of co-enzyme Q reduction at the Q i-site of the cytochrome bc 1 complex. Sci Rep 2016; 6:33607. [PMID: 27667198 PMCID: PMC5035994 DOI: 10.1038/srep33607] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/30/2016] [Indexed: 01/21/2023] Open
Abstract
The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone – a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.
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8
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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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9
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Slingsby JG, Vyas S, Maupin CM. A charge-modified general amber force field for phospholipids: improved structural properties in the tensionless ensemble. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.985675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Paloncýová M, DeVane RH, Murch BP, Berka K, Otyepka M. Rationalization of reduced penetration of drugs through ceramide gel phase membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13942-13948. [PMID: 25354090 DOI: 10.1021/la503289v] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Since computing resources have advanced enough to allow routine molecular simulation studies of drug molecules interacting with biologically relevant membranes, a considerable amount of work has been carried out with fluid phospholipid systems. However, there is very little work in the literature on drug interactions with gel phase lipids. This poses a significant limitation for understanding permeation through the stratum corneum where the primary pathway is expected to be through a highly ordered lipid matrix. To address this point, we analyzed the interactions of p-aminobenzoic acid (PABA) and its ethyl (benzocaine) and butyl (butamben) esters with two membrane bilayers, which differ in their fluidity at ambient conditions. We considered a dioleoylphosphatidylcholine (DOPC) bilayer in a fluid state and a ceramide 2 (CER2, ceramide NS) bilayer in a gel phase. We carried out unbiased (100 ns long) and biased z-constraint molecular dynamics simulations and calculated the free energy profiles of all molecules along the bilayer normal. The free energy profiles converged significantly slower for the gel phase. While the compounds have comparable affinities for both membranes, they exhibit penetration barriers almost 3 times higher in the gel phase CER2 bilayer. This elevated barrier and slower diffusion in the CER2 bilayer, which are caused by the high ordering of CER2 lipid chains, explain the low permeability of the gel phase membranes. We also compared the free energy profiles from MD simulations with those obtained from COSMOmic. This method provided the same trends in behavior for the guest molecules in both bilayers; however, the penetration barriers calculated by COSMOmic did not differ between membranes. In conclusion, we show how membrane fluid properties affect the interaction of drug-like molecules with membranes.
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Affiliation(s)
- Markéta Paloncýová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
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11
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The challenges of understanding glycolipid functions: An open outlook based on molecular simulations. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1130-45. [DOI: 10.1016/j.bbalip.2013.12.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022]
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12
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Maciejewski A, Pasenkiewicz-Gierula M, Cramariuc O, Vattulainen I, Rog T. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration. J Phys Chem B 2014; 118:4571-81. [PMID: 24745688 DOI: 10.1021/jp5016627] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).
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Affiliation(s)
- Arkadiusz Maciejewski
- Department of Physics, Tampere University of Technology , PO Box 692, FI-33101 Tampere, Finland
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13
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Paloncýová M, DeVane R, Murch B, Berka K, Otyepka M. Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region. J Phys Chem B 2014; 118:1030-9. [DOI: 10.1021/jp4112052] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Markéta Paloncýová
- Department
of Physical Chemistry, Faculty of Science, Regional Centre
of Advanced Technologies and Materials, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Russell DeVane
- Corporate Modeling & Simulation, Procter & Gamble, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Bruce Murch
- Corporate Modeling & Simulation, Procter & Gamble, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Karel Berka
- Department
of Physical Chemistry, Faculty of Science, Regional Centre
of Advanced Technologies and Materials, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Department
