Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. The linear interaction energy (LIE) method is used to explore the energetic properties of the essential process of codon–anticodon recognition on the ribosome. The calculations show the structural and energetic consequences and effects of first, second, and third position mismatches in the ribosomal decoding center. Recognition of stop codons by ribosomal termination complexes is fundamentally different from sense codon recognition. Free energy perturbation simulations are used to study the detailed energetics of stop codon recognition by the bacterial ribosomal release factors RF1 and RF2. The calculations explain the vastly different responses to third codon position A to G substitutions by RF1 and RF2. Also, previously unknown highly specific water interactions are identified. The GGQ loop of ribosomal RFs is essential for its hydrolytic activity and contains a universally methylated glutamine residue. The structural effect of this methylation is investigated. The results strongly suggest that the methylation has no effect on the intrinsic conformation of the GGQ loop, and, thus, that its sole purpose is to enhance interactions in the ribosomal termination complex. A first microscopic, atomic level, analysis of blocker binding to the pharmaceutically interesting potassium ion channel Kv1.5 is presented. A previously unknown uniform binding mode is identified, and experimental binding data is accurately reproduced. Furthermore, problems associated with pharmacophore models based on minimized gas phase ligand conformations are highlighted. Generalized Born and Poisson–Boltzmann continuum models are incorporated into the LIE method to enable implicit treatment of solvent, in an effort to improve speed and convergence. The methods are evaluated and validated using a set of plasmepsin II inhibitors.

Les ataxies épisodiques (EA) d’origine génétique sont un groupe de maladies possédant un phénotype et génotype hétérogènes, mais ont en commun la caractéristique d’un dysfonctionnement cérébelleux intermittent. Les EA de type 1 et 2 sont les plus largement reconnues des ataxies épisodiques autosomiques dominantes et sont causées par un dysfonctionnement des canaux ioniques voltage-dépendants dans les neurones. La présente étude se concentrera sur les mutations causant l'EA-1, retrouvées dans le senseur de voltage (VSD) de Kv1.1, un canal très proche de la famille des canaux Shaker. Nous avons caractérisé les propriétés électrophysiologiques de six mutations différentes à la position F244 et partiellement celles des mutations T284 A/M, R297 K/Q/A/H, I320T, L375F, L399I et S412 C/I dans la séquence du Shaker grâce à la technique du ‘’cut open voltage clamp’’ (COVC). Les mutations de la position F244 situées sur le S1 du canal Shaker sont caractérisées par un décalement des courbes QV et GV vers des potentiels dépolarisants et modifient le couplage fonctionnel entre le domaine VSD et le pore. Un courant de fuite est observé durant la phase d'activation des courants transitoires et peut être éliminé par l'application du 4-AP (4-aminopyridine) ou la réinsertion de l'inactivation de type N mais pas par le TEA (tétraéthylamonium). Dans le but de mieux comprendre les mécanismes moléculaires responsables de la stabilisation d’un état intermédiaire, nous avons étudié séparément la neutralisation des trois premières charges positives du S4 (R1Q, R2Q et R3Q). Il en est ressorti l’existence d’une interaction entre R2 et F244. Une seconde interface entre S1 et le pore proche de la surface extracellulaire agissant comme un second point d'ancrage et responsable des courants de fuite a été mis en lumière. Les résultats suggèrent une anomalie du fonctionnement du VSD empêchant la repolarisation normale de la membrane des cellules nerveuses affectées à la suite d'un potentiel d'action. / The genetic episodic ataxias form a group of disorders with heterogeneous phenotype and genotype, but share the common feature of intermittent cerebellar dysfunction. Episodic ataxia (EA) types 1 and 2 are most widely recognised amongst the autosomal dominant episodic ataxias and are caused by dysfunction of neuronal voltage-gated ion channels. The present study focuses on mutations causing EA-1 located in the voltage sensor domains (VSDs) of Kv1.1. A member of the Shaker channel family. Here, we have characterised the electrophysiological properties of six different mutations at the position of F244 and we also reported the partiality effects of these following mutations T284A/M, R297K/Q/A/H, I320T, L375F, L399I S412C/I on Shaker sequence using the cut open voltage clamp technique (COVC). We have shown that mutations of F244 in the S1 of the Shaker Kv channel positively shift the voltage dependence of the VSD movement and alter functional coupling between VSD and pore domain. The mutations causing immobilization