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Journal articles on the topic 'Nucleotides binding'

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Published: 4 June 2021

Last updated: 11 February 2022

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1

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 nucleo

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2

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 interactio

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3

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.

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4

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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5

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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6

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

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7

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

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8

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 tw

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9

Gromadski, Kirill B., Tobias Schümmer, Anne Strømgaard, Charlotte R. Knudsen, Terri Goss Kinzy та Marina V. Rodnina. "Kinetics of the Interactions between Yeast Elongation Factors 1A and 1Bα, Guanine Nucleotides, and Aminoacyl-tRNA". Journal of Biological Chemistry 282, № 49 (9 жовтня 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

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10

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·AT

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11

Mortensen, E. R., J. Drachman, and G. Guidotti. "Guanosine nucleotides regulate hormone binding of insulin receptors." Biochemical Journal 281, no. 3 (February 1, 1992): 735–43. http://dx.doi.org/10.1042/bj2810735.

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Insulin receptors in turkey erythrocyte and rat adipocyte plasma membranes display non-linear hormone binding by Scatchard analysis. This result is consistent with evidence that the insulin-binding sites are heterogeneous and have at least two affinities for the hormone. Mild reduction of plasma membranes with dithiothreitol, before insulin binding, increased the fraction of hormone binding with high affinity without significantly changing the total number of receptor-binding sites. In the presence of guanosine 5′-[gamma-thio]triphosphate, the amount of receptor with high affinity for insulin

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12

Liu, Qi, Reed F. Johnson, and Julian L. Leibowitz. "Secondary Structural Elements within the 3′ Untranslated Region of Mouse Hepatitis Virus Strain JHM Genomic RNA." Journal of Virology 75, no. 24 (December 15, 2001): 12105–13. http://dx.doi.org/10.1128/jvi.75.24.12105-12113.2001.

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ABSTRACT Previously, we characterized two host protein binding elements located within the 3′-terminal 166 nucleotides of the mouse hepatitis virus (MHV) genome and assessed their functions in defective-interfering (DI) RNA replication. To determine the role of RNA secondary structures within these two host protein binding elements in viral replication, we explored the secondary structure of the 3′-terminal 166 nucleotides of the MHV strain JHM genome using limited RNase digestion assays. Our data indicate that multiple stem-loop and hairpin-loop structures exist within this region. Mutant and

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13

Eraso, Jesus M., and Samuel Kaplan. "Half-Site DNA Sequence and Spacing Length Contributions to PrrA Binding to PrrA Site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1." Journal of Bacteriology 191, no. 13 (May 1, 2009): 4353–64. http://dx.doi.org/10.1128/jb.00244-09.

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ABSTRACT The consensus DNA binding sequence for PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, is poorly defined. We have performed mutational analysis of PrrA site 2, of the RSP3361 gene, to which PrrA binds in vitro (J. M. Eraso and S. Kaplan, J. Bacteriol. 191:4341-4352, 2009), to further define the consensus sequence for DNA binding. Two half-sites of equal length, containing 6 nucleotides each, were required for PrrA binding to this DNA sequence. Systematic nucleotide substitutions in both inverted half-sites led to a decrease in binding affinity of phosphorylated PrrA in vitr

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14

Sun, Jie, and Ke Chen. "NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches." Computational and Mathematical Methods in Medicine 2017 (2017): 1–16. http://dx.doi.org/10.1155/2017/5471607.

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Nucleotides play a central role in life-form metabolism, by interacting with proteins and mediating the function of proteins. It is estimated that nucleotides constitute about 15% of the biologically relevant ligands included in PDB. Prediction of binding sites of nucleotides is useful in understanding the function of proteins and can facilitate the in silico design of drugs. In this study, we propose a nucleotide-binding site predictor, namely, NSiteMatch. The NSiteMatch algorithm integrates three different strategies: geometrical analysis, energy calculation, and template comparison. Unlike

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15

Weinreich, Frank, John R. Riordan, and Georg Nagel. "Dual Effects of Adp and Adenylylimidodiphosphate on Cftr Channel Kinetics Show Binding to Two Different Nucleotide Binding Sites." Journal of General Physiology 114, no. 1 (July 1, 1999): 55–70. http://dx.doi.org/10.1085/jgp.114.1.55.