of Physical Chemistry, Faculty of Science, Regional Centre
of Advanced Technologies and Materials, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
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14
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Theoretical studies of the interaction between influenza virus hemagglutinin and its small molecule ligands. J Mol Model 2013; 19:5561-8. [DOI: 10.1007/s00894-013-2036-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
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15
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Bhatnagar N, Kamath G, Potoff JJ. Biomolecular Simulations with the Transferable Potentials for Phase Equilibria: Extension to Phospholipids. J Phys Chem B 2013; 117:9910-21. [DOI: 10.1021/jp404314k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Navendu Bhatnagar
- Department of Chemical Engineering
and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Ganesh Kamath
- Department of Chemistry, University of Missouri−Columbia, Columbia, Missouri
65211-7600, United States
| | - Jeffrey J. Potoff
- Department of Chemical Engineering
and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
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16
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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17
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Pöyry S, Cramariuc O, Postila PA, Kaszuba K, Sarewicz M, Osyczka A, Vattulainen I, Róg T. Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:769-78. [DOI: 10.1016/j.bbabio.2013.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/05/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
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18
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Parameterization of the prosthetic redox centers of the bacterial cytochrome bc 1 complex for atomistic molecular dynamics simulations. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1370-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:761-8. [PMID: 23428399 DOI: 10.1016/j.bbabio.2013.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/24/2013] [Accepted: 02/11/2013] [Indexed: 12/21/2022]
Abstract
Cytochrome (cyt) bc1 complex, which is an integral part of the respiratory chain and related energy-conserving systems, has two quinone-binding cavities (Qo- and Qi-sites), where the substrate participates in electron and proton transfer. Due to its complexity, many of the mechanistic details of the cyt bc1 function have remained unclear especially regarding the substrate binding at the Qo-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc1 complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH2) and quinone (Q). The QH2 binding at the Qo-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits. In this arrangement water molecules are positioned suitably in relation to the hydroxyls of the QH2 ring to act as the primary acceptors of protons detaching from the oxidized substrate. In contrast, water does not have a similar role in the Q binding at the Qo-site. Moreover, the coordinated water molecule is also a prime candidate to act as a structural element, gating for short-circuit suppression at the Qo-site.
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20
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Jämbeck JPM, Lyubartsev AP. Another Piece of the Membrane Puzzle: Extending Slipids Further. J Chem Theory Comput 2012; 9:774-84. [PMID: 26589070 DOI: 10.1021/ct300777p] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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21
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Kirschner KN, Lins RD, Maass A, Soares TA. A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation. J Chem Theory Comput 2012; 8:4719-31. [DOI: 10.1021/ct300534j] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl N. Kirschner
- Fraunhofer-Institute for Algorithms
and Scientific Computing (SCAI), Department of Bioinformatics, Schloss
Birlinghoven, 53754 Sankt Augustin, Germany
| | - Roberto D. Lins
- Department of Fundamental Chemistry,
Federal University of Pernambuco, Cidade Universitária, Recife,
PE 50740-560 Brazil
| | - Astrid Maass
- Fraunhofer-Institute for Algorithms
and Scientific Computing (SCAI), Department of Simulation Engineering,
Schloss Birlinghoven, 53754 Sankt Augustin, Germany
| | - Thereza A. Soares
- Department of Fundamental Chemistry,
Federal University of Pernambuco, Cidade Universitária, Recife,
PE 50740-560 Brazil
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22
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Skjevik ÅA, Madej BD, Walker RC, Teigen K. LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B 2012; 116:11124-36. [PMID: 22916730 DOI: 10.1021/jp3059992] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy, and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that LIPID11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.