of the VSD movement during activation and deactivation and responsible for creating a leak current during activation, are removed by the application of 4-AP (4-aminopyridine) or by reinsertion of N-type inactivation but not by TEA (tetraethylamonium). Insights into the molecular mechanisms responsible for the stabilization of the intermediate state have been investigated by separately neutralizing the first three charges (R1Q, R2Q and R3Q) in the S4 segment. The result suggests an interaction between R2 and F244 mutants. It was established that a second co-evolved interface exists between S1 and the pore helix near the extracellular surface and it acts as a second anchor point. It is also responsible for generation of leak currents. The results suggest a dysfunction of the VSD in which the affected nerve cells cannot efficiently repolarize following an action potential because of altered delayed rectifier function

Les canaux sodiques dépendants du voltage, ou canaux Nav, jouent un rôle capital dans l'excitabilité neuronale, dans la genèse et dans la propagation des potentiels d'action. Le canal Nav1.9 se distingue par une expression restreinte aux nocicepteurs et par des propriétés électrophysiologiques uniques qui, si elles excluent sa contribution à la phase dépolarisante du potentiel d'action, lui confèreraient un rôle dans la modulation de l'excitabilité des nocicepteurs. Ce travail de thèse vise à caractériser son implication dans la physiopathologie de la douleur par une approche comportementale, moléculaire et fonctionnelle. La première partie de ce travail consiste à étudier la contribution du canal Nav1.9 à la douleur inflammatoire. Nous avons donc réalisé différents tests comportementaux chez des souris knock-out (KO) et des rats traités par antisens (knock-down) modèles de douleur inflammatoire (aigu, subaigu, chronique). L'expression du canal ainsi que ses propriétés électrophysiologiques sont ensuite analysées chez ces mêmes modèles animaux. Notre premier constat est que le canal Nav1.9 n'est pas impliqué dans la réponse à une stimulation mécanique ou thermique chaude nociceptive chez des animaux sains. En revanche, l'hypersensibilité douloureuse thermique et mécanique induite par une inflammation subaiguë (carragénine intraplantaire) ou chronique (monoarthrite) est significativement réduite chez la souris KO Nav1.9. Un résultat similaire est obtenu par traitement antisens chez le rat, sur le modèle d'inflammation subaiguë. Chez la souris, suite à l'induction d'une inflammation subaiguë, une légère diminution suivie d'une forte augmentation de l'expression protéique du canal Nav1.9 est observée dans les ganglions rachidiens innervant la patte enflammée. Une augmentation de la quantité de canaux est également observée au niveau des troncs nerveux cutanés innervant cette même zone. Les canaux néosynthétisés ne contribuent pas au courant sodique enregistré en patch clamp dans les corps cellulaires des neurones des ganglions rachidiens, mais nos données suggèrent qu'ils sont exportés en direction des terminaisons nerveuses, où ils pourraient devenir fonctionnels et augmenter l'excitabilité cellulaire. La deuxième partie de ce travail de thèse consiste à caractériser l'implication de canal Nav1.9 dans la perception du froid et dans l'hypersensibilité au froid induite par l'oxaliplatine. Nous avons en effet observé de manière inattendue que les souris KO Nav1.9 présentent des seuils de douleur au froid (<10°C) plus élevés que les souris sauvages. Ce phénomène est confirmé par plusieurs tests comportementaux chez les souris KO et chez des rats traités par antisens anti-Nav1.9. L'oxaliplatine, prescrit dans le traitement des cancers colorectaux, est connu pour induire une hypersensibilité au froid invalidante chez la majorité des patients. Nous avons donc décidé d'étudier la contribution du canal Nav1.9 à ce symptôme. Suite à une injection unique d'oxaliplatine, une forte hypersensibilité au froid apparait chez les souris dès 20°C. Nous montrons que le KO Nav1.9 permet de supprimer l'hypersensibilité au froid aux températures normalement non douloureuses (20 et 15°C, allodynie), et de réduire l'hypersensibilité aux températures douloureuses (10 et 5°C, hyperalgie). Le même effet est observé chez le rat après traitement antisens. En conclusion, ce travail permet de mettre en évidence l'intérêt du canal Nav1.9 en tant que cible pharmacologique potentielle pour le traitement de douleurs inflammatoires et de l'hypersensibilité au froid induite par l'oxaliplatine. Il est de plus intéressant de constater que les seuils de réponse à des stimuli nociceptifs ne sont pas perturbés chez les souris KO Nav1.9 saines, à l'exception de la douleur provoquée par des températures froides extrêmes. Le blocage du canal Nav1.9 aurait donc des propriétés anti-hyperalgiques plutôt qu'antalgique, ce qui est conceptuellement intéressant.

