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1
Herzog, Mario. "Thermophoresis and cooperative binding of nucleotides." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-149751.
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Johansson, Kenth. "Structural studies of four nucleotide binding proteins : aldehyde dehydrogenase, NADP-malate dehydrogenase and two deoxynucleoside kinases /." Uppsala : Swedish University of Agricultural Sciences, 2000. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=009416200&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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Kennedy, Eileen Jeanne. "Understanding modulation of nucleotide binding by PKA and regulation of extracellular nucleotides in saccharomyces cerevisiae /." Diss., Connect to a 24 p. preview or request complete full text in PDF formate. Access restricted to UC campuses, 2005. http://wwwlib.umi.com/cr/ucsd/fullcit?p3208636.
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Worth, Graham Alan. "The energetics of nucleotide binding to RAS proteins." Thesis, University of Oxford, 1992. http://ora.ox.ac.uk/objects/uuid:44524415-2f2b-4601-998c-56110f332153.
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Ras proteins are a special class of proteins that mediate cell growth signals. Their importance lies in the fact that they are products of a proto-oncogene. This means that under certain conditions the gene that determines its structure is altered and a mutant protein results that is involved in the transformation of normal cells to cancer cells. The actual function by which the protein acts in the signal pathway is not known. However it is known that they act as a switch, undergoing a cycle involving the exchange of guaninosine nucleotides in the binding site. This thesis uses computer simulations to study the energetics of this binding, with the long term aim of developing a drug to inhibit the transforming activity of the oncogenic protein. To begin with, a model of the protein based on a crystal structure is built. Using Molecular dynamics the motion of this model is studied. A possible mechanism by which one half of the nucleotide cycle could be induced is investigated, with the result that phosphorylation of the protein may be involved. The main part of the thesis is then devoted to using the free energy perturbation (FEP) method to calculate the difference in Gibbs binding free energy between the nucleotides in the protein. Using histamine as a model, a method of dealing with charged, flexible molecules is developed; namely the inclusion of a reaction field and comprehensive conformational analysis. The results from the associated calculations are seen to be very close to experimental data. The same procedures are then applied to the much more complex ras: nucleotide system with less successful results, the reason for which is mostly due to the restriction of limited computer resources to tackle such a problem. The conclusion is that given the resources and by using the techniques developed in this thesis, this type of calculation is a feasible way to study such systems.
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Herzog, Mario [Verfasser], and Dieter [Akademischer Betreuer] Braun. "Thermophoresis and cooperative binding of nucleotides / Mario Herzog. Betreuer: Dieter Braun." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2012. http://d-nb.info/1027669522/34.
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Law, Wing-lun, and 羅永倫. "Expression, purification and preliminary x-ray crystallographic studies of two nucleotide binding proteins." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46939118.
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Peake, Sarah Jayne. "Structure and function of the NADP(H)-binding component (dIII) of human heart transhydrogenase." Thesis, University of Birmingham, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367626.
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Jeans, David Richard. "Properties of the nucleotide binding sites of the Ca²⁺-ATPase of sarcoplasmic reticulum." Master's thesis, University of Cape Town, 1988. http://hdl.handle.net/11427/26592.
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Properties of the nucleotide binding site of the Ca²⁺-ATPase of skeletal muscle sarcoplasmic reticulum have been investigated. The study centred around interaction of the high affinity ATP analog, 2'-3'-0-(2,4,6-trinitrophenyl)adenosine 5'-triphosphate, (TNP-ATP), with the Ca²⁺-ATPase. Defined fractions of the sarcoplasmic reticulum (SR), corresponding to the terminal cisternae (TC) and light SR (LSR), were isolated. The TC were shown to have distinctive morphological characteristics that differ from the LSR. The TC vesicles contained electron dense intravesicular material representative of Ca²⁺ binding proteins, and visible membranous "feet" structures, which are reported to interconnect with the transverse tubule. Functional characterisation of the isolated fractions provided evidence for the predominant localisation of Ca²⁺ release channels in TC, and concentration of Ca²⁺-ATPase molecules in LSR. These conclusions were based on the following observations: (a) decreased Ca²⁺ transport of TC versus LSR; ruthenium red, a Ca²⁺ channel blocker, enhanced Ca²⁺ transport and pumping efficiency in TC, (b) higher Ca²⁺-ATPase activity for LSR in the presence and absence of ionophore, (c) rapid Ca²⁺ efflux from TC which is inhibited by ruthenium red. Of special interest was the characterisation of the TC and LSR with respect to turnover-dependent TNP-ATP fluorescence. Fluorescence observed for TC was approximately 65% of that for LSR. This phenomenon may be attributable to either the decreased Ca²⁺ ATPase content of the TC vesicles or open Ca²⁺ release channels. Hence the TNP-ATP fluorescence characteristics appear to reflect the morphological and functional subspecialisation of the defined SR fractions.
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Montgomery, Kyle Everett. "MOLECULAR FACTORS THAT INFLUENCE THE BINDING OF AGONISTS TO AMPA RECEPTORS." OpenSIUC, 2009. https://opensiuc.lib.siu.edu/dissertations/297.
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AMPA receptors mediate excitatory synaptic transmission throughout the central nervous system via activation by their natural agonist glutamate. Several other molecules have been recognized as receptor agonist or antagonist, and recently allosteric modulators have been developed that potentiate the currents generated by these receptors. The goal of this thesis has been to address specific and as yet unresolved questions regarding the binding interactions between the AMPA receptors and these classes of molecules. For instance AMPA receptors are seemingly converted to have lower affinity for agonist as they move towards synapses and we evaluate two hypotheses put forward to explain the molecular mechanisms responsible for this. Additionally, guanine nucleotides competitively inhibit AMPA receptors and a second goal has been to further characterize guanine nucleotide binding, and to create mutations that selectively diminish this so that the function of the inhibition can be evaluated. A third goal has been to characterize the molecular factors that influence the effects of the allosteric modulators in order to explain why their efficacy differs greatly between brain regions. Experiments pertaining to these three goals were carried out sequentially and are described below as Projects 1 (guanine nucleotide inhibition), Project 2 (agonist affinity), and Project 3 (allosteric modulators). Project 1. Guanine nucleotides competitively inhibit AMPA-Rs (AMPA receptors) and because this inhibition is ubiquitous among virtually all types of glutamate receptors from fish to mammals, it likely serves a physiological function. Evaluation of this would be greatly facilitated if nucleotide binding could be eliminated through mutations without altering other aspects of receptor function, or if compounds were discovered that selectively prevent nucleotide binding. It was previously reported that a lysine in the chick kainate binding protein (cKBP) is specifically involved in guanine nucleotide binding. Therefore we mutated the homologous lysine (K445) in AMPA-R subunit GluR1 plus 12 additional residues around the glutamate binding pocket with the expectation that this would reduce nucleotide binding even further. Nucleotide affinity was determined by measuring the displacement of [3H]fluorowillardiine. As expected, the guanine nucleotide affinity was decreased about five-fold in R1-K445A mutants and the agonist affinity was seemingly unchanged. However, when tested by electrophysiology, characteristics of the mutant such as desensitization and the EC50 for glutamate were found to be altered. None of the other mutations were more successful at decreasing nucleotide affinity selectively. Nonetheless, these studies have given new insight into the docking mode of guanine nucleotides. The loss of binding in R1-K445A was much larger for GTP and GDP than for GMP, and guanosine binding, which is much lower, was unaffected by the mutation. These data suggest that the first phosphate of GMP determines the higher affinity of the phosphorylated nucleotides, and that K445 stabilizes the binding of the second and third phosphates of GDP and GTP. This along with various other observations suggest that the guanine base docks deep within the agonist binding pocket and that bulky additions, such as the phosphates, are accommodated by projecting out of the cleft in the vicinity of lysine 445. However, the exact docking mode of guanine nucleotides would have to be determined by crystallography. Project 2. Agonist binding to AMPA-R in brain consists of a high and low affinity components with KDs of 9-28 nM and 190-700 nM. Previous studies have