No description available.

No description available.

The characterization of biomolecules and biomolecular complexes represents an area of significant research activity because of the link between structure and function. Drug development relies on structural information in order to target certain domains. Many traditional biochemical techniques, however, are limited by their ability to characterize only certain stable forms of a molecule. As a result, multidimensional approaches, such as ion mobility mass spectrometry coupled to mass spectrometry (IMS-MS), are becoming very attractive tools as they provide fast separation, detection and identification of molecules, in addition to providing three-dimensional shape for structural elucidation. The present work expands the use and application of trapped ion mobility spectrometry-coupled to mass spectrometry (TIMS-MS) by analyzing a range of biomolecules (including proteoforms, intrinsically disordered peptides, DNA and molecular complexes). The aim is to i) evaluate the TIMS platform measuring sensitivity, selectivity, and separation of targeted compounds, ii) pioneer new applications of TIMS for a more efficient and higher throughput methodologies for identification and characterization of biomolecular ions, and iii) characterize the dynamics of selected biomolecules for insight into the folding pathways and the intra-or intermolecular interactions that define their conformational space.

A mitoxantrona (MXT) é um antineoplásico utilizado no tratamento de tumores como leucemias, linfoma não-Hodgkin e câncer de mama e próstata. Ela é classificada como uma antracenodiona, sendo um análogo estrutural das antraciclinas, como a doxorrubicina (DOX), cujo mecanismo de ação é baseado na inibição da enzima topoisomerase II (Topo II), através da formação dos complexos estabilizados Topo II-DNA. As antraciclinas e a MXT também são capazes de formar lesões do tipo adutos, pontes intercadeias de DNA (interstrand crosslink – ICL) e espécies reativas de oxigênio (ERO). Estudos têm demonstrado que a via de reparo por excisão de nucleotídeos (Nucleotide Excision Repair – NER) está envolvido na remoção de lesões no DNA induzidas pela DOX. Considerando as similaridades estruturais e de mecanismo de ação entre a MXT e a DOX, o objetivo deste trabalho foi avaliar a influência da via NER na citotoxicidade da MXT, a fim de elucidar possíveis mecanismos envolvidos na resistência tumoral a esta droga. Os resultados encontrados demonstraram que células deficientes na via NER (XPA, XPD, XPC e CSB) apresentam elevada sensibilidade a MXT comparadas a células proficientes em reparo (MRC5). Apesar disso, células CSB (deficientes na subvia associada à transcrição - Transcription coupled – TCR-NER) são mais sensíveis a MXT que células XPC (deficientes na subvia de reparo global do genoma – Global genome repair – GGR-NER) e também apresentam diferenças no perfil de ciclo celular, síntese de DNA e formação dos complexos Topo II-DNA após tratamento com MXT. Células XPC, da mesma forma que as células proficientes MRC5 apresentam parada de ciclo celular em G2/M, recuperação da síntese de DNA e sinal semelhante para formação dos complexos Topo II-DNA, enquanto células CSB apresentam acúmulo de células na fase S, diminuição na síntese de DNA e sinal mais intenso para formação dos complexos Topo II-DNA. Além disso, a complementação das células CSB com a proteína CSB recuperou a resistência das células a MXT e também diminuiu a intensidade do sinal dos complexos Topo II-DNA. Estes resultados indicaram que a via NER está envolvida na resistência das células ao tratamento com MXT e que a proteína CSB ou a subvia TCR-NER tem um papel chave no processamento dos complexos Topo II-DNA. / Mitoxantrone (MXT) is an antineoplastic drug used in treatment of tumors like leukemia, non-Hodgkin lymphoma and breast and prostate cancer. It is classified as an anthracenedione, being a