Compromised calcium homeostasis in the central nervous system (CNS) is implicated as a major contributor in the pathology of neurodegeneration. Dysregulation of Ca2+ homeostasis initiates downstream Ca2+–dependent events that lead to apoptotic and/or necrotic cell death. Increases in the intracellular free calcium concentration ([Ca2+]i) may be the result of Ca2+ influx from the extracellular environment or Ca2+ release from intracellular Ca2+ stores such as the endoplasmic reticulum (ER). Influx from the extracellular environment is controlled predominantly by voltage gated calcium channels (VGCC), such as L–type calcium channels (LTCC) and ionotropic glutamate receptors, such as the N–methyl–D–aspartate (NMDA) receptors. Ca2+ release from the ER occurs through the inositol–1,4,5–triphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) via IP3–induced or Ca2+–induced mechanisms. Mitigation of Ca2+ overload through these Ca2+ channels offers an opportunity for pharmacological interventions that may protect against neuronal death. In the present study the ability of a novel series of polycyclic compounds, both the pentacycloundecylamines and triquinylamines, to regulate calcium influx through LTCC was evaluated in PC12 cells using calcium imaging with Fura–2/AM in a fluorescence microplate reader. We were also able for the first time to determine IC50 values for these compounds as LTCC blockers. In addition, selected compounds were evaluated for their ability to offer protection in apoptosis–identifying assays such as the lactate dehydrogenase release assay (LDH–assay), trypan blue staining assay and immunohistochemistry utilizing the Annexin V–FITC stain for apoptosis. We were also able to obtain single crystal structures for the tricyclo[6.3.0.02,6]undecane–4,9–dien–3,11–dione (9) and tricyclo[6.3.0.02,6]undecane–3,11–dione (10) scaffolds as well as a derivative, N–(3–methoxybenzyl)–3,11–azatricyclo[6.3.0.02,6]undecane (14f). We also evaluated the possibility that the polycyclic compounds might be able to modulate Ca2+ flux through intracellular Ca2+ channels. Computational methods were utilized to accurately predicted IC50 values and develop a QSAR model with marginal error. The linear regression model delivered r2 = 0.83, which indicated a favorable correlation between the predicted and experimental IC50 values. This model could thus serve as valuable predictor for future structural design and optimization efforts. Data obtained from the crystallographic analysis confirmed the NMR–data based structural assignments done for these compounds in previous studies. Obtaining structural information gave valuable insight into the differences in size and geometric constrains, which are key features for the LTCC activity of these compounds. vii In conclusion, we found that all of the compounds evaluated were able to attenuate Ca2+ influx through the LTCC, with some compounds having IC50 values comparable with known LTCC blockers such as nimodipine. Representative compounds were evaluated for their ability to afford protection against apoptosis induced by 200 ?M H2O2. With the exception of compound 14c (the most potent LTCC blocker in the series, IC50 = 0.398 ?M), most compounds were able to afford protection at two or more concentrations evaluated. Compound 14c displayed inherent toxicity at the highest concentrations evaluated (100 ?M). We concluded that compounds representing both types of structures (pentacycloudecylamines and triquinylamines) have the ability to attenuate excessive Ca2+ influx through the LTCC. In general the aza–pentacycloundecylamines (8a–c) were the most potent LTCC blocker which also had the ability to offer protection in the cell viability assays. However, NGP1–01 (7a) had the most favorable pharmacological profile overall with good activity as an LTCC blocker (IC50 = 86 ?M) and the ability to significantly attenuate cell death in the cell viability assays, exhibiting no toxicity. In addition to their ability to modulate Ca2+ influx from the extracellular environment, these compounds also displayed the ability to modulate Ca2+ flux through intracellular Ca2+ channels. The mechanisms by which they act on intracellular Ca2+ channels still remains unclear, but from this preliminary study it would appear that these compounds are able to partially inhibiting Ca2+–ATPase activity whilst possibly simultaneously inhibiting the IP3R. In the absence of extracellular Ca2+ these compounds showed the ability in inhibit voltage–induced Ca2+ release (VICaR), possibly by modulating the gating charge of the voltage sensor being the dihydropyridine receptors. In future studies it might be worthwhile to do an expanded QSAR study and evaluate the aza–pentacycloundecylamines. To clarify the mechanisms by which the polycyclic compounds interact with intracellular Ca2+ channels we should examine the direct interaction with the individual Ca2+ channels independently. The polycyclic compounds evaluated in this study demonstrate potential as multifunctional drugs due to their ability to broadly regulate calcium homeostasis through multiple pathways of Ca2+ entry. This may prove to be more effective in diseases where perturbed Ca2+ homeostasis have devastating effects eventually leading to excitotoxicity and cell death. / Thesis (Ph.D. (Pharmaceutical Chemistry))--North-West University, Potchefstroom Campus, 2012.

