+publisher:"Indian Institute of Science" +contributor:("Vishveshwara, Saraswathi")

Indian Institute of Science

1. Ghosh, Soma. A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis.

Degree: PhD, Faculty of Science, 2018, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/3519

► Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), has remained the largest killer among infectious diseases for over a century. The increasing emergence of… (more)

▼ Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), has remained the largest killer among infectious diseases for over a century. The increasing emergence of drug resistant varieties such as the multidrug resistant (MDR) and extremely drug resistant (XDR) strains are only increasing the global burden of the disease. Available statistics indicate that nearly one-third of the world’s population is infected, where the bacteria remains in the latent state but can reactivate into an actively growing stage to cause disease when the individual is immunocompromised. It is thus immensely important to rethink newer strategies for containing and combating the spread of this disease. Extraction of iron from the host cell is one of the many factors that enable the bacterium to survive in the harsh environments of the host macrophages and promote tuberculosis. Host–pathogen interactions can be interpreted as the battle of two systems, each aiming to overcome the other. From the host’s perspective, iron is essential for diverse processes such as oxygen transport, repression, detoxification and DNA synthesis. Infact, during infection, both the host and the pathogen are known to fight for the available iron, thereby influencing the outcome of the infection. It is of no surprise therefore, that many studies have investigated several components of the iron regulatory machinery of M.tb and the host. However, very few attempts have been made to study the interactions between these components and how such interactions lead to a better adapted phenotype. Such studies require exploration at multiple levels of structural and functional complexity, thereby necessitating the use of a multiscale approach. Systems biology adopts an integrated approach to study and understand the function of biological systems. It involves building large scale models based on individual biochemical interactions, followed by model validation and predictions of the system’s response to perturbations, such as a gene knock-out or exposure to drug. In multiscale modeling, an approach employed in this thesis, a particular biological phenomenon is studied at different spatiotemporal levels. Studying responses at multiple scales provides a broader picture of the communications that occur between a host and pathogen. Moreover, such an analysis also provides valuable insights into how perturbation at a particular level can elicit responses at another level and help in the identification of crucial inter-level communications that can possibly be hindered or activated for a desired physiological outcome. The broad objectives of this thesis was to obtain a comprehensive in silico understanding of mycobacterial iron homeostasis and metabolism, the influence of iron on host-pathogen interactions, identification of key players that mediate such interactions, determination of the molecular consequences of inhibiting the key players and finally the global response of M.tb to altered iron concentration. Perturbation of iron homeostasis holds a strong… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Mycobacterium Tubercolosis; Mycobacterial Iron Homeostasis; Systems Biology; Host-Pathogen Interaction (HPI) Model; Protein Structure Network; Molecular Dynamics; Tuberculosis Infections; Mycobacterium Tuberculosis Iron Metabolism; Protein Interaction Networks; Iron Dependant Repressor; IdeR-DNA Interactions; Tuberculosis - Iron Homeostasis; IdeR; Molecular Biophysics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ghosh, S. (2018). A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/3519

Chicago Manual of Style (16^th Edition):

Ghosh, Soma. “A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis.” 2018. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/3519.

MLA Handbook (7^th Edition):

Ghosh, Soma. “A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis.” 2018. Web. 18 Jan 2021.

Vancouver:

Ghosh S. A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2018. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/3519.

Council of Science Editors:

Ghosh S. A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis. [Doctoral Dissertation]. Indian Institute of Science; 2018. Available from: http://etd.iisc.ac.in/handle/2005/3519

Indian Institute of Science

2. Vijayabaskar, M S. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.

Degree: PhD, Faculty of Science, 2013, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1904

► Proteins orchestrate a number of cellular processes either alone or in concert with other biomolecules like nucleic acids, carbohydrates, and lipids. They exhibit an intrinsic… (more)

