Práca sa zaoberá in silico dizajnom a validáciou peptidov založených na konotoxíne - MrIA, izolovaného z morských slimákov druhu Conus marmoreus a možnosti využitia týchto peptidov v liečbe neuroblastómu pomocou cielenia norepinefrínového transportéru. Päť peptidov založených na tomto konotoxíne bolo simulovaných pomocou simulácii molekulárnej dynamiky, ich trajektórie boli analyzované pre zistenie vlastností týchto peptidov. Dva homologické modely ľudského norepinefrínového transportéru boli vytvorené pre analýzu väzobných vlastností peptidov založených na konotoxíne ku norepinefrínovému transportéru. Peptidy boli následne syntetizované a použité na pokrytie apoferitínových nanočastíc s elipticínom uväzneným vnútri apoferitínu. Vytvorené peptidy a nanočastice boli ďalej skúmané pre objasnenie ich fyzikálo-chemických vlastností. Interakcie a cytotoxicita boli skúmané aplokáciou nanočastíc na bunky neuroblastómu a epitelu. Z in silico a in vitro analýz vyšiel YKL-6 peptid ako najlepší kandidát na ďalší výskum.

STAT5 est une protéine de la signalisation cellulaire normale, qui peut jouer un rôle important dans la transformation, la survie et à la résistance aux inhibiteurs de tyrosine kinase des cellules tumorales. Son activation constitutive par phosphorylation est liée à la présence de protéines oncogéniques comme la protéine de fusion BCR/ABL1 (leucémie myéloïde chronique) ou de formes mutées de KIT (mastocytoses), par exemple. L’inhibition pharmacologique de STAT5 constitue donc un enjeu thérapeutique majeur pour plusieurs pathologies malignes. Nous avons réalisé la première modélisation et les simulations de dynamique moléculaire des principales formes de STAT5 : la forme monomérique cytoplasmique phosphorylée ou non, et la forme dimérique phosphorylée et liée à l’ADN. Nous avons caractérisé les propriétés dynamiques et le réseau allostérique intramoléculaire des monomères de STAT5. Les résultats générés montrent des variations structurales et dynamiques liées à la différence de séquence primaire des isoformes de STAT5 et/ou à la présence du groupement phosphate. Deux poches à la surface des protéines ont également été caractérisées. Leur localisation à proximité de voies de communication allostériques suggère que ces poches pourraient constituer des sites de modulation des fonctions de STAT5. Nous avons également caractérisé les liaisons hydrogènes entre les monomères constituant les dimères de STAT5 et leur reconnaissance de l’ADN. En outre, nous avons identifié des résidus clés aux interfaces entre les entités moléculaires, nous permettant de mieux comprendre les effets de mutations de STAT5 observées en clinique dans certaines pathologies malignes. / STAT5 is a protein involved in normal cell signalling that is crucial for transformation, survival and resistance to tyrosine kinase inhibitors of tumour cells. The constitutive phosphorylation activates STAT5 and is related to oncogenic proteins like the hybrid protein BCR/ABL1 (chronic myeloid leukaemia) or mutated KIT receptor (mastocytosis). The pharmacologic inhibition of STAT5 is thus a major therapeutic concern in several malignant pathologies. We performed the first modelling and molecular dynamics simulations of the main cellular species of STAT5: the cytoplasmic phosphorylated or unphosphorylated monomer, and the phosphorylated dimer bound to DNA. We characterized the dynamical properties and the intramolecular allosteric network of the monomers. The generated results show structural and dynamic variations linked to the primary sequence changes between the two STAT5 isoforms and/or to the phosphate group. Two pockets were characterized at the surface of STAT5. Their location at close proximity of allosteric communication pathways suggests new putative inhibition sites to modulate STAT5 functions. We also described the hydrogen bonds network between the monomers of the dimeric species and the recognition of the DNA. We identified key residues at the interfaces, allowing us to better understand the effects of clinically relevant STAT5 mutations observed in malignancies.