Compromised calcium homeostasis in the central nervous system (CNS) is implicated as a major contributor in the pathology of neurodegeneration. Dysregulation of Ca2+ homeostasis initiates downstream Ca2+–dependent events that lead to apoptotic and/or necrotic cell death. Increases in the intracellular free calcium concentration ([Ca2+]i) may be the result of Ca2+ influx from the extracellular environment or Ca2+ release from intracellular Ca2+ stores such as the endoplasmic reticulum (ER). Influx from the extracellular environment is controlled predominantly by voltage gated calcium channels (VGCC), such as L–type calcium channels (LTCC) and ionotropic glutamate receptors, such as the N–methyl–D–aspartate (NMDA) receptors. Ca2+ release from the ER occurs through the inositol–1,4,5–triphosphate receptors (IP3Rs) or ryanodine receptors (RyRs) via IP3–induced or Ca2+–induced mechanisms. Mitigation of Ca2+ overload through these Ca2+ channels offers an opportunity for pharmacological interventions that may protect against neuronal death. In the present study the ability of a novel series of polycyclic compounds, both the pentacycloundecylamines and triquinylamines, to regulate calcium influx through LTCC was evaluated in PC12 cells using calcium imaging with Fura–2/AM in a fluorescence microplate reader. We were also able for the first time to determine IC50 values for these compounds as LTCC blockers. In addition, selected compounds were evaluated for their ability to offer protection in apoptosis–identifying assays such as the lactate dehydrogenase release assay (LDH–assay), trypan blue staining assay and immunohistochemistry utilizing the Annexin V–FITC stain for apoptosis. We were also able to obtain single crystal structures for the tricyclo[6.3.0.02,6]undecane–4,9–dien–3,11–dione (9) and tricyclo[6.3.0.02,6]undecane–3,11–dione (10) scaffolds as well as a derivative, N–(3–methoxybenzyl)–3,11–azatricyclo[6.3.0.02,6]undecane (14f). We also evaluated the possibility that the polycyclic compounds might be able to modulate Ca2+ flux through intracellular Ca2+ channels. Computational methods were utilized to accurately predicted IC50 values and develop a QSAR model with marginal error. The linear regression model delivered r2 = 0.83, which indicated a favorable correlation between the predicted and experimental IC50 values. This model could thus serve as valuable predictor for future structural design and optimization efforts. Data obtained from the crystallographic analysis confirmed the NMR–data based structural assignments done for these compounds in previous studies. Obtaining structural information gave valuable insight into the differences in size and geometric constrains, which are key features for the LTCC activity of these compounds. vii In conclusion, we found that all of the compounds evaluated were able to attenuate Ca2+ influx through the LTCC, with some compounds having IC50 values comparable with known LTCC blockers such as nimodipine. Representative compounds were evaluated for their ability to afford protection against apoptosis induced by 200 ?M H2O2. With the exception of compound 14c (the most potent LTCC blocker in the series, IC50 = 0.398 ?M), most compounds were able to afford protection at two or more concentrations evaluated. Compound 14c displayed inherent toxicity at the highest concentrations evaluated (100 ?M). We concluded that compounds representing both types of structures (pentacycloudecylamines and triquinylamines) have the ability to attenuate excessive Ca2+ influx through the LTCC. In general the aza–pentacycloundecylamines (8a–c) were the most potent LTCC blocker which also had the ability to offer protection in the cell viability assays. However, NGP1–01 (7a) had the most favorable pharmacological profile overall with good activity as an LTCC blocker (IC50 = 86 ?M) and the ability to significantly attenuate cell death in the cell viability assays, exhibiting no toxicity. In addition to their ability to modulate Ca2+ influx from the extracellular environment, these compounds also displayed the ability to modulate Ca2+ flux through intracellular Ca2+ channels. The mechanisms by which they act on intracellular Ca2+ channels still remains unclear, but from this preliminary study it would appear that these compounds are able to partially inhibiting Ca2+–ATPase activity whilst possibly simultaneously inhibiting the IP3R. In the absence of extracellular Ca2+ these compounds showed the ability in inhibit voltage–induced Ca2+ release (VICaR), possibly by modulating the gating charge of the voltage sensor being the dihydropyridine receptors. In future studies it might be worthwhile to do an expanded QSAR study and evaluate the aza–pentacycloundecylamines. To clarify the mechanisms by which the polycyclic compounds interact with intracellular Ca2+ channels we should examine the direct interaction with the individual Ca2+ channels independently. The polycyclic compounds evaluated in this study demonstrate potential as multifunctional drugs due to their ability to broadly regulate calcium homeostasis through multiple pathways of Ca2+ entry. This may prove to be more effective in diseases where perturbed Ca2+ homeostasis have devastating effects eventually leading to excitotoxicity and cell death. / Thesis (Ph.D. (Pharmaceutical Chemistry))--North-West University, Potchefstroom Campus, 2012.