structural analogue of anthracyclines, like doxorubicin (DOX), which action mechanism is based on topoisomerase II (Topo II) inhibition and formation of stabilized Topo II-DNA complexes. Anthracyclines and MXT also can form lesions like DNA adducts, interstrand crosslinks (ICL) and reactive oxygen species (ROS). Studies have shown that nucleotide excision repair (NER) pathway is involved in removal of lesions induced by DOX. Due to structural and action mechanism similarities between MXT and DOX, the aim of this work was to evaluate the influence of NER pathway in cytotoxicity of MXT, in order to elucidate possible mechanisms involved in tumor resistance to this drug. The results demonstrated that NER-deficient cells (XPA, XPD, XPC and CSB) show high sensitivity to MXT compared to repair proficient cells (MRC5). However, CSB cells (deficient in Transcription coupled repair – TCR) were more sensitive to MXT than XPC cells (deficient in Global genome repair – GGR) and also showed differences in cell cycle, DNA synthesis and Topo II-DNA complexes formation upon MXT treatment. XPC cells, in the same way as MRC5 proficient cells present G2/M cell cycle arrest, DNA synthesis recovery and similar signal for Topo II-DNA complexes formation, while CSB cells present accumulation of cells in S phase, reduced DNA synthesis and a more intense signal for Topo II-DNA complexes formation. Moreover, CSB cells complementation recovery MXT-resistance and also diminished Topo II-DNA complexes signal intensity. These results indicate that NER pathway is involved in cells resistance to MXT treatment and that CSB protein or TCR-NER sub pathway has a key role in processing of MXT induced Topo II-DNA complexes.

A mitoxantrona (MXT) é um antineoplásico utilizado no tratamento de tumores como leucemias, linfoma não-Hodgkin e câncer de mama e próstata. Ela é classificada como uma antracenodiona, sendo um análogo estrutural das antraciclinas, como a doxorrubicina (DOX), cujo mecanismo de ação é baseado na inibição da enzima topoisomerase II (Topo II), através da formação dos complexos estabilizados Topo II-DNA. As antraciclinas e a MXT também são capazes de formar lesões do tipo adutos, pontes intercadeias de DNA (interstrand crosslink – ICL) e espécies reativas de oxigênio (ERO). Estudos têm demonstrado que a via de reparo por excisão de nucleotídeos (Nucleotide Excision Repair – NER) está envolvido na remoção de lesões no DNA induzidas pela DOX. Considerando as similaridades estruturais e de mecanismo de ação entre a MXT e a DOX, o objetivo deste trabalho foi avaliar a influência da via NER na citotoxicidade da MXT, a fim de elucidar possíveis mecanismos envolvidos na resistência tumoral a esta droga. Os resultados encontrados demonstraram que células deficientes na via NER (XPA, XPD, XPC e CSB) apresentam elevada sensibilidade a MXT comparadas a células proficientes em reparo (MRC5). Apesar disso, células CSB (deficientes na subvia associada à transcrição - Transcription coupled – TCR-NER) são mais sensíveis a MXT que células XPC (deficientes na subvia de reparo global do genoma – Global genome repair – GGR-NER) e também apresentam diferenças no perfil de ciclo celular, síntese de DNA e formação dos complexos Topo II-DNA após tratamento com MXT. Células XPC, da mesma forma que as células proficientes MRC5 apresentam parada de ciclo celular em G2/M, recuperação da síntese de DNA e sinal semelhante para formação dos complexos Topo II-DNA, enquanto células CSB apresentam acúmulo de células na fase S, diminuição na síntese de DNA e sinal mais intenso para formação dos complexos Topo II-DNA. Além disso, a complementação das células CSB com a proteína CSB recuperou a resistência das células a MXT e também diminuiu a intensidade do sinal dos complexos Topo II-DNA. Estes resultados indicaram que a via NER está envolvida na resistência das células ao tratamento com MXT e que a proteína CSB ou a subvia TCR-NER tem