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Fundamental to the complexity of the nervous system is the precise regulation in space and time of the production, maturation, and migration of neurons in the developing embryo. This is eloquently seen in the forming cranial sensory ganglia (CSG) of the peripheral nervous system. Placodes, which are transient pseudostratified neuroepithelia in the surface ectoderm of the embryo, are responsible for generating most of the neurons of the CSG. Placodal progenitors commit to the neuronal fate and delaminate from the epithelium as immature, multipolar neuroblasts. These neuroblasts reside in a staging area immediately outside the placode. Differentiation of the neuroblasts is intimately coupled to their adoption of a bipolar morphology and migration away from the staging area to the future site of the CSG. Thus the forming CSG is a highly tractable model to anatomically separate the three phases of a neuroblast’s lifetime: from neuroepithelial progenitor (in the placode), to immature neuroblast (in the staging area), to mature neuron (in the migratory stream). In this thesis, I used the forming CSG as a model to investigate the role of Regulator of G protein Signalling 3 (RGS3) in neuroblast commitment and differentiation. Promoters within introns of the RGS3 locus generate isoforms in which N-terminal sequences are sequentially truncated, but C-terminal sequences are preserved. Intriguingly, I found that expression of these isoforms in the forming CSG is temporally co-linear with their genomic orientation: longer isoforms are exclusively expressed in the progenitor placode; a medium isoform is expressed exclusively in the neuroblast staging area; and the shortest isoforms are expressed in the neuronal migratory stream. Furthermore, through loss- and gain-of-function experiments, I demonstrated that each of these isoforms plays a specific role in the differentiation state in which it is expressed: placode-expressed isoforms negatively regulate neurogenesis; the neuroblast-expressed isoform negatively regulates differentiation; and the neuron-expressed isoforms negatively regulate neuronal migration. The negative regulatory role which all isoforms play in different cell-biological contexts is intriguing in light of the fact that they all share a C-terminal RGS domain, which canonically negatively regulates G protein signalling. Through domain mutation and deletion, I showed that the RGS and N-terminal domains are important for the function of each isoform. Thus temporally co-linear expression within the RGS3 locus generates later-expressed isoforms which lack the regulatory N-terminal domains of the earlier-expressed isoforms, giving them new license to perform different biochemical functions. Lastly, I investigated the conservation and evolution of RGS3 and its isoforms. RGS3 was found to be present in all extant metazoans, and results from this thesis implicate it as the founding member of the R4 subfamily of RGS proteins. Furthermore, in the early vertebrate lineage, a critical domain was lost. This is intriguing in light of the fact that placodes in their stereotypic forms also emerged early in the vertebrate lineage. Ectopic overexpression of the full-length invertebrate RGS3 protein prevented pseudostratification of the vertebrate placode, suggesting that the domain loss in the early vertebrate lineage was important for the evolution of pseudostratified placodes and the expansion of the vertebrate nervous system. In summary, the work in this thesis has uncovered a previously unseen model of transcriptional regulation of a single locus: intragenic temporal co-linearity. Furthermore, the demonstrated functions of this regulation have profound implications on the generation and differentiation of vertebrate neurons, as well as the evolution of the vertebrate nervous system.