Receptores purinérgicos e canais de cálcio voltagem-dependentes estão envolvidos em diversos processos biológicos como na gastrulação, durante o desenvolvimento embrionário, e na diferenciação neural. Quando ativados, canais de cálcio voltagem-dependentes e receptores purinérgicos do tipo P2, ativados por nucleotídeos, desencadeiam transientes de cálcio intracelulares controlando diversos processos biológicos. Neste trabalho, nós estudamos a participação de canais de cálcio voltagem-dependentes e receptores do tipo P2 na geração de transientes de cálcio espontâneos e sua regulação na expressão de fatores de transcrição relacionados com a neurogênese utilizando como modelo células tronco (CTE) induzidas à diferenciação em células tronco neurais (NSC) com ácido retinóico. Descrevemos que CTE indiferenciadas podem ter a proliferação acelerada pela ativação de receptores P2X7, enquanto que a expressão e a atividade desse receptor precisam ser inibidas para o progresso da diferenciação em neuroblasto. Além disso, ao longo da diferenciação neural, por análise em tempo real dos níveis de cálcio intracelular livre identificamos 3 padrões de oscilações espontâneas de cálcio (onda, pico e unique), e mostramos que ondas e picos tiveram a frequência e amplitude aumentadas conforme o andamento da diferenciação. Células tratadas com o inibidor do receptor de inositol 1,4,5-trifosfato (IP3R), Xestospongin C, apresentaram picos mas não ondas, indicando que ondas dependem exclusivamente de cálcio oriundo do retículo endoplasmático pela ativação de IP3R. NSC de telencéfalo de embrião de camundongos transgênicos ou pré-diferenciadas de CTE tratadas com Bz-ATP, o agonista do receptor P2X7, e com 2SUTP, agonista de P2Y2 e P2Y4, aumentaram a frequência e a amplitude das oscilações espontâneas de cálcio do tipo pico. Dados, obtidos por microscopia de luminescência, da expressão em tempo real de gene repórter luciferase fusionado à Mash1 e Ngn2 revelou que a ativação dos receptores P2Y2/P2Y4 aumentou a expressão estável de Mash1 enquanto que ativação do receptor P2X7 levou ao aumento de Ngn2. Além disso, células na presença do quelante de cálcio extracelular (EGTA) ou do depletor dos estoques intracelulares de cálcio do retículo endoplasmático (thapsigargin) apresentaram redução na expressão de Mash1 e Ngn2, indicando que ambos são regulados pela sinalização de cálcio. A investigação dos canais de cálcio voltagem-dependentes demonstrou que o influxo de cálcio gerado por despolarização da membrana de NSC diferenciadas de CTE é decorrente da ativação de canais de cálcio voltagem-dependentes do tipo L. Além disso, esse influxo pode controlar o destino celular por estabilizar expressão de Mash1 e induzir a diferenciação neuronal por fosforilação e translocação do fator de transcrição CREB. Esses dados sugerem que os receptores P2X7, P2Y2, P2Y4 e canais de cálcio voltagem-dependentes do tipo L podem modular as oscilações espontâneas de cálcio durante a diferenciação neural e consequentemente alteram o padrão de expressão de Mash1 e Ngn2 favorecendo a decisão do destino celular neuronal. / Purinergic receptors and voltage gated Ca2+ channels have been attributed with developmental functions including gastrulation and neural differentiation. Upon activation, nucleotide-activated P2 purinergic receptor and voltage-gated Ca2+ channel subtypes trigger intracellular calcium transients controlling cellular processes. Here, we studied the participation of voltage-gated calcium channels and P2 receptor activity in spontaneous calcium transients and consequent regulation expression of transcription factors related to retinoic acid-induced neurogenesis of mouse neural stem and embryonic stem cells (ESC). In embryonic pluripotent stem cells, proliferation is accelerated by P2X7 receptor activation, while receptor expression / activity needs to be down-regulated for the progress of neuroblast differentiation. Moreover, along neural differentiation time lapse imaging with means of a cytosolic calcium-sensitive fluorescent probe provided different patterns of spontaneous calcium transients (waves and spikes) showing that both, frequency and amplitude increased along