um papel chave no processamento dos complexos Topo II-DNA. / Mitoxantrone (MXT) is an antineoplastic drug used in treatment of tumors like leukemia, non-Hodgkin lymphoma and breast and prostate cancer. It is classified as an anthracenedione, being a structural analogue of anthracyclines, like doxorubicin (DOX), which action mechanism is based on topoisomerase II (Topo II) inhibition and formation of stabilized Topo II-DNA complexes. Anthracyclines and MXT also can form lesions like DNA adducts, interstrand crosslinks (ICL) and reactive oxygen species (ROS). Studies have shown that nucleotide excision repair (NER) pathway is involved in removal of lesions induced by DOX. Due to structural and action mechanism similarities between MXT and DOX, the aim of this work was to evaluate the influence of NER pathway in cytotoxicity of MXT, in order to elucidate possible mechanisms involved in tumor resistance to this drug. The results demonstrated that NER-deficient cells (XPA, XPD, XPC and CSB) show high sensitivity to MXT compared to repair proficient cells (MRC5). However, CSB cells (deficient in Transcription coupled repair – TCR) were more sensitive to MXT than XPC cells (deficient in Global genome repair – GGR) and also showed differences in cell cycle, DNA synthesis and Topo II-DNA complexes formation upon MXT treatment. XPC cells, in the same way as MRC5 proficient cells present G2/M cell cycle arrest, DNA synthesis recovery and similar signal for Topo II-DNA complexes formation, while CSB cells present accumulation of cells in S phase, reduced DNA synthesis and a more intense signal for Topo II-DNA complexes formation. Moreover, CSB cells complementation recovery MXT-resistance and also diminished Topo II-DNA complexes signal intensity. These results indicate that NER pathway is involved in cells resistance to MXT treatment and that CSB protein or TCR-NER sub pathway has a key role in processing of MXT induced Topo II-DNA complexes.

A mitoxantrona (MXT) é um antineoplásico utilizado no tratamento de tumores como leucemias, linfoma não-Hodgkin e câncer de mama e próstata. Ela é classificada como uma antracenodiona, sendo um análogo estrutural das antraciclinas, como a doxorrubicina (DOX), cujo mecanismo de ação é baseado na inibição da enzima topoisomerase II (Topo II), através da formação dos complexos estabilizados Topo II-DNA. As antraciclinas e a MXT também são capazes de formar lesões do tipo adutos, pontes intercadeias de DNA (interstrand crosslink – ICL) e espécies reativas de oxigênio (ERO). Estudos têm demonstrado que a via de reparo por excisão de nucleotídeos (Nucleotide Excision Repair – NER) está envolvido na remoção de lesões no DNA induzidas pela DOX. Considerando as similaridades estruturais e de mecanismo de ação entre a MXT e a DOX, o objetivo deste trabalho foi avaliar a influência da via NER na citotoxicidade da MXT, a fim de elucidar possíveis mecanismos envolvidos na resistência tumoral a esta droga. Os resultados encontrados demonstraram que células deficientes na via NER (XPA, XPD, XPC e CSB) apresentam elevada sensibilidade a MXT comparadas a células proficientes em reparo (MRC5). Apesar disso, células CSB (deficientes na subvia associada à transcrição - Transcription coupled – TCR-NER) são mais sensíveis a MXT que células XPC (deficientes na subvia de reparo global do genoma – Global genome repair – GGR-NER) e também apresentam diferenças no perfil de ciclo celular, síntese de DNA e formação dos complexos Topo II-DNA após tratamento com MXT. Células XPC, da mesma forma que as células proficientes MRC5 apresentam parada de ciclo celular em G2/M, recuperação da síntese de DNA e sinal semelhante para formação dos complexos Topo II-DNA, enquanto células CSB apresentam acúmulo de células na fase S, diminuição na síntese de DNA e sinal mais intenso para formação dos complexos Topo II-DNA. Além disso, a complementação das células CSB com a proteína CSB recuperou