Teoretická studie nekovalentních interakcí, od malých molekul k biomolekuklám

xv Abstract The aim of this thesis is to investigate the accurate stabilization energy and binding free energy in various non-covalent complexes spanned from small organic molecules to biomolecules. Non-covalent interactions such as H-bonds, π...π stacking and halogen bonds are mainly responsible for understanding of most biological processes, such as small molecule interactions with surface, protein-ligand binding in the cell machinery, etc. In the thesis, different non-covalent complexes such as graphene…electron donor- acceptor complexes, DNA base pair interaction with silica surface, etc, were investigated. The reference stabilization energies were calculated at ab initio level, e.g., CCSD(T)/CBS method wherever possible. On the other hand, more approximated scaled MP2 method (MP2.5/CBS/6-31G*(0.25)) is taken as reference instead of CCSD(T)/CBS due to the size of the complexes. Further, the DFT and MM energies were also tested towards the reference one. The knowledge of non- covalent interaction is required for rationalizing of any association processes in nature which requires accurate description of the free energy change. The state-of- the-art molecular dynamics simulation in full atomic scale and biased metadynamics free energy method is used for binding free energy calculations. The well tempered...xvi Abstrakt Cílem této práce je prozkoumat přesné stabilizační energie a volné vazebné energie pro různé nekovalentní komplexy počínaje malými organickými molekulami a konče biomolekulami. Nekovalentní interakce např. vodíkové vazby, π…π patrové interakce či halogenové vazby jsou zodpovědné za pochopení většiny biologických procesů, jako jsou interakce malých molekul s povrchem, protein-ligand interakce v buňkách atd. V práci byly vypočteny stabilizační energie pro různé nekovalentní komplexy, jako elektronové donor-akceptorové komplexy grafenu, páry bazí DNA interagující s povrchem oxidu křemičitého atd. Referenční stabilizační energie, kdekoli to bylo možné, byly výpočteny pomocí metody CCSD(T)/CBS. Vzhledem k velikosti studovaných komplexů byly v některých případech použity jako referenční metody místo CCSD(T)/CBS více aproximativni metody, např. škálované MP2 (MP2.5/CBS/6-31G*(0.25)). Mimo jiné byly stabilizační energie také počítané pomocí metod DFT a MM. Znalost nekovalentních interakcí je nevyhnutelná pro racionalizaci asociačních procesů v přírodě a vyžaduje přesný popis změn volné energie. Nejmodernější molekulově dynamické simulace s plně atomistickým popisem a "biased" metadynamické simulace byly použity pro výpočet volné vazebné energie. "well" temperované metadynamické simulace byly použity...Department of Physical and Macromolecular ChemistryKatedra fyzikální a makromol. chemieFaculty of SciencePřírodovědecká fakult

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes

Visible-light photoswitching of ligand binding mode suggests G-quadruplex DNA as a target for photopharmacology

We report the selective targeting of telomeric G4 DNA with a dithienylethene ligand and demonstrate the robust visible-light mediated switching of the G4 ligand binding mode and G-tetrad structure in physiologically-relevant conditions. The toxicity of the ligand to cervical cancer cells is modulated by the photoisomeric state of the ligand, indicating for the first time the potential of G4 to serve as a target for photopharmacological strategies.MPO thanks the Bristol Chemical Synthesis Centre forDoctoral Training, funded by EPSRC (EP/L015366/1) and theUniversity of Bristol, for a PhD studentship, JRS acknowledges aMSCA fellowship (project 843720-BioNanoProbes). SH and AJMthanks EPSRC for support (grant numbers EP/M015378/1 andEP/M022609/1). This work was carried out using the computationalfacilities of the Advanced Computing Research Centre, University ofBristol – http://www.bris.ac.uk/acrc/ SS thanks the Bristol Centre ForFunctional Nanomaterials (EPSRC EP/L016648/1). JCMS thanks theSpanish Ministerio de Economı ́a y Competitividad (Grant CTQ2015-64275-P and RTI2018-099036-B-I00). MCG thanks the EuropeanResearch Council (ERC-COG: 64823

Ligand-induced unfolding mechanism of an RNA G-quadruplex

The cationic porphyrin, TMPyP4, is a well-established DNA G-quadruplex (G4) binding ligand that can stabilize different topologies via multiple binding modes. However, TMPyP4 has completely opposite destabilizing and unwinding effect on RNA G4 structures. The structural mechanisms that mediate RNA G4 unfolding remains unknown. Here, we report on the TMPyP4-induced RNA G4 unfolding mechanism studied by well-tempered metadynamics (WT-MetaD) with supporting biophysical experiments. The simulations predict a two-state mechanism of TMPyP4 interaction via a groove-bound and a top-face bound conformation. The dynamics of TMPyP4 stacking on the top tetrad disrupts Hoogsteen H-bonds between guanine bases resulting in the consecutive TMPyP4 intercalation from top-to-bottom G-tetrads. The results reveal a striking correlation between computational and experimental approaches and validate WT-MetaD simulations as a powerful tool for studying RNA G4-ligand interactions