Οι οπιοειδείς υποδοχείς (OR), μ, δ, κ και NOP, είναι μέλη των επταελικοειδών υποδοχέων που συζεύγνυνται με G πρωτεΐνες (7ΤΜ ή GPCR), οι οποίοι αποτελούν τη μεγαλύτερη υπεροικογένεια υποδοχέων και έναν από τους κύριους φαρμακολογικούς στόχους λόγω της υψηλής φυσιολογικής τους σημασίας. Οι OR ρυθμίζουν μια ποικιλία φυσιολογικών αποκρίσεων στο νευρικό σύστημα, με κυριότερη την αναλγησία. Τα οπιοειδή φάρμακα είναι τα πιο ισχυρά και αποτελεσματικά αναλγητικά έναντι στον οξύ πόνο, όμως η παρατεταμένη χρήση τους οδηγεί σε φαινόμενα ανοχής και εξάρτησης. Γι’ αυτό υπάρχει έντονο ενδιαφέρον στην αποσαφήνιση των μηχανισμών που εμπλέκονται στα φαινόμενα αυτά προκειμένου να σχεδιαστούν πιο αποτελεσματικά φάρμακα χωρίς τέτοιες παρενέργειες. Η σηματοδότηση των οπιοειδών υποδοχέων γίνεται κυρίως μέσω της ενεργοποίησης των Gi/o πρωτεϊνών που με τη σειρά τους ρυθμίζουν κατάλληλους τελεστές. Πέρα όμως από αυτούς τους κλασσικούς αλληλεπιδρώντες εταίρους οι OR έχουν την ικανότητα να αλληλεπιδρούν και με πολλές άλλες πρωτεΐνες κυρίως μέσω των περιοχών της τρίτης ενδοκυτταρικής τους θηλιάς (i3L) και του καρβοξυτελικού τους άκρου (CT) (Georgoussi et al., 2006- Georgoussi, 2008- Georgoussi et al., 2012). Οι αλληλεπιδράσεις αυτές επηρεάζουν όχι μόνο την σηματοδότηση των OR αλλά και την εν γένει εύρυθμη λειτουργία τους. Μια σημαντική πρωτεϊνική οικογένεια που ελέγχει τη μεταγωγή σήματος από τις G πρωτεΐνες βρέθηκε να είναι οι πρωτεΐνες Ρυθμιστές της κυτταρικής Σηματοδότησης μέσω G πρωτεϊνών ή RGS πρωτεΐνες (Regulators of G protein signaling, RGS). Ο πρωταρχικός τους ρόλος είναι η αλληλεπίδραση τους με τις Gα υπομονάδες των G πρωτεϊνών και η επιτάχυνση της υδρόλυσης του GTP από τις τελευταίες οδηγώντας στη μείωση της σηματοδότησης των GPCR. Μέλη της οικογένειας των RGS πρωτεϊνών είχε δειχθεί ότι πέρα από τις Gα πρωτεΐνες αλληλεπιδρούν επίσης με υποδοχείς GPCR, τελεστές αλλά και με άλλες ρυθμιστικές πρωτεΐνες, προσδίδοντας τους έναν ιδιαίτερο οργανωτικό ρόλο στη λειτουργία του κυττάρου και καθιστώντας τις RGS πρωτεΐνες μόρια υψηλού φαρμακολογικού ενδιαφέροντος. Παρελθόντα πειράματα in vitro συγκατακρήμνισης, του εργαστηρίου Κυτταρικής Σηματοδότησης και Μοριακής Φαρμακολογίας, με τη χρήση GST-χιμαιρικών πεπτιδίων των καρβοξυτελικών άκρων των μ-OR και δ-OR (μ-CT και δ-CT αντίστοιχα) και της τρίτης ενδοκυτταρικής θηλιάς του δ-OR (δ-i3L), έδειξαν ότι η RGS4, ένα μέλος της B/R4 υποοικογένειας, αλληλεπιδρά και με τους δυο υποδοχείς στις περιοχές αυτές (Georgoussi et al., 2006- Leontiadis et al., 2009). Η αλληλεπίδραση της RGS4 στα καρβοξυτελικά άκρα των υποδοχέων αυτών γίνεται στην περιοχή που σχηματίζει μια 8η αμφιπαθική α-έλικα (έλικα VIII), σημείο επαφής των OR και για άλλες πρωτεϊνικές αλληλεπιδράσεις όπως αυτή των STAT5A/B ((Mazarakou and Georgoussi, 2005- Georganta et al., 2010), της σπινοφιλίνης (Fourla et al., 2012) και άλλων πρωτεϊνών (Georgoussi et al., 2012). Βρέθηκε επίσης ότι η RGS4 είναι αρνητικός ρυθμιστής της κυτταρικής σηματοδότησης των μ-OR και δ-OR (Georgoussi et al., 2006- Leontiadis et al., 2009). Τέλος, αποδείχθηκε για πρώτη φορά ότι η RGS4 παίξει το ρόλο «μοριακού φίλτρου» καθοδηγώντας τους μ-OR και δ-OR να αλληλεπιδράσουν με συγκεκριμένο διαφορετικό υποπληθυσμό Gα υπομονάδων των G πρωτεϊνών (Leontiadis et al., 2009). Καμία πληροφορία για τον ρόλο των RGS πρωτεϊνών δεν υπάρχει για τον κ-OR. Για τον λόγο αυτό σκοπός της παρούσας διατριβής ήταν να ελέγξουμε αν οι RGS πρωτεΐνες της Β/R4 υποοικογένειας αλληλεπιδρούν με τον κ-OR και αν ναι, ποιος είναι ο ρόλος τους στη σηματοδότηση του κ-OR και των G πρωτεϊνών με τις οποίες ο τελευταίος συζεύγνυται. Τα αποτελέσματά μας έδειξαν ότι ο κ-OR μπορεί να αλληλεπιδράσει και με την RGS4 και με την RGS2 τόσο in vitro όσο και in vivo. Η δημιουργία GST-χιμαιρικών πεπτιδίων του καρβοξυτελικού άκρου του κ-OR (κ-CT) έδειξε ότι η RGS4 αλληλεπιδρά επίσης εντός της έλικας VIII ενώ η RGS2 αλληλεπιδρά με το τελικό μη συντηρημένο άκρο του κ-CT όσο και του δ-CT. Επιπλέον η συνέκφραση της RGS4 ή της RGS2 σε κύτταρα 293F που εκφράζουν τον κ-OR έδειξε ότι και οι δυο RGS πρωτεΐνες προάγουν την επιλεκτική και διαφορική σύζευξη του κ-OR με συγκεκριμένο υποπληθυσμό των Gαi/o υπομονάδων. Σε ότι αφορά τον φυσιολογικό ρόλο των RGS4 και RGS2 στις ελεγχόμενες από τον κ-OR κυτταρικές αποκρίσεις βρήκαμε ότι τόσο η RGS4 όσο και η RGS2 ανέστειλαν την καταστολή της αδενυλικής κυκλάσης που ελέγχει ο κ-OR, αλλά όχι ο δ-OR, με την RGS2 να έχει ισχυρότερη επίδραση στο μονοπάτι αυτό. Επίσης οι RGS4 και RGS2 μείωσαν την ενεργοποίηση των ERK1,2 κινασών που σηματοδοτούσε ο κ-OR. Τέλος, βρήκαμε ότι παρόλο που καμία από τις δυο RGS δεν επηρεάζει την εσωτερίκευση του κ-OR, η RGS4 επιταχύνει την εσωτερίκευση του δ-OR. Τα ευρήματά μας καταδεικνύουν ότι οι RGS4 και RGS2 πρωτεΐνες είναι δυο νέοι αρνητικοί ρυθμιστές