a resistência das células a MXT e também diminuiu a intensidade do sinal dos complexos Topo II-DNA. Estes resultados indicaram que a via NER está envolvida na resistência das células ao tratamento com MXT e que a proteína CSB ou a subvia TCR-NER tem um papel chave no processamento dos complexos Topo II-DNA. / Mitoxantrone (MXT) is an antineoplastic drug used in treatment of tumors like leukemia, non-Hodgkin lymphoma and breast and prostate cancer. It is classified as an anthracenedione, being a structural analogue of anthracyclines, like doxorubicin (DOX), which action mechanism is based on topoisomerase II (Topo II) inhibition and formation of stabilized Topo II-DNA complexes. Anthracyclines and MXT also can form lesions like DNA adducts, interstrand crosslinks (ICL) and reactive oxygen species (ROS). Studies have shown that nucleotide excision repair (NER) pathway is involved in removal of lesions induced by DOX. Due to structural and action mechanism similarities between MXT and DOX, the aim of this work was to evaluate the influence of NER pathway in cytotoxicity of MXT, in order to elucidate possible mechanisms involved in tumor resistance to this drug. The results demonstrated that NER-deficient cells (XPA, XPD, XPC and CSB) show high sensitivity to MXT compared to repair proficient cells (MRC5). However, CSB cells (deficient in Transcription coupled repair – TCR) were more sensitive to MXT than XPC cells (deficient in Global genome repair – GGR) and also showed differences in cell cycle, DNA synthesis and Topo II-DNA complexes formation upon MXT treatment. XPC cells, in the same way as MRC5 proficient cells present G2/M cell cycle arrest, DNA synthesis recovery and similar signal for Topo II-DNA complexes formation, while CSB cells present accumulation of cells in S phase, reduced DNA synthesis and a more intense signal for Topo II-DNA complexes formation. Moreover, CSB cells complementation recovery MXT-resistance and also diminished Topo II-DNA complexes signal intensity. These results indicate that NER pathway is involved in cells resistance to MXT treatment and that CSB protein or TCR-NER sub pathway has a key role in processing of MXT induced Topo II-DNA complexes.

This work explores the equilibrium structure and thermodynamic phase behavior of complexes formed by charged polymer chains (polyelectrolytes) and oppositely charged spheres (macroions). Polyelectrolyte-macroion complexes form a common pattern in soft-matter physics, chemistry and biology, and enter in numerous technological applications as well. From a fundamental point of view, such complexes are interesting in that they combine the subtle interplay between electrostatic interactions and elastic as well as entropic effects due to conformational changes of the polymer chain, giving rise to a wide range of structural properties. This forms the central theme of theoretical studies presented in this thesis, which concentrate on a number of different problems involving strongly coupled complexes, i.e. complexes that are characterized by a large adsorption energy and small chain fluctuations. <br><br> In the first part, a global analysis of the structural phase behavior of a single polyelectrolyte-macroion complex is presented based on a dimensionless representation, yielding results that cover a wide range of realistic system parameters. Emphasize is made on the interplay between the effects due to the polyelectrolytes chain length, salt concentration and the macroion charge as well as the mechanical chain persistence length. The results are summarized into generic phase diagrams characterizing the wrapping-dewrapping behavior of a polyelectrolyte chain on a macroion. A fully wrapped chain state is typically obtained at intermediate salt concentrations and chain lengths, where the amount of polyelectrolyte charge adsorbed on the macroion typically exceeds the bare macroion charge leading thus to a highly