suggested that newly synthesized receptors have high affinity and are converted to lower affinity by a secondary process. Two particular processes have been implicated, namely the conversion of receptor glycosylation from immature to complex, and modulation by receptor associated proteins. Both hypotheses were evaluated in this project using homomeric receptors GluR1-4 expressed in HEK 293 cells. The role of glycosylation was tested mostly with GluR4 receptors because they are expressed in distinct populations that exhibit either immature or complex glycans and their binding consists of high and low affinity components similar to those previously seen in brain receptors. Cells were treated with castanospermine or deoxymannojirimycin to decrease the proportion of receptors with complex glycosylation, or with cycloheximide plus chloroquine to increase the number of receptors with complex glycosylation. Although 70% of receptors from cells treated with cyloheximide/chloroquine exhibited complex glycans compared to <5% with other treatments, the affinity decreased at most 2-fold. Also, the low affinity component was nearly 80% of the total binding in receptors that exhibited virtually no complex glycans. Taken together these data indicate that complex glycosylation is not the key factor that confers low affinity. To test the second hypothesis GluR1i or GluR2i were co-expressed with stargazin which associates to receptors in neurons and affects their kinetics and trafficking. Considering the affinities of the two components seen in brain, we expected stargazin to cause a 20-fold or greater decrease in binding affinity. This was not the case, however our results did suggest that stargazin caused the appearance of a low affinity component but this was small and remained largely masked by the more abundant high affinity component. Recently, experiments with brain membranes have revealed preliminary evidence that an associated protein of ~85kDa may cause receptors to have low affinity. This hypothesis is currently under investigation. Project 3. Ampakines are cognitive enhancers that potentiate AMPA receptor currents at excitatory synapses. The efficacy of these drugs varies substantially among neurons in different brain regions, being for example about three times larger in the hippocampus than in the thalamus. Binding assays have shown that these compounds also increase the affinity of receptors for agonists. Importantly, the efficacy of these drugs to increase synaptic responses and agonist binding exhibit a positive correlation. Indeed, we have found that the increase in agonist binding (Emax) induced by the prototypical ampakine CX546 is highly variable across eight brain regions and that there is a 3-fold difference between the hippocampus and the thalamus which is similar to the difference reported for physiological efficacy. Therefore, binding assays or receptor autoradiography can potentially be used to predict the physiological efficacy of these drugs in a particular brain region. An important goal of this project has been to identify factors that may be responsible for the regionally different efficacies. Ampakines show some preference for receptor subunits but various considerations suggest that other factors must be involved. In this project we evaluated the role of a novel class of proteins called TARPs (transmembrane AMPA receptor regulatory proteins) that have recently been discovered to be tightly associated with AMPA receptors and to regulate their kinetics. Four of these proteins, named lambda;2(stargazin),λ3,λ4,and λ8 are abundant in the brain, but they exhibit highly selective regional distribution. We determined the maximum increase in agonist binding (Emax ) caused by saturating CX546 in three different AMPA receptor subunits, GluR1i, GluR2i, and GluR4i without and with co-expression of the four TARPs. Without TARPs, both Glu2i and GluR4i showed an Emax value of 100% over baseline binding. Co-expression of TARPs increased the Emax in GluR2i and this was largest for λ3 and λ8 (~130%). However, TARPs decreased the Emax of CX546 in GluR4i and this was most notable with λ2 and λ4 (~72%). Agonist binding in GluR1i was increased by only 15% and it was not significantly changed by TARPs. The expression patterns of TARPs and AMPA-R subunits in the brain have been partially characterized in the literature. Thus, it was previously reported that GluR4i transcripts are abundant in the thalamus but minor in the hippocampus. Using western blots we confirmed that this is also true for protein content; in the thalamus expression of GluR1, GluR2, GluR3, and GluR4 was 4%, 33%, 40%, and 147% respectively, of that in the hippocampus. When considering the known expression patterns of TARP variants, the hippocampus can be described as being enriched in GluR2, λ3 and λ8 while GluR4, λ2 and λ4 are prevalent in the thalamus. In comparison between these specific subunit/TARP combinations, the Emax values for those representative of the hippocampus (GluR2i/λ3 or λ8) were ~2-times larger than the Emax values of thalamic combinations (R4i/λ2 or λ4). Thus we can conclude that the differences in the expression of both TARP variants and AMPA-R subunits are critical factors for determining the variable efficacy of ampakines across brain regions.
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Aung-Htut, May Thandar Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "Characterisation of Escherichia coli GTPase Der reveals previously unknown regulation by RNA." Publisher:University of New South Wales. Biotechnology & Biomolecular Sciences, 2008. http://handle.unsw.edu.au/1959.4/41840.
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GTPases are found in all domains of life and are highly conserved. In eukaryotes, they serve as signalling molecules for many cellular processes. However, the prokaryotic GTPases play a very different role and are found to be associated with ribosome function. Among the 11 conserved GTPases, Der is the most interesting in prokaryotes. It possesses a unique structure with two GTPase domains (G-Domains) tethered by a variable length acidic linker and a carboxyl terminal KH-like domain. The exact function of Der is still under investigation and most of the data suggest that it is important for 50S ribosomal assembly or stability. In order to investigate the function of Escherichia coli Der (Ec-Der), expression plasmids for wild-type and mutated proteins were created and the proteins were successfully expressed. The expression of the mutant protein that lacked G-Domain 1 was toxic to the cells and it was found that some large ribosomal proteins were missing from the ribosomes of these cells. In addition, other macromolecular complexes such as the GroEL/GroES chaperonin appeared not to be assembled under these conditions. The activities of both wild-type and mutated proteins were also tested and found to be dependent on potassium ions (K+), which enhanced nucleotide binding. Additionally, intra-molecular control over nucleotide binding and release was also observed for Ec-Der. The in vitro selection of RNA aptamers with nanomolar affinity for Ec-Der produced aptamers that contained short variable sequences. These aptamers affected the growth of the E. coli cells and caused a change in cellular morphology that had been noted previously during Ec-Der over-expression. Ec-Der showed high affinity (nM) to both selected RNA and the unselected RNA library. The activity of Ec-Der and Era was inhibited in the presence of any sequence of RNA that has the length of greater than 16 nucleotides. RNA was also cross-linked to Ec-Der in the presence of GTP, but not GDP, suggesting that RNA was a regulator of the Ec-Der GTPase cycle. Based on these results, it is speculated that Ec-Der might be involved in more than one function. It may be acting at the level of the membrane (based on cellular morphology reported here and by Hwang and Inouye 2001) and may also take part in processes related to ribosome function. Regulation of protein activity by RNA length has not been predicted or described and this may represent a novel mean of regulation of the Era subfamily of GTPases.
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Seebregts, Christopher J. "Photoaffinity labeling the nucleotide sites of the sarcoplasmic reticulum Ca²⁺-ATPase." Doctoral thesis, University of Cape Town, 1989. http://hdl.handle.net/11427/27167.
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We have synthesized a new class of photoaffinity analogs, 2',3'-O-(2,4,6-trinitrophenyl)-8-azido-ATP, -ADP and -AMP (TNP- 8N₃ATP, -ADP and -AMP), and their radiolabeled derivatives, and characterized their interaction with the sarcoplasmic reticulum Ca²⁺-ATPase. The TNP-8N₃-nucleotides were synthesized from ATP in three steps involving bromination in the 8-position of the adenine ring followed by displacement with an azido group and then trinitrophenylation of the resulting 8N₃-nucleotide with TNBS. Inclusion of the oxidizing agent, DTNB, in the final reaction was found to be necessary to prevent reduction of the azido group by the released sulfite anion and also elevated the yield of trinitrophenylation to about 80%. Purity was determined spectrophotometrically, as well as by anion exchange TLC and reversed phase HPLC. In the dark, the compounds were found to display most of the features of the parent TNP-nucleotides and interacted with the Ca²⁺-ATPase in a similar way. When activated by illumination, the probes were specifically incorporated into SR vesicles with high efficiency at alkaline pH. The site of labeling was identified as being on the A₁ tryptic fragment.
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Sehgal, Rippa. "Binding of Oxaliplatin and its Analogs with DNA Nucleotides at Variable pH and Concentration Levels." TopSCHOLAR®, 2016. http://digitalcommons.wku.edu/theses/1602.