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Affiliation(s)
- Åge A Skjevik
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
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23
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Jämbeck JPM, Lyubartsev AP. An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. J Chem Theory Comput 2012; 8:2938-48. [PMID: 26592132 DOI: 10.1021/ct300342n] [Citation(s) in RCA: 346] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) is a necessity. Here, we report the results of our extension of earlier developed all-atomistic FF parameters for fully saturated phospholipids that complements an earlier parameter set for saturated phosphatidylcholine lipids (J. Phys. Chem. B, 2012, 116, 3164-3179). The FF, coined Slipids (Stockholm lipids), now also includes parameters for unsaturated phosphatidylcholine and phosphatidylethanolamine lipids, e.g., POPC, DOPC, SOPC, POPE, and DOPE. As the extended set of parameters is derived with the same philosophy as previously applied, the resulting FF has been developed in a fully consistent manner. The capabilities of Slipids are demonstrated by performing long simulations without applying any surface tension and using the correct isothermal-isobaric (NPT) ensemble for a range of temperatures and carefully comparing a number of properties with experimental findings. Results show that several structural properties are very well reproduced, such as scattering form factors, NMR order parameters, thicknesses, and area per lipid. Thermal dependencies of different thicknesses and area per lipid are reproduced as well. Lipid diffusion is systematically slightly underestimated, whereas the normalized lipid diffusion follows the experimental trends. This is believed to be due to the lack of collective movement in the relatively small bilayer patches used. Furthermore, the compatibility with amino acid FFs from the AMBER family is tested in explicit transmembrane complexes of the WALP23 peptide with DLPC and DOPC bilayers, and this shows that Slipids can be used to study more complex and biologically relevant systems.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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24
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Andoh Y, Ito T, Okazaki S. An application of improved force field to fully hydrated DPPC and POPC bilayers in a tensionless NPT ensemble: a test of CHARMM 27-based new force field by Högberg et al. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2010.548385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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25
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Jämbeck JPM, Lyubartsev AP. Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J Phys Chem B 2012; 116:3164-79. [PMID: 22352995 PMCID: PMC3320744 DOI: 10.1021/jp212503e] [Citation(s) in RCA: 418] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/18/2012] [Indexed: 11/29/2022]
Abstract
An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.
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Affiliation(s)
- Joakim P. M. Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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26
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Nesterenko AM, Krasilnikov PM, Ermakov YA. Molecular-dynamic simulation of DPPC bilayer in different phase state: Hydration and electric field distribution in the presence of Be2+ cations. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2011. [DOI: 10.1134/s1990747811050084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Parthasarathi R, Tian J, Redondo A, Gnanakaran S. Quantum Chemical Study of Carbohydrate–Phospholipid Interactions. J Phys Chem A 2011; 115:12826-40. [DOI: 10.1021/jp204015j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- R. Parthasarathi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jianhui Tian
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Antonio Redondo
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - S. Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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28
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Gruenbaum SM, Skinner JL. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables. J Chem Phys 2011; 135:075101. [PMID: 21861584 PMCID: PMC3172989 DOI: 10.1063/1.3615717] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/02/2011] [Indexed: 11/15/2022] Open
Abstract
The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.
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Affiliation(s)
- S M Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave. University of Wisconsin, Madison, Wisconsin 53706, USA
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29
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Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: a molecular dynamics study. Biophys Chem 2010; 154:18-25. [PMID: 21227568 DOI: 10.1016/j.bpc.2010.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 11/24/2022]
Abstract
Local anesthetics (LAs) are drugs that cause reversible loss of nociception during surgical procedures. Articaine is a commonly used LA in dentistry that has proven to be exceptionally effective in penetrating bone tissue and induce anesthesia on posterior teeth in maxilla and mandibula. In the present study, our aim was to gain a deeper understanding of the penetration of articaine through biological membranes by studying the interactions of articaine with a phospholipid membrane. Our approach involves Langmuir monolayer experiments combined with molecular dynamics simulations. Membrane permeability of LAs can be modulated by pH due to a titratable amine group with a pKa value close to physiological pH. A change in protonation state is thus known to act as a lipophilicity switch in LAs. Our study shows that articaine has an additional unique lipophilicity switch in its ability to form an intramolecular hydrogen bond. We suggest this intramolecular hydrogen bond as a novel and additional solvent-dependent mechanism for modulation of lipophilicity of articaine which may enhance its diffusion through membranes and connective tissue.
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30
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Klauda JB, Venable RM, Freites JA, O’Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 2010; 114:7830-43. [PMID: 20496934 PMCID: PMC2922408 DOI: 10.1021/jp101759q] [Citation(s) in RCA: 3189] [Impact Index Per Article: 227.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and X-ray diffraction experiments. NMR deuterium order parameters (S(CD)) are well predicted with the new FF, including proper splitting of the S(CD) for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of (13)C NMR relaxation rates of DPPC and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.
