Статті в журналах: "Nucleotide Binding Proteins"

1

Katada, Toshiaki, and Michio Ui. "Guanine nucleotide-binding proteins." Japanese Journal of Pharmacology 49 (1989): 26. http://dx.doi.org/10.1016/s0021-5198(19)55959-5.

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2

Möller, W., and R. Amons. "Phosphate-binding sequences in nucleotide-binding proteins." FEBS Letters 186, no. 1 (July 1, 1985): 1–7. http://dx.doi.org/10.1016/0014-5793(85)81326-0.

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3

Ye, Zhengmao, John D. Lich, Christopher Moore, Kristi L. Williams, Joseph A. Duncan, and Jenny P. _Y Ting. "ATP-binding to the CATERPILLER protein Monarch-1, is required for its inhibitory function (44.19)." Journal of Immunology 178, no. 1_Supplement (April 1, 2007): S51. http://dx.doi.org/10.4049/jimmunol.178.supp.44.19.

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Abstract The newly discovered CATERPILLER (NOD, NLR) family is defined by a nucleotide-binding domain (NBD) that consists of the Walker A and B motifs and ten additional motifs. It is conserved from plants to humans, and is important in immune regulation and several genetic disorders. Although the NBD is a defining feature of this family, there is a paucity of data to indicate that these proteins bind nucleotides, or the binding of nucleotides modulate their functions. Monarch-1/Pypaf7 is a negative regulator of IRAK-1 and NIK. In this report, we successfully purified recombinant Monarch-1 proteins to homogeneity. Purified Monarch-1 binds ATP but not CTP, GTP and UTP and exhibits ATP hydrolysis activity. Intact Walker A/B sequences are required for nucleotide binding. Overexpression of Monarch-1 nucleotide-binding defective mutant in THP-1 cells resulted in a dramatic increase of IL-6, chemokine CCL1, CXCL6 and CXCL13 to the extent that is comparable to the THP-1 Monarch-1 shRNA knock down cells in response to TLR2 agonist. This indicates that ATP binding is required for the inhibitory function of Monarch-1 and the nucleotide binding-defective mutant displays a dominant negative effect. Intact nucleotide-binding domain is also required for IRAK-1 dephosphorylation and p100 processing suggesting a nucleotide binding-dependent mechanism of Monarch-1 function in both canonical and non-canonical NF-κB pathway.

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4

Hatley, M. E., S. W. Lockless, S. K. Gibson, A. G. Gilman, and R. Ranganathan. "Allosteric determinants in guanine nucleotide-binding proteins." Proceedings of the National Academy of Sciences 100, no. 24 (November 17, 2003): 14445–50. http://dx.doi.org/10.1073/pnas.1835919100.

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5

Milligan, G. "Guanine nucleotide binding proteins and cellular control." Current Opinion in Cell Biology 1, no. 2 (April 1989): 196–200. http://dx.doi.org/10.1016/0955-0674(89)90086-0.

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6

Spiegel, Allen M. "Signal transduction by guanine nucleotide binding proteins." Molecular and Cellular Endocrinology 49, no. 1 (January 1987): 1–16. http://dx.doi.org/10.1016/0303-7207(87)90058-x.

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7

Davis, Beckley, Suzanna Talento, Aaron Tocker, and Joseph Duncan. "Nucleotide binding characteristics of NOD2 proteins (INM1P.442)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 56.19. http://dx.doi.org/10.4049/jimmunol.194.supp.56.19.

