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Academic literature on the topic 'Nucleotides binding'

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Published: 4 June 2021
Last updated: 11 February 2022

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Journal articles on the topic "Nucleotides binding"

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McIlroy, Patrick J. "Effects of cations on binding of human choriogonadotropin." Biochemistry and Cell Biology 66, no. 12 (December 1, 1988): 1258–64. http://dx.doi.org/10.1139/o88-145.

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The effect of various salts on the binding of human choriogonadotropin to rat luteal membranes has been examined. Increasing salt concentrations had biphasic effects, initially increasing binding, then decreasing it. With NaCl, these effects were on both the affinity and the number of receptor sites. The affinity increased with increasing NaCl concentrations, to a maximum at 40 mM, and then decreased. Above 40 mM NaCl, the number of binding sites increased. NaCl also altered the effects of Mg2+ and guanyl nucleotides. At low ionic strength, Mg2+ was necessary to observe binding. Guanine nucleotides modulated this binding by decreasing the affinity. At 40 mM NaCl, Mg2+ increased receptor number without altering affinity. Guanyl nucleotides modulated this binding by reducing the number of sites to that observed in the absence of Mg2+. At 150 mM NaCl, Mg2+ and guanine nucleotides had no effect. The results suggest the presence of two pools of human choriogonadotropin receptor in rat corpus luteum, one coupled to the guanine nucleotide regulatory protein (Ns) and being Mg2+ dependent and guanine nucleotide sensitive, and the other not coupled to Ns and being Mg2+ independent and guanine nucleotide insensitive.
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Hause, Lara L., and Kevin S. McIver. "Nucleotides Critical for the Interaction of the Streptococcus pyogenes Mga Virulence Regulator with Mga-Regulated Promoter Sequences." Journal of Bacteriology 194, no. 18 (July 6, 2012): 4904–19. http://dx.doi.org/10.1128/jb.00809-12.

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ABSTRACTThe Mga regulator ofStreptococcus pyogenesdirectly activates the transcription of a core regulon that encodes virulence factors such as M protein (emm), C5a peptidase (scpA), and streptococcal inhibitor of complement (sic) by directly binding to a 45-bp binding site as determined by an electrophoretic mobility shift assay (EMSA) and DNase I protection. However, by comparing the nucleotide sequences of all established Mga binding sites, we found that they exhibit only 13.4% identity with no discernible symmetry. To determine the core nucleotides involved in functional Mga-DNA interactions, the M1T1 Pemm1binding site was altered and screened for nucleotides important for DNA bindingin vitroand for transcriptional activation using a plasmid-based luciferase reporterin vivo. Following this analysis, 34 nucleotides within the Pemm1binding site that had an effect on Mga binding, Mga-dependent transcriptional activation, or both were identified. Of these critical nucleotides, guanines and cytosines within the major groove were disproportionately identified clustered at the 5′ and 3′ ends of the binding site and with runs of nonessential adenines between the critical nucleotides. On the basis of these results, a Pemm1minimal binding site of 35 bp bound Mga at a level comparable to the level of binding of the larger 45-bp site. Comparison of Pemmwith directed mutagenesis performed in the M1T1 Mga-regulated PscpAand Psicpromoters, as well as methylation interference analysis of PscpA, establish that Mga binds to DNA in a promoter-specific manner.
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Chander, Preethi, Kari M. Halbig, Jamie K. Miller, Christopher J. Fields, Heather K. S. Bonner, Gail K. Grabner, Robert L. Switzer, and Janet L. Smith. "Structure of the Nucleotide Complex of PyrR, the pyr Attenuation Protein from Bacillus caldolyticus, Suggests Dual Regulation by Pyrimidine and Purine Nucleotides." Journal of Bacteriology 187, no. 5 (March 1, 2005): 1773–82. http://dx.doi.org/10.1128/jb.187.5.1773-1782.2005.

