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Opis: Coarse-grained molecular dynamics simulations are highly valuable for studying protein-protein interactions. Unfortunately, commonly used force fields often overestimate these interactions. Here, we investigate the performance of the Martini 3 force field in predicting the self-interaction behavior of lysozyme and subtilisin using Metadynamics. The original Martini 3, despite improvements over its predecessor, overestimates interaction strength. Through reparameterization of bead interactions, we achieve good agreement with experimental data of the second virial coefficient and the diffusion coefficient. The new, refined force field enables more accurate CG-MD simulations, with potential applications in understanding and prediction of protein stability, aggregation tendencies, and solubility, with the possibility to aid in the development of protein-based drugs.
Ključne besede: coarse-grained molecular dynamics, Martini 3 force field, protein-protein interactions, B22, reparameterization, NMR, diffusion coefficient
Objavljeno v DKUM: 20.03.2025; Ogledov: 0; Prenosov: 2
Celotno besedilo (6,83 MB)

Ključne besede: molecular dynamics simulations, personalized therapy, single nucleotide polymorphisms, SNPs, linear interaction energy, LIE, multiple sclerosis, MS
Objavljeno v DKUM: 03.02.2025; Ogledov: 0; Prenosov: 3
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Opis: Manganese Superoxide Dismutase (MnSOD) represents a mitochondrial protein that scavenges reactive oxygen species (ROS) responsible for oxidative stress. A known single nucleotide polymorphism (SNP) rs4880 on the SOD2 gene, causing a mutation from alanine to valine (Ala16Val) in the primary structure of immature MnSOD, has been associated with several types of cancer and other autoimmune diseases. However, no conclusive correlation has been established yet. This study aims to determine the effect of the alanine to valine mutation on the secondary structure of the MnSOD mitochondrial targeting sequence (MTS). A model for each variant of the MTS was prepared and extensively simulated with molecular dynamics simulations using the CHARMM36m force field. The results indicate that the alanine variant of the MTS preserves a uniform α-helical secondary structure favorable for the protein transport into mitochondria, whereas the valine variant quickly breaks down its α-helix. Thus, the alanine MTS represents the more active MnSOD variant, the benefits of which have yet to be determined experimentally.
Ključne besede: manganese superoxide dismutase, polymorphism rs4880, mutation Ala16Val, molecular dynamics simulations, oxidative stress
Objavljeno v DKUM: 21.08.2023; Ogledov: 370; Prenosov: 18
Celotno besedilo (5,14 MB)
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Opis: The last two decades have been determined by the development in the field of tissue engineering. Beside the constant progress in new biomaterials and scaffold fabrication methods, currently the main focus is to understand scaffolds biocompatibility. In our thesis, physical aspects of scaffold biocompatibility were studied by correlating molecular to macro scale physical properties of scaffolds with cell attachment and cell growth. In order to focus on scaffold physical properties, scaffolds were prepared by the same chemical composition of natural polymer gelatin excluding biochemical effects on the cell response. Scaffold with different physical properties were obtained by changing the temperature, pH and crosslinker degree during the cryogelation and populated by the fibroblast cells. Advanced experimental biophysical methods were applied to determine the polymer mobility via electron paramagnetic resonance (EPR) with spin labelling, the scaffold mechanical properties via rheometry, dynamic mechanical analysis (DMA) and nanoindentation using atomic force microscope (AFM) and the scaffold porosity via confocal fluorescence microscopy (CFM). The anisotropy of the molecular mobility of the side chains of polymers in the crosslinked gelatin structure was found to correlate with the initial cell growth (throughout the first week) the best of all the physical properties measured. About five times less efficient cell growth was measured on the scaffolds with highly mobile, spatially nonrestricted dynamics of the polymer side chains, in comparison with cell growth on the scaffolds with the restricted rotational motion of polymers. The result indicates that cells identify and respond to the degree of polymer mobility, where partially immobile phase is necessary for efficient cell attachment and efficient cell growth. So far, the molecular mobility of polymers constituting tissue engineering materials has never been studied thoroughly with respect to its influence on cell response, and therefore may represent a new experimental approach in understanding biocompatibility. To further understand cell-scaffold interaction, the study focused also on the first events during cell attachment - bond formation between the cell surface proteins and the specific binding sites on the material. In our thesis, cell adhesion dynamics was investigated in real-time on the surfaces of gelatin scaffolds with different physical properties using spatially-controlled cell manipulation by the optical tweezers and the confocal fluorescence microscopy detection. Our goal was to elucidate, if the adhesion dynamics can be correlated with cell growth and if it can be dependent on the scaffold polymer molecular mobility. Quantitative characterization of the optical tweezers force applied during cell-scaffold adhesion analysis was done by viscous drag force calibration and dynamic cell sequential trapping of individual cells. The maximal force on a trapped cell not causing the thermal damage was measured up to 200 pN, with nearly linearly increasing force profile across the cell towards the plasma membrane. By submicron spatial resolution of cell manipulation, we managed to quantify probability of cell adhesion, cell adhesion strength and mechanism of cell attachment, including the formation of the membrane tethers, which slow down the adhesion process. Adhesion strength was classified according to the displacement of the attached cell under the force of optical tweezers measured in the direction of the scaffold surface.Cell adhesion was shown to significantly correlate with cell growth in the first days of culture, while the adhesion itself seems to be dependent on the molecular mobility of surface polymers. The result indicates that the interactions during the first seconds may markedly direct further cell response. The developed methodology for cell adhesion analysis on the surfaces of 3D scaffolds serves as a good tool to forecast scaffold biocompatibility.
Ključne besede: polymer molecular mobility, mechanical response, morphology, scaffold biocompatibility, cell growth, single cell manipulation, cell adhesion dynamics, optical tweezers, electron paramagnetic resonance, dynamical mechanical analysis, nanoindentation, fluorescence microscopy and microspectroscopy
Objavljeno v DKUM: 06.10.2015; Ogledov: 2496; Prenosov: 181
Celotno besedilo (5,95 MB)