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Abstract Nucleotide binding and oligomerization domain containing protein 2 (NOD2) is an intracellular protein that is involved in the recognition of bacterial cell wall derived muramyl-dipeptide. Mutations in the gene encoding NOD2 are associated with inherited inflammatory disorders including Crohn’s disease and Blau syndrome. NOD2 is a member of the Nucelotide-binding domain and leucine-rich repeat containing protein gene family (NLR). Nucleotide binding is thought to play a critical role in signaling by NLR family members. However, the molecular mechanisms underlying signal transduction by pathogenic NOD2 proteins remains unknown. Mutations in the nucleotide-binding domain of NOD2 have been shown to alter its signal transduction properties in response to muramyl-dipeptide in cellular assay. We demonstrate that nucleotide binding is necessary for wild type and pathogenic NOD2 protein activation of the NF-κB signaling pathway. Mutations of the Walker A motif inhibit binding to RIP2k in wild type NOD2, Crohn’s disease-associated NOD2 and Blau syndrome-associated NOD2. Loss of RIP2k binding correlates with decreased NF-κB-dependent luciferase activity. These data suggest that nucleotide binding is necessary for NOD2 function.

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8

Cheng, Y. S., C. E. Patterson, and P. Staeheli. "Interferon-induced guanylate-binding proteins lack an N(T)KXD consensus motif and bind GMP in addition to GDP and GTP." Molecular and Cellular Biology 11, no. 9 (September 1991): 4717–25. http://dx.doi.org/10.1128/mcb.11.9.4717-4725.1991.

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The primary structures of interferon (IFN)-induced guanylate-binding proteins (GBPs) were deduced from cloned human and murine cDNAs. These proteins contained only two of the three sequence motifs typically found in GTP/GDP-binding proteins. The N(T)KXD motif, which is believed to confer guanine specificity in other nucleotide-binding proteins, was absent. Nevertheless, the IFN-induced GBPs exhibited a high degree of selectivity for binding to agarose-immobilized guanine nucleotides. An interesting feature of IFN-induced GBPs is that they strongly bound to GMP agarose in addition to GDP and GTP agaroses but failed to bind to ATP agarose and all other nucleotide agaroses tested. Both GTP and GMP, but not ATP, competed for binding of murine GBP-1 to agarose-immobilized GMP. The IFN-induced GBPs thus define a distinct novel family of proteins with GTP-binding activity. We further demonstrate that human and murine cells contain at least two genes encoding IFN-induced GBPs. The cloned murine cDNA codes for GBP-1, an IFN-induced protein previously shown to be absent from mice of Gbp-1b genotype.

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9

Cheng, Y. S., C. E. Patterson, and P. Staeheli. "Interferon-induced guanylate-binding proteins lack an N(T)KXD consensus motif and bind GMP in addition to GDP and GTP." Molecular and Cellular Biology 11, no. 9 (September 1991): 4717–25. http://dx.doi.org/10.1128/mcb.11.9.4717.

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The primary structures of interferon (IFN)-induced guanylate-binding proteins (GBPs) were deduced from cloned human and murine cDNAs. These proteins contained only two of the three sequence motifs typically found in GTP/GDP-binding proteins. The N(T)KXD motif, which is believed to confer guanine specificity in other nucleotide-binding proteins, was absent. Nevertheless, the IFN-induced GBPs exhibited a high degree of selectivity for binding to agarose-immobilized guanine nucleotides. An interesting feature of IFN-induced GBPs is that they strongly bound to GMP agarose in addition to GDP and GTP agaroses but failed to bind to ATP agarose and all other nucleotide agaroses tested. Both GTP and GMP, but not ATP, competed for binding of murine GBP-1 to agarose-immobilized GMP. The IFN-induced GBPs thus define a distinct novel family of proteins with GTP-binding activity. We further demonstrate that human and murine cells contain at least two genes encoding IFN-induced GBPs. The cloned murine cDNA codes for GBP-1, an IFN-induced protein previously shown to be absent from mice of Gbp-1b genotype.

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10

Manji, Husseini K., Guang Chen, William Potter, and Thomas R. Kosten. "Guanine nucleotide binding proteins in opioid-dependent patients." Biological Psychiatry 41, no. 2 (January 1997): 130–34. http://dx.doi.org/10.1016/s0006-3223(96)00216-8.