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ABSTRACT PyrR is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. PyrR acts by binding to specific sequences on pyr mRNA and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. PyrR from Bacillus subtilis has been purified and extensively studied. In this work, we describe the purification to homogeneity and characterization of recombinant PyrR from the thermophile Bacillus caldolyticus and the crystal structures of unliganded PyrR and a PyrR-nucleotide complex. The B. caldolyticus pyrR gene was previously shown to restore normal regulation of the B. subtilis pyr operon in a pyrR deletion mutant. Like B. subtilis PyrR, B. caldolyticus PyrR catalyzes the uracil phosphoribosyltransferase reaction but with maximal activity at 60°C. Crystal structures of B. caldolyticus PyrR reveal a dimer similar to the B. subtilis PyrR dimer and, for the first time, binding sites for nucleotides. UMP and GMP, accompanied by Mg2+, bind specifically to PyrR active sites. Nucleotide binding to PyrR is similar to other phosphoribosyltransferases, but Mg2+ binding differs. GMP binding was unexpected. The protein bound specific sequences of pyr RNA 100 to 1,000 times more tightly than B. subtilis PyrR, depending on the RNA tested and the assay method; uridine nucleotides enhanced RNA binding, but guanosine nucleotides antagonized it. The new findings of specific GMP binding and its antagonism of RNA binding suggest cross-regulation of the pyr operon by purines.
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Schulz, Georg E. "Binding of nucleotides by proteins." Current Opinion in Structural Biology 2, no. 1 (February 1992): 61–67. http://dx.doi.org/10.1016/0959-440x(92)90178-a.

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Schulz, Georg E. "Binding of nucleotides by proteins." Current Biology 2, no. 2 (February 1992): 81. http://dx.doi.org/10.1016/0960-9822(92)90208-r.

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Csanády, László, and Vera Adam-Vizi. "Antagonistic Regulation of Native Ca2+- and ATP-sensitive Cation Channels in Brain Capillaries by Nucleotides and Decavanadate." Journal of General Physiology 123, no. 6 (June 1, 2004): 743–57. http://dx.doi.org/10.1085/jgp.200309008.

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Regulation by cytosolic nucleotides of Ca2+- and ATP-sensitive nonselective cation channels (CA-NSCs) in rat brain capillary endothelial cells was studied in excised inside-out patches. Open probability (Po) was suppressed by cytosolic nucleotides with apparent KI values of 17, 9, and 2 μM for ATP, ADP, and AMP, as a consequence of high-affinity inhibition of channel opening rate and low-affinity stimulation of closing rate. Cytosolic [Ca2+] and voltage affected inhibition of Po, but not of opening rate, by ATP, suggesting that the conformation of the nucleotide binding site is influenced only by the state of the channel gate, not by that of the Ca2+ and voltage sensors. ATP inhibition was unaltered by channel rundown. Nucleotide structure affected inhibitory potency that was little sensitive to base substitutions, but was greatly diminished by 3′-5′ cyclization, removal of all phosphates, or complete omission of the base. In contrast, decavanadate potently (K1/2 = 90 nM) and robustly stimulated Po, and functionally competed with inhibitory nucleotides. From kinetic analyses we conclude that (a) ATP, ADP, and AMP bind to a common site; (b) inhibition by nucleotides occurs through simple reversible binding, as a consequence of tighter binding to the closed-channel relative to the open-channel conformation; (c) the conformation of the nucleotide binding site is not directly modulated by Ca2+ and voltage; (d) the differences in inhibitory potency of ATP, ADP, and AMP reflect their different affinities for the closed channel; and (e) though decavanadate is the only example found to date of a compound that stimulates Po with high affinity even in the presence of millimolar nucleotides, apparently by competing for the nucleotide binding site, a comparable mechanism might allow CA-NSC channels to open in living cells despite physiological levels of nucleotides. Decavanadate now provides a valuable tool for studying native CA-NSC channels and for screening cloned channels.
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Sullivan, S. M., R. Mishra, R. R. Neubig, and J. R. Maddock. "Analysis of Guanine Nucleotide Binding and Exchange Kinetics of the Escherichia coli GTPase Era." Journal of Bacteriology 182, no. 12 (June 15, 2000): 3460–66. http://dx.doi.org/10.1128/jb.182.12.3460-3466.2000.

