Glycosaminoglycans (GAGs) are linear polysaccharides, built of periodically occurring disaccharide units. GAGs are ubiquitous in the extracellular matrix (ECM), where they exhibit multifarious biological activities. This diversity arises from - among others - their ability to interact with and regulate a large number of proteins, such as cytokines, chemokines, and growth factors. As of the huge variety in their chemical configuration, GAGs are further sub-classified into different types (heparin, for instance, is one of these sub-classes). Hence, GAGs are a diverse class of molecules, which surely contributes to the broadness of their spectrum of biological functions. Through varying arrangements of sulfate groups and different types of saccharide units, individual GAG molecules can establish specific atomic contacts to proteins. One of the best-studied examples is antithrombin-heparin, whose biologically relevant interaction requires a specific pentasaccharide sequence. It is valid to assume, however, that various proteins are yet to be discovered whose biological functions are in some way affected by GAGs. In other cases, and this is true for the cytokine interleukin-10 (IL-10), there are already experimental indications for a biologically relevant protein-GAG interaction, but the details are still obscure and the fundamental molecular interaction mechanism has still not been clarified. IL-10 has been shown to bind GAGs. So far, however, no structural detail about IL-10-GAG interaction is known. Function-wise, IL-10 is mainly considered to be immunosuppressive and therefore anti-inflammatory, but it in fact has the pleiotropic ability to influence the immune system in both directions, i.e. it constitutes a complex regulation system on its own. Therefore, the role of GAGs in this system is potentially substantial, but is yet to be clarified. In vitro experiments have yielded indications for GAGs being able to modulate IL-10\'s biological function, and obviously IL-10 and GAGs are simultaneously present in the ECM. This gives rise to the assumption that IL-10-GAG interaction is of biological significance, and that understanding the impact of GAGs on IL-10 biology is important - from the basic research point of view, but also for the development of therapies, potentially involving artificially designed ECMs. A promising approach for obtaining knowledge about the nature of IL-10-GAG interaction is its investigation on the structural level, i.e. the identification and characterization of the molecular interaction mechanisms that govern the IL-10-GAG system. In this PhD project it was my goal to reveal structural and molecular details about IL-10-GAG interaction with theoretical and computational means, and with the help of experiments performed by collaborators in the framework of the Collaborative Research Centre DFG Transregio 67. For achieving this, I developed three methods for the in silico investigation of protein-GAG systems in general and subsequently applied them to the IL-10-GAG system. Parts of that work have been published in scientific journals, as outlined further below. I proposed and validated a systematic approach for predicting GAG binding regions on a given protein, based on the numerical simulation and analysis of its Coulomb potential. One advantage of this method is its intrinsic ability to provide clues about the reliability of the resulting prediction. Application of this approach to IL-10 lead to the observation that its Coulomb attraction for GAGs is significantly weaker than in case of exemplary protein-GAG systems (such as FGF2-heparin). Still, a distinct IL-10-GAG binding region centered on the residues R102, R104, R106, R107 of the human IL-10 sequence was identified. This region can be assumed to play a major role in IL-10-GAG interaction, as described in chapter 3. Molecular docking methods are used to generate binding mode predictions for a given receptor-ligand system. In chapter 4, I clarify the importance of data clustering as an essential step for post-processing docking results and present a clustering methodology optimized for GAG molecules. It allows for a reproducible analysis, enabling systematic comparisons among different docking studies. The approach has become standard procedure in our research group. It has been applied in a variety of studies, and served as an essential tool for studying IL-10-GAG interaction, as described in chapter 3. Motivated by the shortcomings of classical docking approaches, especially with respect to protein-GAG systems, I worked on the development of a molecular dynamics-based docking method with less radical approximations than usually applied in classical docking. The goal was to make the computational model properly account for the special physical properties of GAGs, and to include the effects of receptor flexibility and solvation. The methodology was named Dynamic Molecular Docking (DMD) and published in the Journal of Chemical Information and Modeling-together with a validation study. The subsequent application of DMD in a variety of studies required enormous amounts of computational resources. For tackling this challenge, I established a graphics processing unit-based high-performance computing environment in our research group and developed a software framework for reliably performing DMD studies on this hardware, as well as on other computing resources of the TU Dresden. The investigation of the IL-10-GAG system via DMD was focused on the IL-10-GAG binding region predicted earlier, and made heavy usage of the optimized clustering approach named above. An important result of this endeavor is that IL-10's amino acid residue R107 significantly stands out compared to all other residues and supposedly plays a particularly important role in IL-10-GAG recognition. The collaboration with the NMR laboratory of Prof. Daniel Huster at the Universität Leipzig was fruitful: I post-processed nuclear Overhauser effect data and obtained heparin structure models, which revealed that IL-10-heparin interaction has a measurable impact on the backbone structure of the heparin molecule. These results were published in Glycobiology. In chapter 8, I propose two different scenarios about how GAG-binding to IL-10 might affect its biological function, based on the findings made in this thesis project. In conclusion, a set of methods has been developed, all of which are generically applicable for the investigation of protein-GAG systems. Regarding the IL-10-GAG system, valuable structural insights for increasing the understanding about its molecular mechanisms were derived. These observations pave the way towards unraveling GAG-mediated bioactivity of IL-10, which may then be specifically exploited, for instance in artificial ECMs for improved wound healing.