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11

Gilman, Alfred G. "Guanine Nucleotide-Binding Regulatory Proteins and Adenylate Cyclase." Japanese Journal of Pharmacology 40 (1986): 7. http://dx.doi.org/10.1016/s0021-5198(19)58890-4.

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12

Harnett, W., and M. M. Harnett. "Heterotrimeric Guanine Nucleotide-binding Proteins in Eukaryotic Parasites." Parasitology Today 14, no. 1 (January 1998): 27–31. http://dx.doi.org/10.1016/s0169-4758(97)01167-8.

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13

Dolphin, A. C. "Nucleotide binding proteins in signal transduction and disease." Trends in Neurosciences 10, no. 2 (February 1987): 53–57. http://dx.doi.org/10.1016/0166-2236(87)90021-x.

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14

Clerk, Angela, and Peter H. Sugden. "Small Guanine Nucleotide-Binding Proteins and Myocardial Hypertrophy." Circulation Research 86, no. 10 (May 26, 2000): 1019–23. http://dx.doi.org/10.1161/01.res.86.10.1019.

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15

Brenner, Charles, Pawel Bieganowski, Helen C. Pace, and Kay Huebner. "The histidine triad superfamily of nucleotide-binding proteins." Journal of Cellular Physiology 181, no. 2 (November 1999): 179–87. http://dx.doi.org/10.1002/(sici)1097-4652(199911)181:2<179::aid-jcp1>3.0.co;2-8.

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16

Manji, Husseini K. "Guanine Nucleotide-Binding Proteins in Bipolar Affective Disorder." Archives of General Psychiatry 52, no. 2 (February 1, 1995): 135. http://dx.doi.org/10.1001/archpsyc.1995.03950140053007.

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17

Bandorowicz-Pikula, Joanna, Rene Buchet, and Slawomir Pikula. "Annexins as nucleotide-binding proteins: Facts and speculations." BioEssays 23, no. 2 (January 17, 2001): 170–78. http://dx.doi.org/10.1002/1521-1878(200102)23:2<170::aid-bies1024>3.0.co;2-#.

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18

Bellamacina, Cornelia R. "The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins." FASEB Journal 10, no. 11 (September 1996): 1257–69. http://dx.doi.org/10.1096/fasebj.10.11.8836039.

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19

Saito, Mihoko, Mitiko Go, and Tsuyoshi Shirai. "An empirical approach for detecting nucleotide-binding sites on proteins." Protein Engineering, Design and Selection 19, no. 2 (January 10, 2006): 67–75. http://dx.doi.org/10.1093/protein/gzj002.

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20

Danieluk, M., R. Buś, S. Pikuła, and J. Bandorowicz-Pikuła. "Affinity labeling of annexin VI with a triazine dye, Cibacron blue 3GA. Probable interaction of the dye with C-terminal nucleotide-binding site within the annexin molecule." Acta Biochimica Polonica 46, no. 2 (June 30, 1999): 419–29. http://dx.doi.org/10.18388/abp.1999_4174.

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Annexin VI (AnxVI) from porcine liver, a member of the annexin family of Ca(2+)- and membrane-binding proteins, has been shown to bind ATP in vitro with a K(d) in the low micromolar concentration range. However, this protein does not contain within its primary structure any ATP-binding consensus motifs found in other nucleotide-binding proteins. In addition, binding of ATP to AnxVI resulted in modulation of AnxVI function, which was accompanied by changes in AnxVI affinity to Ca2+ in the presence of ATP. Using limited proteolytic digestion, purification of protein fragments by affinity chromatography on ATP-agarose, and direct sequencing, the ATP-binding site of AnxVI was located in a C-terminal half of the AnxVI molecule. To further study AnxVI-nucleotide interaction we have employed a functional nucleotide analog, Cibacron blue 3GA (CB3GA), a triazine dye which is commonly used to purify multiple ATP-binding proteins and has been described to modulate their activities. We have observed that AnxVI binds to CB3GA immobilized on agarose in a Ca(2+)-dependent manner. Binding is reversed by EGTA and by ATP and, to a lower extent, by other adenine nucleotides. CB3GA binds to AnxVI also in solution, evoking reversible aggregation of protein molecules, which resembles self-association of AnxVI molecules either in solution or on a membrane surface. Our observations support earlier findings that AnxVI is an ATP-binding protein.