differentiation. Cells treated with the inositol 1,4,5-trisphosphate receptor (IP3R) inhibitor Xestospongin C showed spikes but not waves, indicating that waves exclusively depended on calcium release from endoplasmic reticulum by IP3R activation. Cells treated with the P2X7 receptor subtype agonist Bz-ATP and the P2Y2 and P2Y4 receptor 2-S-UTP increased frequency and amplitudes of calcium transients, mainly spikes, in embryonic telencephalon neural stem cells (NSC) and NSC pre-differentiated from ESC. Data obtained by luminescence time lapse imaging of stable transfected cells with Mash1 or Ngn2 promoter-protein fusion to luciferase reporter construct revealed increased Mash1 expression due to activation of P2Y2/P2Y4 receptor subtypes, while increased expression of Ngn2 was observed following P2X7 receptor activation. In addition, cells imaged in presence of the extracellular calcium chelator EGTA or following endoplasmic reticulum calcium store depletion by thapsigargin showed a decrease in Mash1 and Ngn2 expression, indicating that both are regulated by calcium signaling. Investigation of the roles of voltage gated Ca2+ channels in neural differentiation showed that Ca2+ influx in NSC pre-differentiated from ESC is due to membrane depolarization and L-type voltage gated Ca2+ channel activation, thereby controlling cell fate decision, by stabilizing the expression of MASH1 and inducing differentiation, by phosphorylation of the transcription factor CREB. Altogether these data suggest that P2X7, P2Y2, P2Y4 receptors and L-type voltage gated Ca2+ channels can modulate spontaneous calcium oscillations during neural differentiation and consequently change the Mash1 and Ngn2 expression patterns, thus favoring the cell fate decision to the neuronal phenotype.

KCNE1 (E1) peptide is the founding member of the KCNE family (1-5), which is a class of type I transmembrane ß-subunits. KCNE1 peptides assemble with and modulate the gating, ion conducting properties and pharmacology of a variety of voltage-gated K+ channel a-subunits, including KCNQ1 (Q1). Mutations that interfere with the function of either E1 and/or Q1 and disrupt the assembly and trafficking of KCNE1- KCNQ1 channel complexes give rise to diseases such as Romano-Ward (RW) and Jervell Lange Nielsen Syndrome (JLNS), two different forms of Long QT Syndrome (LQTS). Using enzymatic deglycosylation assays, immunofluorescence techniques and quantitative cell surface labeling, we showed that KCNE1 peptides are retained in the early stages of the secretory pathway as immaturely N-linked glycosylated proteins. KCNE1 co-assembly with KCNQ1 leads to E1 progression through the secretory pathway and glycan maturation, resulting in cell surface expression. N-linked glycosylation of some membrane proteins is critical for proper folding, co-assembly and subsequent trafficking through the biosynthetic pathway. Previous studies have shown that genetic mutations that disrupt one of the two N-linked glycosylation sites on KCNE family members lead to LQTS (T7I, KCNE1 and T8A, KCNE2) (Schulze-Bahr et al., 1997; Sesti et al., 2000a; Park et al., 2003). Having confirmed that KCNE1 proteins acquire N-linked glycans, we examined the kinetics and efficiency of N-linked glycan addition to KCNE1. We showed that KCNE1 has two distinct N-linked glycosylation sites. The N-terminal sequon is a traditional co-translational site. The internal sequon (which is only ~ 20 residues away from the N-terminal sequon) acquires N-linked glycans primarily after protein synthesis (post-translationally). Surprisingly, mutations that prevent N-glycosylation at the cotranslational site also reduce the glycosylation efficiency of post-translational glycosylation at the internal sequon, resulting in a large population of unglycosylated KCNE1 peptides that are retained in the early stages of the secretory pathway and do not reach the cell surface with their cognate K+ channel. We showed that KCNE1 post-translational N-glycosylation in the endoplasmic reticulum is a cellular mechanism that ensures E1 proteins acquire the maximal number of glycans needed for proper channel assembly and trafficking. Our findings provide a new biogenic