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The CFTR chloride channel is regulated by phosphorylation by protein kinases, especially PKA, and by nucleotides interacting with the two nucleotide binding domains, NBD-A and NBD-B. Giant excised inside-out membrane patches from Xenopus oocytes expressing human epithelial cystic fibrosis transmembrane conductance regulator (CFTR) were tested for their chloride conductance in response to the application of PKA and nucleotides. Rapid changes in the concentration of ATP, its nonhydrolyzable analogue adenylylimidodiphosphate (AMP-PNP), its photolabile derivative ATP-P3-[1-(2-nitrophenyl)ethyl]est

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16

WANG, Guichun, Roxana PINCHEIRA, Mei ZHANG, and Jian-Ting ZHANG. "Conformational changes of P-glycoprotein by nucleotide binding." Biochemical Journal 328, no. 3 (December 15, 1997): 897–904. http://dx.doi.org/10.1042/bj3280897.

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P-glycoprotein (Pgp) is a membrane protein that transports chemotherapeutic drugs, causing multidrug resistance in human cancer cells. Pgp is a member of the ATP-binding cassette superfamily and functions as a transport ATPase. It has been suggested that the conformation of Pgp changes in the catalytic cycle. In this study, we tested this hypothesis by using limited proteolysis as a tool to detect different conformational states trapped by binding of nucleotide ligands and inhibitors. Pgp has high basal ATPase activity; that is, ATP hydrolysis by Pgp is not rigidly associated with drug transpo

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17

Tuvshinjargal, Narankhuu, Wook Lee, Byungkyu Park, and Kyungsook Han. "Predicting protein-binding RNA nucleotides with consideration of binding partners." Computer Methods and Programs in Biomedicine 120, no. 1 (June 2015): 3–15. http://dx.doi.org/10.1016/j.cmpb.2015.03.010.

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18

Dawicki, D. D., J. McGowan-Jordan, S. Bullard, S. Pond, and S. Rounds. "Extracellular nucleotides stimulate leukocyte adherence to cultured pulmonary artery endothelial cells." American Journal of Physiology-Lung Cellular and Molecular Physiology 268, no. 4 (April 1, 1995): L666—L673. http://dx.doi.org/10.1152/ajplung.1995.268.4.l666.

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Adenosine, ATP, and various nucleotides were examined for their effects on the adherence of leukocytes to bovine pulmonary artery endothelial cells. Extracellular ATP enhanced adherence of HL-60 cells and human neutrophils to endothelial cells in a dose-dependent fashion. Maximal adherence occurred after 15 min coincubation of ATP and HL-60 cells or neutrophils with endothelial cells. ATP stimulation was mediated by direct effects on both HL-60 cells and endothelial cells. The potency profile of various nucleotides was ATP = 2-MeSATP > beta,gamma-CH2ATP, indicative of a P2y receptor. Intere

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19

Katwa, L. C., C. D. Parker, J. K. Dybing, and A. A. White. "Nucleotide regulation of heat-stable enterotoxin receptor binding and of guanylate cyclase activation." Biochemical Journal 283, no. 3 (May 1, 1992): 727–35. http://dx.doi.org/10.1042/bj2830727.

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Certain nucleotides were found to regulate the binding of the Escherichia coli heat-stable enterotoxin (STa) to its receptor in pig intestinal brush border membranes. ATP and adenine nucleotide analogues inhibited 125I-STa binding, while guanine nucleotide analogues stimulated binding, with maximal effects at 0.5-1.0 mM. The strongest inhibitors were adenosine 5′-[beta gamma-imido]triphosphate (App[NH]p) (36%) and adenosine 5′-[beta-thio]diphosphate (ADP[S]) (41%). Inhibition did not require Mg2+, and was blocked by p-chloromercuribenzenesulphonate (PCMBS). Stimulation of binding required Mg2+

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20

Huang, Ji, Vinh H. Nguyen, Karleigh A. Hamblin, Robin Maytum, Mark van der Giezen, and Marie E. Fraser. "ATP-specificity of succinyl-CoA synthetase fromBlastocystis hominis." Acta Crystallographica Section D Structural Biology 75, no. 7 (June 26, 2019): 647–59. http://dx.doi.org/10.1107/s2059798319007976.