στην σηματοδότηση των κ-OR και δ-OR. Εμφανίζουν διαφορικό ρυθμιστικό ρόλο στα σηματοδοτικά μονοπάτια καθενός OR, με ρόλο κλειδί στην καθοδήγηση της σύζευξής τους με τις Gα υπομονάδες και μπορούν να αποτελέσουν ενδιαφέροντες φαρμακολογικούς στόχους για τον έλεγχο της δράσης των οπιοειδών. / Οpioid receptors (OR) (subtypes μ, δ, κ and NOP) belong to the superfamily of the Heptahelical G protein-coupled receptors (7TM or GPCRs), the largest class of receptors in the human genome and common targets for therapeutics. ORs mediate their responses in the nervous system via coupling to members of the Gi/Go proteins to regulate the activity of various effector systems. Opioids are the most potent analgesics but prolonged administration leads to phenomena of tolerance and dependence thus there is a great interest towards understanding of OR signalling in an effort to develop new drugs devoid of adverse effects. Extended observations have demonstrated that the cytoplasmic face of the ORs is critical in mediating their signal through interactions not only with G proteins but also with multiple other proteins. These regulatory proteins play distinct roles in the regulation of the OR signalling, and in the fine tuning of these receptors. Regulators of G protein signalling (RGS) proteins is a class of proteins that modulate G protein signalling events by directly interacting with Gα subunits and accelerating the GTP hydrolysis, thus reducing GPCR signalling towards their effectors. RGS can also interact with many GPCRs, effectors and auxiliary proteins thus playing a key role in the cell functions, making them highly attractive as pharmacological targets (Abramow-Newerly et al., 2006). Our previous in vitro studies have shown that a member of the B/R4 subfamily of RGS proteins such as RGS4 interacts directly with μ-OR and δ-OR within a conserved region in their C-termini (μ-CT and δ-CT), forming a helix VIII, as well as within the δ-third intracellular loop (δ-i3L). RGS4 associates with μ-OR and δ-OR in living cells and forms selective complexes with Gαi/o proteins in a receptor dependent manner. Expression of RGS4 in HEK293 cells attenuated adenylyl cyclase inhibition mediated by μ-OR and agonist-mediated ERK1,2 phosphorylation for both receptors (Georgoussi et al., 2006- Leontiadis et al., 2009), suggesting for the first time that RGS4 is a negative modulator of μ-OR and δ-OR signalling. To deduce whether similar effects also occur for the κ-opioid receptor (κ-ΟR) and define the ability of other members of the B/R4 subfamily of RGS proteins, such as RGS2, to interact with OR we generated fusion peptides encompassing the C-terminus of κ-OR (κ-CT). Results from pull down experiments indicated that RGS2 interacts with the κ-CT, the δ-CT and the δ-i3L but fails to interact with the μ-CT. RGS4-N-terminal domain is responsible for OR interaction. Mapping the sites of RGS2 interaction indicated that RGS2 interacts with the non conserved portion of the C-termini of ORs exhibiting a different docking site as compared to that of RGS4. Co-precipitation studies in living cells indicated that RGS2 and RGS4 associate with κ-ΟR constitutively and upon receptor activation and confer selectivity for coupling with a specific subset of G proteins in an RGS protein dependent manner. Expression of both RGS2 and/or RGS4, in 293F cells attenuated agonist mediated-adenylyl cyclase inhibition for κ-ΟR, but not δ-OR, with RGS2 exhibiting a more robust effect. RGS4 and RGS2 reduced κ-ΟR-mediated ERK1,2 phosphorylation whereas, RGS4 accelerated agonist-induced internalization of the δ-OR but not of the κ-OR. Collectively, our observations demonstrate that RGS2 and RGS4 are novel interacting partners and negative modulators of κ-ΟR and δ-OR signalling. These two RGS proteins display a differential modulatory effect in each signalling pathway tested and play a key functional role by conferring selectivity for both κ-OR and δ-OR coupling with a specific subset of G proteins. Therefore they can be considered as attractive new pharmacological targets to manipulate opioid receptors signalling.