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Oxaliplatin is one of the three FDA-approved platinum anticancer drugs and considered a third generation drug, discovered after the first generation drug cisplatin and second generation drug carboplatin. It is known to react with proteins and DNA nucleotides in the body. Reaction with DNA occurs primarily at guanosine residues and secondarily at adenine residues for oxaliplatin and other platinum drugs. We have previously studied oxaliplatin and an analog with additional steric hindrance in the amine ligand and found that the analog had different reactivity with methionine. Now, we have prepared oxaliplatin and its three analogs Pt(Me2dach)(ox), Pt(en)(ox) and Pt(Me4en)(ox) and have reacted each platinum compound with both guanine and adenine nucleotides at pH 4 and pH 7 at different molar ratios. These reactions have been characterized by Nuclear Magnetic Resonance (NMR) spectroscopy equipment over time to observe the formation of products and compare them on the basis of their kinetics and binding affinities. NMR has shown that even under the conditions of excess platinum, the dominant products are usually those with two nucleotides coordinated to one platinum center. Reactions are faster at pH 7 than pH 4 due to deprotonation of phosphate group. Reactions of GMP with a platinum center are faster than reaction with AMP because of the chelate formed by the oxalate ligand. The extra methyl groups on the oxaliplatin analogs do not appear to slow down the reactions with nucleotides considerably. The pH generally affects the rate but does not substantially affect the product distribution.
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Davidson, George Alexander. "Properties of the non-catalytic nucleotide site of the Ca²⁺-ATPase of sarcoplasmic reticulum." Doctoral thesis, University of Cape Town, 1986. http://hdl.handle.net/11427/27199.
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Properties of the regulatory nucleotide binding site of the Ca²⁺-ATPase of skeletal muscle sarcoplasmic reticulum have been investigated. Previously, several lines of evidence have indicated the existence of both catalytic and regulatory nucleotide binding sites on the same polypeptide species. The present study concentrates on the interaction of the ATP analogue, 2'-3'-0-(2,4,6-trinitrocyclohexadienylidine) adenosine 5'-triphosphate, (TNP-ATP), with sites on the non-phosphorylated and phosphorylated enzyme. In particular those conformational transitions linking TNP-ATP fluorescence to the phosphoenzyme subspecies have been sought. Previous studies have demonstrated a close relationship between TNP-ATP fluorescence and phosphoenzyme formed from ATP plus Ca²⁺, or from inorganic phosphate (Pi) in the absence of Ca²⁺, in the reverse direction of the cycle. However, the precise relationship of TNP-ATP fluorescence to the energy transducing conformations of the ATPase is controversial. TNP-ATP binding was investigated by spectrophotometric methods and by the synthesis of [ ¹⁴C] TNP-ATP. [ ¹⁴C] TNP-ATP bound to the ATPase site with high affinity ([TNP-ATP] 0. 5 = 0.12 uM), and · a stoichiometry of 5.4 nmol/mg. [ ¹⁴C] ATP binding stoichiometry was 6.1 nmol/mg, demonstrating that TNP-ATP binds to a single family of sites. The nature of the phosphoenzyme intermediate species that results in enhanced TNP-ATP fluorescence was investigated. NEM derivitization, Sr²⁺-transport and Ca²⁺-oxalate uptake have previously been found to alter the distribution or relative levels of phosphoenzyme intermediates. Modification of thiol groups responsible for phosphoenzyme decomposition (SHd), using N-ethylmaleimide (NEM) (0.4 mM) with 50 uM Ca²⁺, 1 mM AMP-PNP at pH 7.0, resulted in a 50% decrease in Ca²⁺-uptake, Ca²⁺-ATPase activity and ADP-insensitive E-P (E₂-P), while total EP (E₁-P + E₂-P = 3.2 nmol/mg), remained unaltered. ATP-dependent TNP-ATP enhanced fluorescence decreased by 50% under these conditions. Ca²⁺-oxalate induced turnover has previously been shown to decrease steady-state E₂-P levels by prevention of Ca²⁺ gradient formation. Oxalate (5 mM) caused a 40% decrease in ATP-induced TNP-ATP fluorescence levels while total EP levels remained relatively unaltered. Previous studies have shown that Sr²⁺-induced turnover favours higher levels of E₂-P by inhibiting the reverse reaction from E₂-P to E₁-P. Strontium-induced turnover increased TNP-ATP fluorescence by 10% as compared to that of Ca²⁺, without affecting steady-state E-P levels, consistent with an E₂-P conformation relationship to enhanced TNP-ATP fluorescence. The binding site for TNP-ATP on the enzyme was investigated by chase studies using millimolar concentrations of nucleotides. ATP and ADP diminished TNP-ATP fluorescence competitively, with apparent Km values of 1.25 and 0.54 mM respectively, consistent with their affinities of binding to the regulatory site. The rates of decrease of fluorescence (25 and 34 sec⁻¹ at 5 ᵒC, respectively), were of the same order of magnitude as the derived "off" rate of TNP-ATP from the site of enhanced fluorescence (33 sec⁻¹), consistent with TNP-ATP being bound to the regulatory site of the enzyme. Enhanced TNP-ATP fluorescence has previously been related to decreased water activity of the probe site. Alteration of water activity by structure- forming (Deuterium oxide) and structure-breaking solutes (KSCN) in relation to fluorescence were explored. Replacement of H₂O by D₂O altered the fluorescence of unbound TNP-ATP. The apparent for TNP-ATP binding to the E₂-P conformation of the regulatory site. The regulatory site appears to be a modified form of the phosphorylated catalytic site. It is proposed that TNP-ATP fluorescence monitors an enzyme conformation related to Ca²⁺ binding to an inward oriented site of low affinity. The mechanism of K⁺ fluorescence quenching appears to be via an acceleration of dephosphorylation, as opposed to a change in affinity of the enzyme for TNP-ATP, as previously suggested. The K⁺ sensitivity of TNP-ATP fluorescence has proved useful in demonstrating a direct interaction of valinomycin with the enzyme through the monovalent cation binding site. Valinomycin appears to bind directly to the enzyme and to selectively accelerate the "off" rate of K⁺ from this site.
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Dahan, Albert. "Receptor binding of somatostatin-14 and somatostatin-28 in rat brain differential modulation by nucleotides and ions." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=66121.
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Hatcher, Mary Elana. "A solid-state deuterium NMR investigation of the local dynamics of nucleotides in the EcoRI restriction endonuclease binding site /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/8640.
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Shyy, Yeun-Jund. "Nuclear magnetic resonance studies on the interaction of metal ions with adenine nucleotides and substrates binding to adenylate kinase /." The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487329662147312.
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Levine, Kara B. "Identification of the Human Erythrocyte Glucose Transporter (GLUT1) ATP Binding Domain: A Dissertation." eScholarship@UMMS, 1999. https://escholarship.umassmed.edu/gsbs_diss/247.
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The human erythrocyte glucose transport protein (GLUT1) interacts with, and is regulated by, cytosolic ATP. This study asks the following questions concerning ATP modulation of GLUT1 mediated sugar transport. 1) Which region(s) of GLUT1 form the adenine nucleotide-binding domain? 2) What factors influence ATP modulation of sugar transport? 3) Is ATP interaction with GLUT1 sufficient for sugar transport regulation?
The first question was addressed through peptide mapping, n-terminal sequencing, and alanine scanning mutagenesis of GLUT1 using [32P]-azidoATP, a photoactivatable ATP analog. We then used a combination of transport measurements and photolabeling strategies to examine how glycolytic intermediates, pH, and transporter oligomeric structure affect ATP regulation of sugar transport. Finally, GLUT1 was reconstituted into proteoliposomes to determine whether ATP is sufficient for the modulation of GLUT1 function in-vitro.
This thesis presents data supporting the hypothesis that residues 332-335 contribute to the efficiency of adenine nucleotide binding to GLUT1. In addition, we show that AMP, acidification, and conversion of the transporter to its dimeric form antagonize ATP regulation of sugar transport. Finally, we present results that support the proposal that ATP interaction with GLUT1 is sufficient for transport modulation.
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Butler, Michelle Marie. "Probing the dNTP Binding Region of Bacillus subtilis: DNA Polymerase III with Site-Directed Inhibitors: A Dissertation." eScholarship@UMMS, 1992. https://escholarship.umassmed.edu/gsbs_diss/132.
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6-(p-Hydroxyphenylhydrazino) uracil (H2-HPUra) is a selective and potent inhibitor of the replication-specific DNA polymerase III (pol III) of Gram+ bacteria such as Bacillus subtilis. Although a pyrimidine, H2-HPUra derives its inhibitory activity from its specific capacity to mimic the purine nucleotide, dGTP. The project described in this thesis dissertation involves the use of H2-HPUra-like inhibitors to probe the structure and function of the pol III active site. It consists of two separate problems which are summarized below.