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21

Datta, S., R. Krishna, N. Ganesh, Nagasuma R. Chandra, K. Muniyappa, and M. Vijayan. "Crystal Structures of Mycobacterium smegmatis RecA and Its Nucleotide Complexes." Journal of Bacteriology 185, no. 14 (July 15, 2003): 4280–84. http://dx.doi.org/10.1128/jb.185.14.4280-4284.2003.

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ABSTRACT The crystal structures of Mycobacterium smegmatis RecA (RecAMs) and its complexes with ADP, ATPγS, and dATP show that RecAMs has an expanded binding site like that in Mycobacterium tuberculosis RecA, although there are small differences between the proteins in their modes of nucleotide binding. Nucleotide binding is invariably accompanied by the movement of Gln 196, which appears to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding loops. These observations provide a framework for exploring the known properties of the RecA proteins.

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22

Lin, Bin, Kelly L. Covalle, and Janine R. Maddock. "The Caulobacter crescentus CgtA Protein Displays Unusual Guanine Nucleotide Binding and Exchange Properties." Journal of Bacteriology 181, no. 18 (September 15, 1999): 5825–32. http://dx.doi.org/10.1128/jb.181.18.5825-5832.1999.

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ABSTRACT The Caulobacter crescentus CgtA protein is a member of the Obg-GTP1 subfamily of monomeric GTP-binding proteins. In vitro, CgtA specifically bound GTP and GDP but not GMP or ATP. CgtA bound GTP and GDP with moderate affinity at 30°C and displayed equilibrium binding constants of 1.2 and 0.5 μM, respectively, in the presence of Mg2+. In the absence of Mg2+, the affinity of CgtA for GTP and GDP was reduced 59- and 6-fold, respectively.N-Methyl-3′-O-anthranoyl (mant)–guanine nucleotide analogs were used to quantify GDP and GTP exchange. Spontaneous dissociation of both GDP and GTP in the presence of 5 to 12 mM Mg2+ was extremely rapid (kd = 1.4 and 1.5 s−1, respectively), 103- to 105-fold faster than that of the well-characterized eukaryotic Ras-like GTP-binding proteins. The dissociation rate constant of GDP increased sevenfold in the absence of Mg2+. Finally, there was a low inherent GTPase activity with a single-turnover rate constant of 5.0 × 10−4s−1 corresponding to a half-life of hydrolysis of 23 min. These data clearly demonstrate that the guanine nucleotide binding and exchange properties of CgtA are different from those of the well-characterized Ras-like GTP-binding proteins. Furthermore, these data are consistent with a model whereby the nucleotide occupancy of CgtA is controlled by the intracellular levels of guanine nucleotides.

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23

KALDENBERG-STASCH, Sylvia, Michael BADEN, Barbara FESSELER, Karl H. JAKOBS, and Thomas WIELAND. "Receptor-stimulated guanine-nucleotide-triphosphate binding to guanine-nucleotide-binding regulatory proteins. Nucleotide exchange and beta-subunit-mediated phosphotransfer reactions." European Journal of Biochemistry 221, no. 1 (April 1994): 25–33. http://dx.doi.org/10.1111/j.1432-1033.1994.tb18711.x.

