This thesis explores how basic region/leucine zipper (bZIP) transcription factors target gene regulatory sequences. The GCN4 bZIP binds to more than one target site [CRE (TGACGTCA) and cognate AP-1 (TGACTCA)] and exhibits flexibility in -helical structure. These observations suggest that the GCN4 bZIP can establish sequence-selective DNA binding at noncognate target sites. Studies on such noncognate but sequence-selective binding can provide insights into how bZIP proteins search for and localize to their cognate target sites. This thesis investigates DNA binding by the GCN4 bZIP and its structural and functional mimic, the wild-type (wt) bZIP, at noncognate gene regulatory sequences C/EBP (TTGCGCAA), E-box (CACGTG), HRE (GCACGTAG), XRE1 (TTGCGTGA), and related DNA sequences. These DNA-binding activities are sequence-selective, as confirmed by DNase I footprinting and electrophoretic mobility shift assay (EMSA). Full- and half-site DNA-binding affinities, determined by EMSA titrations, decrease from cognate to noncognate binding. At noncognate target sites, the bZIP proteins form a dimer of -helices, as indicated by circular dichroism (CD) spectroscopy and EMSA. These results demonstrate that the bZIP proteins can establish noncognate but sequence-selective DNA binding, and suggest such DNA binding potentially contributes to structure preorganization and rapid translocation of the bZIP proteins when they search for their cognate target sites, to which they then bind with high affinity. This thesis also indicates a highly dynamic DNA-binding model for the bZIP proteins to establish strong and sequence-selective DNA binding. The C/EBP site includes two 5H-LR (TTGCG) half-sites, each of which comprises two 4-bp subsites. The in vitro and in silico results together demonstrate that the basic region at 5H-LR recognizes the 4-bp subsites alternately as distinct units, which requires it to translocate between the subsites, potentially by sliding or hopping. Taken as a whole, this thesis provides further insights into how bZIP transcription factors accomplish sequence-selective DNA binding.

This thesis explores how basic region/leucine zipper (bZIP) transcription factors target gene regulatory sequences. The GCN4 bZIP binds to more than one target site [CRE (TGACGTCA) and cognate AP-1 (TGACTCA)] and exhibits flexibility in -helical structure. These observations suggest that the GCN4 bZIP can establish sequence-selective DNA binding at noncognate target sites. Studies on such noncognate but sequence-selective binding can provide insights into how bZIP proteins search for and localize to their cognate target sites. This thesis investigates DNA binding by the GCN4 bZIP and its structural and functional mimic, the wild-type (wt) bZIP, at noncognate gene regulatory sequences C/EBP (TTGCGCAA), E-box (CACGTG), HRE (GCACGTAG), XRE1 (TTGCGTGA), and related DNA sequences. These DNA-binding activities are sequence-selective, as confirmed by DNase I footprinting and electrophoretic mobility shift assay (EMSA). Full- and half-site DNA-binding affinities, determined by EMSA titrations, decrease from cognate to noncognate binding. At noncognate target sites, the bZIP proteins form a dimer of -helices, as indicated by circular dichroism (CD) spectroscopy and EMSA. These results demonstrate that the bZIP proteins can establish noncognate but sequence-selective DNA binding, and suggest such DNA binding potentially contributes to structure preorganization and rapid translocation of the bZIP proteins when they search for their cognate target sites, to which they then bind with high affinity. This thesis also indicates a highly dynamic DNA-binding model for the bZIP proteins to establish strong and sequence-selective DNA binding. The C/EBP site includes two 5H-LR (TTGCG) half-sites, each of which comprises two 4-bp subsites. The in vitro and in silico results together demonstrate that the basic region at 5H-LR recognizes the 4-bp subsites alternately as distinct units, which requires it to translocate between the subsites, potentially by sliding or hopping. Taken as a whole, this thesis provides further insights into how bZIP transcription factors accomplish sequence-selective DNA binding.