Production of a potent bona fide dGTP form of inhibitor. A method was devised to successfully convert the H2-HPUra inhibitor prototype to a bona fide purine, using N2-benzyl guanine as the basis. Structure-activity relationships of benzyl guanines carrying a variety of substituents on the aryl ring identified N2-(3,4-dichlorobenzyl) guanine (DCBG) as a compound equivalent to H2-HPUra with respect to potency and inhibitor mechanism. DCBdGTP, the 2'-deoxyribonucleoside 5'-triphosphate form of DCBG, was synthesized and characterized with respect to its action on wild-type and mutant forms of pol III. DCBdGTP acted on pol III by the characteristic inhibitor mechanism and formally occupied the dNTP binding site with a fit which permitted its polymerization. The latter experiment identified the site for the binding of the inhibitor's aryl moiety as a distinct site located at a distance of approximately 6-7 Å from the base-paired 2-NH group of a bound dGTP.
Attempt to covalently label amino acid residue 1175, a putative participant in inhibitor binding. Azp-12, a point mutation of serine 1175, yields a form of pol III whose inhibitior sensitivity varies specifically as a function of the composition of the para substituent of the inhibitor's aryl ring. On the basis of the latter behavior, residue 1175 was hypothesized to be a residue directly involved in the binding of the inhibitor's aryl moiety. To test this hypothesis, residue 1175 was specifically mutated to either cysteine or lysine, each of which presents a side chain amenable to covalent bond formation with appropriately reactive inhibitor forms. Of the two mutant pol III forms, only the cysteine form (pol III-cys) was catalytically active. The kinetic properties and inhibitor sensitivity profile of pol III-cys identified it as a target suitable for potentially irreversible inhibitor forms containing the following groups in the meta position of the aryl ring: -CH2Br, -CH2C1, and -CH2SH. None of the several inhibitors tested selectively or irreversibly inactivated pol III-cys. Possible bases for the failure of this group of inhibitors and for the redesign of more useful covalently reactive inhibitor forms are considered.
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Lin, Chien-Ling. "Studies on the Regulation of Cytoplasmic Polyadenylation Element-Binding Protein: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/583.
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Post-transcriptional regulation of gene expression sits at the core of proteomic complexity; trans-acting factors that regulate RNA localization and translation capacity are thus indispensible. In this thesis, I present studies of the cytoplasmic polyadenylation element binding protein (CPEB), a sequence specific RNA-binding protein important for cell cycle progression and neural synaptic plasticity. I focus on CPEB because the activity of RNA-binding proteins affects the destiny of their mRNA substrates. As presented in Chapter II, CPEB, though mostly cytoplasmic at steady state, shuttles between the nucleus and the cytoplasm. Surprisingly, the RNA recognition motifs are essential for the nuclear localization. CPEB associates with the polyadenylation machinery in both compartments, suggesting it is involved in both nuclear mRNA processing and cytoplasmic translational regulation. Moreover, the nuclear translocalization is critical to relay a tight translation repression on CPE-containing mRNAs. Chapter III focuses on the regulation of CPEB dimerization. CPEB dimerizes through the RNA-binding domains to inhibit its own RNA binding ability in a cell cycle-dependent manner. By dimerizing, CPEB has enhanced binding to protein destruction factors so that robust active degradation occurs in the later cell cycle. The degradation of CPEB is required for translation activation of a subset of mRNAs and cell cycle progression. In addition, dimerization protects cells from being overloaded with excess CPEB. In sum, the localization and dimerization status of CPEB is dynamic and highly regulated; they in turn regulate the activity of CPEB, which results in responsive translation control. These studies provide a strong foundation to decipher CPEB-mediated gene expression.
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Madera, Dmitri. "Cooperating Events in Core Binding Factor Leukemia Development: A Dissertation." eScholarship@UMMS, 2011. https://escholarship.umassmed.edu/gsbs_diss/532.
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Leukemia is a hematopoietic cancer that is characterized by the abnormal differentiation and proliferation of hematopoietic cells. It is ranked 7th by death rate among cancer types in USA, even though it is not one of the top 10 cancers by incidence (USCS, 2010). This indicates an urgent need for more effective treatment strategies. In order to design the new ways of prevention and treatment of leukemia, it is important to understand the molecular mechanisms involved in development of the disease.
In this study, we investigated mechanisms involved in the development of acute myeloid leukemia (AML) that is associated with CBF fusion genes. The RUNX1 and CBFB genes that encode subunits of a transcriptional regulator complex CBF, are mutated in a subset (20 – 25%) of AML cases. As a result of these mutations, fusion genes called CBFB-MYH11 and RUNX1-ETO arise. The chimeric proteins encoded by the fusion genes provide block in proliferation for myeloid progenitors, but are not sufficient for AML development. Genetic studies have indicated that activation of cytokine receptor signaling is a major oncogenic pathway that cooperates in leukemia development. The main goal of my work was to determine a role of two factors that regulate cytokine signaling activity, the microRNA cluster miR-17-92 and the thrombopoietin receptor MPL, in their potential cooperation with the CBF fusions in AML development.
We determined that the miR-17-92 miRNA cluster cooperates with Cbfb-MYH11 in AML development in a mouse model of human CBFB-MYH11 AML. We found that the miR-17-92 cluster downregulates Pten and activates the PI3K/Akt pathway in the leukemic blasts. We also demonstrated that miR-17-92 provides an anti-apoptotic effect in the leukemic cells, but does not seem to affect proliferation. The anti-apoptotic effect was mainly due to activity of miR-17 and miR-20a, but not miR-19a and miR-19b.
Our second study demonstrated that wild type Mpl cooperated with RUNX1-ETO fusion in development of AML in mice. Mpl induced PI3K/Akt, Ras/Raf/Erk and Jak2/Stat5 signaling pathways in the AML cells. We showed that PIK3/Akt pathway plays a role in AML development both in vitro and in vivo by increasing survival of leukemic cells. The levels of MPL transcript in the AML samples correlated with their response to thrombopoietin (THPO). Moreover, we demonstrated that MPL provides pro-proliferative effect for the leukemic cells, and that the effect can be abrogated with inhibitors of PI3K/AKT and MEK/ERK pathways.
Taken together, these data confirm important roles for the PI3K/AKT and RAS/RAF/MEK pathways in the pathogenesis of AML, identifies two novel genes that can serve as secondary mutations in CBF fusions-associated AML, and in general expands our knowledge of mechanisms of leukemogenesis.
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Tisi, Dominic John Guiseppe. "Structural studies on nucleotide binding proteins." Thesis, Birkbeck (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391822.
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Belk, Jonathan Philip. "A Characterization of Substrates and Factors Involved in Yeast Nonsense-Mediated mRNA Decay: A Dissertation." eScholarship@UMMS, 2002. https://escholarship.umassmed.edu/gsbs_diss/65.
Full textAbstract:
Many intricate and highly conserved mechanisms have evolved to safeguard organisms against errors in gene expression. The nonsense-mediated mRNA decay pathway (NMD) exemplifies one such mechanism, specifically by eliminating mRNAs containing premature translation termination codons within their protein coding regions, thereby limiting the synthesis of potentially deleterious truncated polypeptides. Studies in Saccharomyces Cerevisiae have found that the activity of at least three trans-acting factors, known as UPF1, UPF2/NMD2, and UPF3is necessary for the proper function of the NMD pathway. Further research conducted in yeast indicates that the degradation of substrates of the NMD pathway is dependent on their translation, and that the sub-cellular site of their degradation in the cytoplasm.
Although most evidence in yeast suggests that substrates of the NMD pathway are degraded in the cytoplasm while in association with the translation apparatus, some mammalian studies have found several mRNAs whose decay appears to occur within the nucleus or before their transport to the cytoplasm has been completed. In addition, study of the mammalian TPI mRNA found that this transcript was unavailable as a substrate for the NMD pathway once it had been successfully exported to the cytoplasm, further supporting the notion that the degradation of mammalian substrates of the NMD pathway occurs in association with the nucleus, or during export from the nucleus to the cytoplasm.
