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No description available.

No description available.

It has been discovered during the past few years that demosponges of the order Verongida such as Aplysina cavernicola exhibit chitin-based skeletons. Verongida sponges are well known to produce bioactive brominated tyrosine derivatives. We could recently demonstrate that brominated compounds do not exclusively occur in the cellular matrix but also in the skeletons of the marine sponges Aplysina cavernicola and Ianthella basta. Our measurements imply that these yet unknown compounds are strongly, possibly covalently bound to the sponge skeletons. In the present work, we determined the skeletal amino acid composition of the demosponge A. cavernicola especially with respect to the presence of halogenated amino acids. The investigations of the skeletons before and after MeOH extraction confirmed that only a small amount of the brominated skeleton-bound compounds dissolves in MeOH. The main part of the brominated compounds is strongly attached to the skeletons but can be extracted for example by using Ba(OH)2. Various halogenated tyrosine derivatives were identified by GC-MS and LC-MS in these Ba(OH)2 extracts of the skeletons.

Demosponges of the order Verongida such as Ianthella basta exhibit skeletons containing spongin, a collagenous protein, and chitin. Moreover, Verongida sponges are well known to produce bioactive brominated tyrosine derivatives. We recently demonstrated that brominated compounds do not only occur in the cellular matrix but also in the skeletons of the marine sponges Aplysina cavernicola and I. basta. Further investigations revealed the amino acid composition of the skeletons of A. cavernicola including the presence of several halogenated amino acids. In the present work, we investigated the skeletal amino acid composition of the demosponge I. basta, which belongs to the Ianthellidae family, and compared it with that of A. cavernicola from the Aplysinidae family. Seventeen proteinogenic and five non-proteinogenic amino acids were detected in I. basta. Abundantly occurring amino acids like glycine and hydroxyproline show the similarity of I. basta and A. cavernicola and confirm the collagenous nature of their sponging fibers. We also detected nine halogenated tyrosines as an integral part of I. basta skeletons. Since both sponges contain a broad variety of halogenated amino acids, this seems to be characteristic for Verongida sponges. The observed differences of the amino acid composition confirm that spongin exhibits a certain degree of variability even among the members of the order Verongida.

Die Adsorption von Additiven an den Oberflächen eines Kristallisates wird als eine hauptsächliche Ursache für die Beeinflussung von Kristallwachstum und Morphologie angesehen und spielt bei vielen Kristallisationsprozessen eine entscheidende Rolle. Gerade für die Calciumsulfate, die im Millionen-Tonnen-Maßstab jährlich in Deutschland verarbeitet werden, stellt der Additiv-Einsatz einen Hauptkostenfaktor dar, während gleichzeitig die Additivwirkung mechanistisch nicht ausreichend gut verstanden und damit derzeit nicht vorhersagbar ist. Zur Erlangung eines besseren Verständnisses wurden mit Hilfe von molekulardynamischen Computersimulationen die Prozesse in den Grenzflächen zwischen festen Calciumsulfaten und wässriger Additivlösung auf atomarer Ebene analysiert. Wesentlicher Untersuchungsschwerpunkt war dabei die Rolle des polaren Lösungsmittels Wasser auf die Wechselwirkung zwischen verschiedenen ionischen Additivspezies und den Salzkristallen.:1. Einleitung und Zielsetzung 1 2. Literatur 6 2.1. Kristallstrukturen der Calciumsulfate 7 2.2. Kristallmorphologie und relevante Kristallflächen 10 2.2.1. Kristallwachstum und Morphologie der Calciumsulfate 10 2.2.2. Theoretische Methoden zur Morphologievorhersage 13 2.2.3. Morphologievorhersage für die Calciumsulfate 18 2.3. Struktur von