Thesis advisor: Evan R. Kantrowitz / The enzyme aspartate transcarbamoylase (ATCase) is an enzyme in the pyrimidine nucleotide biosynthetic pathway. It was once an attractive target for anti-proliferation drugs but has since become a teaching model due to kinetic properties such as cooperativity and allostery exhibited by the Escherichia coli form of the enzyme. ATCase from E. coli has been extensively studied over that last 60 years and is the textbook example of allosteric enzymes. Through this past research it is understood that ATCase is allosterically inhibited by CTP, the end product of pyrimidine biosynthesis, and allosterically activated by ATP, the end product of the parallel purine biosynthetic pathway. Part of the work discussed in this dissertation involves further understanding the catalytic properties of ATCase by examining an unregulated trimeric form from Bacillus subtilis, a bacterial ATCase that more closely resembles the mammalian form than E. coli ATCase. Through X-ray crystallography and molecular modeling, the complete catalytic cycle of B. subtilis ATCase was visualized, which provided new insights into the manifestation of properties such as cooperativity and allostery in forms of ATCase that are regulated. Most of the work described in the following chapters involves understanding allostery in E. coli ATCase. The work here progressively builds a new model of allostery through new X-ray structures of ATCase*NTP complexes. Throughout these studies it has been determined that the allosteric site is bigger than previously thought and that metal ions play a significant role in the kinetic response of the enzyme to nucleotide effectors. This work proves that what is known about ATCase regulation is inaccurate and that currently accepted, and taught, models of allostery are wrong. This new model of allostery for E. coli ATCase unifies all old and current data for ATCase regulation, and has clarified many previously unexplainable results. / Thesis (PhD) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

In order to maintain genetic stability in eukaryotes, tight regulation of the relative sizes of deoxyribonucleoside triphosphate (dNTP) levels inside the cell is essential for optimal fidelity of DNA replication. Ribonucleotide reductase (RNR) is the enzyme responsible for proportional production of DNA precursors. Studies on regulation of this enzyme, the focus of this thesis, are important because mutations affecting RNR control mechanisms result in dNTP pool imbalance, thus promoting mutagenesis. By using mouse RNR as a model for mammalian forms of the enzyme, three major factors--allosteric effectors, rNDP substrate concentrations, and hypoxic conditions--that influence the substrate specificity of RNR have been investigated. Allosteric regulation has been studied by the four-substrate assay, which permits simultaneous monitoring of the four reactions catalyzed by this enzyme in one reaction mixture. Individual dNTPs affect the four activities differentially in a concentration-dependent manner with discrete effects of dTTP and dGTP on reduction of ADP and GDP, respectively. Ribonucleoside diphosphate (rNDP) substrate concentrations are equally important, as their variations lead to different product ratios. Results from nucleotide binding assays indicate that rNDPs directly influence binding of dNTP effectors at the specificity site, one of the two classes of allosteric sites, whereas ADP has an indirect effect, displacing other substrates at the catalytic site and consequently removing effects of those substrates upon dNTP binding. Hence, this is the first evidence of a two-way communication between the catalytic site and the specificity site. Oxygen limitation also plays an important role in controlling the enzyme specificity. Reactivation of the enzyme at different oxygen tensions, after treatment of the enzyme with hydroxyurea (HU) followed by removal of HU, reveals a distinct sensitivity of GDP reductase to low 0��� levels. Although the basis for specific inhibition of GDP reduction remains to be determined, some possibilities have been ruled out. This research proves that in addition to allosteric regulation by nucleoside triphosphates, mouse RNR is also controlled by other factors. Since these components can simultaneously exert their effects upon enzyme specificity, complex regulatory patterns of RNR to provide a proportional supply of the DNA building blocks in vivo are suggested. / Graduation date: 2003