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24

Shydlovskyi, Sergii, Anke Y. Zienert, Semra Ince, Christine Dovengerds, Annika Hohendahl, Julia M. Dargazanli, Ailisa Blum, et al. "Nucleotide-dependent farnesyl switch orchestrates polymerization and membrane binding of human guanylate-binding protein 1." Proceedings of the National Academy of Sciences 114, no. 28 (June 23, 2017): E5559—E5568. http://dx.doi.org/10.1073/pnas.1620959114.

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Dynamin-like proteins (DLPs) mediate various membrane fusion and fission processes within the cell, which often require the polymerization of DLPs. An IFN-inducible family of DLPs, the guanylate-binding proteins (GBPs), is involved in antimicrobial and antiviral responses within the cell. Human guanylate-binding protein 1 (hGBP1), the founding member of GBPs, is also engaged in the regulation of cell adhesion and migration. Here, we show how the GTPase cycle of farnesylated hGBP1 (hGBP1F) regulates its self-assembly and membrane interaction. Using vesicles of various sizes as a lipid bilayer model, we show GTP-dependent membrane binding of hGBP1F. In addition, we demonstrate nucleotide-dependent tethering ability of hGBP1F. Furthermore, we report nucleotide-dependent polymerization of hGBP1F, which competes with membrane binding of the protein. Our results show that hGBP1F acts as a nucleotide-controlled molecular switch by modulating the accessibility of its farnesyl moiety, which does not require any supportive proteins.

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25

Schünke, Sven, and Matthias Stoldt. "Structural snapshot of cyclic nucleotide binding domains from cyclic nucleotide-sensitive ion channels." Biological Chemistry 394, no. 11 (November 1, 2013): 1439–51. http://dx.doi.org/10.1515/hsz-2013-0228.

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Abstract Cyclic nucleotide-binding domains (CNBDs) that are present in various channel proteins play crucial roles in signal amplification cascades. Although atomic resolution structures of some of those CNBDs are available, the detailed mechanism by which they confer cyclic nucleotide-binding to the ion channel pore remains poorly understood. In this review, we describe structural insights about cyclic nucleotide-binding-induced conformational changes in CNBDs and their potential coupling with channel gating.

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26

Altenberg, Guillermo A. "The Engine of ABC Proteins." Physiology 18, no. 5 (October 2003): 191–95. http://dx.doi.org/10.1152/nips.01445.2003.

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Proteins that belong to the ATP-binding cassette superfamily span from bacteria to humans and comprise one of the largest protein families. These proteins are characterized by the presence of two nucleotide-binding domains, and recent studies suggest that association and dissociation of these domains is a common basic molecular mechanism of operation that couples ATP binding/hydrolysis to substrate transport across membranes.

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27

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 of the nucleotide-binding domain in complex with Mg2+-ADP was determined, as well as the structures of four proteins with single mutations, K46βE, K114βD, V113βL and L227βF, and one with two mutations, K46βE/K114βD. The crystal structures show that the enzyme is specific for ADP/ATP because of interactions between the nucleotide and the binding site. Nucleotide-specificity is provided by hydrogen-bonding interactions between the adenine base and Gln20β, Gly111β and Val113β. The O atom of the side chain of Gln20β interacts with N6 of ADP, while the side-chain N atom interacts with the carbonyl O atom of Gly111β. It is the different conformations of the backbone at Gln20β, of the side chain of Gln20β and of the linker that make the enzyme ATP-specific. This linker connects the two subdomains of the ATP-grasp fold and interacts differently with adenine and guanine bases. The mutant proteins have similar conformations, although the L227βF mutant shows structural changes that disrupt the binding site for the magnesium ion. Although the K46βE/K114βD double mutant ofBlastocystis hominisSCS binds GTP better than ATP according to kinetic assays, only the complex with Mg2+-ADP was obtained.

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28

Exton, John H. "Cell Signalling Through Guanine-Nucleotide-Binding Regulatory Proteins (G Proteins) and Phospholipases." European Journal of Biochemistry 243, no. 1-2 (January 1997): 10–20. http://dx.doi.org/10.1111/j.1432-1033.1997.t01-1-00010.x.