Cellular response to environmental changes involves a wide repertoire of complex signalling systems often resulting in up and down regulation of various genes. These mechanisms are generally conserved in a variety of organisms. These pathways are also constantly rewired in various organisms, which aid them in maintaining homeostasis and result in species-specific adaptation mechanisms. Protein kinases are central to these mechanisms and orchestrate a multitude of these pathways. This thesis aims to understand the selective forces behind evolution of signalling pathways. More specifically, this thesis focuses on structural and domain architecture differences of protein kinases. Protein kinases are one of the most populated families of proteins in many organisms and it constitutes about 2-3% of proteomes of most of the eukaryotic organisms. These kinases have evolved over ~400 million years and regulate nearly all major signalling pathways. Classification of kinases enables convenient association of kinases to the function and signalling pathway in which they participate. The current scheme of classification is based on the amino acid sequence of the catalytic region, which consists of about 200-300 residues. This scheme proposes division into 7 groups which show gross level similarities in function such as the TK group, which constitutes all tyrosine kinases, or AGC group which constitutes kinases regulated by second messengers. These groups are further divided into ~280 subfamilies providing us insights into function and regulation at a much finer level. This enables ascertaining information about signalling pathways, protein-protein interactions or substrates the kinase phosphorylates. Chapter 1 provides an elaborate introduction to the various types of protein kinases and their roles in signalling processes. This chapter discusses how protein kinases work in a concerted manner with several other players of a signalling pathway to generate a regulated response to external stimuli. Furthermore, it highlights both the evolutionary aspects and dynamical nature of such pathways. The subsequent part of this chapter deals with protein kinases, their evolution, regulation and structural features crucial to catalysis. Protein kinases are regulated in many ways ¬regulation is achieved from within the catalytic domain and also by means of additional domains tethered to the catalytic domain. The regulatory switch is triggered by various cellular and molecular events such as phosphorylation of specific residues, changes in spatial-temporal localization and altered redox states to name a few. The effects of regulatory domains on the overall function have also been discussed. The chapter concludes by highlighting structural analysis carried out to understand the regulatory aspect of kinases and uses this information in rational drug discovery. Chapters 2 and 3 report identification and analysis of a repertoire of protein kinases encoded in the genomes of two of the organisms which are frequently used in comparative genomics. Chapter 2 focuses on the distribution of kinases in Takifugu rubripes, a teleost fish which is a widely used model system for studying human genes. Use of remote homology detection methods identified 519 kinases in fugu. Although the group-wise distribution of kinases shows high similarity to that of human kinases, subfamily distribution shows considerable differences in 22 subfamilies. They are either under or over-represented in fugu. Most noticeable difference is seen for the DYRK subfamily, which is eight times higher in fugu than human. Detailed analysis of the DYRKs revealed interesting insights into and explained partially their high representation in fugu. Only about ten of these kinases classified into these subfamilies showed high sequence similarity and conserved localization signals to the human kinases and kinases commonly found in other eukaryotes such as C.elegans, S.cereviseae and D.melanogaster. Disparity at the level of genome may be attributed to the observation of unique domain architectures characteristic of this genome. A comparison of domain architectures of kinases documented in Pfam with that of the kinases in Takifugu also revealed two kinases with unique domain architectures in fugu; they are associated with Galectin domain and YkyA domains. Despite inconsistencies in the distribution, human and Takifugu kinases subfamilies remarkable similarity is observed in the MAP kinase pathway, which is ubiquitously found across eukaryotic organisms. Nearly 83% of the proteins in this pathway show more than 30% sequence identity between the two organisms thus, validating the use of Takifugu as a model system to study human signalling pathways. While addressing the possibilities of similar expansions of kinases in other teleosts, it was noticed that the Danio rerio genome (zebrafish) had a massively expanded kinome with ~1200 kinases. Chapter 3 explores the possible reasons for the expansion of kinome with kinases specific to Zebrafish. For e.g., the number of kinases from one subfamily (CAMK) is roughly similar to the total number of protein kinases encoded in the human genome. Further, the PIM kinase subfamily is the sole subfamily, which is massively over-represented (~30 times) in this genome. A detailed analysis of PIM kinases of zebrafish revealed that the sequences are divergent from the canonical PIM