mechanism for human disease by showing that the JLNS mutation, T7I, not only inhibits glycosylation of the N-terminal sequon, but also indirectly prevents the glycosylation of the internal sequon, giving rise to a large population of assembly incompetent hypoglycosylated KCNE1 peptides. To further investigate the two N-linked glycosylation sites on KCNE1, we generated structure-function deletion scans of KCNE1 and performed positional glycosylation scanning mutagenesis. We examined the glycosylation pattern of glycosylation mutants in an effort to define the glycosylation window important for proper KCNE1 assembly and trafficking. Our findings suggested a nine amino acid periodicity to serve as a desirable glycosylation site and a better substrate for N-glycosylation. Appendix II shows work on the characterization of the C-terminally HA-tagged KCNE1 protein, which was used throughout the experiments presented in Chapter II, Chapter III and Chapter IV. Analysis of the C-terminally HA-tagged KCNE1 protein revealed that in heterologous expression systems KCNE1 had an internal translational start site, a methionine at position 27. A proteolytic cleavage site was also identified at the arginine cluster spanning residues 32 through 38 bearing the two known Long QT mutations (R32H and R36H) (Splawski et al., 2000; Napolitano et al., 2005). My work in Professor Craig C. Mello’s lab during the first four years of my graduate study is presented in Appendix I. The highly conserved Wnt/Wingless glycoproteins regulate many aspects of animal development. Wnt signaling specifies endoderm fate by controlling the fate of EMS blastomere daughters in 4-cell stage Caenorhabditis elegans embryos. A suppressor genetic screen was performed using two temperature sensitive alleles of mom-2/Wnt to identify additional regulators of the Wnt/Wingless signaling pathway during C. elegans endoderm specification. Five intragenic suppressors and three extragenic suppressors of mom-2/Wnt embryonic lethality were identified. We cloned ifg-1, eIF4G homologue, as one of the extragenic suppressors suggesting an intriguing connection between the Wnt signaling pathway and the translational machinery.

No description available.

Analyses of the evolution and function of voltage-gated sodium channel proteins (Navs) have largely been limited to mutations from individual people with diagnosed neuromuscular disease. This project investigates the carboxyl-terminus of the Nav paralog (locus scn4aa 3’) that is preferentially expressed in electric organs of Neotropical weakly-electric fishes (Order Gymnotiformes). As a model system, I used the genus Gymnotus, a diverse clade of fishes that produce species-specific electric organ discharges (EODs). I clarified evolutionary relationships among Gymnotus species using mitochondrial (cytochrome b, and 16S ribosome) and nuclear (rag2, and scn4aa) gene sequences (3739 nucleotide positions from 28 Gymnotus species). I analyzed the molecular evolution of scn4aa 3’, and detected evidence for positive selection at eight amino acid sites in seven Gymnotus lineages. These eight amino acid sites are located in motifs that may be important for modulation of EOD frequencies.

Analyses of the evolution and function of voltage-gated sodium channel proteins (Navs) have largely been limited to mutations from individual people with diagnosed neuromuscular disease. This project investigates the carboxyl-terminus of the Nav paralog (locus scn4aa 3’) that is preferentially expressed in electric organs of Neotropical weakly-electric fishes (Order Gymnotiformes). As a model system, I used the genus Gymnotus, a diverse clade of fishes that produce species-specific electric organ discharges (EODs). I clarified evolutionary relationships among Gymnotus species using mitochondrial (cytochrome b, and 16S ribosome) and nuclear (rag2, and scn4aa) gene sequences (3739 nucleotide positions from 28 Gymnotus species). I analyzed the molecular evolution of scn4aa 3’, and detected evidence for positive selection at eight amino acid sites in seven Gymnotus lineages. These eight amino acid sites are located in motifs that may be important for modulation of EOD frequencies.