Mineral-Wasser-Grenzflächen 20 2.3.1. Experimentelle Untersuchungen 20 2.3.2. Simulationen 25 2.4. Morphologiebeeinflussung der Calciumsulfate durch Additive 26 2.4.1. Additive für Calciumsulfate und deren Wirkungsweise 26 2.4.2. Beeinflussung der Gipsmorphologie durch Zitronensäure und Aminosäuren 28 2.5. Stand der Technik von Adsorptionssimulationen 31 2.5.1. Methodenüberblick 31 2.5.2. Molekulardynamische Adsorptionssimulationen 33 2.5.3. Modellierungen und Simulationen der Calciumsulfat-Additiv- Wechselwirkung 44 3. Methodik 47 3.1. Simulationsbasis 49 3.1.1. Randbedingungen und Annahmen 49 3.1.2. Simulationsmethoden und -parameter 51 3.1.3. Kraftfeld 55 3.1.4. Erstellen von Simulationsboxen 60 3.2. Simulationen zur Morphologievorhersage 65 3.2.1. Durchgeführte Simulationen 66 iiiInhaltsverzeichnis 3.2.2. Berechnung der Morphologie im Vakuum 68 3.2.3. Berechnung der Morphologie in Lösung 69 3.2.4. Zusammenfassung 72 3.3. Simulationen der CaSO 4 -Wasser-Grenzfläche 74 3.3.1. Durchgeführte Simulationen 74 3.3.2. Charakterisierung der Oberflächenstabilität 75 3.3.3. Strukturelle Charakterisierung der Hydratationsschichten 77 3.3.4. Kinetische Charakterisierung der Hydratationsschichten 82 3.3.5. Thermodynamische Charakterisierung der Hydratations- schichten 83 3.3.6. Zusammenfassung 87 3.4. Simulation der Adsorption 89 3.4.1. Durchgeführte Simulationen 89 3.4.2. Berechnung der Adsorptionsenergie 103 3.4.3. Berechnung der Freien Adsorptionsenergie 106 3.4.4. Zusammenfassung 112 4. Ergebnisse und Diskussion 114 4.1. Morphologievorhersage und Flächenauswahl 115 4.1.1. Die Morphologie im Vakuum 115 4.1.2. Die Morphologie in Lösung 123 4.1.3. Flächenauswahl 126 4.2. Die Mineral-Wasser-Grenzfläche 127 4.2.1. Oberflächenstabilität 127 4.2.2. Strukturelle Charakterisierung der Hydratationsschichten 133 4.2.3. Kinetische Charakterisierung der Hydratationsschichten 153 4.2.4. Thermodynamische Charakterisierung der Hydratations- schichten 162 4.2.5. Einfluss der Simulationsmethodik 166 4.3. Die Adsorption 167 4.3.1. Einfluss des Lösungsmittels 167 4.3.2. Einfluss des Additivs 176 4.3.3. Einfluss der Fläche 186 4.3.4. Einfluss der Simulationsmethodik 201 5. Zusammenfassung und Ausblick 211 ivInhaltsverzeichnis Abkürzungsverzeichnis V-1 Literaturverzeichnis V-6 Abbildungsverzeichnis V-34 Tabellenverzeichnis V-38 A. Methoden A-1 A.1. Erstellen von Simulationsboxen mit Kristallschichten A-2 A.1.1. Randbedingungen A-2 A.1.2. Erstellen der Elementarzelle A-3 A.1.3. Erstellen der Oberflächenelementarzelle A-3 A.2. Voruntersuchungen zur Adsorption A-8 A.2.1. Ausgangssituation A-8 A.2.2. Finden energetisch günstiger Konformationen A-11 A.2.3. Berechnung der Freien Adsorptionsenergie A-13 A.2.4. Berechnung der Adsorptionsenergie A-23 A.3. Clusteranalyse A-24 B. Tabellen B-1 C. Abbildungen C-1

The progress in genome research demands for an adequate infrastructure to analyze the data sets. Database systems reflect a key technology to organize data and speed up the analysis process. This paper discusses the role of a relational database system based on the problem of finding frequent substructures in multi-dimensional protein databases. The specific problem consists of producing a set of association rules regarding frequent substructures with different lengths and gaps between the amino acid residues of a protein. From a database point of view, the process of finding association rules building the base for a more in-depth analysis of the data material is split into two parts. The first part performs a discretization of the conformational angle space of a single amino acid residue by computing the nearest neighbor of a given set of representatives. The second part consists in adapting a well-known association rule algorithm to determine the frequent substructures. Both steps within this comprehensive analysis task requires substantial support of the underlying database in order to reduce the programming overhead at the application level.

