Molecular modelling

In this thesis atomistic level modelling is conducted to investigate the design of an environmentally adaptable self-cleaning polymer paint coating that incorporates biomimetics to remain clean in various environmental setting. This work will be used to aid in the development of stay-clean polymer paint coating.

116p runthenight07 01-03-2023 9 3   Download

In this Masters thesis computational modelling techniques were employed to investigate iron-free apo-Lactoferrin (apo-Lf) structural conformation changes in the presence of variant temperature and pH. These conditions represent the environment most milk protein goes through in food processing and the production of food products.

162p runthenight04 02-02-2023 8 3   Download

Master's thesis of Science "Investigation into the modulation of circadian clock proteins by dietary compounds and small molecules" is structured as follows: Chapter 1 Introduction; Chapter 2 Identification of novel bioactive compounds from Olea europaea by evaluation of chemical compounds in the OliveNetTM library: in silico bioactivity and molecular modelling, and in vitro validation of hERG activity; Chapter 3 Modulation of circadian core clock proteins by dietary compounds; Chapter 4 Molecular mechanisms of action of selected olive phenolics against epigenetic modifiers and the structur...

235p runthenight04 02-02-2023 5 3   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 11 3   Download

The research in this thesis follows two directions: The first, using high performance computing currently available, we studied atomic and molecular emissions in astrophysical environment. The radiative transfer model was applied to explain the characteristics of the recombination line masers Hnα in the envelope of the star MWC 349A.

27p beloveinhouse01 15-08-2021 19 4   Download

In this work, we have analyzed this problem for the example of N,N-dialkylamides in the presence of uranyl nitrate experimentally. Furthermore, we present a minimal model at nanoscale that allows rationalizing the experimental phenomena by connecting the molecular, mesoscopic and macroscopic scale and that allows predicting qualitative trends in viscosity.

18p christabelhuynh 29-05-2020 11 2   Download

The quantum-chemical modeling mechanism of the [4+2]-cycloaddition reaction of 2,3 dimethylbuta-1,3-diene and methyl acrylate was conducted. Its qualitative aspects were analyzed at the molecular level by the program MOPAC2012 and semiempirical method RM1.

6p tocectocec 25-05-2020 7 1   Download

In this paper a molecular dynamics simulation of nano-metric cutting of copper with a diamond tool is presented. MD simulations require the determination of the interaction of the involved atoms through a function of potential for the materials involved in the analysis and the accurate topography of the studied area, leading to high demand of computational time.

12p tohitohi 19-05-2020 29 1   Download

In  Molecular simulation of nanoparticle diffusion at fluid interfaces molecular dynamics simulations are used to exam- ine the transport properties of a nanoparticle in both bulk solvent and at a liquid–liquid interface. Specifically it aims to address the effect of interfacial adsorption on the diffusion of nanoparticles (at low concentration).

5p hoquangbio 22-07-2015 27 2   Download

The design of b-glycosidases with planed substrate specificity for biotechnological application has received little attention. This is mostly a consequence of the lack of data on the molecular basis of the b-glycosidase specificity, namely data on the energy of the noncovalent interactions in the enzymetransition state complex. In an attempt to fill this gap, sitedirected mutagenesis and enzyme steady-state kinetic experiments with different substrates were conducted, using as model a digestive b-glycosidase (glycoside hydrolase family 1) from Spodoptera frugiperda (Lepidoptera) (Sfbgly50).

10p system191 01-06-2013 44 4   Download

A recombinant lipase cloned from Pseudomonas fragi strain IFO 3458 (PFL) was found to retain significant activity at low temperature. In an attempt to elucidate the structural basis of this behaviour, a model of its three-dimensional structure was built by homology and compared with homologous mesophilic lipases, i.e. the Pseudomonas aeruginosa lipase (45% sequence identity) and Burkholderia cepacia lipase (38%).