Degradation of mRNA is a highly regulated step important for proper gene expression. Degradation of eukaryotic mRNA is initiated by shortening of the 3’ end located poly(A) tail. Poly(A)-specific ribonuclease (PARN) is an oligomeric enzyme that degrades the poly(A) tail with high processivity. A unique property of PARN is its ability to interact not only with the poly(A) tail but also with the 5’ end located mRNA cap structure. A regulatory role in protein synthesis has been proposed for PARN based on its ability to bind the cap that is required for efficient initiation of eukaryotic mRNA translation. Here we have investigated how the cap structure influences PARN activity and how PARN binds the cap. We show that the cap activates PARN and enhances the processivity of PARN. Further we show that the cap binding complex (CBC) inhibits PARN activity through a protein-protein interaction. To investigate the cap binding property of PARN, we identified the cap binding site at the molecular level using site-directed mutagenesis and fluorescence spectroscopy. We identified tryptophan 475, located within the RNA recognition motif (RRM) of PARN, as crucial for cap binding. A crystal structure of PARN bound to cap revealed that cap binding is mediated by the nuclease domain and the RRM of PARN. Tryptophan 475 binds the inverted 7-Me-guanosine residue through a stacking interaction. Involvement of the nuclease domain in cap binding suggests that the cap site and the active site overlap. Mutational analysis showed that indeed amino acids involved in cap binding are crucial for hydrolytic activity of PARN. Taken together, we show that PARN is an allosteric enzyme that is activated by the cap structure and that the allosteric cap binding site in one PARN subunit corresponds to the active site in the other PARN subunit.

Phosphofructokinase from Escherichia coli (EcPFK) is allosterically regulated by MgADP and phospho(enol)pyruvate (PEP). Both molecules compete for binding to the same allosteric site, however, MgADP activates and PEP inhibits the binding of fructose-6-phosphate (F6P) to the active site. The mode by which this enzyme can differentiate between the two ligands and cause the appropriate response is important for the understanding of the basis of allosteric regulation. We studied the interactions between an active site and an allosteric site (heterotropic interactions) within the protein, and found that each of the four unique heterotropic interactions is unique and the magnitudes of the coupling free energies for MgADP activation sum up to 100% that of wildtype EcPFK without homotropic cooperativity in F6P binding. We took on the kinetic and structural characterization of phosphofructokinase from Lactobacillus bulgaricus (LbPFK) to reveal an enzyme that exhibits allosteric properties in spite of previous kinetic studies performed by Le Bras et al. (1991). We have identified residues in EcPFK (Asp59, Gly184 and Asp273), which are important for the allosteric responses to both MgADP and PEP. Interestingly, Lys214 is only important in PEP inhibition and not MgADP activation. We can also differentially disrupt the MgADP heterotropic interactions with the introduction of G184C within the protein. These results suggest that there are different pathways for allosteric communication within the enzyme: different paths for MgADP activation and PEP inhibition, and different paths for each heterotropic interaction with Gly184 being important for the 33Å MgADP heterotropic interaction.

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.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 105-119).

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2004. / Vita. Bibliography: 154-163.

Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Embargoed. Vita. Bibliography: References located at the end of each chapter.