The field of DNA nanotechnology offers a wide range of design strategies with which nanometer-sized structures with a desired shape, size and aspect ratio can be built. The most established techniques in the field rely on close-packed 'solid' DNA nanostructures produced with either the DNA origami or the single-stranded tile techniques. These structures depend on high-salt buffer solutions and require more material than comparable size hollow wireframe structures. This dissertation explores the construction of hollow wireframe DNA nanostructures composed of equilateral triangles. To achieve maximal material efficiency the design is restricted to use a single DNA double helix per triangle edge. As a proof of principle, the DNA origami technique is extended to produce a series of truss structures including the flat, tetrahedral, octahedral, or irregular dodecahedral truss designs. In contrast to close packed DNA origami designs these structures fold at low-salt buffer conditions. These structures have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. The design process of these structures is simplified by a custom design software. Next, the triangulated construction motif is extended to the single-stranded DNA tile technique. A collection of finite structures, as well as one-dimensional crystalline assemblies is explored. The ideal assembly conditions are determined experimentally and using molecular dynamics simulations. A custom design software is presented to simplify the design and handling of these structures. At last, the cost-effective prototyping of triangulated wireframe DNA origami structures is explored. This is achieved through the introduction of single-stranded “gap” regions along the triangle edges. These gap regions are then filled using a DNA polymerase rather than by synthetic oligonucleotides. This technique also allows the mechanical transformation of these structures, which is exemplified by the transition of a bent into a straight structure upon completion of the gap filling.:Abstract v Publications vii Acknowledgements ix Contents xi Chapter 1 A short introduction into DNA nanotechnology 1 1.1 Nanotechnology 1 1.1.1 Top down 1 1.1.2 Bottom up 3 1.2 Deoxyribonucleic acid (DNA) 4 1.3 DNA Nanotechnology 6 1.3.1 Tile based assembly 9 1.3.2 DNA origami and single-stranded tiles 10 1.3.3 Some applications of DNA nanotechnology 12 1.3.4 Wireframe structures 15 1.3.5 Computational tools and DNA nanotechnology. 17 Chapter 2 Motivation and objectives 19 Chapter 3 Design and Synthesis of Triangulated DNA Origami Trusses 20 3.1 Introduction 20 3.2 Results and Discussion 21 3.2.1 Design 21 3.2.2 Nomenclature and parameters of the tube structures 23 3.2.3 Gel electrophoreses analysis 25 3.2.4 Imaging of the purified structures 26 3.2.5 Optimizing the folding conditions 28 3.2.6 Comparison to vHelix 29 3.3 Conclusions 29 3.4 Methods 30 3.4.1 Standard DNA origami assembly reaction. 30 3.4.2 Gel purification. 30 3.4.3 AFM sample preparation. 31 3.4.4 TEM sample preparation. 31 3.4.5 Instructions for mixing the staple sets. 31 Chapter 4 Triangulated wireframe structures assembled using single-stranded DNA tiles 33 4.1 Introduction 33 4.2 Results and Discussion 35 4.2.1 Designing the structures 35 4.2.2 Synthesis of test structures 37 4.2.3 Molecular dynamics simulations of 6-arm junctions 38 4.2.4 Assembly of the finite structures 40 4.2.5 Influence of salt concentration and folding times 42 4.2.6 Molecular dynamics simulations of the rhombus structure 43 4.2.7 1D SST crystals 44 4.2.8 Controlling the crystal growth 46 4.3 Conclusions 48 4.4 Methods 49 4.4.1 SST Folding 49 4.4.2 Agarose Gel Electrophoresis 49 4.4.3 tSEM Characterization 49 4.4.4 AFM Imaging 49 4.4.5 AGE-Based Folding-Yield Estimation 49 4.4.6 Molecular Dynamics Simulations 50 Chapter 5 Structural transformation of wireframe DNA origami via DNA polymerase assisted gap-filling 52 5.1 Introduction 52 5.2 Results and Discussion 54 5.2.1 Design of the Structures 54 5.2.2 Folding of Gap-Structures 56 5.2.3 Inactivation of Polymerase. 57 5.2.4 Secondary Structures. 58 5.2.5 Folding Kinetics of Gap Origami. 60 5.3 Conclusions 61 5.4 Methods 62 5.4.1 DNA origami folding 62 5.4.2 Gap filling of the wireframe DNA origami structures 63 5.4.3 Agarose gel electrophoresis 63 5.4.4 PAGE gel analysis 63 5.4.5 tSEM characterization 64 5.4.6 AFM imaging 64 5.4.7 AGE based folding-yield estimation 64 5.4.8 Gibbs free energy simulation using mfold 65 5.4.9 List of sequence for folding the DNA origami triangulated structures 65 Chapter 6 Summary and outlook 67 Appendix 69 A.1 Additional figures from chapter 369 A.2 Additional figures from chapter 4 77 A.3 Additional figures from chapter 5 111 Bibliography 127 Erklärung 138