α-Isopropylmalate synthase (α-IPMS) catalyses the first committed step in leucine biosynthesis in bacteria, including Neisseria meningitidis and Mycobacterium tuberculosis. It catalyses the condensation of α-ketoisovalerate (α-KIV) and acetyl coenzyme A (AcCoA) to form α-isopropylmalate (α-IPM). Like many key enzymes in biosynthesis, α-IPMS is inhibited by the end-product of the biosynthetic pathway, in this case leucine. α-IPMS is homodimeric, with monomers consisting of a (β/α)8-barrel catalytic domain, two subdomains and a C-terminal regulatory domain, responsible for binding leucine and providing feedback inhibition for leucine biosynthesis. The exact mechanism of feedback inhibition in this enzyme is unknown, despite the elucidation of crystal structures with and without leucine bound. This thesis explores the nature of allosteric regulation in α-IPMS, including the effects of the regulatory domain and the importance of structural asymmetry on catalytic activity. Chapter 2 details the characterisation of wild-type α-IPMS from N. meningitidis (NmeIPMS). This protein was successfully cloned, expressed and purified by metal-affinity and size-exclusion chromatography. NmeIPMS has similar characteristics to previously characterised α-IPMSs, being a dimer and demonstrating substrate binding affinities in the micromolar range. This enzyme has a turnover number of 13s⁻¹ and is sensitive to mixed, non-competitive inhibition by the amino acid leucine. Small angle X-ray scattering experiments reveal that the solution-phase structure of this protein is likely similar to existing crystal structures of other α-IPMSs. In Chapter 3, substitutions of residues potentially involved in the binding and transmission of the leucine regulatory mechanism are described. Most of these amino acid substituted variants reduce enzyme sensitivity to leucine, and one variant is almost entirely insensitive to this inhibitor. Another of these variants demonstrates an unexpected decrease in substrate affinity, despite the substituted residue being located far from the active site. The independence of α-IPMS domains is investigated in Chapter 4. The catalytic domains were isolated from NmeIPMS and the α-IPMS from M. tuberculosis (MtuIPMS), and found to be unable to catalyse the condensation of substrates, despite maintaining the wild-type structural fold. Complementation studies with Escherichia coli cells lacking the gene for α-IPMS show that the truncated variants are unable to rescue growth in these cells. Binding of α-KIV in the truncated NmeIPMS variant is much stronger than in the wild-type, and this may be the reason for lack of competent catalysis. A crystal structure was solved for the truncated variant of NmeIPMS and indicates that the regulatory domain is required for proper positioning of large regions of the protein. Two isolated regulatory domains from NmeIPMS were cloned, but with limited success in characterisation. Finally, Chapter 5 describes substitutions made in MtuIPMS to affect relative domain orientations within the protein. Dimer asymmetry is investigated by substituting residues at the domain interfaces. These substitutions did have some effect on catalysis and inhibition, but did not show any change in average solution-phase structure. These results are drawn together in the greater context of allostery in general in Chapter 6, along with ideas for future research in this field. This chapter reviews the insights gained into protein structure from this thesis, particularly the importance of residues at protein domain interfaces. The asymmetry in the α-IPMS structure is discussed, along with small-molecule binding regulatory domains.

This study revolves around a family in which 4 male members have metabolic profiles similar to that of atypical 3–methylcrotonyl–CoA carboxylase (MCC) deficiency, an inborn error of leucine catabolism. This profile consists of high urinary 3–hydroxyisovaleric acid (3–HIVA) and trace amounts of 3–methylcrotonylglycine. One of the individuals also had clinical symptoms of chronic fatigue and muscle weakness, symptoms also related to MCC–deficiency. Further investigation showed that these individuals were negative for MCC–deficiency. The inheritance pattern of the abnormal metabolic profile seemed to indicate a link to the X–chromosome. In this study the single nucleotide polymorphism (SNP) and copy number variation (CNV) profiles of the X–chromosomes of participating members of the family were investigated for a possible link to the abnormal metabolic profile, using SNP6 DNA microarrays. The data generated by the SNP6 arrays was of good quality. The small sample size available for this study necessitated an unorthodox method for analysing the SNP6 data. No clear link between the SNP6 data and the abnormal metabolic profile was found. Selected SNP calls made by the SNP6 arrays were verified by sequencing. The origin of the elevated 3–HIVA detected in the urine of the male family members was also investigated. This was done by culturing fibroblasts from case individuals in culture medium supplemented with deuterium labelled leucine. The culture medium was analysed using GC–MS after an organic acid extraction. The resulting data seems to indicate at least two sources of 3–HIVA formation by the cells, one originating from leucine and another from a source other than leucine. The mevalonate shunt is one possible source of 3–HIVA, which does not originate from leucine catabolism. / Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.