▼ Proteins orchestrate a number of cellular processes either alone or in concert with other biomolecules like nucleic acids, carbohydrates, and lipids. They exhibit an intrinsic ability to fold de novo to their functional states. The three–dimensional structure of a protein, dependent on its amino acid sequence, is important for its function. Understanding this sequence– structure–function relationship has become one of the primary goals in biophysics. Various experimental techniques like X–ray crystallography, Nuclear Magnetic Resonance (NMR), and site–directed mutagenesis have been used extensively towards this goal. Computational studies include mainly sequence based, and structure based approaches. The sequence based approaches such as sequence alignments, phylogenetic analysis, domain identification, statistical coupling analysis etc., aim at deriving meaningful information from the primary sequence of the protein. The structure based approaches, on the other hand, use structures of folded proteins. Recent advances in structure determination and efforts by various structural consortia have resulted in an enormous amount of structures available for analysis. Innumerable observations such as the allowed and disallowed regions in the conformations of a peptide unit, hydrophobic core in globular proteins, existence of regular secondary structures like helices, sheets, and turns and a limited fold space have been landmarks in understanding the characteristics of protein structures. The uniqueness of protein structure is attained through non–covalent interactions among the constituent amino acids. Analyses of protein structures show that different types of non–covalent interactions like hydrophobic interactions, hydrogen bonding, salt bridges, aromatic stacking, cation–π interactions, and solvent interactions hold protein structures together. Although such structure analyses have provided a wealth of information, they have largely been performed at a pair–wise level and an investigation involving such pair–wise interactions alone is not sufficient to capture all the determinants of protein structures, since they happen at a global level. This consideration has led to the development of graphs/networks for proteins. Graphs or Networks are a collection of nodes connected by edges. Protein Structure Networks (PSNs) can be constructed using various definitions of nodes and edges. Nodes may vary from atoms to secondary structures in Synopsis proteins, and the edges can range from simple atom–atom distances to distance between secondary structures. To study the interplay of amino acids in structure formation, the most commonly used PSNs consider amino acids as nodes. The criterion for edge definition, however, varies. PSNs can be constructed at a course grain level by considering the distances between Cα/Cβ atoms, any side–chain atoms, or the centroids of the amino acids. At a finer level, PSNs can be constructed using atomic details by considering the interaction types or by computing the extent of interaction between… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Proteins-DNA Graphs (PDGs); Protein Structures; Protein Side–chain Networks (PScNs); Protein–DNA Graphs (PDGs); Protein Energy Networks (PENs); Dps; Mycobacterium smegmatis; Structure Network Analysis; Protein Structure Networks; GraProStr; Structure Networks; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vijayabaskar, M. S. (2013). Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1904

Chicago Manual of Style (16^th Edition):

Vijayabaskar, M S. “Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.” 2013. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/1904.

MLA Handbook (7^th Edition):

Vijayabaskar, M S. “Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.” 2013. Web. 18 Jan 2021.

Vancouver:

Vijayabaskar MS. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2013. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/1904.

Council of Science Editors:

Vijayabaskar MS. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. [Doctoral Dissertation]. Indian Institute of Science; 2013. Available from: http://etd.iisc.ac.in/handle/2005/1904

Indian Institute of Science

3. Bhattacharyya, Moitrayee. Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory.

Degree: PhD, Faculty of Science, 2014, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/2341

► The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of… (more)

▼ The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of different interesting phenomena of biological relevance, ranging from enzyme specificity to allosteric communication, from selection of fold to structural organization / states of oligomerization, from half-sites-reactivity to reshuffling of the conformational free energy landscape, encompassing the dogma of sequence-structure dynamics-function of macromolecules. The role of striking an optimal balance between rigidity and flexibility in macromolecular 3D structural organisation is yet another concept that needs attention from the functional perspective. Needless to say that the variety of protein structures and conformations naturally leads to the diversity of their function and consequently many other biological functions in general. Classical models of allostery like the ‘MWC model’ or the ‘KNF model’ and the more recently proposed ‘population shift model’ have advanced our understanding of the underlying principles of long range signal transfer in macromolecules. Extensive studies have also reported the importance of the fold selection and 3D structural organisation in the context of macromolecular function. Also ligand induced conformational changes in macromolecules, both subtle and drastic, forms the basis for controlling several biological processes in an ordered manner by re-organizing the free energy landscape. The above mentioned biological phenomena have been observed from several different biochemical and biophysical approaches. Although these processes may often seem independent of each other and are associated with regulation of specialized functions in macromolecules, it is worthwhile to investigate if they share any commonality or interdependence at the detailed atomic level of the 3D structural organisation. So the nagging question is, do these diverse biological processes have a unifying theme, when probed at a level that takes into account even subtle re-orchestrations of the interactions and energetics at the protein/nucleic acid side-chain level. This is a complex problem to address and here we have made attempts to examine this problem using computational tools. Two methods have been extensively applied: Molecular Dynamics (MD) simulations and network theory and related parameters. Network theory has been extensively used in the past in several studies, ranging from analysis of social networks to systems level networks in biology (e.g., metabolic networks) and have also found applications in the varied fields of physics, economics, cartography and psychology. More recently, this concept has been applied to study the intricate details of the structural organisation in proteins, providing a local view of molecular interactions from a global perspective. On the other hand, MD simulations capture the dynamics of interactions and the conformational space associated with a given state (e.g., different… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Protein Structure; Protein - Non Covalent Interactions; Nucleic Acids- Non Covalent Interactions; Bacterial LuxS Protein; Protein-Ligand Interactions; Protein Structure Networks; Proteins - Conformation; Allosteric Proteins; Energy-Weighted Network Formalism; Proteins - Allosterism; Protein Structure Network (PSN); Protein Structure Graph (PSN); Protein Complex Energy Network (PcEN); Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bhattacharyya, M. (2014). Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/2341