kinases. Despite this difference, the specific residues, which dictate the functional properties specific to PIM kinases, are highly conserved. These PIM kinases are usually constitutively active, features of which are conserved in PIM kinases of zebrafish as well. Unlike canonical PIM kinases in other eukaryotes, the post-transcriptional regulation of these PIM kinases might be different due to the absence of regulatory regions in the 3'UTR regions of the PIM gene. However, conservation of a S261 phosphorylation site highlights regulation by phosphorylation, which compensates for the constitutively active nature. A massive expansion of the substrate pool of PIM kinases in this genome seems to correlate well with the expansion. Since PIM kinases regulate large number of growth related pathways, we believe that, this might be associated with high regenerative capacity of organs observed in this fish, which makes it an ideal model to study most cancers. While the earlier two chapters primarily focused on the kinase catalytic domain and organism specific changes; the next two chapters address the contribution of domains tethered to the catalytic domain in the overall function of the kinase. Deviations from canonical kinase domain architectures indicate expansion in the functional repertoire of kinases. Chapter 4 is a study on human kinases from the latest revised version of the human genome sequence data. The initial part of the chapter focuses on the differences in the kinase repertoire upon revision of the human genomic data. Seven sequences gleaned from the earlier genomic data are absent and 16 new sequences are added to the kinome dataset according to the latest human genome sequence data. In addition, differences in transcripts for 23 kinases have led to differences in overall length and sub-family classification of these kinases. The identification of the kinome data from this latest version was a mandatory step prior to the study of outlier kinases due to variations in gene transcripts. The domain architectures of the human kinases have been compared with known subfamily-specific domain architectures, in order to identify outliers. Based on the type of domain architecture these outliers have been classified as “rogue” or “hybrid” kinases. Hybrid architecture represent kinases showing high sequence similarity within the kinase domain to a known sub¬family of kinases with the acquisition of non-kinase domains typically found in one of the other subfamilies of kinases. On the other hand rogue architectures belong to kinases with domain architectures not observed in any of the kinase sub-families. A total of 23 outliers have been identified in the human genome-13 hybrids and 10 rogues. The presence of such "hybrid" and "rogue" kinases makes classification of kinases into subfamilies a daunting task and hence necessitates a new method for classification using the full-length sequences. The use of one such alignment-free method, ClaP (Appendix), using full length sequences has been validated for classification of kinases. A similarity metric obtained from full protein sequence comparison further improved the existing methods of classification for 29 kinases, which utilize only the catalytic domain of kinases. Classification based on catalytic domain is incomplete without the knowledge of associated domains, which also have an important role in function. This necessitates a new approach in classification of kinases for function annotation-an integrated one that uses information from the full-length sequence of each kinase. Chapter 5 extends the learning from chapter 4 and aids in identification of 74 "Hybrid" and 18 "Rogue" kinases in other model eukaryotes, Mus musculus, C.elegans, S. Cerevisiae, D. melanogaster and Takifugu rubripes which show significant variations in the overall functions. These sequences due to their hybrid nature might facilitate cross-talk between signalling pathways. Thus annotating the function of each of these 92 outliers has highlighted the use of domain recombination in wiring new pathways and re-wiring existing pathways. Also, these sequences because of their hybrid nature cannot be classified under any of the existing sub-families. Therefore, it has been proposed in this chapter that they be classified as separate sub-family containing sequences with hybrid properties. To validate this, the ClaP method has been extended where the pair-wise distances between two sequences (using full length sequence) has been used to generate phylogenetic trees which have then been subjected to hierarchical clustering to generate sub-family based clusters. Further, a Shannon entropy based score has been used to identify clusters that contain sequences from diverse sub-families grouped