overcharged complex. <br><br> Perhaps the most striking features occur when a single long polyelectrolyte chain is complexed with many oppositely charged spheres. In biology, such complexes form between DNA (which carries the cell's genetic information) and small oppositely charged histone proteins serving as an efficient mechanism for packing a huge amount of DNA into the micron-size cell nucleus in eucaryotic cells. The resultant complex fiber, known as the chromatin fiber, appears with a diameter of 30~nm under physiological conditions. Recent experiments indicate a zig-zag spatial arrangement for individual DNA-histone complexes (nucleosome core particles) along the chromatin fiber. A numerical method is introduced in this thesis based on a simple generic chain-sphere cell model that enables one to investigate the mechanism of fiber formation on a systematic level by incorporating electrostatic and elastic contributions. As will be shown, stable complex fibers exhibit an impressive variety of structures including zig-zag, solenoidal and beads-on-a-string patterns, depending on system parameters such as salt concentration, sphere charge as well as the chain contour length (per sphere). The present results predict fibers of compact zig-zag structure within the physiologically relevant regime with a diameter of about 30~nm, when DNA-histone parameters are adopted. <br><br> In the next part, a numerical method is developed in order to investigate the role of thermal fluctuations on the structure and thermodynamic phase behavior of polyelectrolyte-macroion complexes. This is based on a saddle-point approximation, which allows to describe the experimentally observed reaction (or complexation) equilibrium in a dilute solution of polyelectrolytes and macroions on a systematic level. This equilibrium is determined by the entropy loss a single polyelectrolyte chain suffers as it binds to an oppositely charged macroion. This latter quantity can be calculated from the spectrum of polyelectrolyte fluctuations around a macroion, which is determined by means of a normal-mode analysis. Thereby, a stability phase diagram is obtained, which exhibits qualitative agreement with experimental findings. <br><br> At elevated complex concentrations, one needs to account for the inter-complex interactions as well. It will be shown that at small separations, complexes undergo structural changes in such a way that positive patches from one complex match up with negative patches on the other. Furthermore, one of the polyelectrolyte chains may bridge between the two complexes. These mechanisms lead to a strong inter-complex attraction. As a result, the second virial coefficient associated with the inter-complex interaction becomes negative at intermediate salt concentrations in qualitative agreement with recent experiments on solutions of nucleosome core particles. / In dieser Arbeit werden Gleichgewichtsstrukturen und die thermodynamischen Phasen von Komplexen aus geladenen Polymeren (Polyelektrolyten) und entgegengesetzt geladenen Kugeln (Makroionen) untersucht. Polyelektrolyt-Makroion-Komplexe bilden ein grundlegendes und wiederkehrendes Prinzip in der Physik weicher Materie sowie in Chemie und Biologie. In zahlreichen technologischen Prozessen finden sich ebenfalls Anwendungsbeispiele für derartige Komplexe. Zusätzlich zu ihrem häufigen Auftreten sind sie aufgrund ihrer Vielfalt von strukturellen Eigenschaften von grundlegendem Interesse. Diese Vielfalt wird durch ein Zusammenspiel von elektrostatischen Wechselwirkungen sowie elastischen und entropischen Effekten aufgrund von Konformationsänderungen in der Polymerkette bedingt und bildet das zentrale Thema der theoretischen Studien, die mit dieser Arbeit vorgelegt werden. Verschiedene Strukturen und Prozesse, die stark gekoppelte Komplexe beinhalten - das sind solche, für die eine hohe Adsorptionsenergie und geringe Fluktuationen in den Polymerketten