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ABSTRACT Era is an essential Escherichia coli guanine nucleotide binding protein that appears to play a number of cellular roles. Although the kinetics of Era guanine nucleotide binding and hydrolysis have been described, guanine nucleotide exchange rates have never been reported. Here we describe a kinetic analysis of guanine nucleotide binding, exchange, and hydrolysis by Era using the fluorescent mant (N-methyl-3′-O-anthraniloyl) guanine nucleotide analogs. The equilibrium binding constants (KD ) for mGDP and mGTP (0.61 ± 0.12 μM and 3.6 ± 0.80 μM, respectively) are similar to those of the unmodified nucleotides. The single turnover rates for mGTP hydrolysis by Era were 3.1 ± 0.2 mmol of mGTP hydrolyzed/min/mol in the presence of 5 mM MgCl2 and 5.6 ± 0.3 mmol of mGTP hydrolyzed/min/mol in the presence of 0.2 mM MgCl2. Moreover, Era associates with and exchanges guanine nucleotide rapidly (on the order of seconds) in both the presence and absence of Mg2+. We suggest that models of Era function should reflect the rapid exchange of nucleotides in addition to the GTPase activity inherent to Era.
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Lew, Chih M., and Jay D. Gralla. "Mechanism of Stimulation of Ribosomal Promoters by Binding of the +1 and +2 Nucleotides." Journal of Biological Chemistry 279, no. 19 (March 9, 2004): 19481–85. http://dx.doi.org/10.1074/jbc.m401285200.

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The rate of transcription ofEscherichia coliribosomal RNA promoters is central to adjusting the cellular growth rate to nutritional conditions. The +1 initiating nucleotide and ppGpp are regulatory effectors of these promoters. The data herein show thatin vitrotranscription is also regulated by the +2 nucleotide. Both the +1 and +2 nucleotides act by driving polymerase into an altered conformation rather than by increasing the lifetime of transcription complexes. The unique design of the ribosomal promoters may stabilize a distorted state of polymerase that is relieved by the binding of the two nucleotides required for transcription initiation.
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Gromadski, Kirill B., Tobias Schümmer, Anne Strømgaard, Charlotte R. Knudsen, Terri Goss Kinzy, and Marina V. Rodnina. "Kinetics of the Interactions between Yeast Elongation Factors 1A and 1Bα, Guanine Nucleotides, and Aminoacyl-tRNA." Journal of Biological Chemistry 282, no. 49 (October 9, 2007): 35629–37. http://dx.doi.org/10.1074/jbc.m707245200.

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The interactions of elongation factor 1A (eEF1A) from Saccharomyces cerevisiae with elongation factor 1Bα (eEF1Bα), guanine nucleotides, and aminoacyl-tRNA were studied kinetically by fluorescence stopped-flow. eEF1A has similar affinities for GDP and GTP, 0.4 and 1.1 μm, respectively. Dissociation of nucleotides from eEF1A in the absence of the guanine nucleotide exchange factor is slow (about 0.1 s–1) and is accelerated by eEF1Bα by 320-fold and 250-fold for GDP and GTP, respectively. The rate constant of eEF1Bα binding to eEF1A (107–108m–1 s–1) is independent of guanine nucleotides. At the concentrations of nucleotides and factors prevailing in the cell, the overall exchange rate is expected to be in the range of 6 s–1, which is compatible with the rate of protein synthesis in the cell. eEF1A·GTP binds Phe-tRNAPhe with a Kd of 3 nm, whereas eEF1A·GDP shows no significant binding, indicating that eEF1A has similar tRNA binding properties as its prokaryotic homolog, EF-Tu.
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Demeuse, Philippe, Reinhold Penner, and Andrea Fleig. "TRPM7 Channel Is Regulated by Magnesium Nucleotides via its Kinase Domain." Journal of General Physiology 127, no. 4 (March 13, 2006): 421–34. http://dx.doi.org/10.1085/jgp.200509410.