together. Upon analysis of these clusters, it was observed that the hybrid and rogue kinases specifically cluster within four clusters with high entropy (constitute large number of sub-families) validating their status as emergent sub-families. In addition, more hybrids and rogues have been identified in these clusters, which have long regions without any domain assignments. Such sequences may contain domain families deviant from those that are currently known and information on their function can be obtained from further genomic studies in future. Lastly, the prevalence of such hybrid and rogue kinases in the genome of a protozoan parasite, P. falciparum has been studied in detail. The role of hybrids and rogues in host-pathogen interaction has been explored. Chapter 6 presents an in-depth analysis of the possible role of charge-neutralization around phosphosites in protein kinases and its substrates. This analysis was a follow up of a study and in collaboration with Dr.Warwicker's group in Manchester, which identified positively charged residues around phosphosites in kinase substrates. The current study not only aims to address the importance of charge neutralization around phosphosites, but also uses this feature for prediction of phosphosites in known structures of kinase substrates. A dataset of phosphosites mapped on a 3-D structure has been used to calculate peak electrostatic potentials around phosphosites based on the solution of a non-linear Poisson-Boltzmann equation. A comparison of peak potentials around phosphosites with that of non-phosphosites reveals a higher positive peak potential at ~10.0 Å radius around the phosphosite. This variation is significantly higher around tyrosine residues in comparison to Ser/Thr residues phosphosites. Further, this distinction in peak potential around the phosphosite is attributed to only certain families like protein kinases and pyruvate kinases. The concept of charge neutralization will therefore show greater success in prediction of phosphosites in such families in comparison to other families with phosphosites. The functional importance of such charge neutralizations has been studied in great detail in the protein kinase domain family due to prior knowledge that certain phosphorylation events contribute to conformational change, which may be correlated to the changes in peak potentials upon phosphorylation. Phosphorylation at certain sites within the kinase catalytic domain often mediates onset of certain signalling events including regulating activity levels of kinases, mediating protein-protein interactions and altering their localization. Therefore, by means of studying conservation patterns of such phosphosites or neutralizing residues, the variations in signalling pathways in homologues with differences in conservation patterns, have been highlighted. Among domain families which do not show clear differences in peak potentials between phosphosites and non-phosphosites, it was noted, in a few cases, that negatively charged ligands bind to the protein in the vicinity of phosphosites, in the un-phosphorylated forms of the protein. Structural studies on a few cases in ligand bound forms indicate a competitive mechanism between phosphorylation and ligand binding which helps in switching between different functional forms. Therefore, the role of phosphorylation as a regulatory mechanism for modulating ligand binding in such domain families has been highlighted. Chapter 7 of the thesis reports a study on disease causing mutations in kinases. So far 180 kinases have been reported to contain disease causing mutations. This chapter particularly focuses on understanding the deleterious effects of non-synonymous missense mutations in kinases. Mutations at certain sites are enriched as seen by the concentration of disease phenotypes upon mutations at these sites in comparison to others. Interactions involving Arginines in sub-domains VIB, VIII, IX and XI are perturbed which affect catalysis. Structural explanation of 10 such mutations, which occur in important sub-domains and not directly implicated in catalysis has been provided. Apart from analyzing the various evolutionary and structural aspects of protein kinases in this thesis an attempt has been made to provide a deeper structural understanding of Msh (MutS Homologues) proteins involved in eukaryotic chromosomal segregation. Chapter 8 deals with Msh4-Msh5 complex, which are eukaryotic homologues of the MutS family of proteins in bacteria. MutS proteins form homodimeric complexes in bacteria that aid in mismatch repair process. There are six MutS homologues in eukaryotes, which form hetero-dimers. Two of the homologues are Msh4 and Msh5, which form hetero-dimeric complexes which is a