6 Abstract This master's thesis provides study of individual helixes from C-terminal pore-forming domain (CTD) of colicin U and their behavior in lipid bilayer on atomic level. For this purpose the all-atom molecular simulation method was used. Later the study was extended an applied on CTD of published structures of other pore-forming colicins. On the base of study extension the ability of disruption of lipid bilayer integrity by helixes H1 and H10 was successfully observed. Helix H1 was synthesized and its activity was experimentally proved on black lipid membranes. The other helixes are often too short to be able to keep position in lipid bilayer and their behavior could be affected by artificial termini, therefore they were not synthesized. The MD simulations of pairs of helixes show that structure stability and their ability to stay in the membrane depends on binding partners. The results of the thesis show the importance of H10 for colicin pore-formation, which has not been observed yet. The results also support the toroidal pore model suggested previously for colicin E1. The results prove that colicins contain specific secondary structures, which are able to disrupt the inner bacterial membrane not only in its native form but also when artificially separated from the rest of the protein. Klíčová...

The two-phase MD technique employed in this work determines the liquid and vapor phase densities from a histogram of molecular densities within phase clusters in the simulation cell using a new Monte Carlo (MC) sampling method. These equilibrium densities are then fitted in conjunction with known critical-point scaling laws to obtain the critical temperature, and the critical density. This MC post-processing method was found to be more easily implemented in code, and it is efficient and easily applied to complex, structured molecules. This method has been successfully applied and benchmarked for a simple Lennard-Jones (LJ) fluid and a structured molecule, propane. Various degrees of internal flexibility in the propane models showed little effect on the coexisting densities far from critical point, but internal flexibility (angle bending and bond vibrations) seemed to affect the saturated liquid densities in the near-critical region, changing the critical temperature by approximately 20 K. Shorter cutoffs were also found to affect the phase dome and the location of the critical point. The developed MD+MC method was then used to test the efficacy of two all-atom, site-site pair potential models (with and without point charges) developed solely from the energy landscape obtained from high-level ab initio pair interactions for the first time. Both models produced equivalent phase domes and critical loci. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here. Lastly, the transferability of the ab initio potential model was evaluated by applying it to 1-pentanol. An attempt has been made to separate the errors due to transferability of the potential model from errors due to the use of a true-pair potential. The results suggested a good level of transferability for the site-site model. The lack of multi-body effects appears to be dominant weakness in using the generalized ab initio potential model for determination of the phase dome and critical properties of larger alcohols.