This study revolves around a family in which 4 male members have metabolic profiles similar to that of atypical 3–methylcrotonyl–CoA carboxylase (MCC) deficiency, an inborn error of leucine catabolism. This profile consists of high urinary 3–hydroxyisovaleric acid (3–HIVA) and trace amounts of 3–methylcrotonylglycine. One of the individuals also had clinical symptoms of chronic fatigue and muscle weakness, symptoms also related to MCC–deficiency. Further investigation showed that these individuals were negative for MCC–deficiency. The inheritance pattern of the abnormal metabolic profile seemed to indicate a link to the X–chromosome. In this study the single nucleotide polymorphism (SNP) and copy number variation (CNV) profiles of the X–chromosomes of participating members of the family were investigated for a possible link to the abnormal metabolic profile, using SNP6 DNA microarrays. The data generated by the SNP6 arrays was of good quality. The small sample size available for this study necessitated an unorthodox method for analysing the SNP6 data. No clear link between the SNP6 data and the abnormal metabolic profile was found. Selected SNP calls made by the SNP6 arrays were verified by sequencing. The origin of the elevated 3–HIVA detected in the urine of the male family members was also investigated. This was done by culturing fibroblasts from case individuals in culture medium supplemented with deuterium labelled leucine. The culture medium was analysed using GC–MS after an organic acid extraction. The resulting data seems to indicate at least two sources of 3–HIVA formation by the cells, one originating from leucine and another from a source other than leucine. The mevalonate shunt is one possible source of 3–HIVA, which does not originate from leucine catabolism. / Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.

Relaxin and insulin-like peptide-3 (INSL3) are closely related reproductive hormones that are derived from a common ancestor. Relaxin was initially named for its ability to relax the pubic symphysis in pregnant guinea pigs at parturition. Since then relaxin has been found to be involved in many physiological processes based on its ability to stimulate the breakdown and remodeling of collagen fibers. INSL3 is also known as Leydig insulin-like hormone and the relaxin-like factor, and is produced by the Leydig cells in the testis, the thecal and luteal cells of the ovary, the thyroid, placenta and mammary gland. INSL3 induces transabdominal testicular descent by stimulating the development of the gubernacular ligament, which subsequently swells and contracts to pull the fetal testes towards the inguinal wall. In adults however, evidence suggests that INSL3 is involved in reproductive function, acting to promote the survival of male and female germ cells.

Thesis (Ph.D.)--Baylor University, 2008. / Includes bibliographical references (p. 121-133)

Thesis (Ph.D. in Pharmacology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 148-159). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