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Proteins have an indispensable role in the cell. They carry out a wide variety of structural, catalytic and signaling functions in all known biological systems. To perform their biological functions, proteins establish interactions with other bioorganic molecules including other proteins. Therefore, protein-protein interactions is one of the central topics in molecular biology. My thesis is devoted to three different topics in the field of protein-protein interactions. The first one focuses on solvent contribution to protein interfaces as it is an important component of protein complexes. The second topic discloses the structural and functional potential of fluorine's unique properties, which are attractive for protein design and engineering not feasible within the scope of canonical amino acids. The last part of this thesis is a study of the impact of charged amino acid residues within the hydrophobic interface of a coiled-coil system, which is one of the well-established model systems for protein-protein interactions studies. I. The majority of proteins interact in vivo in solution, thus studies of solvent impact on protein-protein interactions could be crucial for understanding many processes in the cell. However, though solvent is known to be very important for protein-protein interactions in terms of structure, dynamics and energetics, its effects are often disregarded in computational studies because a detailed solvent description requires complex and computationally demanding approaches. As a consequence, many protein residues, which establish water-mediated interactions, are neither considered in an interface definition. In the previous work carried out in our group the protein interfaces database (SCOWLP) has been developed. This database takes into account interfacial solvent and based on this classifies all interfacial protein residues of the PDB into three classes based on their interacting properties: dry (direct interaction), dual (direct and water-mediated interactions), and wet spots (residues interacting only through one water molecule). To define an interaction SCOWLP considers a donor–acceptor distance for hydrogen bonds of 3.2 Å, for salt bridges of 4 Å, and for van der Waals contacts the sum of the van der Waals radii of the interacting atoms. In previous studies of the group, statistical analysis of a non-redundant protein structure dataset showed that 40.1% of the interfacial residues participate in water-mediated interactions, and that 14.5% of the total residues in interfaces are wet spots. Moreover, wet spots have been shown to display similar characteristics to residues contacting water molecules in cores or cavities of proteins. The goals of this part of the thesis were: 1. to characterize the impact of solvent in protein-protein interactions 2. to elucidate possible effects of solvent inclusion into the correlated mutations approach for protein contacts prediction To study solvent impact on protein interfaces a molecular dynamics (MD) approach has been used. This part of the work is elaborated in section 2.1 of this thesis. We have characterized properties of water-mediated protein interactions at residue and solvent level. For this purpose, an MD analysis of 17 representative complexes from SH3 and immunoglobulin protein families has been performed. We have shown that the interfacial residues interacting through a single water molecule (wet spots) are energetically and dynamically very similar to other interfacial residues. At the same time, water molecules mediating protein interactions have been found to be significantly less mobile than surface solvent in terms of residence time. Calculated free energies indicate that these water molecules should significantly affect formation and stability of a protein-protein complex. The results obtained in this part of the work also suggest that water molecules in protein interfaces contribute to the conservation of protein interactions by allowing more sequence variability in the interacting partners, which has important implications for the use of the correlated mutations concept in protein interactions studies. This concept is based on the assumption that interacting protein residues co-evolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. The study presented in section 2.2 has been carried out to prove that an explicit introduction of solvent into the correlated mutations concept indeed yields qualitative improvement of existing approaches. For this, we have used the data on interfacial solvent obtained from the SCOWLP database (the whole PDB) to construct a “wet” similarity matrix. This matrix has been used for prediction of protein contacts together with a well-established “dry” matrix. We have analyzed two datasets containing 50 domains and 10 domain pairs, and have compared the results obtained by using several combinations of both “dry” and “wet” matrices. We have found that for predictions for both intra- and interdomain contacts the introduction of a combination of a “dry” and a “wet” similarity matrix improves the predictions in comparison to the “dry” one alone. Our analysis opens up the idea that the consideration of water may have an impact on the improvement of the contact predictions obtained by correlated mutations approaches. There are two principally novel aspects in this study in the context of the used correlated mutations methodology : i) the first introduction of solvent explicitly into the correlated mutations approach; ii) the use of the definition of protein-protein interfaces, which is essentially different from many other works in the field because of taking into account physico-chemical properties of amino acids and not being exclusively based on distance cut-offs. II. The second part of the thesis is focused on properties of fluorinated amino acids in protein environments. In general, non-canonical