8p system191 01-06-2013 49 4   Download

The case of homologous monomeric c-type and oligomeric b-type crystallins has been described and analyzed in evolutionary terms. Data and hypotheses from molecular genetics and structural investigations converge and suggest a novel three-phase model for the evolutionary history of crystallin-type proteins. In the divergent cascades of monomeric and oligomeric crystallins, a pivotal role was played by alterations in the gene segments encoding the C-terminal extensions and the intermotif or interdomain linker peptides.

9p system191 01-06-2013 42 4   Download

Oligomerization into multimeric complexes is a prerequisite for the chaperone function of almost all a-crystallin type heat shock proteins (a-Hsp), but the molecular details of complex assembly are poorly understood. The a-Hsp proteins from Bradyrhizobium japonicum are suitable bacterial models for structure-function studies of these ubiquitous stress proteins. They fall into two distinct classes, A and B, display chaperone activity in vitro and form oligomers of  24 subunits.

9p research12 01-06-2013 50 6   Download

A comparative study of thermodynamic and kinetic aspects of Cu(II) and Ni(II) binding at the N-terminal binding site of human and bovine serum albumins (HSA and BSA, respectively) and short peptide analogues was performed using potentiometry and spectroscopic techniques. It was found that while qualitative aspects of interaction (spectra and structures of complexes, order of reactions) could be reproduced, the quantitative parameters (stability and rate constants) could not.

9p research12 01-06-2013 38 4   Download

Lipoprotein lipase (LPL) plays a key role in lipid metabo-lism. Molecular modeling of dimeric LPL was carried out usingINSIGHT IIbased upon the crystal structures of human, porcine, and horse pancreatic lipase. The dimeric model reveals a saddle-shaped structure and the key heparin-binding residues in the amino-terminal domain located on the top of this saddle.

10p research12 29-04-2013 47 4   Download

It is scientifically and industrially important 1 to clarify the stabilizing mechanism of proteases in extraordinary envi-ronments. We used subtilisins ALPI and Sendai as models to study the mechanism. Subtilisin ALPI is extremely sensitive to highly alkaline conditions, even though the enzyme is produced by alkalophilicBacillus, whereas sub-tilisin Sendai from alkalophilic Bacillusis stable under conditions of high alkalinity.

9p research12 23-04-2013 45 1   Download

We used parameter scanning to emulate changes to the limitingrate for steps inafittedmodel of glucose-derepressed yeast glycolysis. Three flux-control regimes were observed, two of which were under the dominant control of hexose transport, in accordance with various experimental studies andothermodel predictions.

11p research12 23-04-2013 43 2   Download

Upon mutation of Asp153 by asparagine, the catalytic activity of agmatinase (agmatine ureohydrolase, EC 3.5.3.11)fromEscherichia coliwas reduced to about 5% of wild-type activity. Tryptophan emission fluorescence (kmax ¼340 nm), and CD spectra were nearly identical for wild-type and D153N agmatinases. TheKmvalue for agmatine (1.6 ± 0.1 mM),aswellastheKi for putrescine inhibition (12 ± 2 mM)and the interaction of the enzyme with the requiredmetal ion,werealsonot alteredbymutation.

5p tumor12 22-04-2013 22 3   Download

Protein molecular modelling and ligand docking were employed for the design of anthraquinone galactosyl-bio-mimetic dye ligands (galactosyl-mimodyes) for the target enzyme galactose dehydrogenase (GaDH). Using appro-priate modelling methodology, a GaDH model was build based on a glucose-fructose oxidoreductase (GFO) protein template.

15p tumor12 22-04-2013 47 2   Download

We examined the microenvironment of the single trypto-phan and the tyrosine residues of PsbQ, one of the three main extrinsic proteins of green algal and higher plant photosystem II. On the basis of this information and the previous data on secondary structure [Balsera, M., Arel-lano, J.B., Gutie´rrez, J.R., Heredia, P., Revuelta, J.L. & De Las Rivas, J. (2003)Biochemistry42, 1000–1007], we screened structural models derived by combining various threading approaches.

12p tumor12 20-04-2013 33 1   Download