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Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
| | - Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - J. Alfredo Freites
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Joseph W. O’Connor
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
| | - Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025
| | - Carlos Mondragon-Ramirez
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Igor Vorobyov
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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31
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Lupyan D, Mezei M, Logothetis DE, Osman R. A molecular dynamics investigation of lipid bilayer perturbation by PIP2. Biophys J 2010; 98:240-7. [PMID: 20338845 DOI: 10.1016/j.bpj.2009.09.063] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 10/19/2022] Open
Abstract
Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP(2)) are negatively charged lipids that play a pivotal role in membrane trafficking, signal transduction, and protein anchoring. We have designed a force field for the PIP(2) headgroup using quantum mechanical methods and characterized its properties inside a lipid bilayer using molecular dynamics simulations. Macroscopic properties such as area/headgroup, density profiles, and lipid order parameters calculated from these simulations agree well with the experimental values. However, microscopically, the PIP(2) introduces a local perturbation of the lipid bilayer. The average PIP(2) headgroup orientation of 45 degrees relative to the bilayer normal induces a unique, distance-dependent organization of the lipids that surround PIP(2). The headgroups of these lipids preferentially orient closer to the bilayer normal. This perturbation creates a PIP(2) lipid microdomain with the neighboring lipids. We propose that the PIP(2) lipid microdomain enables the PIP(2) to function as a membrane-bound anchoring molecule.
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Affiliation(s)
- Dmitry Lupyan
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, USA
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32
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Shushkov P, Tzvetanov S, Velinova M, Ivanova A, Tadjer A. Structural aspects of lipid monolayers: computer simulation analyses. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:8081-8092. [PMID: 20337413 DOI: 10.1021/la904734b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand. The packing pattern and cluster size dispersion were studied by means of Voronoi tessellation and radial distribution functions. Speculations regarding structural changes upon phase-state changes during film compression were made. Individual characteristics for surfactant heads and tails as well as for interfacial water were outlined and related to the available experimental data. An analysis of the diffusion coefficients revealed the limiting factors for lipid lateral and normal diffusion. Structural arguments in support of changes in monolayer dielectric properties with the area per molecule were provided.
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Affiliation(s)
- Philip Shushkov
- Laboratory of Quantum and Computational Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Sofia, 1 James Bourchier Avenue, 1164 Sofia, Bulgaria
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33
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Wei C, Pohorille A. Permeation of membranes by ribose and its diastereomers. J Am Chem Soc 2009; 131:10237-45. [PMID: 19621967 DOI: 10.1021/ja902531k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
It was recently found that ribose permeates membranes an order of magnitude faster than its diastereomers arabinose and xylose (Sacerdote, M. G.; Szostak, J. W. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6004). On this basis it was hypothesized that differences in membrane permeability to aldopentoses provide a mechanism for preferential delivery of ribose to primitive cells for subsequent selective incorporation into nucleotides and their polymers. However, the origins of these unusually large differences have not been well understood. We address this issue in molecular dynamics simulations combined with free energy calculations. It is found that the free energy of transferring ribose from water to the bilayer is lower by 1.5-2 kcal/mol than the barrier for transferring the other two aldopentoses. The calculated and measured permeability coefficients are in excellent agreement. The sugar structures that permeate the membrane are beta-pyranoses, with a possible contribution of the alpha-anomer for arabinose. The furanoid form of ribose is not substantially involved in permeation, even though it is non-negligibly populated in aqueous solution. The differences in free energy of transfer between ribose and arabinose or xylose are attributed, at least in part, to stronger highly cooperative, intramolecular interactions between consecutive exocyclic hydroxyl groups, which are stable in nonpolar media but rare in water. Water/hexadecane partition coefficients of the sugars obtained from separate molecular dynamics simulations correlate with the calculated permeability coefficients, in qualitative agreement with the Overton rule. The relevance of our calculations to understanding the origins of life is discussed.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Mail Stop 229-1, Moffett Field, California 94035, USA
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