charakteristisch sind -, bilden das Hauptthema der Arbeit. <br><br> Basierend auf einer dimensionslosen Darstellung wird im ersten Teil der Arbeit in einer umfassenden Analyse das strukturelle Phasenverhalten einzelner Polyelektrolyt-Makroion-Komplexe behandelt. Der Schwerpunkt wird hier auf das Wechselspiel zwischen Effekten aufgrund der Polyelektrolytkettenlänge, ihrer mechanischen Persistenzlänge, der Salzkonzentration und der Ladung des Makroions gelegt. Die Ergebnisse werden in allgemeinen Phasendiagrammen zusammengestellt, das das Aufwickeln-Abwickeln-Verhalten der Polyelektrolytkette auf einem Makroion beschreibt. Ein Zustand mit komplett aufgewickelter Kette tritt typischerweise bei mittleren Salzkonzentrationen und Kettenlängen auf; häufig ist hier die auf dem Makroion adsorbierte Gesamtladung des Polyelektrolyts größ er als die Ladung des nackten Makroions, d.h. es findet in hohem Grad Ladungsinversion statt. <br><br> Äußerst bemerkenswerte Eigenschaften treten auf, wenn eine einzelne lange Polyelektrolytkette viele, ihr entgegengesetzt geladene Kugeln komplexiert. In biologischen Systemen findet man solche Komplexe zwischen DNS, die die genetische Information einer Zelle trägt, und kleinen, entgegengesetzt geladenen Histonproteinen. Diese Komplexe dienen als effizienter Mechanismus, die groß e Menge an DNS im Mikrometer-groß en Zellkern eukaryotischer Zellen zu komprimieren. Die dadurch erhaltene komplexe Faser, eine Chromatinfaser, hat unter physiologischen Bedingungen einen Durchmesser von nur etwa 30~nm. Neue Experimente haben gezeigt, dass eine räumliche Zickzack-Anordnung einzelner DNA-Histon-Komplexe entlang der Chromatinfaser vorliegt. In der hier vorgelegten Arbeit wird eine numerische Methode vorgestellt, die auf einem einfachen Ketten-Kugel-Zell-Modell basiert und die die systematische Untersuchung des Mechnismus zur Faserbildung ermöglicht, wobei sowohl elektrostatische als auch elastische Wechselwirkungen berücksichtigt werden. Es wird gezeigt, dass stabile Komplexfasern in Abhängigkeit von der Salzkonzentration, der Kugelladung und der Kettenkonturlänge eine Vielfalt von Strukturen aufweisen, darunter Zickzack-, Solenoid- und Perlenkettenformen. Für physiologisch relevante Bedingungen werden mit dieser Methode für DNA-Histon-Komplexe Fasern kompakter Zickzack-Struktur mit einem Durchmesser von etwa 30~nm erhalten. <br><br> Im folgenden Teil wird eine numerische Methode entwickelt, um den Einfluss thermischer Fluktuationen auf Struktur und thermodynamisches Phasenverhalten der Polyelektrolyt-Makroion-Komplexe zu untersuchen. Basierend auf der Sattelpunktsnäherung werden die experimentell beobachteten Reaktionsgleichgewichte in verdünnten Lösungen von Polyelektrolyten und Makroionen systematisch beschrieben. Das Gleichgewicht ist durch einen Verlust an Entropie für die einzelne Polyelektrolytkette durch die Bindung an das entgegengesetzt geladene Makroion gekennzeichnet. Diese Größ e wurde aus dem Spektrum der Polyelektrolytfluktuationen um das Makroion erhalten und mittels einer Analyse der Normalmoden berechnet. Hierüber wird ein Phasendiagramm zur Stabilität der Komplexe erhalten, das qualitativ gute Übereinstimmungen mit experimentellen Ergebnissen aufweist. <br><br> Bei höheren Komplexkonzentrationen müssen auch die Wechselwirkungen zwischen den Komplexen berücksichtigt werden. Es wird gezeigt, dass sich die Struktur der Komplexe bei kleinen Abständen so ändert, dass positiv geladene Bereiche eines Komplexes mit negativ geladenen auf einem Nachbarkomplex räumlich korrelieren. Weiterhin können einzelne Polyelektrolytketten als verbrückendes Element zwischen zwei Komplexen dienen. Dieser Mechanismus führt zu starker effektiver Anziehung zwischen den Komplexen. In Übereinstimmung mit kürzlich durchgeführten Experimenten ist als Folge davon der zweite Virialkoeffizient der Wechselwirkung zwischen Komplexen bei mittleren Salzkonzentrationen negativ.