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29

Ohyanagi, Mitsumasa, and Tadaaki Iwasaki. "The guanine nucleotide-binding regulatory proteins (G proteins) in myocardium with ischemia." Molecular and Cellular Biochemistry 160-161, no. 1 (1996): 153–58. http://dx.doi.org/10.1007/bf00240045.

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30

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. Interestingly, UTP was as potent as ATP in stimulating HL-60 cell adherence, suggesting the presence of a pyrimidine nucleotide receptor. Photoaffinity labeling of endothelial cells with 8-Az-[alpha-32P]ATP showed the presence of two ATP binding proteins of 48 and 87 kDa. ATP and 2-MeSATP inhibited binding by both proteins. Labeling of the 87-kDa protein was inhibited by beta,gamma-CH2ATP, whereas UTP blocked binding by the 48-kDa protein. Thus photoaffinity labeling experiments support the proposal that endothelial cells possess two ATP receptors, one of which is a P2u nucleotide receptor. These findings show that extracellular nucleotides enhance leukocyte adherence to endothelial cells. Nucleotide release into the extracellular space may be one mechanism of exacerbating vascular cell injury relevant to conditions such as adult respiratory distress syndrome and septic shock.

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31

Hoffman, Paula L., and Boris Tabakoff. "Ethanol and guanine nucleotide binding proteins: a selective interaction." FASEB Journal 4, no. 9 (January 1990): 2612–22. http://dx.doi.org/10.1096/fasebj.4.9.2161371.

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32

Kuno, Takayoshi, Shinya Hasimoto, Midori Hirai, and Chikako Tanaka. "A rapid filtration assay for cyclic nucleotide binding proteins." Japanese Journal of Pharmacology 43 (1987): 140. http://dx.doi.org/10.1016/s0021-5198(19)58224-5.

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33

Buss, J. E., S. M. Mumby, P. J. Casey, A. G. Gilman, and B. M. Sefton. "Myristoylated alpha subunits of guanine nucleotide-binding regulatory proteins." Proceedings of the National Academy of Sciences 84, no. 21 (November 1, 1987): 7493–97. http://dx.doi.org/10.1073/pnas.84.21.7493.

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34

Tsuchimoto, Daisuke, Teruaki Iyama, Mari Nonaka, Nona Abolhassani, Eiko Ohta, Kunihiko Sakumi, and Yusaku Nakabeppu. "A comprehensive screening system for damaged nucleotide-binding proteins." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 703, no. 1 (November 2010): 37–42. http://dx.doi.org/10.1016/j.mrgentox.2010.06.005.

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35

Ali, Nawab, and Devendra K. Agrawal. "Guanine nucleotide binding regulatory proteins: Their characteristics and identification." Journal of Pharmacological and Toxicological Methods 32, no. 4 (December 1994): 187–96. http://dx.doi.org/10.1016/1056-8719(94)90086-8.

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36

MILLNER, P. A. "Guanine nucleotide binding proteins associated with chloroplast thylakoid membranes." Biochemical Society Transactions 17, no. 1 (February 1, 1989): 224–25. http://dx.doi.org/10.1042/bst0170224.

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37

Graziano, Michael P., and Alfred G. Gilman. "Guanine nucleotide-binding regulatory proteins; mediators of transmembrane signaling." Trends in Pharmacological Sciences 8, no. 12 (December 1987): 478–81. http://dx.doi.org/10.1016/0165-6147(87)90042-3.

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38

Shabb, J. B., and J. D. Corbin. "Cyclic nucleotide-binding domains in proteins having diverse functions." Journal of Biological Chemistry 267, no. 9 (March 1992): 5723–26. http://dx.doi.org/10.1016/s0021-9258(18)42609-9.