Chicago Manual of Style (16^th Edition):

Bhattacharyya, Moitrayee. “Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory.” 2014. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/2341.

MLA Handbook (7^th Edition):

Bhattacharyya, Moitrayee. “Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory.” 2014. Web. 18 Jan 2021.

Vancouver:

Bhattacharyya M. Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2014. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/2341.

Council of Science Editors:

Bhattacharyya M. Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory. [Doctoral Dissertation]. Indian Institute of Science; 2014. Available from: http://etd.iisc.ac.in/handle/2005/2341

Indian Institute of Science

4. Jha, Anupam Nath. Topology-based Sequence Design For Proteins Structures And Statistical Potentials Sensitive To Local Environments.

Degree: PhD, Faculty of Science, 2013, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1886

► Proteins, which regulate most of the biological activities, perform their functions through their unique three-dimensional structures. The folding process of this three dimensional structure from… (more)

▼ Proteins, which regulate most of the biological activities, perform their functions through their unique three-dimensional structures. The folding process of this three dimensional structure from one dimensional sequence is not well understood. The available facts infer that the protein structures are mostly conserved while sequences are more tolerant to mutations i.e. a number of sequences can adopt the same fold. These arch of optimal sequences for a chosen conformation is known as inverse protein folding and this thesis takes this approach to solve the enigmatic problem. This thesis presents a protein sequence design method based on the native state topology of protein structure. The structural importance of the amino acid positions has been converted into the topological parameter of the protein conformation. This scheme of extraction of topology of structures has been successfully applied on three dimensional lattice structures and in turn sequences with minimum energy for a given structure are obtained. This technique along with the reduced amino cid alphabet(A reduced amino acid alphabet is any clustering of twenty amino acids based on some measure of the irrelative similarity) has been applied on the protein structures and hence designed optimal amino acid sequences for a given structure. These designed sequences are energetically much better than the native amino acid sequence. The utility of this method is further confirmed by showing the similarity between naturally occurring and the designed sequences. In summary, a computationally efficient method of designing optimal sequences for a given structure is given. The physical interaction energy between the amino acids is an important part of study of protein-protein interaction, structure prediction, modeling and docking etc. The local environment of amino acids makes a difference between the same amino acid pairs in the protein structure and so the pair-wise interaction energy of amino acid residues should depend on the irrespective environment. A local environment depended knowledge based potential energy function is developed in this thesis. Two different environments, one of these is the local degree (number of contacts) and the other is the secondary structural element of amino acids, have been considered. The investigations have shown that the environment-based interaction preferences for amino acids is able to provide good potential energy functions which perform exceedingly well in discriminating the native structure from the structures with random interactions. Further, the membrane proteins are located in a completely different physico-chemical environment with different amino acid composition than the water soluble proteins. This work provides reliable potential energy functions which take care of different environment for the investigation(model/predict) of the structure of helical membrane proteins. Three different environments, parallel and perpendicular to the lipid bilayer and number of amino acid contacts, are explored to analyze the… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Protein Structure; Membrane Proteins; Protein Folding; Protein Design; Amino Acid Sequence; Membrane Proteins - Helix Packing; Protein Sequences; Globular Proteins; Protein Sequence Design; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Jha, A. N. (2013). Topology-based Sequence Design For Proteins Structures And Statistical Potentials Sensitive To Local Environments. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1886

Chicago Manual of Style (16^th Edition):

Jha, Anupam Nath. “Topology-based Sequence Design For Proteins Structures And Statistical Potentials Sensitive To Local Environments.” 2013. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/1886.

