Specific recognition of ligands including metal ions by proteins is the key of many crucial biological functions and systems. Accurate prediction of the binding strength not only sheds light on the mechanism of the molecular recognition but also provides the most important prerequisite of drug discovery. Computational modeling of molecular binding has gained a great deal of attentions in the last few decades since the advancement of computer power and availability of high-resolution crystal structures. However there still exist two major challenges in the field of molecular modeling, i.e. sampling issue and accuracy of the models. In this work, I have dedicated to tackling these two problems with a noval polarizable force field which is believed to produce more accurate description of molecular interactions than classic non-polarizable force fields. We first developed the model for divalent cations Mg²⁺ and Ca²⁺, deriving the parameters from quantum mechanics. To understand the hydration thermodynamics of these ions we have performed molecular dynamics simulations using our AMOEBA force field. Both the water structures around ions and the solvation free energies were in great accordance with experiment data. We have also simulated and calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin using explicit solvent approach by free energy perturbation. The calculated binding free energies are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. Finally, we computed the hydration free energies of a few organic molecules and automated the calculation procedure. / text

abstract: Na+/H+ antiporters are vital membrane proteins for cell homeostasis, transporting Na+ ions in exchange for H+ across the lipid bilayer. In humans, dysfunction of these transporters are implicated in hypertension, heart failure, epilepsy, and autism, making them well-established drug targets. Although experimental structures for bacterial homologs of the human Na+/H+ have been obtained, the detailed mechanism for ion transport is still not well-understood. The most well-studied of these transporters, Escherichia coli NhaA, known to transport 2 H+ for every Na+ extruded, was recently shown to bind H+ and Na+ at the same binding site, for which the two ion species compete. Using molecular dynamics simulations, the work presented in this dissertation shows that Na+ binding disrupts a previously-unidentified salt bridge between two conserved residues, suggesting that one of these residues, Lys300, may participate directly in transport of H+. This work also demonstrates that the conformational change required for ion translocation in a homolog of NhaA, Thermus thermophilus NapA, thought by some to involve only small helical movements at the ion binding site, is a large-scale, rigid-body movement of the core domain relative to the dimerization domain. This elevator-like transport mechanism translates a bound Na+ up to 10 Å across the membrane. These findings constitute a major shift in the prevailing thought on the mechanism of these transporters, and serve as an exciting launchpad for new developments toward understanding that mechanism in detail. / Dissertation/Thesis / Doctoral Dissertation Physics 2016

Ca2+ is an important messenger that affects almost all cellular processes. Ca2+ signaling involves events that happen at various time-scales such as Ca2+ diffusion, trans-membrane Ca2+ transport and Ca2+-mediated protein-protein interactions. In this work, we utilized multi-scale computational methods to quantitatively characterize Ca2+ diffusion efficiency, Ca2+ binding thermodynamics and molecular bases of Ca2+-dependent protein-protein interaction. Specifically, we studied 1) the electrokinetic transport of Ca2+ in confined sub-µm geometry with complicated surfacial properties. We characterized the effective diffusion constant of Ca2+ in a cell-like environment, which helps to understand the spacial distribution of cytoplasmic Ca2+. 2) the association kinetics and activation mechanism of the protein phosphatase calcineurin (CaN) by its activator calmodulin (CaM) in the presence of Ca2+. We found that the association between CaM and CaN peptide is diffusion-limited and the rate could be tuned by charge density/distribution of CaN peptite. Moreover, we proposed an updated CaM/CaN interaction model in which a secondary interaction between CaN’s distal helix motif and CaM was highlighted. 3) the roles of Mg2+ and K+ in the active transport of Ca2+ by sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) pump. We found that Mg2+ most likely act as inhibitor while K+ as agonist in SERCA’s transport process of Ca2+. Results reported in this work shed insights into various aspects of Ca2+ signaling from molecular to cellular level.

No / Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening. / EPSRC

No description available.

Thesis (M.Sc. (Physics)) -- University of Limpopo, 2022 / The gas sensing performance of two-dimensional (2D) hexagonal boron nitride nanosheets (h-BNNSs) has being studied by means of computational and experimental methods. The structural, stability and vacancies properties of both defect free and defected 2D h-BNNSs were studied using the classical molecular dynamics (MD) approach. The calculations were performed in the NVT Evans and NPT hoover ensembles using the Tersoff potentials with the Verlet leapfrog algorithm to obtain reliable structural properties and energies for defect free, boron (B) and nitrogen (N) vacancies. B and N defect energies were calculated relative to the bulk defect free total energies, and the results suggest that N vacancy is the most stable vacancy as compared to the B vacancy. The radial distribution functions and structure factors were used to predict the most probable structural form. Mean square displacements suggests the mobility of B and N atoms in the system is increasing with an increase in the surface area of the nanosheets. Results obtained are compared with the bulk defect free h-BNNSs. Experimentally, 2D h-BNNSs were synthesised using the wet chemical reaction method through chemical vapour deposition (CVD) catalyst free approach. The X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM), Fourier Transform Infrared Spectroscopy (FTIR), Raman Spectroscopy (RM), UV-visible Spectroscopy (UV-VIS), dynamic light scattering (DLS), Energy Dispersion Spectroscopy (EDS) and Brunauer-Emmett Teller (BET) were adopted to attain the structural properties of the nanosheets. Each spectroscopic technique affirmed unique features about the surface morphology of h BNNSs. The crystallinity of the nanosheets with the stacking of the B and N vii honeycomb lattice was validated by the XRD, while the TEM disclosed the specimen orientations and chemical compositions of phases with the number of layers of a planar honeycomb BN sheet, the EDS express the atoms present in the samples and BET validated the surface area of the materials. The FTIR, RM, DLS and the UV-vis expressed the formation of the in-plane, out-of-plane h-BN vibrations and, the nature of the surface with the thickness, particles stability together with the optical properties of the nanosheets. From TEM, FTIR, RS and BET the material fabricated at 800°C showed different morphologies, large number of disordering together with high surface area, which enhances the sensing properties of the nanosheets. However, with an increase in temperature the sensitivity of the nanosheets was found to decrease. Additionally, the UV-vis results, confirmed a lower energy band gap of 4.79, 4.55 and 4.70 eV for materials fabricated at 800, 900 and 1000 °C, that improved the semiconducting properties of the materials, which in return enhanced the sensing properties of the nanosheets. The gas sensing properties of the 2D h BNNSs were also investigated on hydrogen sulphide (H2S) and carbon monoxide (CO). The fabricated sensor based on 800 – 900 °C h-BNNSs showed good sensitivity towards ppm of H2S at 250 °C. The excellent gas sensing properties could be attributed to high surface area, small crystallite size, defect/disordering of h BNNSs. Overall, the h-BNNSs were found to be more sensitive to H2S over CO. / University of Limpopo (UL) Mintek Council for Scientific and Industrial Research (CSIR) Center for High Performance Computing (CHPC)