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Succinyl-CoA synthetase (SCS) catalyzes the only step of the tricarboxylic acid cycle that leads to substrate-level phosphorylation. Some forms of SCS are specific for ADP/ATP or for GDP/GTP, while others can bind all of these nucleotides, generally with different affinities. The theory of `gatekeeper' residues has been proposed to explain the nucleotide-specificity. Gatekeeper residues lie outside the binding site and create specific electrostatic interactions with incoming nucleotides to determine whether the nucleotides can enter the binding site. To test this theory, the crystal structure

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21

Ohmori, Senri, Marina Wani, Saki Kitabatake, Yuka Nakatsugawa, Tadashi Ando, Takuya Umehara, and Koji Tamura. "RNA Aptamers for a tRNA-Binding Protein from Aeropyrum pernix with Homologous Counterparts Distributed Throughout Evolution." Life 10, no. 2 (February 1, 2020): 11. http://dx.doi.org/10.3390/life10020011.

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In the present in vitro selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon Aeropyrum pernix. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in diverse types of proteins from different organisms. They likely arose early in evolution and have played important roles in evolution through interactions with key RNA structures. RNA aptamers specific for A. pernix Trbp were successfully selected from a pool of RNAs composed of 60 nucleotides, including a random 30-nucleotide region. From

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22

Hosoi, K., M. Fujishita, K. Sugita, K. Kurihara, T. Atsumi, T. Murai, and T. Ueha. "P2 purinergic receptors and cellular calcium metabolism in A 431 human epidermoid carcinoma cells." American Journal of Physiology-Cell Physiology 262, no. 3 (March 1, 1992): C635—C643. http://dx.doi.org/10.1152/ajpcell.1992.262.3.c635.

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Stimulation of P2 purinergic receptors on A 431 human epidermoid cells with ATP rapidly mobilized intracellular calcium and increased cytosolic free Ca2+ ([Ca2+]i). Incorporation of 45Ca2+ was also stimulated by ATP at a rate less than that of [Ca2+]i elevation. Among a number of nucleosides, nucleotides, and their analogues examined, ATP, GTP, UTP, ADP, UDP, adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S), and 5'-adenylylimidodiphosphate (AMP-PNP) increased both [Ca2+]i and 45Ca2+ influx, whereas others did not; these latter two analogues (ATP gamma S and AMP-PNP) blocked the ATP-stimulated

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23

Beslin, A., M. P. Vié, J. P. Blondeau, and J. Francon. "Identification by photoaffinity labelling of a pyridine nucleotide-dependent tri-iodothyronine-binding protein in the cytosol of cultured astroglial cells." Biochemical Journal 305, no. 3 (February 1, 1995): 729–37. http://dx.doi.org/10.1042/bj3050729.

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High-affinity 3,3′,5-tri-iodo-L-thyronine (T3) binding (Kd approximately 0.3 nM) to the cytosol of cultured rat astroglial cells was strongly activated in the presence of pyridine nucleotides. A 35 kDa pyridine nucleotide-dependent T3-binding polypeptide (35K-TBP) was photoaffinity labelled using underivatized [125I]T3 in the presence of pyridine nucleotides and the free-radical scavenger dithiothreitol. Maximum activations of T3 binding and 35K-TBP photolabelling were obtained at approx. 1 x 10(-7) M NADP+ or NADPH, or 1 x 10(-4) M NADH. NAD+ and other nucleotides were without effect. NADPH i

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24

Cameron, Angus J. M. "Occupational hazards: allosteric regulation of protein kinases through the nucleotide-binding pocket." Biochemical Society Transactions 39, no. 2 (March 22, 2011): 472–76. http://dx.doi.org/10.1042/bst0390472.

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Targeting the protein kinase ATP-binding pocket provides a significant opportunity for the treatment of disease. Recent studies have revealed a central activity-independent role for nucleotide pocket occupation in the allosteric behaviour of diverse kinases. Regulation of nucleotide pocket conformation with either nucleotides or ATP competitive inhibitors has revealed an added dimension to the targeting of kinases. In the present paper, using PKC (protein kinase C) as a paradigm, the liabilities and opportunities associated with the occupation of the nucleotide pocket are explored.