MLA Handbook (7^th Edition):

Jha, Anupam Nath. “Topology-based Sequence Design For Proteins Structures And Statistical Potentials Sensitive To Local Environments.” 2013. Web. 18 Jan 2021.

Vancouver:

Jha AN. Topology-based Sequence Design For Proteins Structures And Statistical Potentials Sensitive To Local Environments. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2013. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/1886.

Council of Science Editors:

Jha AN. Topology-based Sequence Design For Proteins Structures And Statistical Potentials Sensitive To Local Environments. [Doctoral Dissertation]. Indian Institute of Science; 2013. Available from: http://etd.iisc.ac.in/handle/2005/1886

Indian Institute of Science

5. Dighe, Anasuya. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.

Degree: PhD, Faculty of Science, 2019, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/4236

► Molecular recognition between proteins and their associated ligands constitutes ligand-induced protein rewiring thereby enabling the formation of a stable protein-ligand complex. The studies presented in… (more)

▼ Molecular recognition between proteins and their associated ligands constitutes ligand-induced protein rewiring thereby enabling the formation of a stable protein-ligand complex. The studies presented in this thesis address the conformational plasticity inherent to proteins by virtue of which they adapt to diverse ligands and orchestrate complex biological processes like signal transduction, transcription and protein-protein interaction. Adopting network theory based formalisms for understanding protein-ligand associations involve deconstructing the three-dimensional structure of a protein in terms of nodes and edges. With this view, Protein Structure Networks (PSNs) of ligand-bound complexes are studied by considering their side-chain non-covalent interactions. Agonist and antagonist-bound G-Protein Coupled Receptors (GPCRs) are investigated to gain mechanistic insights into allostery and its role in signal transduction. The degree of similarity between PSNs of these complexes is quantified by means of Network Similarity Score (NSS). The physical nature of these networks is inspected by subjecting them to perturbations and major players in maintaining the stability of such networks are identified. Residue-wise groupings (at backbone and side-chain level) are obtained by applying graph spectral methods. All-atom Molecular Dynamics (MD) simulations are carried out to gain a better understanding of protein-ligand binding by analysing conformational ensembles of these complexes. In this scenario, two members from a highly versatile ligand-inducible transcription factor superfamily, i.e., Nuclear Receptors (NR) are studied, that are known to exhibit extremes of ligand binding behavior ranging from promiscuity to specificity. Diverse ligands are known to bind to proteins and the overall nature of their binding site is investigated. In particular, similarities among binding sites of diverse proteins are analysed by using PocketMatch. Percolation of these similarities to regions surrounding the binding site is reported and examples depicting this extended similarity are discussed. Overall, studies presented in this thesis provide a structural perspective into the adaptability of proteins for recognizing diverse ligands and undergoing local or global re-organizations in their framework to regulate complex biological processes. Advisors/Committee Members: Vishveshwara, Saraswathi (advisor), Chandra, Nagasuma (advisor).

Subjects/Keywords: Protein-ligand Interactions; Protein Ligand Interactions; Protein Structure Networks (PSNs); Graph Theory; Protein Side-chain Networks (PScN); Muscarinic Acetylcholine Receptors; Muscarinic Receptor Cmplexes; Protein-Protein Interactions; Pregnane X Receptor; G-Protein Coupled Receptors (GPCRs); Network Similarity Score (NSS); Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dighe, A. (2019). Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/4236

Chicago Manual of Style (16^th Edition):

Dighe, Anasuya. “Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.” 2019. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/4236.

MLA Handbook (7^th Edition):

Dighe, Anasuya. “Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.” 2019. Web. 18 Jan 2021.

Vancouver:

Dighe A. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2019. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/4236.

Council of Science Editors:

Dighe A. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. [Doctoral Dissertation]. Indian Institute of Science; 2019. Available from: http://etd.iisc.ac.in/handle/2005/4236

Indian Institute of Science

6. Gupta, Garima. Structural, Biophysical And Biochemical Studies On Mannose-Specific Lectins.

Degree: PhD, Faculty of Science, 2013, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1885

► For a long time, the scientific community underestimated the value of carbohydrates and the approach of most scientists to the complex world of glycans was… (more)