Theoretical Study of Non-covalent Interaction from small molecules to Biomolecules

xv Abstract The aim of this thesis is to investigate the accurate stabilization energy and binding free energy in various non-covalent complexes spanned from small organic molecules to biomolecules. Non-covalent interactions such as H-bonds, π...π stacking and halogen bonds are mainly responsible for understanding of most biological processes, such as small molecule interactions with surface, protein-ligand binding in the cell machinery, etc. In the thesis, different non-covalent complexes such as graphene…electron donor- acceptor complexes, DNA base pair interaction with silica surface, etc, were investigated. The reference stabilization energies were calculated at ab initio level, e.g., CCSD(T)/CBS method wherever possible. On the other hand, more approximated scaled MP2 method (MP2.5/CBS/6-31G*(0.25)) is taken as reference instead of CCSD(T)/CBS due to the size of the complexes. Further, the DFT and MM energies were also tested towards the reference one. The knowledge of non- covalent interaction is required for rationalizing of any association processes in nature which requires accurate description of the free energy change. The state-of- the-art molecular dynamics simulation in full atomic scale and biased metadynamics free energy method is used for binding free energy calculations. The well tempered..

Genetic and Functional Diversities of Bacterial Communities in the Rhizosphere of Arachis Hypogaea

Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alphaproteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes.Most bacterial isolates from the groundnutrhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system

A novel high symmetry interlocking micro-architecture design for polymer composites with improved mechanical properties

Development and design of novel materials based on their micro-structural arrangements are being intensely investigated due to their wide range of real and potential applications. One of the key objectives of such design is to achieve multiple properties, which are often competing in nature (such as high stiffness-high damping, high strength-high toughness etc.), within a single composite material. In the present work we propose a novel interlocking micro-architecture design to achieve high symmetry in a plane within a composite. The present study shows that constraining a very low volume fraction of high damping polymer within this micro-architecture, together with a stiff polymer, results in a simultaneously high stiffness and high damping polymer composite. The proposed micro-architecture design possesses high symmetry that is not commonly found in fiber-reinforced polymer composites. The interlocking feature avoids use of extra adhesives for holding two adjacent building blocks. Finite element simulations are performed by considering the micro-architecture made of two widely used polymeric materials such as polymethyl methacrylate (PMMA as the stiffer building block) and polyurethane (PU as the soft viscous material). Our numerical predictions show remarkable stiffness and damping properties for the design over a wide range of frequencies. Simulations are also performed considering contact between two polymer interfaces to establish the fact that the geometric interlocking works well without any use of adhesive for holding the blocks together. Further simulations are performed under high frequency impulse pressure loading to study dynamic wave propagation through the micro-architecture that shows the near-isotropic response of the proposed micro-architecture

A NOVEL ARCHITECTURED POLYMER COMPOSITE FOR NEAR ISOTROPIC CHARACTERISTICS AND IMPROVED COMBINED STIFFNESS€”DAMPING PROPERTIES

A novel micro-architecture is proposed to design multifunctional composite with simultaneous stiffness and damping capabilities. The micro-architecture utilizes the hexagonal symmetry in order to manifest in-plane isotropy in the properties. The micro-architectured composite is made of circular gear and triangular shaped stiff material and a layer of viscoelastic material in between them. The gear and triangular shaped building blocks is designed to utilize the interlocking mechanism for them to transfer load through the interlock under tensile load. The combination of the stiff and the viscoelastic material in the composite yields to both high-stiffness and highdamping, which otherwise are competing in engineering materials. Numerical experiments are performed in order to characterize the design and quantify the performance parameters of the micro-architectured composite using PMMA as the stiff materials and PU as the viscoelastic materials. Quasi-static tensile behavior and damping performance under low frequency load is predicted using finite element analysis. The thickness of the PU layer is varied to investigate the effect of PU volume fraction. The simulation results show that with approximately 7 percent volume fraction of PU the composite retains 55 percent stiffness of PMMA. With the increase in PU volume fraction (layer thickness), the damping of the composite increases and the stiffness decreases. The composite achieves 10 and 50 percent damping of PU with only 7 and 30 volume percent of PU, at 10 Hz loading frequency. The combined performance (i.e. multiplication of stiffness and damping) is found to be close to Wang-Lakes line, which is notable for a polymer-polymer composite