Browsing by Author "Chamati H."

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    Physical properties of phospholipids at low temperatures through Slipid force field
    (2023-01-01) Ivanova N.; Chamati H.
    Slipid (Stockholm lipids) force field is suitable for the description of the physical properties of biological membranes composed of phospholipids at room temperature. So far, its accuracy to reproduce the behavior of the thermodynamic and structural quantities of membranes at low temperatures has not yet been tested in sufficient details. In the present study, we compute some characteristic quantities of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) using GROMACS in conjunction with Slipid force field. The initial configuration of the SOPC system composed of 128 lipid molecules distributed equally in each monolayer and 5120 water molecules was generated with the aid of CHARMM-GUI. Atomistic molecular dynamic (MD) simulations were performed at several temperatures. By virtue of a statistical analysis of trajectories, we computed the main structural parameters of the lipid molecules and thermodynamic quantities characterizing the phase behavior of the bilayer. The results are compared to available experimental data, as well as theoretical predictions. The Slipid force field was found to describe fairly well the structural behavior of the lipids at low temperatures.
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    Probing Slipids Force Field for Phase Transitions in SOPC Lipid Bilayers with Various Cholesterol Concentrations
    (2024-08-01) Ivanova N.; Chamati H.
    We explore the phase behavior of lipid bilayers containing SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with various molar concentrations (0 mol%, 10 mol% and 30 mol%) of cholesterol. To this end, we performed extensive atomistic molecular dynamics simulations in conjunction with the Slipids force field with optimized parameters for the headgroups of phospholipids. We computed thermodynamic and structural quantities describing the ordering of the tails, the mobility of the heads and the arrangement of the lipids in the bilayers. We analyzed the behavior of the named quantities over the temperature range between 271 K and 283 K, where the experimentally determined melting temperature, (Formula presented.) K, lies, as well as at 400 K, which is used as a reference temperature. The obtained results are compared to available experimental data along with the outcome from molecular dynamics simulations of similar phospholipids containing different amounts of cholesterol. In the temperature interval of interest, we found evidence of the occurrence of a thermal-driven phase transition (melting) in both the pure system and the one with the lower concentration of cholesterol, while in the remaining system, the higher amount of cholesterol in the bilayer smears out the transitional behavior. Thus, we demonstrate the ability of the Slipids force field to predict the phase behavior of bilayers of SOPC and SOPC mixed with cholesterol.
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    Silver nanoparticles synthesis and their effect on the SOPC lipid structure
    (2022-04-04) Slavkova Z.; Genova J.; Chamati H.; Boev V.; Yancheva D.
    We focus our attention on the influence of hydrophobic silver nanoparticles (Ag NPs) on the 1-Stearoyl-2-oleoylsn-glycero-3-phosphocholine (SOPC) model system. Results obtained by differential scanning calorimetry (DSC) and infrared (IR) spectroscopy were compared to their counterpart for lipid systems with incorporated hydrophobic gold nanoparticles (AuNPs) and pure SOPC lipid in a water environment. The results show a strong effect of hindering the gel-to-liquid crystalline phase transition for both types of noble metal hydrophobic NPs. The effect of the phase transitions shift to the lower temperatures is more pronounced for the silver particles for the concentrations studied. According to the IR spectral analyses, no negative effect is observed of the NPs on the lipid hydration for the concentration studied, and the plasmon effect of the Ag NPs appears to be more pronounced.
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    The Effect of Cholesterol in SOPC Lipid Bilayers at Low Temperatures
    (2023-03-01) Ivanova N.; Chamati H.
    We study the behavior of lipid bilayers composed of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with different concentrations of cholesterol, ranging from 10 mol% to 50 mol% at 273 K. To this end, we carry out extensive atomistic molecular dynamic simulations with the aid of the Slipid force field aiming at computing basic bilayer parameters, as well as thermodynamic properties and structural characteristics. The obtained results are compared to available relevant experimental data and the outcome of atomistic simulations performed on bilayers composed of analogous phospholipids. Our results show a good quantitative, as well as qualitative, agreement with the main trends associated with the concentration increase in cholesterol. Moreover, it comes out that a change in the behavior of the bilayer is brought about at a concentration of about 30 mol% cholesterol. At this very concentration, some of the bilayer properties are found to exhibit a saturation and a significant long-range ordering of the lipid molecules in the membrane shows up.