To determine if yeast cytoplasmic nonsense-containing mRNA can become immune to the NMD pathway we examined the decay kinetics of two NMDS substrate mRNAs in response to repressing or activating the NMD pathway. Both the ade2-1 and pgk1-UAG-2nonsense-containing mRNAs were stabilized by repressing this pathway, while activation of NMD resulted in the rapid and immediate degradation of each transcripts. These findings demonstrate that nonsense-containing mRNAs residing in the nucleus are potentially susceptible to NMD at each round of translation.
The remainder of this thesis utilizes protein overexpression studies to gain understanding into the function of factors related to the processes of nonsense-mediated mRNA decay and translation in Saccharomyces cerevisiae. Overexpression of a C-terminal truncated form of Nmd3p was found to be dominant-negative for cell viability, translation and the normal course of rRNA biogenesis.
Overexpression studies conducted with mutant forms of the nonsense-mediated mRNA decay protein Upf1p, found that overexpression of mutants in the ATP binding and ATP hydrolysis region ofUpflp were dominant-negative for growth in an otherwise wild-type yeast strain. Furthermore, overexpression of the ATP hydrolysis mutant of Upf1p (DE572AA), resulted in the partial inhibition of NMD and a general perturbation of the translation apparatus. These results support previous studies suggesting a general role for Upf1p function in translation.
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Mutomba, Martha Chengetai. "Guanine nucleotide-binding proteins of Trypanosoma brucei." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308280.
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Schrift, Greta Lynn. "Energetic consequences of structural features and dynamics changes upon nucleotide binding to ribonuclease SA molecular basis for nucleotide binding specificity /." Diss., University of Iowa, 2004. http://ir.uiowa.edu/etd/120.
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Iuga, Adriana. "Solid-state 31P NMR of nucleotide binding proteins." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=973225238.
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Heurtel, Thuswaldner Sophie. "Nucleotide-binding Proteins in the Plant Thylakoid Membrane." Licentiate thesis, Linköping Department of Biomedicine and Surgery, Linköping University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-7934.
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Raper, Jayne. "Guanine nucleotide binding protein function in T.B. Brucei." Thesis, University of Cambridge, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305533.
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Kakraba, Samuel. "A Hierarchical Graph for Nucleotide Binding Domain 2." Digital Commons @ East Tennessee State University, 2015. https://dc.etsu.edu/etd/2517.
Full textAbstract:
One of the most prevalent inherited diseases is cystic fibrosis. This disease is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is known to function as a chloride channel that regulates the viscosity of mucus that lines the ducts of a number of organs. Generally, most of the prevalent mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1). However, some mutations in nucleotide binding domain 2 (NBD2) can equally cause cystic fibrosis. In this work, a hierarchical graph is built for NBD2. Using this model for NBD2, we examine the consequence of single point mutations on NBD2. We collate the wildtype structure with eight of the most prevalent mutations and observe how the NBD2 is affected by each of these mutations.
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Smith, James. "Molecular discrimination analysis for purine nucleotide binding sites." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620247.
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Graham, Heidi C. "Nuclear magnetic resonance studies of a kinase : 3-phosphoglycerate kinase (PGK)." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334917.
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Rodrigues, Daniel Joseph. "Structure-function relationships in the NADP (H) binding component of proton-translocating transhydrogenase from Rhodospirillum rubrum." Thesis, Oxford Brookes University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289256.
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Blanco, Barrera José Antonio. "Structural analysis of nucleotide binding sites of antimicrobial ribonucleases." Doctoral thesis, Universitat Autònoma de Barcelona, 2015. http://hdl.handle.net/10803/311613.
Full textAbstract:
Esta tesis abarca un análisis estructural y funcional de las ribonucleasas antimicrobianas. Se han analizado los centros de interacción de ligandos nucleotídicos con la RNasa A como referencia. Los estudios estructurales, estadísticos y por cristalografía de rayos X, de complejos de RNasas han permitido definir, junto a la triada catalítica, otros subcentros de interacción secundarios. La superfamilia de la RNasa A incluye miembros con funciones no necesariamente relacionadas con la actividad RNasa. En particular, las propiedades antimicrobianas aparecen en miembros con puntos isoeléctricos elevados , que explican asimismo su elevada afinidad por componentes de membrana y estabilidad. No obstante, se ha observado una baja actividad RNasa, probablemente debido a modificaciones en el alineamiento del sustrato.
Se han analizado los patrones de reconocimiento y unión de sustratos nucleotídicos para caracterizar mejor las ribonucleasas citotóxicas de secreción mediante estudios estadísticos generales con complejos estructurales con mono- y dinucleótidos, realizando asimismo una comparativa con las particularidades de familias seleccionadas de endorribonucleasas representativas. Se han establecido modelos generales de interacción entre proteínas y nucleótidos y se han identificado los aminoácidos y átomos presentes en estas interacciones, definiéndose los motivos tridimensionales para los grupos fosfato, ribosa y bases nitrogenadas dentro de la superfamilia de la RNasa A. Junto a la triada catalítica, conservada en el centro activo, se ha visto una variabilidad en los subcentros secundarios, de acuerdo con los patrones de unión preferenciales de las RNasas, alineamiento y especificidad de sustrato o eficiencia catalítica variable. Estos resultados se han completado con predicciones por modelado molecular y comparaciones evolutivas por alineamiento de secuencia y solapamiento estructural. Con una comparación final con la superfamilia de la RNasa T1 (RNasas microbianas) se han analizado las características comunes y particulares para aplicarlas al reconocimiento de biomoléculas polianiónicas y configurar un punto de partida para el diseño de nuevos fármacos.
Finalmente, se han estudiado, por cristalografía de rayos X, distintas RNasas recombinantes nativas (RNasa A, RNasa 3, RNasa 6), así como variantes mutantes, expresadas en un sistema procariota de alto rendimiento. Se han resuelto sus estructuras cristalinas. En particular, el estudio estructural de la ribonucleasa 6 humana (RNasa k6), el primero para el enzima, supone el punto de partida para posteriores análisis de interacciones con potenciales sustratos nucleotídicos y otros ligandos relacionados. Por otra parte, se ha cristalizado un mutante de RNasa A (RNasa A/H7H10), en complejo con 3’-CMP, cuyo centro de unión de fosfatos p2 se ha convertido en un segundo centro activo, ocasionando cambios estructurales próximos. Con un segundo complejo de RNasa A con 3’-CMP, obtenido a resolución atómica, se ha realizado un análisis comparativo más detallado, en comparación con complejos similares a menor resolución, junto con un estudio de cada subcentro en relación al complejo de RNasa A mutante, permitiendo explicar las propiedades catalíticas del mutante. La observación del estado de protonación de los residuos del centro activo ha proporcionado información adicional sobre el mecanismo de catálisis. A continuación se han cristalizado dos mutantes de la RNasa 3/ECP (ECP/H15A, H128N). Los estudios estructurales confirman los estudios cinéticos previos sobre la abolición de la actividad catalítica. Adicionalmente, dos cristales de ECP nativa se utilizaron para la comparación estructural de sendas formas cristalográficas, cadenas laterales o centros de reconocimiento de aniones. Además, con las estructuras de RNasa A, RNasa 3/ECP y RNasa 6 con iones sulfato se compararon los centros de reconocimiento del anión, análogo a los grupos fosfato de nucleótidos. Se ha confirmado la mayor afinidad de la ECP, y se han identificado las regiones potenciales de reconocimiento de nucleótidos o derivados heterosacáridos.This thesis encompasses the structural and functional analysis of antimicrobial ribonucleases. Nucleotide-type ligand interaction sites have been analysed using RNase A as a reference protein. RNase complexes were analysed by statistical structural analysis and X-ray crystallography. Together with the catalytic triad, other secondary interaction subsites were also defined at the protein surface. The RNase A superfamily embraces ribonucleases with diverse functions not necessarily related to RNase activity. In particular, antimicrobial properties are ascribed to members with high isoelectric point values, which also explain their stability and high affinity to membrane components. However, a noticeably lower RNase activity is seen for cationic RNases owing to the lack of key residues important for the correct substrate alignment. The different nucleotide-type substrate binding and recognition patterns were deduced from an overall structure complex statistics’ analysis and compared to the particular traits of selected families of representative endoribonucleases . A large amount of mono- and dinucleotide protein complexes was analysed. The results provided a general model of protein-nucleotide interactions for cytotoxic endoribonucleases. The identification of amino acids and atoms frequently involved in the recognition interactions defined three-dimensional motifs for phosphate, ribose and bases in the RNase A superfamily. Together with the conserved catalytic triad at the active site, residue variability is commonly observed throughout the secondary binding subsites, in agreement with the RNase preferential binding patterns, the different alignment capability, substrate specificity and variable catalytic efficiency. Results were complemented with molecular modelling predictions and evolution comparisons by sequence alignment and structural overlapping. A final side-by-side comparison with the microbial RNase T1 superfamily has allowed an analysis of the common and particular features of substrate recognition processes, thereby building a general interaction architecture applicable to recognition for polyanionic biomolecules that may set a structural basis for the design of new drugs. Additionally, structural studies by X-ray crystallography were carried out. Recombinant wild-type RNases (RNase A, RNase 3, RNase 6) and mutant variants were expressed and purified in a high-yield prokaryotic system andtheir crystal structures were solved. In particular, a crystallisation condition has been discovered for human RNase 6. We report here the first crystal structure of RNase 6, which sets the basis for further analysis of interactions with nucleotide molecules and other putative ligands. On the other hand, the structural analysis of an RNase A mutant (RNase A/H7H10), where the secondary phosphate binding site p2 has been converted into a second active site, in complex with 3’-CMP, enabled the visualisation of induced neighbouring conformational changes. A second RNase A – 3’-CMP complex, obtained at atomic resolution, has enabled a more detailed comparative analysis with lower-resolution protein-nucleotide complexes together with a side-by-side study of subsite environments with the mutant complex, explaining the mutant catalytic properties. The additional visualisation of the protonation state of the active site residues has also provided information about the mechanism of catalysis. Following, two RNase 3/ECP active site mutants (ECP/H15A, ECP/H128N) were crystallised. Structural studies confirmed the conservation of the protein overall three dimensional structure together with previous kinetic experiments related to the abolished catalytic activity. Also, two native ECP crystals obtained by two distinct crystallization conditions were used for a comparison of the different unit cell packing, residue side chain variability and anion recognition sites. Finally, the structures of RNase A, RNase 3/ECP and RNase 6 with bound sulphate anions were compared, and their putative anion recognition sites characterized. The comparison of the binding subsites confirmed the higher affinity of RNase 3/ECP for sulphate/ phosphate anionsand may lead to the identification of protein regions prone to host nucleotides or heterosaccharide compounds.
