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Hryc J, Szczelina R, Markiewicz M, Pasenkiewicz-Gierula M. Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases. Front Mol Biosci 2022; 9:958537. [PMID: 36046609 PMCID: PMC9423040 DOI: 10.3389/fmolb.2022.958537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, carried out using computational methods, the organisation of the lipid/water interface of bilayers composed of galactolipids with both α-linolenoyl acyl chains is analysed and compared in three different lyotropic liquid-crystalline phases. These systems include the monogalactosyldiglyceride (MGDG) and digalactosyldiglyceride (DGDG) bilayers in the lamellar phase, the MGDG double bilayer during stalk phase formation and the inverse hexagonal MGDG phase. For each system, lipid-water and direct and water-mediated lipid-lipid interactions between the lipids of one bilayer leaflet and those of two apposing leaflets at the onset of new phase (stalk) formation, are identified. A network of interactions between DGDG molecules and its topological properties are derived and compared to those for the MGDG bilayer.
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Affiliation(s)
- Jakub Hryc
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Szczelina
- Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Marta Pasenkiewicz-Gierula, ; Michal Markiewicz,
| | - Marta Pasenkiewicz-Gierula
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Marta Pasenkiewicz-Gierula, ; Michal Markiewicz,
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Markiewicz M, Szczelina R, Pasenkiewicz-Gierula M. Data for molecular dynamic simulations in the OPLSAA force field: Partial charges of cholesterol, C7-hydroxycholesterol and C7-hydroperoxycholesterol, torsional parameters for the hydroperoxy group of C7-hydroperoxycholesterol. Data Brief 2021; 39:107483. [PMID: 34712759 PMCID: PMC8528686 DOI: 10.1016/j.dib.2021.107483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
This data article contains partial charges generated for cholesterol, C7-hydroxycholesterol and C7-hydroperoxycholesterol and torsional parameters for hydroperoxy of C7-hydroperoxycholesterol for molecular dynamics simulations in the OPLSAA force field [1] using the package Gromacs [2]. The hydroperoxy group remained unparameterized in the OPLSAA force field and the parameters obtained have the potential for re-use in similar simulations. The atom-centred point charges on each sterol molecule were derived using the restrained electrostatic potential (RESP) approach [3]. The parameters for the C7-OET-OH-HO and C8-C7-OET-OH torsion angles were derived by fitting the parameters of the torsional term (Ryckaert-Bellemans function) of the OPLSAA potential energy function to the quantum mechanical rotational energy profile calculated at CCSD(T)/cc-pVQZ level of theory. This article presents data used in the research article “Chirality affects cholesterol-oxysterol association in water, a computational study” [4].
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Affiliation(s)
- Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Szczelina
- Division of Computational Mathematics, Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
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Markiewicz M, Szczelina R, Milanovic B, Subczynski WK, Pasenkiewicz-Gierula M. Chirality affects cholesterol-oxysterol association in water, a computational study. Comput Struct Biotechnol J 2021; 19:4319-4335. [PMID: 34429850 PMCID: PMC8361299 DOI: 10.1016/j.csbj.2021.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023] Open
Abstract
Cholesterol (Chol) is the most prevalent sterol in the animal kingdom and an indispensable component of mammalian cell membranes. Chol content in the membrane is strictly controlled, although the oxidation of phospholipids may change the relative content of membrane Chol. An excess of it results in the formation of pure Chol microdomains in the membrane. It is likely that some Chol molecules detach from the domains and self-assemble in the aqueous environment. This may promote Chol microcrystallisation, which initiates the development of gallstones and atherosclerotic plaque. In this study, the molecular dynamics, free energy perturbation, umbrella sampling and Voronoi diagram methods are used to reveal the details of self-association of Chol and its oxidised forms (oxChol), namely 7α,β-hydroxycholesterol and 7α,β-hydroperoxycholesterol, in water. In the first part of the study the interactions between a sterol monomer and water over a short and longer timescale as well as the energy of hydration of each sterol are analysed. This helps one to understand Chol-Chol and Chol-OxChol with different chirality self-association in water better, which is analysed in the second part of the study. The Voronoi diagram approach is used to determine the relative arrangement of molecules in the dimer and, most importantly, to analyse the dehydration of the contacting surfaces of the assembling molecules. Free energy calculations indicate that Chol and 7β-hydroxycholesterol associate into the most stable dimer and that Chol-Chol is the next most stable of the five dimers studied. Employing different computational methods enables us to obtain an adequate picture of Chol-sterol self-association in water, which includes dynamic, energetic and temporal aspects of the process.