Orientador: Anete Pereira de Souza / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T21:21:36Z (GMT). No. of bitstreams: 1 Saraiva_AntonioMarcos_D.pdf: 12032714 bytes, checksum: 1262a05ca10735e855fa138a2093d04b (MD5) Previous issue date: 2009 / Resumo: A linhagem 9a5c da bactéria Xylella fastidiosa foi o primeiro fitopatógeno a ter seu genoma completamente sequenciado, o qual gerdu diversas informações sobre seu metabolismo e patogenicidade. Das orfs codificadas por esta bactéria, destaca-se; no presente trabalho, a XF0703, cuja proteína correlata (com 28,3 kDa) possui similaridade com proteínas SurE de várias outras bactérias. Proteínas SurEs são nucleotidases que desfosforilam diversos nucleosideos monofosforilados para seus respectivos nucleosideos. Tal função é de fundamental importância para manter o pool balanceado dos quatro (deoxi)ribonucleosideos para síntese de DNA e RNA, respectivamente. Este trabalho descreve a clonagem da orfXF0703 no vetor pET29a, a expressão da proteína recombinante (XfSurE) em Escheríchia coli BL21(DE3) e a purificação da mesma por cromatografia de afinidade ao níquel. A análise da estrutura secundária foi feita por dicroísmo circular e realizou-se a determinação do estado oligomérico por cromatografia de gel filtração e espalhamento de luz a baixo ângulo (SAXS), os quais revelaram que a proteína é um tetrâmero. Dados de caracterização funcional indicam que a proteína possui maior atividade em pH neutro na presença do íon manganês como cofator, com uma maior afinidade pelo substrato 3'-AMP (K0,5=0,16 mM). Além disso, ensaios cinéticos mostram que a proteína possui um comportamento alostérico com alta cooperatividade positiva (coeficiente de Hill em torno de 2,6) com todos os quatro substratos naturais testados (3'-AMP, 5'-dAMP, 5'-AMP e 5-GMP). Experimentos com a técnica de SAXS permitiram calcular o raio de giro (32,7 ± 0.2 A), distância máxima intramolecular (100 A) e a simetria do envelope da molécula (222). A estrutura de diversas SurEs homólogas já cristalizadas foram superpostas ao envelope obtido, sendo que StSurE (SurE de Salmonella com maior idenjidade de aminoácidos) mostrou ter o melhor ajuste. No entanto, notou-se que havia espaços vazios no envelope de XfSurE e tais espaços podiam ser preenchidos a partir do afastamento das alças responsáveis pela tetramerização e pela rotação dos f dímeros. Estes movimentos (translação e rotação) podem explicar o comportamento alostérico da proteína, facilitando a entrada de substrato ao sítio catalítico da molécula. / Abstract: The 9a5c strain from bacterium Xylella fastidiosa was the first phytopathogen to have its genome completely sequenced, which revealed a lot of information about its metabolism and its pathogenicity. 'From a variety of orfs encoded by this bacterium, we highlight, in this work, the XF0703, which correlated protein (with 28.3 kDa) has similarity with SurE proteins from several other bacteria. The SurE proteins *are nucleotidases that dephosphorylate various monophosphorylated nucleosides to their respective nucleosides. This function is critical for maintaining the balanced pool of four (deoxy) ribonucleosides for DNA and RNA synthesis. In this work, we describes the cloning of the XF0703 orf into the vector pET29a, the recombinant protein overexpression (XfSurE) in Escherichia coli BL21(DE3) and the protein purification by nickel affinity chromatography. The secondary structure analysis was done by circular dichroism, while oligomeric state determination was achieved by gel filtration chromatography and small-angle X-ray light scattering (SAXS), which showed that the protein is a tetramer. Functional characterization data indicate that the protein has a highest activity at neutral pH in the presence of manganese as a cofactor, with a highest affinity for the 3-AMP substrate (K0,5 = 0,16 mM). Furthermore, kinetic tests showed that the protein has a allosteric behavior with a high positive cooperativity (Hill coefficient around 2.6) for all natural substrates screened (3-AMP, 5'-dAMP, 5'-AMP and 5'-GMP). Experiments with SAXS technique have allowed to calculate the radius of gyration (32.7 ± 0.2 A), maximum intramolecular distance (100 A) and molecule symmetry. / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular

Ribonucleotide reductase (RNR) is a key enzyme for de novo dNTP biosynthesis. We have studied nucleotide-dependent oligomerization of the allosterically regulated mammalian RNR using a mass spectrometry–related technique called Gas-phase Electrophoretic Mobility Macromolecule Analysis (GEMMA). Our results showed that dATP and ATP induce the formation of an α6β2 protein complex. This complex can either be active or inactive depending on whether ATP or dATP is bound. In order to understand whether formation of the large complexes is a general feature in the class Ia RNRs, we compared the mammalian RNR to the E. coli enzyme. The E. coli protein is regarded a prototype for all class Ia RNRs. We found that the E. coli RNR cycles between an active α2β2 form (in the presence of ATP, dTTP or dGTP) and an inactive α4β4 form in the presence of dATP or a combination of ATP with dTTP/dGTP. The E. coli R1 mutant (H59A) which needs higher dATP concentrations to be inhibited than the wild-type enzyme had decreased ability to form these complexes. It remains to be discovered how the regulation functions in the mammalian enzyme where both the active and inactive forms are α6β2 complexes. An alternative way to produce dNTPs is via salvage biosynthesis where deoxyribonucleosides are taken up from outside the cell and phosphorylated by deoxyribonucleoside kinases. We have found that the pathogen Trypanosoma brucei, which causes African sleeping sickness, has a very efficient salvage of adenosine, deoxyadenosine and adenosine analogs such as adenine arabinoside (Ara-A). One of the conclusions made was that this nucleoside analog is phosphorylated by the T. brucei adenosine kinase and kills the parasite by causing nucleotide pool imbalances and by incorporation into nucleic acids. Ara-A-based therapies can hopefully be developed into new medicines against African sleeping sickness. Generally, the dNTPs produced from the de novo and salvage pathways can be imported into mitochondria and participate in mtDNA replication. The minimal mtDNA replisome contains DNA polymerase γA, DNA polymerase γB, helicase (TWINKLE) and the mitochondrial single-stranded DNA-binding protein (mtSSB). Here, it was demonstrated that the primase-related domain (N-terminal region) of the TWINKLE protein lacked primase activity and instead contributes to single-stranded DNA binding and DNA helicase activities. This region is not absolutely required for mitochondrial DNA replisome function but is needed for the formation of long DNA products.