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TRPM7 is a Ca2+- and Mg2+-permeable cation channel that also contains a protein kinase domain. While there is general consensus that the channel is inhibited by free intracellular Mg2+, the functional roles of intracellular levels of Mg·ATP and the kinase domain in regulating TRPM7 channel activity have been discussed controversially. To obtain insight into these issues, we have determined the effect of purine and pyrimidine magnesium nucleotides on TRPM7 currents and investigated the possible involvement of the channel's kinase domain in mediating them. We report here that physiological Mg·ATP concentrations can inhibit TRPM7 channels and strongly enhance the channel blocking efficacy of free Mg2+. Mg·ADP, but not AMP, had similar, albeit smaller effects, indicating a double protection against possible Mg2+ and Ca2+ overflow during variations of cell energy levels. Furthermore, nearly all Mg-nucleotides were able to inhibit TRPM7 activity to varying degrees with the following rank in potency: ATP > TTP > CTP ≥ GTP ≥ UTP > ITP ≈ free Mg2+ alone. These nucleotides also enhanced TRPM7 inhibition by free Mg2+, suggesting the presence of two interacting binding sites that jointly regulate TRPM7 channel activity. Finally, the nucleotide-mediated inhibition was lost in phosphotransferase-deficient single-point mutants of TRPM7, while the Mg2+-dependent regulation was retained with reduced efficacy. Interestingly, truncated mutant channels with a complete deletion of the kinase domain regained Mg·NTP sensitivity; however, this inhibition did not discriminate between nucleotide species, suggesting that the COOH-terminal truncation exposes the previously inaccessible Mg2+ binding site to Mg-nucleotide binding without imparting nucleotide specificity. We conclude that the nucleotide-dependent regulation of TRPM7 is mediated by the nucleotide binding site on the channel's endogenous kinase domain and interacts synergistically with a Mg2+ binding site extrinsic to that domain.
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Dissertations / Theses on the topic "Nucleotides binding"

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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 &amp 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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Books on the topic "Nucleotides binding"

1

Bosch, L., B. Kraal, and A. Parmeggiani, eds. The Guanine — Nucleotide Binding Proteins. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-2037-2.

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EMBO-NATO-CEC Advanced Research Workshop on the Guanine-Nucleotide Binding Proteins: Common Structural and Functional Properties (1988 Renesse, Netherlands). The guanine-nucleotide binding proteins: Common structural and functional properties. New York: Plenum Press, 1989.

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Maurer, Brigitte. Expression and purification of the nucleotide binding domains of P-glycoprotein. Ottawa: National Library of Canada, 2001.

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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. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1999.

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Venning, Jamie Derrick. The catalytically-active complex of the nucleotide-binding domains of transhydrogenase from rhodospirillum rubrum. Birmingham: University of Birmingham, 1999.

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Taylor, Catherine Yvonne. Analysis of protein binding motifs in the nucleotide sequence of the human [gamma]-actin gene promoter. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Stilwell, Shaun Nicholas. The involvement of NADP(H) binding and release in energy transduction by proton-translocating nicotinamide nucleotide transhydrogenase from Escherichia coli and Rhodospirillum rubrum. Birmingham: University of Birmingham, 1997.

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NATO, Advanced Research Institute on Biological Signal Transduction (1990 Island of Spetsai Greece). Biological signal transduction. Berlin: Springer-Verlag, 1991.

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Photolabeling the nucleotide binding sites of dog kidney Na,K-ATPase with azido nucleotides. 1993.

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The Guanine - Nucleotide Binding Proteins:Common Structural and Functional Properties. Springer, 1989.

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Book chapters on the topic "Nucleotides binding"

1

Dove, Stefan. "Mammalian Nucleotidyl Cyclases and Their Nucleotide Binding Sites." In Non-canonical Cyclic Nucleotides, 49–66. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/164_2015_34.

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Eccleston, J. F., T. F. Kanagasabai, D. P. Molloy, S. E. Neal, and M. R. Webb. "The Application of Fluorescent and Photosensitive Analogues of Guanine Nucleotides to the Function and Structure of G-Binding Proteins." In The Guanine — Nucleotide Binding Proteins, 87–97. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-2037-2_9.

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Hankin, Joseph A., and Robert C. Murphy. "Covalent Binding of Leukotriene A4 to Nucleosides, Nucleotides, and Nucleic Acids." In Advances in Experimental Medicine and Biology, 29–33. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4419-9194-2_7.