amino acids with newly designed side-chain functionalities are powerful tools that can be used to improve structural, catalytic, kinetic and thermodynamic properties of peptides and proteins, which otherwise are not feasible within the use of canonical amino acids. In this context fluorinated amino acids have increasingly gained in importance in protein chemistry because of fluorine's unique properties: high electronegativity and a small atomic size. Despite the wide use of fluorine in drug design, properties of fluorine in protein environments have not been yet extensively studied. The aims of this part of the dissertation were: 1. to analyze the basic properties of fluorinated amino acids such as electrostatic and geometric characteristics, hydrogen bonding abilities, hydration properties and conformational preferences (section 3.1) 2. to describe the behavior of fluorinated amino acids in systems emulating protein environments (section 3.2, section 3.3) First, to characterize fluorinated amino acids side chains we have used fluorinated ethane derivatives as their simplified models and applied a quantum mechanics approach. Properties such as charge distribution, dipole moments, volumes and size of the fluoromethylated groups within the model have been characterized. Hydrogen bonding properties of these groups have been compared with the groups typically presented in natural protein environments. We have shown that hydrogen and fluorine atoms within these fluoromethylated groups are weak hydrogen bond donors and acceptors. Nevertheless they should not be disregarded for applications in protein engineering. Then, we have implemented four fluorinated L-amino acids for the AMBER force field and characterized their conformational and hydration properties at the MD level. We have found that hydrophobicity of fluorinated side chains grows with the number of fluorine atoms and could be explained in terms of high electronegativity of fluorine atoms and spacial demand of fluorinated side-chains. These data on hydration agrees with the results obtained in the experimental work performed by our collaborators. We have rationally engineered systems that allow us to study fluorine properties and extract results that could be extrapolated to proteins. For this, we have emulated protein environments by introducing fluorinated amino acids into a parallel coiled-coil and enzyme-ligand chymotrypsin systems. The results on fluorination effect on coiled-coil dimerization and substrate affinities in the chymotrypsin active site obtained by MD, molecular docking and free energy calculations are in strong agreement with experimental data obtained by our collaborators. In particular, we have shown that fluorine content and position of fluorination can considerably change the polarity and steric properties of an amino acid side chain and, thus, can influence the properties that a fluorinated amino acid reveals within a native protein environment. III. Coiled-coils typically consist of two to five right-handed α-helices that wrap around each other to form a left-handed superhelix. The interface of two α-helices is usually represented by hydrophobic residues. However, the analysis of protein databases revealed that in natural occurring proteins up to 20% of these positions are populated by polar and charged residues. The impact of these residues on stability of coiled-coil system is not clear. MD simulations together with free energy calculations have been utilized to estimate favourable interaction partners for uncommon amino acids within the hydrophobic core of coiled-coils (Chapter 4). Based on these data, the best hits among binding partners for one strand of a coiled-coil bearing a charged amino acid in a central hydrophobic core position have been selected. Computational data have been in agreement with the results obtained by our collaborators, who applied phage display technology and CD spectroscopy. This combination of theoretical and experimental approaches allowed to get a deeper insight into the stability of the coiled-coil system. To conclude, this thesis widens existing concepts of protein structural biology in three areas of its current importance. We expand on the role of solvent in protein interfaces, which contributes to the knowledge of physico-chemical properties underlying protein-protein interactions. We develop a deeper insight into the understanding of the fluorine's impact upon its introduction into protein environments, which may assist in exploiting the full potential of fluorine's unique properties for applications in the field of protein engineering and drug design. Finally we investigate the mechanisms underlying coiled-coil system folding. The results presented in the thesis are of definite importance for possible applications (e.g. introduction of solvent explicitly into the scoring function) into protein folding, docking and rational design methods. The dissertation consists of four chapters: ● Chapter 1 contains an introduction to the topic of protein-protein interactions including basic concepts and an overview of the present state of research in the field. ● Chapter 2 focuses on the studies of the role of solvent in protein interfaces. ● Chapter 3 is devoted to the work on fluorinated amino acids in protein environments. ● Chapter 4 describes the study of coiled-coils folding properties. The experimental parts presented in Chapters 3 and 4 of this thesis have been performed by our collaborators at FU Berlin. Sections 2.1, 2.2, 3.1, 3.2 and Chapter 4 have been submitted/published in peer-reviewed international journals. Their organization follows a standard research article structure: Abstract, Introduction, Methodology, Results and discussion, and Conclusions. Section 3.3, though not published yet, is also organized in the same way. The literature references are summed up together at the end of the thesis to avoid redundancy within different chapters.