Hydrated polysaccharide systems primarily using xylans along with mutans and alternans were studied using long atomistic simulations over a few microseconds to analyse structure-function relationships and nanoscale interactions with moisture. The influence of various structural and chemical factors such as alignment, nature of glycosidic linkage, effect of moisture / chemical substitutions was explored with a focus on structure-dynamics correlations to aid in the effective functionalisation of biomaterials for the development of a green, circular bioeconomy. The effect of initial geometry in terms of alignment of the xylan chains was observed to affect xylan chain extension and water dynamics significantly. Xylan interaction with moisture studied at high and low moisture contents showed compression along with structural locking, and evolution into segregated water-rich and polymer-rich phases respectively. The effect of chemical heterogeneity in terms of substitutions appeared to improve xylan dispersion in water resulting in faster dynamics for substituted residues with reference to unsubstituted residues along a given polymer chain. In addition, significant correlations between local hydration and polymer dynamics / structure in terms of relaxation times and order parameters was observed across differently substituted hydrated xylan systems, such that the polymer dynamics could be expressed as a local hydration water dependent component and a second partially stochastic component. In addition, the molecular structure of mixed linkage (1,3 and 1,6) as well as 1,3 linked glucans elucidated the effect of the nature of glycosidic linkage on the molecular structure of glucan oligosaccharides. A combination of glucan linkages and the ratio of different conformation states of the hydroxymethyl dihedral angle was observed to yield linear, twisted and extended structures in mutans, or helical coils of varying pitch sizes in alternans. Further modeling of structure-dynamics dependencies in hydrated xylan systems and analysis of the effect of alignment / chemical substitutions at the nanoscale is to be correlated with scattering or related experimental techniques in the future to understand the dynamics of hydrated xylan aggregates in typically aqueous solutions at varying intermediate length / timescales. In addition, the methodologies derived in this work to identify atom-specific, temporally sensitive, structural / dynamical parameters for analysing structural / dynamical variations at the nanoscale can be extended to study other hydrated biopolymeric systems. The role of substitutions, involving its polar nature and interactions with other xylans, can be extended to neutral groups such as arabinose sugars to broaden knowledge in carbohydrate science as well as being analysed further to improve effective functionalisation for tailoring physical properties influencing phenomena like aggregation / dispersion. / Hydrerade polysackaridsystem som primärt använde xylaner, mutaner och alternaner studerades med hjälp av långa atomistiska simuleringar under några mikrosekunder för att analysera struktur-funktionsförhållanden och interaktioner med fukt i nanoskala. Inverkan av olika strukturella och kemiska faktorer såsom placering, karaktären av glykosidbindning, effekten avfukt/kemiska substitutioner undersöktes med fokus på struktur-dynamiska korrelationer för att hjälpa till med en effektiv funktionalisering av biomaterial för utvecklingen av en grön, cirkulär bioekonomi. Effekten av initial geometri i termer av placering av xylan-kedjorna observerades påverka xylan-kedjeförlängningen och vattendynamiken signifikant. Xylaninteraktionen medfukt studerades vid höga och låga fukthalter och visade kompression tillsammans med strukturell låsning och utveckling till segregerade vattenrika och polymerrika faser respektive. Effekten av kemisk heterogenitet i termer av substitutioner verkade förbättra dispersionen av xylan i vatten vilket resulterade i snabbare dynamik för substituerade delar jämfört med osubstituerade delar längs en given polymerkedja. Dessutom observerades signifikanta korrelationer mellan lokal hydratisering och polymerdynamik/struktur i termer av relaxationstider och ordningsparametrar över olika substituerade hydratiserade xylansystem, så att polymerdynamiken kunde uttryckas som en lokal hydreringsvattenberoende komponent och en andra delvis stokastisk komponent. Dessutom klargjorde den molekylära strukturen av blandad koppling (1,3 och 1,6) såväl som 1,3 länkade glukaner effekten av glykosidkopplingens natur på molekylstrukturen hos glukanoligosackarider. En kombination av glukanbindningar och förhållandet mellan olika konformationstillstånd för den hydroximetyldiedriska vinkeln observerades i linjära, vridna och utsträckta strukturer som i mutaner, eller som spiralformade spolar med varierande stigningsstorlekar i alternaner. Ytterligare modellering av struktur-dynamiska beroenden i hydratiserade xylansystem och analys av effekten av inriktning/kemiska substitutioner på nanoskala ska korreleras med spridning av relaterade experimentella tekniker i framtiden för att förstå dynamiken hos hydratiserade xylanaggregat i typiskt vattenhaltiga lösningar vid varierande medellängd /tidsskalor. Dessutom kan de metoder som härrör från detta arbete för att identifiera atomspecifika, tidsmässigt känsliga, strukturella/dynamiska parametrar för analys av strukturella/dynamiska variationer på nanoskala, utvidgas till att studera andra hydratiserade biopolymera system. Substitutionernas roll, som involverar dess polära natur och interaktioner med andra xylaner, kan utvidgas till neutrala grupper som arabinossocker för att bredda kunskapen inom kolhydratvetenskap samt analyseras ytterligare för att förbättra effektiv funktionalisering för att skräddarsy fysiska egenskaper som påverkar fenomen som aggregering / dispersion. / <p>QC 2023-05-22</p>