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De, Wet Heidi. "The nucleotide binding domains of multidrug resistance-p-glycoproteins." Doctoral thesis, University of Cape Town, 2001. http://hdl.handle.net/11427/2690.
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Watson, Dorothy M. A. "Cyclic nucleotide binding and oncogene expression in breast cancer." Thesis, University of Edinburgh, 1989. http://hdl.handle.net/1842/19398.
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Chow, Sarah Sue Wen. "Energetic and structural impact of cyclic nucleotide binding to hyperpolarization-activated cyclic nucleotide-gated channels." Thesis, University of British Columbia, 2013. http://hdl.handle.net/2429/44980.
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Hyperpolarization-activated Cyclic Nucleotide-gated, HCN, channels contribute to the membrane potential of excitable cells including pacemaker cells of the heart and neurons in the brain. By binding to the inner side of the HCN channel, cAMP facilitates channel opening, but
the underlying mechanism has been mainly inferred from relating cAMP concentration to the degree of facilitation. Concentration-response relations reflect the tightly coupled process of cAMP binding and channel opening. The strength of binding and how it is linked to channel
opening is not known. Furthermore, cAMP facilitation is not equal among the four mammalian
HCN isoforms and the extent to which cAMP binding affinity contributes to these differences is
not known.My experiments support the conclusion that cAMP binds to one site of the isolated
tetrameric C-terminus of HCN2 and HCN4 with high affinity and to three sites with low affinity
revealing negative cooperativity. In contrast, only low affinity binding was observed in HCN1
with energetics of binding that were similar to those of the low affinity binding to HCN2. Cyclic
AMP enhanced oligomerization of the HCN2 C-terminus in solution, but had a negligible effect
on oligomerization of the HCN1 C-terminus. Oligomerization in solution is thought to reflect the formation of a gating ring in the intact channel that facilitates opening. Together, this suggests that HCN1 functions as though already disinhibited, explaining its easier opening in the absence of cAMP, its smaller facilitation of opening, and lack of negative cooperativity upon cAMP binding. Lysine substitution at residue 488 of HCN2, initially identified in an individual with
idiopathic generalized epilepsy, eliminated negative cooperativity and reduced oligomerization
of the isolated C-terminus upon cAMP binding. This likely reflects a decrease in its ability to form a gating ring in the intact channel and explains the reported inhibition of opening by this
mutation.The work presented in this thesis demonstrates the value of studying the C-terminus of the HCN channel in isolation to uncover the mechanism by which the HCN C-terminus and cAMP binding control channel opening that would otherwise be hidden by functional experiments.
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Dunaway, Adam Blake. "Characterization of the binding activity of immobilized DNA aptamers for nucleotide and non-nucleotide targets." Thesis, Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/54310.
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Deoxyribonucleic acid (DNA) aptamers are oligonucleotides with high specificity and affinity for non-nucleotide targets ranging from molecular species to cellular proteins. Their high affinity, rapid synthesis, and the ease with which they can be chemically modified to include convenient chemical groups (e.g. amine group on 5’ end) make them excellent adaptable ligands for use in colloidal drug delivery vehicles for both uptake and release of therapeutic agents. This work uses pre-identified aptamers for vascular endothelial growth factor (VEGF) to investigate the design of one such vehicle for controlled uptake and release of target therapeutics and analyzes the ability of particle-immobilized aptamers to bind both nucleotide and non-nucleotide targets. Aptamer sequences are immobilized on colloidal microspheres and binding activity of both the primary DNA and protein targets are directly monitored using flow cytometry. Additionally, the dual nature of aptamer-target binding is further investigated by evaluating the effects of simultaneous and serial incubation of the primary targets. Finally, the ability to recover the functionality of the aptamer is evaluated after displacement of the primary DNA target through DNA mediated interactions. It has been shown that the nature of aptamer-target interactions are complex in nature, requiring optimization for each species incorporated into a delivery vehicle; however, partial recovery of aptamer functionality was achieved after hybridization with the primary DNA target.
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Bramble, Sharyl Elizabeth. "Guanine nucleotide binding properties and attempted immunopurification of ras protein from dictyostelium discoideum." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/26172.
Full textAbstract:
One purpose of this study was to determine whether the ras protein from Dictyostelium discoideum (p23) binds guanine nucleotides
like the ras proteins from mammals (p21) and yeast. The other purpose of this investigation was to purify or enrich for p23ras from D. discoideum by immunoaffinity chromatography.
A number of different approaches were used to determine guanine nucleotide binding by p23RAS . A simple filter binding assay, binding to Western blots, and photoaffinity labeling all failed to demonstrate specific binding with lysates of D. discoideum cells. In contrast p21RAS from transformed NIH-3T3 cell lysate was successfully photoaffinity labeled in the presence
of ³²P-α-guanosine 5¹-triphosphate (GTP) suggesting that the technique had been performed correctly. It was concluded that either p23RAS has a very low affinity for guanine nucleotides
such that GTP binding was not detectable in these experiments
or that the ras protein from D. discoideum simply does not bind guanine nucleotides.
The purification of p23RAS from D. discoideum cells was attempted in order to provide a purified protein preparation for guanine nucleotide binding and for reconstitution studies. An anti-ras monoclonal antibody (Y13-259) was used as the ligand for the immunoaffinity chromatography. This approach was not successful in that the ras protein could not be enriched
relative to other proteins because the immunoaffinity columns did not bind p23RAS.Science, Faculty of
Microbiology and Immunology, Department of
Graduate
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Gao, Enoch N. (Enoch Nuo). "Post-translational lipid modification and nucleotide binding of Myelin 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase (CNP)." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=23889.