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25

Dolgounitcheva, O., V. G. Zakrzewski, and J. V. Ortiz. "Electron binding energies of nucleobases and nucleotides." International Journal of Quantum Chemistry 90, no. 4-5 (2002): 1547–54. http://dx.doi.org/10.1002/qua.10380.

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26

Matthiesen, Karina, and Jacob Nielsen. "Binding of cyclic nucleotides to phosphodiesterase 10A and 11A GAF domains does not stimulate catalytic activity." Biochemical Journal 423, no. 3 (October 12, 2009): 401–9. http://dx.doi.org/10.1042/bj20090982.

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To date eleven human PDE (3′,5′-cyclic nucleotide phosphodiesterase) families have been identified. Of these, five families contain non-catalytic tandem GAF (cGMP-specific and -stimulated phosphodiesterases, Anabaenaadenylate cyclases and Escherichia coliFhlA) domains, GAFa and GAFb, in the N-terminal part of the enzyme. For PDE2A, PDE5A and PDE6 the GAF domains have been shown to bind cGMP with high affinity. For PDE2A and PDE5A this ligand binding has been shown to stimulate the catalytic activity of the enzyme. PDE10A and PDE11A are the two most recently described PDEs and it has been sugge

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27

Mathis, S. A., and L. M. F. Leeb-Lundberg. "Bradykinin recognizes different molecular forms of the B2 kinin receptor in the presence and absence of guanine nucleotides." Biochemical Journal 276, no. 1 (May 15, 1991): 141–47. http://dx.doi.org/10.1042/bj2760141.

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We have previously reported that [3H]bradykinin [(3H]BK) identifies high- and low-affinity B2 kinin receptor sites in bovine myometrial membranes which are sensitive and insensitive respectively to guanine nucleotides. Here we show that these receptor-binding sites are solubilized by the detergent CHAPS. Equilibrium binding in soluble preparations revealed that [3H]BK identified a maximal number of binding sites (Bmax) of 1119 +/- 160 fmol/mg of protein, with an equilibrium dissociation constant (KD) of 314 +/- 70 pM and with a typical B2 kinin receptor specificity. Dissociation of equilibrium

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28

Query, C. C., R. C. Bentley, and J. D. Keene. "A specific 31-nucleotide domain of U1 RNA directly interacts with the 70K small nuclear ribonucleoprotein component." Molecular and Cellular Biology 9, no. 11 (November 1989): 4872–81. http://dx.doi.org/10.1128/mcb.9.11.4872.

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We have defined the nucleotide sequence of a protein-binding domain within U1 RNA that specifically recognizes and binds both to a U1 small nuclear ribonucleoprotein component (the 70K protein) and to the previously defined RNA-binding domain of the 70K protein. We have investigated direct interactions between purified U1 RNA and 70K protein by reconstitution in vitro. Thirty-one nucleotides of U1 RNA, corresponding to stem-loop I, were required for this interaction. Nucleotides at the 5' end of U1 RNA that are involved in base pairing with the 5' splice site of pre-mRNA were not required for

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29

Query, C. C., R. C. Bentley, and J. D. Keene. "A specific 31-nucleotide domain of U1 RNA directly interacts with the 70K small nuclear ribonucleoprotein component." Molecular and Cellular Biology 9, no. 11 (November 1989): 4872–81. http://dx.doi.org/10.1128/mcb.9.11.4872-4881.1989.

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We have defined the nucleotide sequence of a protein-binding domain within U1 RNA that specifically recognizes and binds both to a U1 small nuclear ribonucleoprotein component (the 70K protein) and to the previously defined RNA-binding domain of the 70K protein. We have investigated direct interactions between purified U1 RNA and 70K protein by reconstitution in vitro. Thirty-one nucleotides of U1 RNA, corresponding to stem-loop I, were required for this interaction. Nucleotides at the 5' end of U1 RNA that are involved in base pairing with the 5' splice site of pre-mRNA were not required for

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Frey, Stephan, Adriane Leskovar, Jochen Reinstein, and Johannes Buchner. "The ATPase Cycle of the Endoplasmic Chaperone Grp94." Journal of Biological Chemistry 282, no. 49 (October 9, 2007): 35612–20. http://dx.doi.org/10.1074/jbc.m704647200.