Potential parameters that can handle multi-component oxide glass systems especially boron oxide are very limited in literature. One of the main goals of my dissertation is to develop empirical potentials to simulate multi-component oxide glass systems with boron oxide. Two approaches, both by introducing the composition dependent parameter feature, were taken and both led to successful potentials for boron containing glass systems after extensive testing and fitting. Both potential sets can produce reasonable glass structures of the multi-component oxide glass systems, with structure and properties in good agreement with experimental data. Furthermore, we have tested the simulation settings such as system size and cooling rate effects on the results of structures and properties of MD simulated borosilicate glasses. It was found that increase four-coordinated boron with decreasing cooling rate and system size above 1000 atoms is necessary to produce converged structure. Another application of the potentials is to simulate a six-component nuclear waste glass, international simple glass (ISG), which was for first time simulated using the newly developed parameters. Structural features obtained from simulations agree well with the experimental results. In addition, two series of sodium borosilicate and boroaluminosilicate glasses were simulated with the two sets of potentials to compare and evaluate their applicability and deficiency. Various analyses on the structures and properties such as pair distribution function, total correlation function, coordination number analysis, Qn distribution function, ring size distribution function, vibrational density of states and mechanical properties were performed. This work highlights the challenge of MD simulations of boron containing glasses and the capability of the new potential parameters that enable simulations of wide range of mixed former glasses to investigate new structure features and design of new glass compositions for various applications.

Both ammonia and phosphine are widely used in industrial processes, and yet they are noxious and exhibit detrimental effects on human health. Despite the remarkable progress on sensors development, there are still some limitations, for instance, the requirement of high operating temperatures, and that most sensors are solely dedicated to individual gas monitoring. Herein, an ultrasensitive, highly discriminative platform is demonstrated for the detection and identification of ammonia and phosphine at room temperature using a graphene nanosensor. Graphene is exfoliated and successfully functionalized by copper phthalocyanine derivate. In combination with highly efficient machine learning techniques, the developed graphene nanosensor demonstrates an excellent gas identification performance even at ultralow concentrations: 100 ppb NH3 (accuracy—100.0%, sensitivity—100.0%, specificity—100.0%) and 100 ppb PH3 (accuracy—77.8%, sensitivity—75.0%, and specificity—78.6%). Molecular dynamics simulation results reveal that the copper phthalocyanine derivate molecules attached to the graphene surface facilitate the adsorption of ammonia molecules owing to hydrogen bonding interactions. The developed smart gas sensing platform paves a path to design a highly selective, highly sensitive, miniaturized, low-power consumption, nondedicated, smart gas sensing system toward a wide spectrum of gases.

The development of medicine is generally a long and costly process, and one big factor is estimating the affinity of protein-drug binding. Leveraging machine learning in this field is a promising approach as it can streamline the prediction process and reduce the need for expensive experimental methods. Machine learning methods have already enabled significant advances in predicting protein-drug binding affinity, yet there remains room for improvement. The primary challenge is the quality of data used for these machine learning models. In this work, two ensemble machine learning models, Random Forest and Extreme Gradient Boosting Machine, have been tested and compared with a recent database of protein-ligand complex features calculated from molecular dynamics simulation. Additional features were also extracted from the PDB database through PLIP (Protein-Ligand interaction Profiler), aiming to improve the predictions further. The results indicate that while the features from the PDB database provided strong predictive power, including features from molecular dynamic simulations did not improve the models’ performance.

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