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39

Rosenblum, Jonathan S., Tyzoon K. Nomanbhoy, and John W. Kozarich. "Functional interrogation of kinases and other nucleotide-binding proteins." FEBS Letters 587, no. 13 (May 15, 2013): 1870–77. http://dx.doi.org/10.1016/j.febslet.2013.05.008.

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40

Molski, T. F. P., and R. I. Sha'afi. "Intracellular acidification, guanine-nucleotide binding proteins, and cytoskeletal actin." Cell Motility and the Cytoskeleton 8, no. 1 (1987): 1–6. http://dx.doi.org/10.1002/cm.970080102.

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41

Hentze, Matthias W. "Enzymes as RNA-binding proteins: a role for (di)nucleotide-binding domains?" Trends in Biochemical Sciences 19, no. 3 (March 1994): 101–3. http://dx.doi.org/10.1016/0968-0004(94)90198-8.

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42

Grucela, Paulina Katarzyna, Tobias Fuhrer, Uwe Sauer, Yanjie Chao, and Yong Everett Zhang. "Ribose 5-phosphate: the key metabolite bridging the metabolisms of nucleotides and amino acids during stringent response in Escherichia coli?" Microbial Cell 10, no. 7 (July 3, 2023): 141–44. http://dx.doi.org/10.15698/mic2023.07.799.

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The bacterial stringent response and its effector alarmone guanosine penta- or tetra – phosphates (p)ppGpp are vital for bacterial tolerance and survival of various stresses in environments (including antibiotics) and host cells (virulence). (p)ppGpp does so by binding to its numerous target proteins and reprograming bacterial transcriptome to tune down the synthesis of nucleotides and rRNA/tRNA, and up-regulate amino acid biosynthesis genes. Recent identification of more novel (p)ppGpp direct binding proteins in Escherichia coli and their deep studies have unveiled unprecedented details of how (p)ppGpp coordinates the nucleotide and amino acid metabolic pathways upon stringent response; however, the mechanistic link between nucleotide and amino acid metabolisms remains still incompletely understood. Here we propose the metabolite ribose 5’-phosphate as the key link between nucleotide and amino acid metabolisms and a working model integrating both the transcriptional and metabolic effects of (p)ppGpp on E. coli physiological adaptation during the stringent response.

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43

BORDES, Patricia, Siva R. WIGNESHWERARAJ, Xiaodong ZHANG, and Martin BUCK. "sigma54-dependent transcription activator phage shock protein F of Escherichia coli: a fragmentation approach to identify sequences that contribute to self-association." Biochemical Journal 378, no. 3 (March 15, 2004): 735–44. http://dx.doi.org/10.1042/bj20031464.

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Proteins that belong to the AAA (ATPases associated with various cellular activities) superfamily of mechanochemical enzymes are versatile and control a wide array of cellular functions. Many AAA proteins share the common property of self-association into oligomeric structures and use nucleotide binding and hydrolysis to regulate their biological output. The Escherichia coli transcription activator PspF (phage shock protein F) is a member of the σ54-dependent transcriptional activators that belong to the AAA protein family. Nucleotide interactions condition the functional state of PspF, enabling it to self-associate and interact with its target, the σ54–RNAP (RNA polymerase) closed complex. The self-association determinants within the AAA domain of σ54-dependent activators remain poorly characterized. In the present study, we have used a fragment of the AAA domain of PspF as a probe to study the nucleotide-conditioned self-association of PspF. Results show that the PspF fragment acts in trans to inhibit specifically self-association of PspF. The PspF fragment prevented efficient binding of nucleotides to PspF, consistent with the observation that the site for nucleotide interactions within an oligomer of AAA proteins is created between two protomers. Using proximity-based footprinting and cross-linking techniques, we demonstrate that the sequences represented in this fragment are close to one protomer–protomer interface within a PspF oligomer. As the sequences represented in this PspF fragment also contain a highly conserved motif that interacts with the σ54–RNAP closed complex, we suggest that PspF may be organized to link nucleotide interactions and self-association to σ54–RNAP binding and transcription activation.