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The myelin protein CNP $(2 sp prime,3 sp prime$-Cyclic Nucleotide 3$ sp prime$-Phosphodiesterase) is thio-palmitoylated. Since acylation plays an important role in the protein-membrane interaction, CNP palmitoylation was further investigated. Seven cysteine residues in CNP were individually converted into serines and the palmitoylation was analyzed in either COS-7 cells or an in vitro acylation reaction. No single Cys to Ser mutation could reduce substantially the level of palmitoylation, which may indicate that the turnover of palmitate on CNP is high and that there are multiple palmitoylation sites. Immunostaining and subcellular fractionation showed that isoprenylation is the major factor to control the membrane association of CNP while palmitoylation may serve as a fine tuning mechanism. A double mutation of Cys 231 to Ser and Thr 374 to Pro greatly reduced CNPase activity and the level of palmitoylation. CNP was expressed in Sf9 cells and the mutant C397S was purified to near homogeneity. Since CNP contains several ATPase consensus motifs, we investigated in a preliminary way its ATPase/ATP-binding properties. CNP was affinity-photolabeled by $ lbrack alpha- sp{32}$P) 8-azido ATP in a specific and saturable way, although no apparent ATPase activity was detected. The binding of 8N3 ATP could be competed by ATP, GTP and CTP at different concentrations.
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Laine, Jennifer M. "Protein Ligand Interactions Probed by NMR: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/617.
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Molecular recognition, defined as the specific interactions between two or more molecules, is at the center of many biological processes including catalysis, signal transduction, gene regulation and allostery. Allosteric regulation is the modification of function caused by an intermolecular interaction. Allosteric proteins modify their activity in response to a biological signal that is often transmitted through the interaction with a small effector molecule. Therefore, determination of the origins of intermolecular interactions involved in molecular recognition and allostery are essential for understanding biological processes. Classically, molecular recognition and allosteric regulation have been associated to structural changes of the system. NMR spectroscopic methods have indicated that changes in protein dynamics may also contribute to molecular recognition and allostery. This thesis is an investigation of the contributions of both structure and dynamics in molecular binding phenomena.
In chapter I, I describe molecular recognition, allostery and examples of allostery and cooperativity. Then I discuss the contribution of protein dynamics to function with a special focus on allosteric regulation. Lastly I introduce the hemoglobin homodimer, HbI of Scapharca inaequivalvis and the mRNA binding protein TIS11d.
Chapter II is the primary focus of this thesis on the contribution of protein dynamics to allostery in the dimeric hemoglobin of scapharca inaequivalvis, HbI. Thereafter I concentrate on the mechanism of adenine recognition of the Tristetraprolin-like (TTP) protein TIS11d; this study is detailed in Chapter III. In Chapter IV I discuss broader impacts and future directions of my research.
This thesis presents an example of the use of protein NMR spectroscopy to probe ligand binding. The studies presented in this thesis emphasize the importance of dynamics in understanding protein function. Measurements of protein motions will be an element of future studies to understand protein function in health and disease.
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De, Zutter Julie Kelley. "Allosteric Regulation of Recombination Enzymes E. coli RecA and Human Rad51: A Dissertation." eScholarship@UMMS, 2000. https://escholarship.umassmed.edu/gsbs_diss/192.
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ATP plays a critical role in the regulation of many enzyme processes. In this work, I have focused on the ATP mediated regulation of the recombination processes catalyzed by the E. coliRecA and the human Rad51 proteins. The RecA protein is a multifunctional enzyme, which plays a central role in the processes of recombinational DNA repair, homologous genetic recombination and in the activation of the cellular SOS response to DNA damage. Each of these functions requires a common activating step, which is the formation of a RecA-ATP-ssDNA nucleoprotein filament. The binding of ATP results in the induction of a cooperative, high affinity ssDNA binding state within RecA (Menetski & Kowalczykowski, 1985b; Silver & Fersht, 1982). Data presented here identifies Gln194 as the NTP binding site "γ-phosphate sensor", in that mutations introduced at this residue disrupt all ATP induced RecA activities, while basal enzyme function is maintained. Additionally, we have dissected the parameters contributing to cooperative nucleoprotein filament assembly in the presence of cofactor. We show that the dramatic increase in the affinity of RecA for ssDNA in the presence of ATP is a result of a significant increase in the cooperative nature of filament assembly and not an increase in the intrinsic affinity of a RecA monomer for ssDNA.
Previous work using both mutagenesis and engineered disulfides to study the subunit interface of the RecA protein has demonstrated the importance of Phe217 for the maintenance of both the structural and functional properties of the protein (Skiba & Knight, 1994; Logan et al., 1997; Skiba et al., 1999). A Phe217Tyr mutation results in a striking increase in cooperative filament assembly. In this work, we identify Phe217 as a key residue within the subunit interface and clearly show that Phe217 is required for the transmission of ATP mediated allosteric information throughout the RecA nucleoprotein filament.
The human Rad51 (hRad51) protein, like its bacterial homolog RecA, catalyzes genetic recombination between homologous single and double stranded DNA substrates. This suggests that the overall process of homologous recombination may be conserved from bacteria to humans. Using IAsys biosensor technology, we examined the effect of ATP on the binding of hRad51 to ssDNA. Unlike RecA, we show that hRad51 binds cooperatively and with high affinity to ssDNA both in the presence and absence of nucleotide cofactor. These results show that ATP plays a fundamentally different role in hRad51 vs.RecA mediated processes.
In summary, through the work presented in this dissertation, we have defined the critical molecular determinants for ATP mediated allosteric regulation within RecA. Furthermore, we have shown that ATP is not utilized by Rad51 in the same manner as shown for RecA, clearly defining a profound mechanistic difference between the two proteins. Future studies will define the requirement for ATP in hRad51 mediated processes.
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Guy, E. C. "Nucleotide binding to type-M1̲ pyruvate kinase from rabbit muscle." Thesis, University of Southampton, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235158.
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Yakamavich, Joseph Andrew. "Control of HslUV protease function by nucleotide binding and hydrolysis." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42397.
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Includes bibliographical references.Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, February 2008.
Many proteins act as molecular machines, using the power of nucleotide binding and hydrolysis to drive conformational changes in themselves and their target substrates. Like other AAA+ proteases, HslUV recognizes, unfolds, translocates, and degrades substrate proteins in an ATP-dependent manner. Understanding how nucleotides interact with HslU and control the activities of both HslU and HslV provides insights into the general mechanism of energy-dependent proteolysis. In order to better understand HslU-nucleotide interactions, I created a variant of HslU unable to hydrolyze ATP. HslU is composed of six identical subunits with a total of six nucleotide-binding sites. Moreover, many crystal structures show HslU with six bound nucleotides. Nevertheless, I found that HslU in solution is only able to bind 3-4 ATPs at saturation. This result rules out a model of ATP hydrolysis in which six nucleotides bind and are hydrolyzed together in a single power stroke and also suggests that many HslU crystal structures represent states that are not populated in the normal ATPase cycle. I also characterized the nucleotide requirement for various HslU activities. I found that at least two ATPs must be bound to HslU to support substrate binding and ATP hydrolysis, but showed that a single nucleotide is sufficient to support HslU-HslV binding and to stimulate HslV peptidase activity. I also found that the nucleotide state of HslU affects its affinity to HslV, weakening it when some subunits have ADP or no nucleotide bound. This effect is offset by an increase in HslU-HslV affinity during substrate degradation. This work suggests a simple model in which binding of a single ATP to HslU drives HslV binding, with further ATP binding acting to stabilize an HslU conformation that can bind protein substrate, hydrolyze ATP, and support substrate unfolding, translocation, and degradation.
by Joseph Andrew Yakamavich.
Ph.D.
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Pagano, John M. Jr. "RNA Recognition by the Caenorhabditis elegans Embryonic Determinants MEX-5 and MEX-3: A Dissertation." eScholarship@UMMS, 2010. https://escholarship.umassmed.edu/gsbs_diss/486.
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Post-transcriptional regulation of gene expression is a mechanism that governs developmental and cellular events in metazoans. In early embryogenesis, transcriptionally quiescent cells depend upon maternally supplied factors such as RNA binding proteins and RNA that control key decisions. Morphogen gradients form and in turn pattern the early embryo generating different cell types and spatial order. In the nematode Caenorhabditis elegans, the early embryo relies upon several RNA binding proteins that control mRNA stability, translation efficiency, and/or mRNA localization of cell fate determinants essential for proper development.