▼ For a long time, the scientific community underestimated the value of carbohydrates and the approach of most scientists to the complex world of glycans was apprehensive. The scenario, however, has changed today. With the development of new research tools and methodologies the study of carbohydrates and glycoconjugates has progressed rapidly, increasing our understanding of these molecules. Carbohydrates are most abundant amongst biological polymers in nature and vital for life processes. In their simplest form, they serve as a primary source of energy to most living organisms. In generalis, they exist as complex structures (glycans), and as conjugates of protein (glycoproteins, proteoglycans), lipids (glycolipids) and nucleosides (UDP-Glucose). Defined in the broadest sense, the study of glycans in all their forms and their interacting partners is termed “Glycobiology”. Glycans are ubiquitously found in nature decorating cells of almost all types with a “sugar coat”. They are also present within the cytoplasm, as well as in the extra-cellular matrix. They have key roles in a broad range of biological processes, including signal transduction, cell development and immune responses. All living organisms have evolved to express proteins that recognize discrete glycans and mediate specific physiological or pathological processes. One major class of such proteins is “Lectins”. Found in all forms of life, they are characterized by their ability to recognize carbohydrates. They are proteins of non-immune origin that bind glycans reversibly with a high degree of stereo-specificity in a non-catalytic manner. It must be emphasized that they are a different class from glycan-specific antibodies. Lectins were first discovered in plants and a large amount of work has been carried out on plant lectins to decipher their structural organization, mode of interaction with substrate and as models to study protein stability and folding. Study on animal and microbial lectins, on the other hand, gathered momentum only recently. In spite of this, more is known about their function in animals and micro-organisms rather than in plants. Lectin-glycan binding is implicated in several important biological processes such as protein folding, trafficking, host-pathogen interactions, immune cell responses and in malignancy and metastasis. Most lectins have one or more carbohydrate recognition domains (CRDs) which often share either 3-D structural features or amino acid sequence. New members of a family can be identified using either sequence or structural homology. Interestingly, it turns out that several plant and microbial lectins have structural or sequential similarity with animal lectins , revealing that these CRDs are evolutionarily related. This thesis, entitled “Structural, Biophysical and Biochemical Studies on Mannose-specific Lectins”, focuses on three lectins, Banana lectin (Banlec), Calreticulin (CRT) and Peptide-N-Glycanase (PNGase). Although all three lectins have distinct biological functions, they share a common ligand… Advisors/Committee Members: Surolia, Avadesha (advisor), Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Lectins; Oligomannosides; Proteins; Glycan-Lectin Interactions; Banana Lectin (Banlec); Calreticulin (CRT); Peptide-N-Glycanase (PNGase); Mannose-Specific Lectins; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gupta, G. (2013). Structural, Biophysical And Biochemical Studies On Mannose-Specific Lectins. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1885

Chicago Manual of Style (16^th Edition):

Gupta, Garima. “Structural, Biophysical And Biochemical Studies On Mannose-Specific Lectins.” 2013. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/1885.

MLA Handbook (7^th Edition):

Gupta, Garima. “Structural, Biophysical And Biochemical Studies On Mannose-Specific Lectins.” 2013. Web. 18 Jan 2021.

Vancouver:

Gupta G. Structural, Biophysical And Biochemical Studies On Mannose-Specific Lectins. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2013. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/1885.

Council of Science Editors:

Gupta G. Structural, Biophysical And Biochemical Studies On Mannose-Specific Lectins. [Doctoral Dissertation]. Indian Institute of Science; 2013. Available from: http://etd.iisc.ac.in/handle/2005/1885

Indian Institute of Science

7. Gadiyaram, Vasundhara. Graph Spectral Methods for Analysis of Protein Structures.

Degree: PhD, Faculty of Science, 2019, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/4280

► Network representation of protein structures is an information-rich mode of examining protein structure, dynamics and its interactions with biomolecules. Graph spectral methods are extremely useful… (more)

Subjects/Keywords: Protein Structure Networks (PSN); Spectral Theory; Protein Structure Models; Spectral Graph Theory; G-Protein Coupled Receptors; Graph Spectral Method; Correspondence Score (CRS); Eigenvalue-Weighted Cosine Score (EWCS); Eigenvalue-Weighted Cosine Score (EWCS); Network Similarity Score (NSS); Mathematics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gadiyaram, V. (2019). Graph Spectral Methods for Analysis of Protein Structures. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/4280

Chicago Manual of Style (16^th Edition):

Gadiyaram, Vasundhara. “Graph Spectral Methods for Analysis of Protein Structures.” 2019. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/4280.