Biological degradable polymers on a basis of renewable raw materials, such as polysaccharides, represent promising alternatives to synthetic polymers used as flocculant or stabilizing agents. Polysaccharides derived from potato starch and chitosan have been modified with benzyl- and the first one with additionally cationic hydroxypropyl-trimethylammonium groups of different degrees of substitution (DS). The aim of this work was to characterize the solution properties of these novel amphiphilic polysaccharides concerning the impact of their DS on charge density, particle size, dynamic surface tension and viscosity behaviour. The work is further focused on investigations on flocculation properties of these amphiphilic polyelectrolytes in dispersions of kaolin and silica to identify the interplay between charge density and hydrophobicity. Flocculation efficiency has been evaluated via joint analysis of charge density measurements (using polyelectrolyte titration), turbidity and TOC measurements, as well as dynamic surface tension measurements applying the drop profile analysis. Particle sizes and particle size distributions have been determined by dynamic light scattering and laser diffraction methods. In addition, these amphiphilic starch derivatives have been used to remove substances which impact negatively the paper production process when using recycled paper, so called stickies. Model suspensions have been studied using a multitude of different measurement techniques with the aim to predict a “sticky potential” and to reduce containing dissolved and colloidal substances such as micro stickies. The surface activity and viscometric behaviour have been studied of solely cationic and moderately and highly substituted, amphiphilic polysaccharides in salt-free and 0.05 M NaCl aqueous solution. For the first time dynamic surface tension measurement results have been correlated with particle sizes and apparent charge density. Rheological investigation of large concentration ranges (0.01–20 g/L) was used to discuss Huggins plots and typical polyelectrolyte behaviour for all polysaccharide derivatives could be found. Overlap concentration and, in dilute aqueous solution, intrinsic viscosity could be determined. For polysaccharide solution in dilute regime semi-empirical equations of Rao and Wolf have been applied, making it possible to get insights to polyelectrolyte conformation in dependence on the DS of both substituents. It is shown that for intrinsic viscosity a change of the impact of both substituents takes place when having derivatives with enhanced hydrophobicity. Data evaluation via the ratio of both DS values had been successfully utilized and thus, the applied method has been identified as being a promising tool to compare a multitude of starch derivatives with substituents of different polarity in various degrees of substitution to get tendencies regarding overall hydrophobicity. Moderate hydrophobic substitution was found to lead to a decrease of the efficient flocculant dose and to an increase of the flocculation window width. Amphiphilic starch derivatives with high DS of hydrophobic moieties showing strong hydrophobic association are effective only at significantly higher doses, but in a broader concentration range compared to cationic starch of the same DS. Joint analysis of adsorption isotherms and flocculation test data has revealed, that the surface coverage required to induce phase separation ranges between 10 and 25 % and is minimal for amphiphilic starch derivatives. This gave the evidence of the complex mechanism of flocculation via combination of electrostatic “charge patch” interactions and bridging. Concerning sticky reduction experiments by systematically studying the interactions between the novel amphiphilic starch derivatives and the model suspension it turned out, that dynamic surface tension is a very suitable property to characterize the surface active compounds in the model suspension giving additional information about the sticky potential of waste water, e.g. white water, being a new and sensitive method to describe the parameter “hydrophobicity”. Moderate cationic and hydrophobic starch derivatives have been proved to be the most effective ones for sticky removal.