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Affiliation(s)
- Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Szczelina
- Division of Computational Mathematics, Faculty of Mathematics and Computer Science, Jagiellonian University, 30-348 Krakow, Poland
| | - Bozena Milanovic
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Witold K. Subczynski
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
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Szczelina R, Baczynski K, Markiewicz M, Pasenkiewicz-Gierula M. Network of lipid interconnections at the interfaces of galactolipid and phospholipid bilayers. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Plesnar E, Szczelina R, Subczynski WK, Pasenkiewicz-Gierula M. Is the cholesterol bilayer domain a barrier to oxygen transport into the eye lens? Biochim Biophys Acta Biomembr 2017; 1860:434-441. [PMID: 29079282 DOI: 10.1016/j.bbamem.2017.10.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
Abstract
In the eye lens, the oxygen partial pressure is very low and the cholesterol (Chol) content in cell membranes is very high. Disturbance of these quantities results in cataract development. In human lens membranes, both bulk phospholipid-Chol domains and the pure Chol bilayer domains (CBDs) were experimentally detected. It is hypothesized that the CBD constitutes a significant barrier to oxygen transport into the lens. Transmembrane profiles of the oxygen diffusion-concentration product, obtained with electron paramagnetic resonance spin-labeling methods, allow evaluation of the oxygen permeability (PM) of phospholipid membranes but not the CBD. Molecular dynamics simulation can independently provide components of the product across any bilayer domain, thus allowing evaluation of the PM across the CBD. Therefore, to test the hypothesis, MD simulation was used. Three bilayers containing palmitoyl-oleoyl-phosphorylcholine (POPC) and Chol were built. The pure Chol bilayer modeled the CBD, the 1:1 POPC-Chol bilayer modeled the bulk membrane in which the CBD is embedded, and the POPC bilayer was a reference. To each model, 200 oxygen molecules were added. After equilibration, the oxygen concentration and diffusion profiles were calculated for each model and multiplied by each other. From the respective product profiles, the PM of each bilayer was calculated. Favorable comparison with experimental data available only for the POPC and POPC-Chol bilayers validated these bilayer models and allowed the conclusion that oxygen permeation across the CBD is ~10 smaller than across the bulk membrane, supporting the hypothesis that the CBD is a barrier to oxygen transport into the eye lens.
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Affiliation(s)
- Elzbieta Plesnar
- Department of Computational Biophysics and Bioinformatics, WBBiB, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
| | - Robert Szczelina
- Department of Bioinformatics, MCB, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.
| | - Witold K Subczynski
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, WBBiB, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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Affiliation(s)
- Robert Szczelina
- Faculty of Mathematics and Computer Science, ‡Malopolska Centre of Biotechnology, and §Faculty of Biochemistry,
Biophysics and Biotechnology, Department of Computational Biophysics
and Bioinformatics, Jagiellonian University, 31-007 Krakow, Poland
| | - Krzysztof Murzyn
- Faculty of Mathematics and Computer Science, ‡Malopolska Centre of Biotechnology, and §Faculty of Biochemistry,
Biophysics and Biotechnology, Department of Computational Biophysics
and Bioinformatics, Jagiellonian University, 31-007 Krakow, Poland
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