pre-requisite for its function. They are involved in chromosomal segregation during meiosis-I and aid in resolving Holliday junction DNA. Till date no structure of this complex is available and the exact mode of binding is unclear. In addition, Msh4 and Msh5 display asymmetry in DNA and ATP binding sites. These insights are derived from the severity in phenotypes upon mutation of various residues in these proteins. This work is in collaboration with Dr. Nishant from IISER, Trivandrum. The questions addressed in chapter 8 of the thesis are: What are the structural features that contribute to the asymmetry in function between Msh4 and Msh5 in DNA and ATP binding? Can a structural explanation be provided for each of the 27 mutations causing severe phenotypes (cross-over defects/viability) to predict their role in function of the Msh4-Msh5 complex? Can a prediction be provided for the mode of binding of the Holliday junction DNA? Can residues occurring at interface regions of Msh4 and Msh5 be identified on the basis of the structure which affects the complexation of Msh4 and Msh5? These questions are addressed by homology modelling of the Msh4-Msh5 complex using the Msh2-Msh6 complex as template. Structural explanations have been provided for 23 out of 27 mutations with severe phenotypes. Certain residues in Msh5 are shown to form tighter network of interactions than their counterparts in Msh4 and therefore likely to have a more prominent role in DNA and ATP binding which corroborate with the observed asymmetry in mutant functions. A volume based calculation has been used to suggest a possible mode of binding of the Holliday junction within the cavity of the complex. Finally, the model has been used to predict interface residues that play a crucial role in complexation and function. Experiments are being carried out in Dr. Nishant's laboratory to mutate these residues to validate the model. Chapter 9 summarizes the entire thesis work and also clearly states the chief conclusions from various chapters. Apart from studies embodied in the thesis, the author has been involved in one other study, which is provided as appendix.

Heart rate changes mediate the embryotoxic effect of antiarrhythmic drugs in the chick embryo A significant increase in cardiovascular medication use during pregnancy has occurred in recent years but only limited evidence on its safety profile is available. We hypothesized that drug-induced bradycardia is the leading mechanism of developmental toxicity. We tested metoprolol, carvedilol, or ivabradine for embryotoxicity and their acute effect on chick embryonic model. We used video microscopy and ultrasound biomicroscopy. Significant dose-dependent mortality was achieved in embryos injected with carvedilol and ivabradine. In ED4 embryos, metoprolol, carvedilol and ivabradine reduced the heart rate by 33%, 27%, and 55%, respectively, compared to controls (6%). In ED8 embryos this effect was more pronounced with a heart rate reduction by 71%, 54%, 53%, respectively (controls 36%). Cardiac output decreased in all tested groups but only proved significant in the metoprolol group in ED8 embryos. The number of -adrenergic receptors showed a downward tendency during embryonic development but a negative chronotropic effect of tested drugs was increasingly pronounced with embryonic maturity. This effect was associated with reduced cardiac output in chick embryos, probably leading to premature death....

Heart rate changes mediate the embryotoxic effect of antiarrhythmic drugs in the chick embryo A significant increase in cardiovascular medication use during pregnancy has occurred in recent years but only limited evidence on its safety profile is available. We hypothesized that drug-induced bradycardia is the leading mechanism of developmental toxicity. We tested metoprolol, carvedilol, or ivabradine for embryotoxicity and their acute effect on chick embryonic model. We used video microscopy and ultrasound biomicroscopy. Significant dose-dependent mortality was achieved in embryos injected with carvedilol and ivabradine. In ED4 embryos, metoprolol, carvedilol and ivabradine reduced the heart rate by 33%, 27%, and 55%, respectively, compared to controls (6%). In ED8 embryos this effect was more pronounced with a heart rate reduction by 71%, 54%, 53%, respectively (controls 36%). Cardiac output decreased in all tested groups but only proved significant in the metoprolol group in ED8 embryos. The number of -adrenergic receptors showed a downward tendency during embryonic development but a negative chronotropic effect of tested drugs was increasingly pronounced with embryonic maturity. This effect was associated with reduced cardiac output in chick embryos, probably leading to premature death....