MLA Handbook (7^th Edition):

Gadiyaram, Vasundhara. “Graph Spectral Methods for Analysis of Protein Structures.” 2019. Web. 18 Jan 2021.

Vancouver:

Gadiyaram V. Graph Spectral Methods for Analysis of Protein Structures. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2019. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/4280.

Council of Science Editors:

Gadiyaram V. Graph Spectral Methods for Analysis of Protein Structures. [Doctoral Dissertation]. Indian Institute of Science; 2019. Available from: http://etd.iisc.ac.in/handle/2005/4280

Indian Institute of Science

8. Hansia, Priti. Structure Function Relationship In Tryptophanyl tRNA Synthetase Through MD Simulations & Quantum Chemical Studies On Unusual Bonds In Biomolecules.

Degree: PhD, Faculty of Science, 2010, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/923

► Biological processes are so complicated that to understand the mechanisms underlying the functioning of biomolecules it is inevitable to study them from various perspectives and… (more)

▼ Biological processes are so complicated that to understand the mechanisms underlying the functioning of biomolecules it is inevitable to study them from various perspectives and with a wide range of tools. Understanding the function at the molecular level obviously requires the knowledge of the three dimensional structure of the biomolecules. Experimentally this can be obtained by techniques such as X‐ray crystallography and NMR studies. Computational biology has also played an important role in elucidating the structure function relationship in biomolecules. Computationally one can obtain the temporal as well as ensemble behavior of biomolecules at atomic level under conditions that are experimentally not accessible. Molecular dynamics(MD) study is a technique that can be used to obtain information of the dynamic behavior of the biomolecules. Dynamics of large systems like proteins can be investigated by classical force fields. However, the changes at the level of covalent bond involve the reorganization of electron density distribution which can be addressed only at Quantum mechanical level. In the present thesis, some of the biological systems have been characterized both at the classical and quantum mechanical level. The systems investigated by MD simulations and the insights brought from these studies are presented in Chapters 3 and 4. The unusual bonds such as pyrophosphate linkage in ATP and short strong hydrogen bonds in proteins, investigated through high level quantum chemical methods, are presented in Chapters 5, 6 and 7. Part of this thesis is aimed to address some important issues related to the dynamics of Tryptophanyl tRNA synthetase (TrpRS) which belongs to classic of aminoacyl‐tRNA synthetases (aaRS). aaRSs are extremely important class of enzymes involved in the translation of genetic code. These enzymes catalyze the aminoacylation of tRNAs to relate the cognate amino acids to the anticodon trinucleotide sequences. aaRSs are modular enzymes with distinct domains on which extensive kinetic and mutational experiments as well as structural analyses have been carried out, highlighting the role of inter‐domain communication (Alexander and Schimmel, 2001). The overall architecture of tRNA synthetases consists of primarily two domains. The active site domain is responsible for the activation of an amino acid with ATP in synthesizing an enzyme‐bound aminoacyl‐adenylate, and transfer of the aminoacyl‐adenylate intermediate to the 3’end of tRNA. The second domain is responsible for selection and binding of the cognate tRNA. aaRSs are allosteric proteins in which the binding of tRNA at the anticodon domain influences the activity at the catalytic region. These two binding sites are separated by a large distance. One of the aims of this thesis is to characterize such long distance communication (allosteric communication) at atomic level in Tryptophanyl tRNA synthetase. This is achieved by generating ensembles of conformations by MD simulations and analyzing the trajectories by novel graph theoretic approach.… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: tRNA; Transfer RNA; Tryptophanyl tRNA; Multidimensional Scaling; Human Tryptophanyl tRNA Synthetase; Aminoacyl-tRNA Synthetases (aaRSs); Short Hydrogen Bonds; Proteins - Molecular Dynamics; Monellin; Adenosine Triphosphate; Biomolecules; Tryptophanyl tRNA synthetase (TrpRS); Biochemical Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hansia, P. (2010). Structure Function Relationship In Tryptophanyl tRNA Synthetase Through MD Simulations & Quantum Chemical Studies On Unusual Bonds In Biomolecules. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/923

Chicago Manual of Style (16^th Edition):

Hansia, Priti. “Structure Function Relationship In Tryptophanyl tRNA Synthetase Through MD Simulations & Quantum Chemical Studies On Unusual Bonds In Biomolecules.” 2010. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/923.