The flow of genetic information from genes to proteins is mediated through proteins which interact with the nucleic acids at several stages to successfully transmit the information from the nucleus to the cell cytoplasm. Unlike in the case of protein-protein interactions, the principles behind protein-nucleic acid interactions are still not very (Pabo and Nekludova, 2000) and efforts are still underway to arrive at the basic principles behind the specific recognition of nucleic acids by proteins (Prabakaran et al., 2006). This is mainly due to the innate complexity involved in recognition of nucleotides by proteins, where, even within a given family of DNA binding proteins, different modes of binding and recognition strategies are employed to suit their function (Luscomb et al., 2000). Such difficulties have also not made possible, a thorough classification of DNA/RNA binding proteins based on the mode of interaction as well as the specificity of recognition of the nucleotides. The availability of a large number of structures of protein-nucleic acids complexes (albeit lesser than the number of protein structures present in the PDB) in the past few decades has provided the knowledge-base for understanding the details behind their molecular mechanisms (Berman et al., 1992). Previously, studies have been carried out to characterize these interactions by analyzing specific non-covalent interactions such as hydrogen bonds, van der Walls, and hydrophobic interactions between a given amino acid and the nucleic acid (DNA, RNA) in a pair-wise manner, or through the analysis of interface areas of the protein-nucleic acid complexes (Nadassy et al., 1998; Jones et al., 1999). Though the studies have deciphered the common pairing preferences of a particular amino acid with a given nucleotide of DNA or RNA, there is little room for understanding these specificities in the context of spatial interactions at a global level from the protein-nucleic acid complexes. The representation of the amino acids and the nucleotides as components of graphs, and trying to explore the nature of the interactions at a level higher than exploring the individual pair-wise interactions, could provide greater details about the nature of these interactions and their specificity. This thesis reports the study of protein-nucleic interactions using graph and network based approaches. The evaluation of the parameters for characterizing protein-nucleic acid graphs have been carried out for the first time and these parameters have been successfully employed to capture biologically important non-covalent interactions as clusters of interacting amino acids and nucleotides from different protein-DNA and protein-RNA complexes. Graph and network based approaches are well established in the field of protein structure analysis for analyzing protein structure, stability and function (Kannan and Vishveshwara, 1999; Brinda and Vishveshwara, 2005). However, the use of graph and network principles for analyzing structures of protein-nucleic acid complexes is so far not accomplished and is being reported the first time in this thesis. The matter embodied in the thesis is presented as ten chapters. Chapter 1 lays the foundation for the study, surveying relevant literature from the field. Chapter 2 describes in detail the methods used in constructing graphs and networks from protein-nucleic acid complexes. Initially, only protein structure graphs and networks are constructed from proteins known to interact with specific DNA or RNA, and inferences with regard to nucleic acid binding and recognition were indirectly obtained . Subsequently, parameters were evaluated for representing both the interacting amino acids and the nucleotides as components of graphs and a direct evaluation of protein-DNA and Protein-RNA interactions as graphs has been carried out. Chapter 3 and 4 discuss the graph and network approaches applied to proteins from a dataset of DNA binding proteins complexed with DNA. In chapter 3, the protein structure graphs were constructed on the basis of the non-covalent interactions existing between the side chains of amino acids. Clusters of interacting side chains from the graphs were obtained using the graph spectral method. The clusters from the protein-DNA interface were analyzed in detail for the interaction geometry and biological importance (Sathyapriya and Vishveshwara, 2004). Chapter 4 also uses the same dataset of DNA binding proteins, but a network-based approach is presented. From the analysis of the protein structure networks from these DNA binding proteins, interesting observations relating the presence of highly connected nodes(or hubs) of the network to functionally important amino acids in the structure, emerged. Also, the comparison between the hubs identified from the protein-protein and the protein-DNA interfaces in terms of their amino acid composition and their connectivity are also presented (Sathyapriya and Vishveshwara, 2006) Chapter 5 and 6 deal with the graph and network applications to a specific system of protein-RNA complex (aminoacyl-tRNA synthetases) to gain insights into their interface biology based on amino acid connectivity. Chapter 5 deals with a dataset of aminoacyl-tRNA synthetase (aaRS) complexes obtained with various ligands like ATP, tRNA and L-amino acids. A graph based identification of side chain clusters from these ligand-bound aaRS structures has highlighted important features of ligand-binding at the catalytic sites of the two structurally different classes of aaRS (Class I and Class II). Side chain clusters from other regions of aaRS such as the anticodon binding region and the ligand-activation sites are discussed. A network approach is used in a specific system of aaRS(E.coli Glutaminyl-tRNA synthetase (GlnRS) complexed with its ligands, to