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Berden, Jan A., Cees M. Edel, and Aloysius F. Hartog. "Number, Localisation and Function of the Non-Catalytic Adenine Nucleotide Binding Sites of Mitochondrial F1-ATPase." In Adenine Nucleotides in Cellular Energy Transfer and Signal Transduction, 47–58. Basel: Birkhäuser Basel, 1992. http://dx.doi.org/10.1007/978-3-0348-7315-4_4.

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Balobanov, V., N. Lekontseva, A. Mikhaylina, and A. Nikulin. "Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface." In Methods in Molecular Biology, 251–62. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0278-2_17.

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Sakurai, Hidehiro, and Toru Hisabori. "Characterization of Nucleotide Binding Sites on Chloroplast Coupling Factor 1 (CF1): Effects of Nucleotides on Nucleotide Triphosphate Formation by Isolated CF1." In Molecular Structure, Function, and Assembly of the ATP Synthases, 267–71. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0593-4_27.

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Moss, J., D. L. Burns, and M. Vaughan. "Mechanism of Action of Choleragen: Effect of Toxin on Binding of Guanyl Nucleotides." In Bacterial Diarrheal Diseases, 153–60. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-4990-4_15.

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Kitabgi, Patrick, and Jean-Pierre Vincent. "Effects of Cations and Nucleotides on Neurotensin Binding to Rat Brain Synaptic Membranes." In Neural and Endocrine Peptides and Receptors, 313–19. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5152-8_21.

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Shrestha, Rojan, Jisu Kim, and Kyungsook Han. "Prediction of RNA-Binding Residues in Proteins Using the Interaction Propensities of Amino Acids and Nucleotides." In Lecture Notes in Computer Science, 114–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87442-3_16.

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Kaziro, Yoshito. "Structure and Function of G Proteins from Mammalian and Yeast Cells." In The Guanine — Nucleotide Binding Proteins, 291–304. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-2037-2_29.

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Conference papers on the topic "Nucleotides binding"

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Sumi, Y., Y. Nakamura, M. Sakai, M. Muramatsu, and N. Aoki. "STRUCTURE OF HUMAN α2-PLASMIN INHIBITOR DEDUCED FROM THAT OF cDNA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644371.

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The complete amino acid sequence of α2-plasmin inhibitor (α2PI) was determined by cDNA cloning. A Agt 10 cDNA library was prepared from poly(A)+mRNA isolated from cultured human liver cells. The labeled oligonucleotides, corresponding to the reported partial amino acid sequences of α2PI, were used as probes to screen the library. One of the positive clones was subcloned into plasmid pUC8. A 2.2 kilobase cDNA clone thus isolated contains a region coding for a portion of a leader sequence, the mature protein, a stop codon (TGA), a 3' noncoding region (733 nucleotides), and a poly(A)tail (37 nucleotides). The amino acid sequence deduced from the cDNA is composed of 452 amino acids starting with an amino-terminal sequence of Asn-Gln-Glu-Gln and ending with a carboxyl-terminal sequence of Gly-Ser-Pro-Lys. The sequence shows approximately 30% homology with those of other plasma serine protease inhibitors. However, α2PI extends 50-52 amino acids beyond the carboxyl-terminal ends of the other inhibitors. This 50-52 carboxyl-terminal amino acid sequence is therefore specific to α2PI, and contains the sequence that is exactly the same as that of the peptide containing the plasminogen binding site. There are three lysine residues possibly involved in the binding to plasminogen in this region. From the homology with the other inhibitors, the inhibitor's reactive-site peptide bond was suggested to be Met-Ser and the same as that of ai-antitrypsin. The Met residue is located at the 362 position from the amino-terminal end.
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Athayde, C. M., and M. C. Scrutton. "ROLE OF GUANINE NUCLEOTIDES IN Ca2+ - DEPENDENT LYSOSOMAL SECRETION FROM ELECTROPERMEABILISED PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644513.