As Stanniocalcinas (STC1 e STC2) são hormônios glicoproteicos originalmente encontrados em peixes teleósteos. Em mamíferos, esses hormônios são expressos em uma variedade de tecidos e estão envolvidos em processos como o transporte de cálcio e fosfato pelos rins e intestino, a carcinogênese, a reprodução e o crescimento. Recentemente, foram encontrados efeitos da STC1 e da STC2 no metabolismo intermediário. Sítios de ligação para a STC1 já foram identificados na membrana mitocondrial e resultados preliminares do nosso laboratório demonstraram que a STC1 possui um efeito inibitório sobre a gliconeogênese renal e tanto a STC1 quanto a STC2 diminuem a incorporação de 14C-glicose em 14CO2 no fígado e no músculo gastrocnêmio, respectivamente, de ratos. No entanto, o papel desses hormônios no metabolismo de aminoácidos permanece desconhecido. No presente trabalho, as ações da STC1 e da STC2 foram avaliadas no fígado e no músculo gastrocnêmio excisados de ratos machos (Rattus norvegicus, n=48 animais) de 300±50g, alimentados ad libitum. Os resultados obtidos mostram que a STC1, no fígado, diminuiu a captação do ácido 2-(metilamino)isobutírico, aumentou a atividade da bomba Na+/K+-ATPase, diminuiu a atividade da enzima malato desidrogenase mitocondrial e estimulou a síntese de glicogênio a partir da alanina. A STC2, no fígado, diminuiu a atividade da enzima malato desidrogenase mitocondrial, estimulou a síntese de proteínas a partir de leucina, e estimulou a síntese de glicogênio a partir de alanina. Já, no músculo, a STC2 estimulou a oxidação de leucina e a incorporação desse aminoácido em proteínas. Esses resultados confirmam a existência de ações das STC1 e STC2 no metabolismo de aminoácidos e sugerem, com exceção da ação da STC2 sobre a enzima malato desidrogenase, um papel anabólico para a STC2 em ambos os tecidos. A mesma afirmação não pode ser feita para a STC1, que apresentou efeitos antagônicos no tecido hepático. Por fim, o trabalho mostrou que as ações da STC1 e da STC2 sobre as vias metabólicas dos aminoácidos ocorrem com a utilização de doses muito baixas desses hormônios. / Stanniocalcins (STC) are glycoprotein hormones that were first discovered in teleostean fishes. In mammals, these hormones are expressed in a variety of tissues. Besides its role on the calcium and phosphate transport by the kidneys and intestine, they are involved in processes such as carcinogenesis, reproduction and growth. Recently it has been shown that STC1 and STC2 affect the control of intermediary metabolism. Binding sites for STC1 have been already identified in the mitochondrial membrane. Preliminary results of our laboratory showed that STC1 has an inhibitory effect on renal gluconeogenesis in rats and both STC1 and STC2 decrease the 14C-glicose incorporation into 14CO2 in the liver and the gastrocnemius muscle, respectively. Despite these evidences that STC1 and STC2 have a role in the control of glucose and lipids metabolism, the function of these hormones in amino acids metabolism remains unknown. In the present study, the STC1 and STC2 actions were evaluated in livers and gastrocnemius muscles excised from male rats (Rattus norvegicus, n=48 animals). The rats weighted 300±50g and were fed ad libitum. The results show that STC1 decreased 2-(metilamine)isobutyric acid uptake, increased Na+/K+-ATPase activity, decreased mitochondrial malate dehydrogenase activity and stimulated glycogen synthesis from alanine. All actions of STC1 were shown in the hepatic tissue and this hormone did not affect any parameter in muscular tissue. In the liver, STC2, decreased the mitochondrial malate dehydrogenase activity, stimulated protein synthesis from leucine and stimulated glycogen synthesis from alanine. In muscle, STC2 stimulated leucine incorporation into CO2 and proteins. These results confirm the regulatory role of STC1 and STC2 on amino acid metabolism in muscle and liver of rats. They suggest, with exception to the STC2 action into the hepatic malate dehydrogenase, an anabolic role for STC2 in both tissues. However this cannot be stated for STC1, which show antagonistic effects in the hepatic tissue. Lastly, another important finding of this study is that STC1 and STC2 actions on amino acid metabolism occur with low hormone concentrations.

Parkinson's Disease (PD) is a late-onset neurodegenerative disease characterized by progressive motor dysfunction caused by a loss of dopaminergic neurons for which there is no known cure. Among the most common genetic causes of PD are mutations in the leucine-rich repeat kinase 2 gene (LRRK2), encoding a multi-domain protein with kinase activity. The LRRK2 G2019S mutation causes hyperactivity of the kinase domain and is the most frequent LRRK2 mutation in patients with familial PD, though its role in PD pathology remains unclear. Preliminary data from the lab of our collaborator, Dr. David Park, demonstrated through a genetic screen in Drosophila melanogaster that the deletion of rbp9 encoding an RNA-binding protein prevented pathology induced by PD-relevant mutations in the LRRK2 kinase domain. The neuronal homolog of RBP9 in humans is HuD, a member of the Hu family of RNA-binding proteins that regulates the expression of many transcripts involved in neuronal development, plasticity, and survival. In addition, HuD has been shown to modify the age-at-onset or risk of developing PD. Here, we studied the effect of LRRK2 on the post-transcriptional regulation of mRNAs bound by HuD in the context of PD. Our findings showed that HuD is a substrate for LRRK2 phosphorylation in vitro, and that LRRK2 G2019S hyperphosphorylates HuD. We demonstrated that LRRK2 kinase activity is required for the binding of several transcripts by HuD that encode PD-relevant proteins such as α-synuclein and neuronal survival factor BDNF. Our findings in human neuroblastoma cells indicated that LRRK2 regulates the protein levels of HuD mRNA targets α-synuclein and BDNF in a mechanism that can by modified by HuD. Finally, we showed that the combination of HuD knockout with LRRK2 G2019S expression in mice rescues aberrant expression of HuD targets in mice with only the LRRK2 G2019S mutation or the knockout of HuD alone. Together, our findings demonstrate that LRRK2 affects the post-transcriptional regulation of HuD-bound mRNAs, and suggest the use of HuD as a potential therapeutic target in patients with PD caused by the LRRK2 G2019S mutation.