MLA Handbook (7^th Edition):

Hansia, Priti. “Structure Function Relationship In Tryptophanyl tRNA Synthetase Through MD Simulations & Quantum Chemical Studies On Unusual Bonds In Biomolecules.” 2010. Web. 18 Jan 2021.

Vancouver:

Hansia P. Structure Function Relationship In Tryptophanyl tRNA Synthetase Through MD Simulations & Quantum Chemical Studies On Unusual Bonds In Biomolecules. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2010. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/923.

Council of Science Editors:

Hansia P. Structure Function Relationship In Tryptophanyl tRNA Synthetase Through MD Simulations & Quantum Chemical Studies On Unusual Bonds In Biomolecules. [Doctoral Dissertation]. Indian Institute of Science; 2010. Available from: http://etd.iisc.ac.in/handle/2005/923

Indian Institute of Science

9. Ghosh, Amit. Structure-Function Correlations In Aminoacyl tRNA Synthetases Through The Dynamics Of Structure Network.

Degree: PhD, Faculty of Science, 2010, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/822

► Aminoacyl-tRNA synthetases (aaRSs) are at the center of the question of the origin of life and are essential proteins found in all living organisms. AARSs… (more)

▼ Aminoacyl-tRNA synthetases (aaRSs) are at the center of the question of the origin of life and are essential proteins found in all living organisms. AARSs arose early in evolution to interpret genetic code and are believed to be a group of ancient proteins. They constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. These enzymes ensure the fidelity of transfer of genetic information from the DNA to the protein. They are responsible for attaching amino acid residues to their cognate tRNA molecules by virtue of matching the nucleotide triplet, which is the first step in the protein synthesis. The translation of genetic code into protein sequence is mediated by tRNA, which accurately picks up the cognate amino acids. The attachment of the cognate amino acid to tRNA is catalyzed by aaRSs, which have binding sites for the anticodon region of tRNA and for the amino acid to be attached. The two binding sites are separated by ≈ 76 Å and experiments have shown that the communication does not go through tRNA (Gale et al., 1996). The problem addressed here is how the information of binding of tRNA anticodon near the anticodon binding site is communicated to the active site through the protein structure. These enzymes are modular with distinct domains on which extensive kinetic and mutational experiments and supported by structural data are available, highlighting the role of inter-domain communication (Alexander and Schimmel, 2001). Hence these proteins present themselves as excellent systems for in-silico studies. Various methods involved for the construction of protein structure networks are well established and analyzed in a variety of ways to gain insights into different aspects of protein structure, stability and function (Kannan and Vishveshwara, 1999; Brinda and Vishveshwara, 2005). In the present study, we have incorporated network parameters for the analysis of molecular dynamics (MD) simulation data, representing the global dynamic behavior of protein in a more elegant way. MD simulations have been performed on the available (and modeled) structures of aaRSs bound to a variety of ligands, and the protein structure networks (PSN) of non-covalent interactions have been characterized in dynamical equilibrium. The changes in the structure networks are used to understand the mode of communication, and the paths between the two sites of interest identified by the analysis of the shortest path. The allosteric concept has played a key role in understanding the biological functions of aaRSs. The rigidity/plasticity and the conformational population are the two important ideas invoked in explaining the allosteric effect. We have explored the conformational changes in the complexes of aaRSs through novel parameters such as cliques and communities (Palla et al., 2005), which identify the rigid regions in the protein structure networks (PSNs) constructed from the non-covalent interactions of amino acid side chains. The thesis consists of 7 chapters. The first chapter… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Aminoacyl tRNA Synthetases (aaRSs); Protein Structure Network Analysis; Molecular Dynamics Simulation; Protein Structure; Methionyl tRNA Synthetase; Cysteinyl tRNA Synthetase; Protein Folding; Intra-Molecular Signaling; Lysozyme; Protein Structure Graphs; Protein-Ligand Binding Energy; Protein Dynamics; Structure Network Analysis; Aminoacyl-tRNA Synthetases; Biochemical Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ghosh, A. (2010). Structure-Function Correlations In Aminoacyl tRNA Synthetases Through The Dynamics Of Structure Network. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/822

Chicago Manual of Style (16^th Edition):

Ghosh, Amit. “Structure-Function Correlations In Aminoacyl tRNA Synthetases Through The Dynamics Of Structure Network.” 2010. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/822.

MLA Handbook (7^th Edition):

Ghosh, Amit. “Structure-Function Correlations In Aminoacyl tRNA Synthetases Through The Dynamics Of Structure Network.” 2010. Web. 18 Jan 2021.