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Grp94, the Hsp90 paralog of the endoplasmic reticulum, plays a crucial role in protein secretion. Like cytoplasmic Hsp90, Grp94 is regulated by nucleotide binding to its N-terminal domain. However, the question of whether Grp94 hydrolyzes ATP was controversial. This sets Grp94 apart from other members of the Hsp90 family where a slow but specific turnover of ATP has been unambiguously established. In this study we aimed at analyzing the nucleotide binding properties and the potential ATPase activity of Grp94. We show here that Grp94 has an ATPase activity comparable with that of yeast Hsp90 wi

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31

Bag, Jnanankur. "Feedback Inhibition of Poly(A)-binding Protein mRNA Translation." Journal of Biological Chemistry 276, no. 50 (October 4, 2001): 47352–60. http://dx.doi.org/10.1074/jbc.m107676200.

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An adenine-richciselement at the 5′-untranslated region (UTR) of Pabp1 mRNA is able to inhibit translation of its own mRNA. Similar inhibition of translation of a reporter β-galactosidase mRNA is observed when the adenine-rich auto regulatory sequence (ARS) is placed within the 5′-UTR of this mRNA. For this translational control the distance of the ARS from the 5′ cap is not important. However, it determines the number of 40 S ribosomal subunits bound to the translationally arrested mRNA. Inhibition of mRNA translation by this regulatory sequence occurs at the step of joining of the 60 S ribos

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32

Volkán-Kacsó, Sándor, and Rudolph A. Marcus. "Theory of single-molecule controlled rotation experiments, predictions, tests, and comparison with stalling experiments in F1-ATPase." Proceedings of the National Academy of Sciences 113, no. 43 (October 10, 2016): 12029–34. http://dx.doi.org/10.1073/pnas.1611601113.

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A recently proposed chemomechanical group transfer theory of rotary biomolecular motors is applied to treat single-molecule controlled rotation experiments. In these experiments, single-molecule fluorescence is used to measure the binding and release rate constants of nucleotides by monitoring the occupancy of binding sites. It is shown how missed events of nucleotide binding and release in these experiments can be corrected using theory, with F1-ATP synthase as an example. The missed events are significant when the reverse rate is very fast. Using the theory the actual rate constants in the c

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BISWAS, Subhasis B., Stephen FLOWERS, and Esther E. BISWAS-FISS. "Quantitative analysis of nucleotide modulation of DNA binding by DnaC protein of Escherichia coli." Biochemical Journal 379, no. 3 (May 1, 2004): 553–62. http://dx.doi.org/10.1042/bj20031255.

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In this study, we have presented the first report of Escherichia coli DnaC protein binding to ssDNA (single stranded DNA) in an apparent hexameric form. DnaC protein transfers DnaB helicase onto a nascent chromosomal DNA replication fork at oriC, the origin of E. coli DNA replication. In eukaryotes, Cdc6 protein may play a similar role in the DNA helicase loading in the replication fork during replication initiation at the origin. We have analysed the DNA-binding properties of DnaC protein and a quantitative analysis of the nucleotide regulation of DnaC–DNA and DnaC–DnaB interactions using flu

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34

Hiriyanna, K. T., J. Varkey, M. Beer, and R. M. Benbow. "Electron microscopic visualization of sites of nascent DNA synthesis by streptavidin-gold binding to biotinylated nucleotides incorporated in vivo." Journal of Cell Biology 107, no. 1 (July 1, 1988): 33–44. http://dx.doi.org/10.1083/jcb.107.1.33.