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Previous studies have shown that the maximal extent of Ca2+ dependent secretion of β-N-acetylglucosaminidase (B-N-AcGlc) from electropermeabilised human platelets can be enhanced by addition of thrombin or of 1-oleyl-2-acetylglycerol or 12-0-tetradecanoyl phorbol-13-acetate without a significant alteration in the EC^q for Ca2+. (Knight et al. Europ. J. Biochem.,143337 (1984)). We have found a similar Ca2+ dependent increase in the maximal extent of β-N-AcGlc and β-galactosidase secretion on addition of metabolically stable analogues of GTP (GTPγS and GppNHp) in the absence of thrombin or of GTP added in the presence of a nonsaturating concentration of thrombin. The EC50 values for GTP and GppNHp do not differ significantly for β-N-AcGlc and 3H-5HT secretion, but GTPγS is significantly more effective for 3H-5HT secretion.The time course of β-N-AcGlc secretion induced by GTPγS shows a significant delay as compared with that induced by thrombin + Ca2+. No significant differences could be detected between the properties of β-N-AcGlc or β-galactosidase secretion in this system. The results are consistent with involvement of a GTP binding protein (Np) in receptor-phospholipase C coupling mediating lysosomal secretion, but provide no indication that an additional protein of this type (Ne) is involved as has been proposed for lysosomal secretion from neutrophils. We have thus far failed to find evidence for heterogeneity in lysosomal secretion in this system (supported by SERC and Ciba-Geigy).
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Asaji, T., E. Murakami, N. Takekoshi, S. Matsui, and T. Imaoka. "EFFECT OF ATRIAL NATRIURETIC POLYPEPTIDES ON PLATELET FUNCTION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644872.

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Atrial natriuretic polypeptides (ANP) have been shown to possess a potent diuretic and natriuretic activity, and medicated to patients with heart insufficiency as a drug to be mediated by cGMPaccumulation in glomeruli. A existence of receptors for ANP have recently beenreported in human platelet. But, whether ANP has a direct effect on platelet function remains to be known.Single stimulation of ANP in any concentration did not induce aggregation in neither platelet rich plasma, nor washed platelets. Also no effect of pretreatment with ANP was observed against aggregation triggered by known mediators of platelet activation (Thrombin, ADP, Epinephrine, Collagen) using platelet rich plasma and washed platelets.Therefore, biochemical parameters such as cyclic nucleotides (cAMP, cGMP), phosphatidylinositol hydrolysis and protein phosphorylation, leading to the early stage of platelet activation were examined to investigate the effect of ANP in receptor linked transducing mechanism. Neither cyclic nucleotides accumulation nor [32 P] phosphatidic acid production were detected in platelets treated with ANP. ANP caused a small increase of 32P incorporation into M 30K protein, but no change on the level of phosphorylation of 47K, 20K protein (Imaoka, T. and Haslam, R.J., J.Biol.Chem.258,11404, 1983) was observed.These results clearly suggested thatANP binding with membrane receptor was not linked with adenylate cyclase, ganulate cyclase and phosphatidylinositol phosphate turnover in human platelet, maybe because of too few numbers of ANP receptor. Mechanism of 30K protein phosphorylation and Ca++ mobilization are important subjects for future study, (supported by MESC of Japan)
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Ueno, H., T. Yasunaga, C. Shingyoji, T. Yamaguchi, and K. Hirose. "Dynein Pulls Microtubules Without Rotating Its Stalk." In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-206430.

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Dynein is a motor protein that hydrolyses ATP and moves toward the minus end of a microtubule (MT). A dynein molecule has one to three heavy chains, each consisting of three domains: a head, a stalk and a tail. ATP is bound and hydrolysed in the head, which has a ring-like structure composed of 6 AAA+ domains. The stalk is an antiparallel coiled-coil, 10–15 nm long, and has a nucleotide-dependent MT-binding domain at the tip (1) (Fig. 1). It has been proposed that the nucleotide-dependent binding affinity of the tubulin-binding site at the tip of the stalk is modulated by the two alpha helices in the coiled-coil sliding over each other (2). However, it is not known how a dynein molecule moves along a microtubule (MT).
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Liao, Jung-Chi, and George Oster. "The Engines of Biomolecular Motors." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46094.