Vancouver:

Ghosh A. Structure-Function Correlations In Aminoacyl tRNA Synthetases Through The Dynamics Of Structure Network. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2010. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/822.

Council of Science Editors:

Ghosh A. Structure-Function Correlations In Aminoacyl tRNA Synthetases Through The Dynamics Of Structure Network. [Doctoral Dissertation]. Indian Institute of Science; 2010. Available from: http://etd.iisc.ac.in/handle/2005/822

Indian Institute of Science

10. Sanjeev, B S. Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations.

Degree: PhD, Faculty of Science, 2011, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1187

Subjects/Keywords: Eosinophil; Ribonucleases - Molecular Dynamics; Catalysis; Molecular Dynamics - Data Processing; RNase A; Angiogenin; Ribonuclease A; Cell Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sanjeev, B. S. (2011). Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1187

Chicago Manual of Style (16^th Edition):

Sanjeev, B S. “Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations.” 2011. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/1187.

MLA Handbook (7^th Edition):

Sanjeev, B S. “Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations.” 2011. Web. 18 Jan 2021.

Vancouver:

Sanjeev BS. Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2011. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/1187.

Council of Science Editors:

Sanjeev BS. Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations. [Doctoral Dissertation]. Indian Institute of Science; 2011. Available from: http://etd.iisc.ac.in/handle/2005/1187

Indian Institute of Science

11. Sathyapriya, R. Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches.

Degree: PhD, Faculty of Science, 2009, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/624

► 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… (more)

▼ 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… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Protein-Nucleic Acid Interactions; Protein-RNA Interactions; Protein Structure Graphs; Protein Nucleotide Graphs (PNG); Protein-DNA Complexes; Protein-RNA Complexes; Aminoacyl-tRNA Synthetase; Glutaminyl-tRNA Synthetase (GlnRS); Proteins - Short Hydrogen Bonds; Protein Structure Networks; Protein-RNA Interaction; Structure Graphs; Protein-RNA Graphs; 70S Ribosome; Biochemical Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sathyapriya, R. (2009). Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/624

Chicago Manual of Style (16^th Edition):

Sathyapriya, R. “Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches.” 2009. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/624.

MLA Handbook (7^th Edition):

Sathyapriya, R. “Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches.” 2009. Web. 18 Jan 2021.

Vancouver:

Sathyapriya R. Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2009. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/624.

Council of Science Editors:

Sathyapriya R. Exploring Protein-Nucleic Acid Interactions Using Graph And Network Approaches. [Doctoral Dissertation]. Indian Institute of Science; 2009. Available from: http://etd.iisc.ac.in/handle/2005/624

Indian Institute of Science

12. Iyer, Lakshmanan K. Molecular Dynamics Simulation Of Transmembrane Helices And Analysis Of Their Packing In Integral Membrane Proteins.

Degree: PhD, Faculty of Science, 2012, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1792

Subjects/Keywords: Integral Membrane Proteins (IMPs); Transmembrane Helices; Bacteriorhodopsin; Rhodopsin; Transmembrane Helix; Proline Helix I1; Proteins - Molecular Dynamics; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Iyer, L. K. (2012). Molecular Dynamics Simulation Of Transmembrane Helices And Analysis Of Their Packing In Integral Membrane Proteins. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1792

Chicago Manual of Style (16^th Edition):

Iyer, Lakshmanan K. “Molecular Dynamics Simulation Of Transmembrane Helices And Analysis Of Their Packing In Integral Membrane Proteins.” 2012. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021. http://etd.iisc.ac.in/handle/2005/1792.

MLA Handbook (7^th Edition):

Iyer, Lakshmanan K. “Molecular Dynamics Simulation Of Transmembrane Helices And Analysis Of Their Packing In Integral Membrane Proteins.” 2012. Web. 18 Jan 2021.

Vancouver:

Iyer LK. Molecular Dynamics Simulation Of Transmembrane Helices And Analysis Of Their Packing In Integral Membrane Proteins. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2012. [cited 2021 Jan 18]. Available from: http://etd.iisc.ac.in/handle/2005/1792.

Council of Science Editors:

Iyer LK. Molecular Dynamics Simulation Of Transmembrane Helices And Analysis Of Their Packing In Integral Membrane Proteins. [Doctoral Dissertation]. Indian Institute of Science; 2012. Available from: http://etd.iisc.ac.in/handle/2005/1792

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