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Biotinylated nucleotides (bio-11-dCTP, bio-11-dUTP, and bio-7-dATP) were microinjected into unfertilized and fertilized Xenopus laevis eggs. The amounts introduced were comparable to in vivo deoxy-nucleoside triphosphate pools. At various times after microinjection, DNA was extracted from eggs or embryos and subjected to electrophoresis on agarose gels. Newly synthesized biotinylated DNA was analyzed by Southern transfer and visualized using either the BluGENE or Detek-hrp streptavidin-based nucleic acid detection systems. Quantitation of the amount of biotinylated DNA observed at various time

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35

KULAKOVSKIY, IVAN, VICTOR LEVITSKY, DMITRY OSHCHEPKOV, LEONID BRYZGALOV, ILYA VORONTSOV, and VSEVOLOD MAKEEV. "FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES." Journal of Bioinformatics and Computational Biology 11, no. 01 (February 2013): 1340004. http://dx.doi.org/10.1142/s0219720013400040.

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Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) became a method of choice to locate DNA segments bound by different regulatory proteins. ChIP-Seq produces extremely valuable information to study transcriptional regulation. The wet-lab workflow is often supported by downstream computational analysis including construction of models of nucleotide sequences of transcription factor binding sites in DNA, which can be used to detect binding sites in ChIP-Seq data at a single base pair resolution. The most popular TFBS model is represented by positional weight matrix (PWM) with s

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Brown, Jessica A., Likui Zhang, Shanen M. Sherrer, John-Stephen Taylor, Peter M. J. Burgers, and Zucai Suo. "Pre-Steady-State Kinetic Analysis of Truncated and Full-LengthSaccharomyces cerevisiaeDNA Polymerase Eta." Journal of Nucleic Acids 2010 (2010): 1–11. http://dx.doi.org/10.4061/2010/871939.

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Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome.Saccharomyces cerevisiaeDNA polymeraseη(yPolη), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolηwhich contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminu

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QIN, PENG-HUA, WEN-CAI LU, PAN-JUAN GUO, WEI QIN, LI-ZHEN ZHAO, and WEI SONG. "INTERACTIONS OF THE NUCLEOTIDES WITH THE METAL IONS Mg2+, Ca2+, Mn2+, Na+, AND K+." Journal of Theoretical and Computational Chemistry 11, no. 06 (December 2012): 1183–99. http://dx.doi.org/10.1142/s0219633612500794.

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The interactions of the four typical nucleotides with the metal ions Mg 2+, Ca 2+, Mn 2+, Na +, and K + were studied by using the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) calculations in the PCM model. A lot of initial binding sites of the metal ions were designed and optimized to determine the most stable structures of the metal ion nucleotide compounds. It has been shown that the metal ions tend to attach at the center of the negatively charged atoms of the nucleotides. Furthermore, the vertical excitation energies of the metal ion nucleotide compounds were calculated at the same level with the

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MISSIAEN, Ludwig, Jan B. PARYS, Humbert DE SMEDT, Ilse SIENAERT, Henk SIPMA, Sara VANLINGEN, Karlien MAES, and Rik CASTEELS. "Effect of adenine nucleotides on myo-inositol-1,4,5-trisphosphate-induced calcium release." Biochemical Journal 325, no. 3 (August 1, 1997): 661–66. http://dx.doi.org/10.1042/bj3250661.

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The effects of a whole series of adenine nucleotides on Ins(1,4,5)P3-induced Ca2+ release were characterized in permeabilized A7r5 smooth-muscle cells. Several adenine nucleotides activated the Ins(1,4,5)P3 receptor. It was observed that 3′-phosphoadenosine 5′-phosphosulphate, CoA, di(adenosine-5′)tetraphosphate (Ap4A) and di(adenosine-5′)pentaphosphate (Ap5A) were more effective than ATP. Ap4A and Ap5A also interacted with a lower EC50 than ATP. In order to find out how these adenine nucleotides affected Ins(1,4,5)P3-induced Ca2+ release, we have measured their effect on the response of perme

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Sakamoto, C., T. Matozaki, M. Nagao, and S. Baba. "Coupling of guanine nucleotide inhibitory protein to somatostatin receptors on pancreatic acinar membranes." American Journal of Physiology-Gastrointestinal and Liver Physiology 253, no. 3 (September 1, 1987): G308—G314. http://dx.doi.org/10.1152/ajpgi.1987.253.3.g308.