specifically understand the effects of different ligand binding., in chapter 6. The structure networks of E.coli GlnRS in the ligand-free and different ligand-bound states are constructed. The ligand-free and the ligand-bound complexes are compared by analyzing their network properties and the presence of hubs to understand the effect of ligand-binding. These properties have elegantly captured the effects of ligand-binding to the GlnRS structure and have also provided an alternate method for comparing three dimensional structures of proteins in different ligand-bound states (Sathyapriya and Vishveshwara, 2007). In contrast to protein structure graphs (PSG), both the interacting amino acids and nucleotides (DNA/RNA) form the components of the protein-nucleic acid graphs (PNG) from protein-nucleic acid complexes. These graphs are constructed based on the non-covalent interactions existing between the side chains of the amino acids and nucleotides. After representing the interacting nucleotides and amino acids as graphs, clusters of the interacting components are identified. These clusters are the strongly interacting amino acids and nucleotides from the protein-nucleic acid complexes. These clusters can be generated at different strengths of interaction between the amino acid side chain and the nucleotide (measured in terms of its atomic connectivity) and can be used for detecting clusters of non-specific as well as specific interactions of amino acids and nucleotides. Though the methodology of graph construction and cluster identification are given in chapter 2, the details of the parameters evaluated for constructing PNG are given in chapter 7. Unlike in the previous chapters, the succeeding chapters deal exclusively with results that are obtained from the analyses of PNG. Two examples of obtaining clusters from a PNG are given, one each for a protein-DNA and a protein-RNA complex. In the first example, a nucleosome core particle is subjected to the graph based analysis and different clusters of amino acids with different regions of the DNA chain such as phosphate, deoxyribose sugar and the base are identified. Another example of aminoacyl-tRNA synthetase complexed with its cognate tRNA is used to illustrate the method with a protein-RNA complex. Further, the method of constructing and analyzing protein-nucleic acid graphs has been applied to the macromolecular machinery of the pre-translocation complex of the T. thermophilus 70S ribosome. Chapter 8 deals exclusively with the results identified from the analysis of this magnificent macromolecular ensemble. The availability of the method that can handle interactions between both amino acids and the nucleotides of the protein-nucleic acid complexes has given us the basis fro evaluating these interactions in a level higher than that of analyzing pair-wise interactions. A study on the evaluation of short hydrogen bonds(SHB) in proteins, which does not fall under the realm of the main objective of the thesis, is discussed in the Chapter 9. The short hydrogen bonds, defined by the geometrical distance and angle parameters, are identified from a non-redundant dataset of proteins. The insights into their occurrence, amino acid composition and secondary structural preferences are discussed. The SHB are present in distinct regions of protein three-dimensional structures, such that they mediate specific geometrical constraints that are necessary for stability of the structure (Sathyapriya and Vishveshwara, 2005). The significant conclusions of various studies carried out are summarized in the last chapter (Chapter 10). In conclusion, this thesis reports the analyses performed with protein-nucleic acid complexes using graph and network based methods. The parameters necessary for representing both amino acids and the nucleotides as components of a graph, are evaluated for the first time and can be used subsequently for other analyses. More importantly, the use of graph-based methods has resulted in considering the interaction between the amino acids and the nucleotides at a global level with respect to their topology of the protein-nucleic acid complexes. Such studies performed on a wide variety of protein-nucleic acid complexes could provide more insights into the details of protein-nucleic acid recognition mechanisms. The results of these studies can be used for rational design of experimental mutations that ascertain the structure-function relationships in proteins and protein-nucleic acid complexes.

(In English) The reaction of highly reactive oxygen radicals with protein solvent-accessible residues can be utilized to map protein landscape. Fast photochemical oxidation of proteins (FPOP) is an MS- based technique, which utilizes highly reactive radical species to oxidize proteins and map protein surface or its interactions with their interaction partners. In this work, FPOP was employed to study protein-DNA interactions. First, a full-length of FOXO4-DBD was successfully expressed and purified. The ability of the protein to bind its DNA-response element was verified by electrophoretic and MS-based techniques, respectively. Optimal experimental conditions were achieved to oxidize the protein itself and in the presence of DNA, respectively. Oxidized samples were analyzed by bottom-up and top-down approach. In the bottom-up experiment, modification of individual residues was precisely located and quantified. Different extend of modification was observed for protein alone and in complex with DNA. To avoid experimental artifacts analyzing multiply oxidized protein, standard bottom up approach was replaced by a progressive top-down technology. Only a singly oxidized protein ion was isolated, and further fragmented by collision-induced dissociation (CID) and electron-capture dissociation (ECD),...