MEX-5 and MEX-3 are two conserved RNA-binding proteins required to pattern the anterior/posterior axis and early embryo. Mutation of either gene results in a maternal effect lethal phenotype with proliferating posterior muscle into the anterior blastomeres (Muscle EXcess). Several cell-fate determinants are aberrantly expressed in mex-5 and mex-3 embryos. Both proteins are thought to interact with cis-regulatory elements present in 3’-UTRs of target RNAs controlling their metabolism. However, previous studies failed to demonstrate that these proteins regulate maternal transcripts directly.
This dissertation presents a thorough assessment of the RNA binding properties of MEX-5 and MEX-3. Quantitative biochemical approaches were used to determine the RNA binding specificity of both proteins. MEX-5 has a relaxed specificity, binding with high affinity to linear RNA containing a tract of six or more uridines within an eight-nucleotide window. This is very different from its mammalian homologs Tristetraprolin (TTP) and ERF-2. I was able to identify two amino acids present within the MEX-5 RNA binding domain that are required for the differential RNA recognition observed between MEX-5 and TTP. MEX-3 on the other hand is a specific RNA binding protein, recognizing a bipartite element with flexible spacing between two four-nucleotide half-sites. I demonstrate that this element is required for MEX-3 dependent regulation in vivo. Previous studies only identify a small number of candidate regulatory targets of MEX-5 and MEX-3. The defined sequence specificity of both proteins is used to predict new putative targets that may be regulated by either protein. Collectively, this study examines the RNA binding properties of MEX-5 and MEX-3 to clarify their role as post-transcriptional regulators in nematode development.
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Burns, David M. "Post-Transcriptional Control of Human Cellular Senescence: A Dissertation." eScholarship@UMMS, 2010. https://escholarship.umassmed.edu/gsbs_diss/491.
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The central dogma of biology asserts that DNA is transcribed into RNA and RNA is translated into protein. However, this overtly simplistic assertion fails to portray the highly orchestrated and regulated mechanisms of transcription and translation. During the process of transcription, RNA provides the template for translation and protein synthesis as well as the structural and sequence specificity of many RNA and protein-based machines. While only 1-5% of the genome will escape the nucleus to be translated as mRNAs, complex, parallel, highly-conserved mechanisms have evolved to regulate specific mRNAs. Trans-acting factors bind cis-elements in both the 5" and 3" untranslated regions of mRNA to regulate their stability, localization, and translation. While a few salient examples have been elucidated over the last few decades, mRNA translation can be reversibly regulated by the shortening and lengthening of the 3" polyadenylate tail of mRNA. CPEB, an important factor that nucleates a complex of proteins to regulate the polyadenylate tail of mRNA, exemplifies a major paradigm of translational control during oocyte maturation and early development. CPEB function is also conserved in neurons and somatic foreskin fibroblasts where it plays an important role in protein synthesis dependent synaptic plasticity and senescence respectively. Focusing on the function of CPEB and its role in mRNA polyadenylation during human cellular senescence, the following dissertation documents the important finding that CPEB is required for the normal polyadenylation of p53 mRNA necessary for its normal translation and onset of senescence. Cells that lack CPEB have abnormal levels of mitochondria and ROS production, which are demonstrated to arise from the direct result of hypomorphic p53 levels. Finally, in an attempt to recapitulate the model of CPEB complex polyadenylation in human somatic cells, I unexpectedly find that Gld-2, a poly(A) polymerase required for CPEB-mediated polyadenylation in Xenopus laevis oocytes, is not required for p53 polyadenylation, but instead regulates the stability of a microRNA that in turn regulates CPEB mRNA translation. Furthermore, I demonstrate that CPEB requires Gld-4 for the normal polyadenylation and translation of p53 mRNA.
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Maurer, Brigitte. "Expression and purification of the nucleotide binding domains of P-glycoprotein." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/MQ63109.pdf.
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Delannoy, Sabine. "Structure-function relationship in the nucleotide-binding domains of ABC transporters." Ann Arbor, Mich. : ProQuest, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3244455.
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Thesis (Ph.D. in Molecular and Cell Biology)--S.M.U., 2007.Title from PDF title page (viewed Mar. 18, 2008). Source: Dissertation Abstracts International, Volume: 67-12, Section: B, page: 6885. Adviser: Pia D. Vogel. Includes bibliographical references.
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Saiu, P. "Structural and functional studies on nucleotide binding to AMP-activated protein kinase." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/645676/.
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AMP-activated protein kinase (AMPK) is an enzyme that senses and regulates cellular energy balance thus playing a key role in homeostasis. As such it is a target for treatment of metabolic disorders such as type II diabetes. AMPK is a hetero-trimeric complex composed of an α, β and γ subunit. α contains the catalytic kinase domain, β is a scaffolding subunit that enables complex formation and γ monitors cellular energy via nucleotide binding to its CBS domains. AMPK is primarily activated by phosphorylation at Thr-172 on the activation loop in the kinase domain. It exerts its cellular effects via phosphorylation of a range of downstream targets involved in different aspects of energy production & utilization. The aim of this thesis is to characterize the mechanistic basis of energy regulation of mammalian AMPK via structural and binding measurements. Fluorescence studies have been facilitated by the use of N-methylanthraniloyl (mant) labelled AMP and of β-Nicotinamide adenine dinucleotide 2’-phosphate (NADPH) to monitor competition with AMP, ADP and ATP. A number of mutations in the γ subunit, which interfere with the normal function of AMPK and cause Wolff-Parkinson- White (WPW) syndrome, have also assessed for changes in nucleotide binding affinities and potential implications for the regulation of kinase activity. Thermal denaturation experiments are used to investigate the stabilizing effects of nucleotides and other small molecule ligands. This method was used in a low throughput screen against an enriched list of compounds selected from an in silico screen to try to identify novel activators. I have also determined the structure of the regulatory fragment of the enzyme bound to 5-aminoimidazole-4-carboximide riboside monophosphate (ZMP), an intermediate on the biosynthetic route to AMP, the fluorescence reporter mant-AMP and the WPW mutants Arg298\rightarrowGly, Arg69\rightarrowGln and His150\rightarrowArg. The structures of the mutants have revealed that nucleotide binding is impaired due to a reduced affinity for the nucleotides thus affecting the regulation of the kinase.
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Akam, Elizabeth Claire. "The activation of guanine nucleotide binding proteins by muscarinic acetylcholine receptor subtypes." Thesis, University of Leicester, 1999. http://hdl.handle.net/2381/29919.
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Agonist-stimulation of human recombinant M1, M2, M3 and M4 receptors, expressed in Chinese hamster ovary cells, was investigated at the level of G protein activation. Functional responses were determined by a number of methods including [35S]-GTPS binding in membranes using both filtration-based and immunoprecipitation-based procedures: Ins(1,4,5)P3 accumulation and 45Ca2+ release from permeabilised cell suspensions; and cAMP accumulation in cell suspensions. M2 and M4 receptors, with equivalent expression levels in this recombinant system, were found only to couple to pertussis toxin-sensitive G proteins with near equal kinetics. Methacholine appeared equipotent when activating the total G protein complement through the M2 and M4 receptors, however, it appeared more potent when activating Gi3/o through the M2 compared to the M4 muscarinic receptor. Using equivalent expression levels of M1 and M3 receptors both the subtypes were found to couple to both pertussis toxin-sensitive and -insensitive G proteins. CHO-M1 and -M3 mediated Ins(1,4,5)P3 generation after pertussis toxin pre-treatment suggested the functional significance of coupling to multiple G protein classes may be in the stimulation of PLC by -subunits derived from Gi-like G proteins. The activation of Gq/11 through the M1 receptor subtype, after methacholine-stimulation, is faster, greater and more potent than that mediated by the M3 receptor subtype, suggesting that the intrinsic activity of the M1 subtype is greater than that of the M3 subtype. The 'partial' agonist pilocarpine also displayed very different G protein activation profiles after stimulation of M1, M2, M3 and M4 receptor subtypes, suggesting that agonists acting at different receptor subtypes may be capable of inducing relatively selective coupling of the occupied receptor to available G proteins. This study therefore concludes that muscarinic receptor subtypes display divergent G protein activation profiles after either 'full' or 'partial' agonist-stimulation.
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Gorman, Christine. "The interaction of Ras with Raf and other potential effectors." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312373.
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Grondin, Ronald Thomas. "Expression, purification, refolding, and ATP binding of the first nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq29275.pdf.
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