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Guanine nucleotides and pertussis toxin were used to investigate whether somatostatin receptors interact with the guanine nucleotide inhibitory protein (Ni) on pancreatic acinar membranes in the rat. Guanine nucleotides reduced 125I-[Tyr1]somatostatin binding to acinar membranes up to 80%, with rank order of potency being 5'-guanylyl imidodiphosphate [Gpp(NH)p] greater than GTP greater than GDP greater than GMP. Scatchard analysis revealed that the decrease in somatostatin binding caused by Gpp(NH)p was due to the decrease in the maximum binding capacity without a significant change in the bin

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Proks, Peter, Heidi de Wet, and Frances M. Ashcroft. "Sulfonylureas suppress the stimulatory action of Mg-nucleotides on Kir6.2/SUR1 but not Kir6.2/SUR2A KATP channels: A mechanistic study." Journal of General Physiology 144, no. 5 (October 27, 2014): 469–86. http://dx.doi.org/10.1085/jgp.201411222.

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Sulfonylureas, which stimulate insulin secretion from pancreatic β-cells, are widely used to treat both type 2 diabetes and neonatal diabetes. These drugs mediate their effects by binding to the sulfonylurea receptor subunit (SUR) of the ATP-sensitive K+ (KATP) channel and inducing channel closure. The mechanism of channel inhibition is unusually complex. First, sulfonylureas act as partial antagonists of channel activity, and second, their effect is modulated by MgADP. We analyzed the molecular basis of the interactions between the sulfonylurea gliclazide and Mg-nucleotides on β-cell and card

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Stawicki, Scott Stevenson, and C. Cheng Kao. "Spatial Perturbations within an RNA Promoter Specifically Recognized by a Viral RNA-Dependent RNA Polymerase (RdRp) Reveal That RdRp Can Adjust Its Promoter Binding Sites." Journal of Virology 73, no. 1 (January 1, 1999): 198–204. http://dx.doi.org/10.1128/jvi.73.1.198-204.1999.

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ABSTRACT RNA synthesis during viral replication requires specific recognition of RNA promoters by the viral RNA-dependent RNA polymerase (RdRp). Four nucleotides (−17, −14, −13, and −11) within the brome mosaic virus (BMV) subgenomic core promoter are required for RNA synthesis by the BMV RdRp (R. W. Siegel et al., Proc. Natl. Acad. Sci. USA 94:11238–11243, 1997). The spatial requirements for these four nucleotides and the initiation (+1) cytidylate were examined in RNAs containing nucleotide insertions and deletions within the BMV subgenomic core promoter. Spatial perturbations between nucleo

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Lee, John H., and Randall K. Holmes. "Characterization of Specific Nucleotide Substitutions in DtxR-Specific Operators of Corynebacterium diphtheriae That Dramatically Affect DtxR Binding, Operator Function, and Promoter Strength." Journal of Bacteriology 182, no. 2 (January 15, 2000): 432–38. http://dx.doi.org/10.1128/jb.182.2.432-438.2000.

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ABSTRACT The diphtheria toxin repressor (DtxR) of Corynebacterium diphtheriae uses Fe2+ as a corepressor. Holo-DtxR inhibits transcription from the iron-regulated promoters (IRPs) designated IRP1 through IRP5 as well as from the promoters for thetox and hmuO genes. DtxR binds to 19-bp operators with the consensus sequence 5′-TTAGGTTAGCCTAACCTAA-3′, a perfect 9-bp palindrome interrupted by a single C · G base pair. Among the seven known DtxR-specific operators, IRP3 exhibits the weakest binding to DtxR. The message (sense) strand of the IRP3 operator (5′-TTAGGTGAGACGCACCCAT-3′ [nonconsensus nuc

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Li, Yuan-Zong, Wen-Bao Chang, and Yun-Xiang Ci. "Structure effect of nucleotides in terbium(III)-nucleotide fluorescent reaction New evidence for the binding sites of terbium(III) on nucleotides." Chinese Journal of Chemistry 11, no. 6 (August 27, 2010): 524–31. http://dx.doi.org/10.1002/cjoc.19930110606.

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Burstein, E. S., and I. G. Macara. "Interactions of the ras-like protein p25rab 3A with Mg2+ and guanine nucleotides." Biochemical Journal 282, no. 2 (March 1, 1992): 387–92. http://dx.doi.org/10.1042/bj2820387.