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The majority of biomolecular motors are powered by nucleoside triphosphate (NTP), especially adenosine triphosphate (ATP). These motors consist of a β-sheet with highly conserved motifs and the nucleotide binding domain around it. The highly conserved protein folds are the engines of these motors, which convert the energy of NTP hydrolysis cycle to mechanical work. Although functions of molecular motors are widely diverse, (including cargo movement, DNA unwinding, protein degradation, ion pumping, etc), the nucleotide binding domains are very similar. In the binding site, NTP undergoes a hydrolysis cycle E+NTP⇄E·NTP⇄E•NTP⇄E•NDP•Pi⇄E•NDP+Pi⇄E+NDP+Pi where E is the enzyme (motor protein), the small dot represents the docking of NTP, and the large dot represents the tightly-bound states. The hydrogen bond network formed in the NTP binding step, as shown in Figure 1 [1], deforms the β-sheet and adjacent structures. The local deformation propagates to conformational changes of functional residues to do mechanical work or to change the affinity to the substrate [2]. For multimeric motor proteins, we must also consider the stress paths among subunits which control the sequence and the activity of the protein. Stress trajectories emanating from a binding site either passes through a circumferential stress loop or a stress loop through the substrate.
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Budmark*, Amber, Michael Catalano*, Tyrel Haley*, Brady Hicks*, Maria Koenen*, Thea Patrick*, Tyler Larson*, et al. "Abstract 490: Single nucleotide variations within and around microRNA-binding sites." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-490.

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Jefferson, J. R., J. T. Harmon, and G. A. Jamieson. "ADP-BINDING SITES IN PLATELETS: CHARACTERIZATION BY PHOTOAFFINITY LABELING AND BINDING STUDIES WITH FIXED PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644463.

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Attempts to photoaffinity label platelet ADP receptors with 2-azidoADP have not been successful possibly due to the absence of a spacer arm between the nucleotide and the photolabile group. We have synthesized a probe having a long spacer arm by coupling 2-(3-aminopropylthio)-ADP to succinimidyl 4-3H-azidobenzoate. Labeling competable by ADP could not demonstrated with intact platelets. With isolated platelet membranes, three bands (Mr 140,000, 110,000 and 46,000) were labeled that were not competed by ADP while three other bands (Mr 188,000, 92,000 and 51,000) were competable by 100 uM ADP.Another problem in characterizing ADP receptors has been complications due to ADP metabolism and secretion from the dense granules. To avoid this problem we have measured the binding of ADP and analogues to formalin-fixed platelets. ADP bound to two sites (Kl, 0.35 ± 0.04 uM; R1, 160,000 ± 20,000 sites/platelet; K2 7.9 ± 2.0 uM; R2, 400,000 ± 40,000 sites/platelet) with low non-specific binding: these values are in agreement with ADP concentrations required for activation. Affinity at the high affinity site was in the sequence ADP(0.35 uM)=ATP(0.4 uM)›2-MeS.ADP(6.8 uM)› GDP(49 uM) › AMP(360 uM); adenosine did not compete. Binding at the high affinity site was blocked by pMBS (EC50 250 uM) and 5-fluoro-sulfonylbenzoyladenosine (EC50 1 mM). This is the first report of photoaffinity labeling of putative ADP receptors. Our experiments with fixed platelets suggest that they may be useful in testing agonists, antagonists and inhibitors in the absence of complications due to secretion and metabolism.
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Perera, Alexandre, Montserrat Vallverdu, Francesc Claria, Jose Manuel Soria, and Pere Caminal. "DNA Binding Sites Characterization by Means of Rényi Entropy Measures on Nucleotide Transitions." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.260482.

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Perera, Alexandre, Montserrat Vallverdu, Francesc Claria, Jose Manuel Soria, and Pere Caminal. "DNA Binding Sites Characterization by Means of Rényi Entropy Measures on Nucleotide Transitions." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4398771.

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Salekin, Sirajul, Jianqiu Michelle Zhang, and Yufei Huang. "A deep learning model for predicting transcription factor binding location at single nucleotide resolution." In 2017 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). IEEE, 2017. http://dx.doi.org/10.1109/bhi.2017.7897204.

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