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The rab3A gene product is a 25 kDa guanine-nucleotide-binding protein which is expressed at high levels in neural tissue and has about 30% sequence similarity to ras. Purified p25rab3A has been used as substrate to examine its kinetics of nucleotide binding and hydrolysis, and to study the effects of Mg2+ on these processes. p25rab3A binds GDP and GTP similarly well, with nanomolar affinity. Mg2+ increases the affinity between p25rab3A and guanine nucleotides by 3- and 7-fold for GTP and GDP respectively, primarily by drastically decreasing the nucleotide off-rates. The Mg2+ binding affinity t

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Xu, Chaoyi, Douglas K. Fischer, Sanela Rankovic, Wen Li, Robert A. Dick, Brent Runge, Roman Zadorozhnyi, et al. "Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis." PLOS Biology 18, no. 12 (December 17, 2020): e3001015. http://dx.doi.org/10.1371/journal.pbio.3001015.

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Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetic

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Reiber, Duane C., and Robert C. Murphy. "Covalent Binding of LTA4 to Nucleosides and Nucleotides." Archives of Biochemistry and Biophysics 379, no. 1 (July 2000): 119–26. http://dx.doi.org/10.1006/abbi.2000.1851.

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Mejillano, Magdalena R., and Richard H. Himes. "Binding of guanine nucleotides and Mg2+ to tubulin with a nucleotide-depleted exchangeable site." Archives of Biochemistry and Biophysics 291, no. 2 (December 1991): 356–62. http://dx.doi.org/10.1016/0003-9861(91)90146-a.

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Haffke, Matthias, Anja Menzel, Yvonne Carius, Dieter Jahn, and Dirk W. Heinz. "Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides." Acta Crystallographica Section D Biological Crystallography 66, no. 9 (August 13, 2010): 979–87. http://dx.doi.org/10.1107/s0907444910028593.

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The human ATP-binding cassette (ABC) transporter ABCB6 is involved in haem-precursor transport across the mitochondrial membrane. The crystal structure of its nucleotide-binding domain (NBD) has been determined in the apo form and in complexes with ADP, with ADP and Mg2+ and with ATP at high resolution. The overall structure is L-shaped and consists of two lobes, consistent with other reported NBD structures. Nucleotide binding is mediated by the highly conserved Tyr599 and the Walker A motif, and induces notable structural changes. Structural comparison with other structurally characterized N

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Sage, Jay M., Anthony J. Cura, Kenneth P. Lloyd, and Anthony Carruthers. "Caffeine inhibits glucose transport by binding at the GLUT1 nucleotide-binding site." American Journal of Physiology-Cell Physiology 308, no. 10 (May 15, 2015): C827—C834. http://dx.doi.org/10.1152/ajpcell.00001.2015.

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Glucose transporter 1 (GLUT1) is the primary glucose transport protein of the cardiovascular system and astroglia. A recent study proposes that caffeine uncompetitive inhibition of GLUT1 results from interactions at an exofacial GLUT1 site. Intracellular ATP is also an uncompetitive GLUT1 inhibitor and shares structural similarities with caffeine, suggesting that caffeine acts at the previously characterized endofacial GLUT1 nucleotide-binding site. We tested this by confirming that caffeine uncompetitively inhibits GLUT1-mediated 3- O-methylglucose uptake in human erythrocytes [ Vmax and Km f

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Coin, Frédéric, Philippe Frit, Benoit Viollet, Bernard Salles, and Jean-Marc Egly. "TATA Binding Protein Discriminates between Different Lesions on DNA, Resulting in a Transcription Decrease." Molecular and Cellular Biology 18, no. 7 (July 1, 1998): 3907–14. http://dx.doi.org/10.1128/mcb.18.7.3907.

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ABSTRACT DNA damage recognition by basal transcription factors follows different mechanisms. Using transcription-competition, nitrocellulose filter binding, and DNase I footprinting assays, we show that, although the general transcription factor TFIIH is able to target any kind of lesion which can be repaired by the nucleotide excision repair pathway, TATA binding protein (TBP)-TFIID is more selective in damage recognition. Only genotoxic agents which are able to induce kinked DNA structures similar to the one for the TATA box in its TBP complex are recognized. Indeed, DNase I footprinting pat

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