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44

Williams, Wynford R. "Dampening of neurotransmitter action: molecular similarity within the melatonin structure." Endocrine Regulations 52, no. 4 (October 1, 2018): 199–207. http://dx.doi.org/10.2478/enr-2018-0025.

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AbstractObjectives. Melatonin initiates physiologic and therapeutic responses in various tissues through binding to poorly defined MT receptors regulated by G-proteins and purine nucleotides. Melatonin’s interaction with other G-protein regulated receptors, including those of serotonin, is unclear. This study explores the potential for the interaction of melatonin with nucleotide and receptor ligand structures. Methods. The study uses a computational program to investigate relative molecular similarity by the comparative superimposition and quantitative fitting of molecular structures to adenine and guanine nucleotide templates. Results. A minimum energy melatonin conformer replicates the nucleotide fits of ligand structures that regulate Gαi and Gαq proteins via serotonin, dopamine, opioid, α-adrenoceptor, and muscarinic receptor classes. The same conformer also replicates the nucleotide fits of ligand structures regulating K+ and Ca2+ ion channels. The acyl-methoxy distance within the melatonin conformer matches a carbonyl-hydroxyl distance in guanine nucleotide. Conclusion. Molecular similarity within the melatonin and ligand structures relates to the established effects of melatonin on cell receptors regulated by purine nucleotides in cell signal transduction processes. Pharmacologic receptor promiscuity may contribute to the widespread effects of melatonin.

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45

Buday, L., and J. Downward. "Epidermal growth factor regulates the exchange rate of guanine nucleotides on p21ras in fibroblasts." Molecular and Cellular Biology 13, no. 3 (March 1993): 1903–10. http://dx.doi.org/10.1128/mcb.13.3.1903-1910.1993.

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Treatment of intact Rat-1 fibroblasts with epidermal growth factor (EGF) leads to rapid activation of cellular ras-encoded proteins. By using the bacterial toxin streptolysin O to permeabilize these cells, it was shown that the low basal rate at which guanine nucleotides bind to, and dissociate from, ras-encoded protein in quiescent fibroblasts was greatly accelerated by EGF treatment. Nucleotide binding to other proteins was not affected. Stimulation of nucleotide exchange on ras-encoded protein required tyrosine kinase but not phospholipase activity. EGF had no effect on total GTPase-activating protein activity. Regulation of ras-encoded protein in Rat-1 fibroblasts is therefore mediated by stimulation, either directly or indirectly, of ras-encoded protein-specific guanine nucleotide exchange factors by the EGF receptor tyrosine kinase.

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46

Buday, L., and J. Downward. "Epidermal growth factor regulates the exchange rate of guanine nucleotides on p21ras in fibroblasts." Molecular and Cellular Biology 13, no. 3 (March 1993): 1903–10. http://dx.doi.org/10.1128/mcb.13.3.1903.

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Treatment of intact Rat-1 fibroblasts with epidermal growth factor (EGF) leads to rapid activation of cellular ras-encoded proteins. By using the bacterial toxin streptolysin O to permeabilize these cells, it was shown that the low basal rate at which guanine nucleotides bind to, and dissociate from, ras-encoded protein in quiescent fibroblasts was greatly accelerated by EGF treatment. Nucleotide binding to other proteins was not affected. Stimulation of nucleotide exchange on ras-encoded protein required tyrosine kinase but not phospholipase activity. EGF had no effect on total GTPase-activating protein activity. Regulation of ras-encoded protein in Rat-1 fibroblasts is therefore mediated by stimulation, either directly or indirectly, of ras-encoded protein-specific guanine nucleotide exchange factors by the EGF receptor tyrosine kinase.

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47

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 a traditional template-based predictor, which identifies global similarity between target structure and template, NSiteMatch concerns the local similarity between a surface patch of the target protein and the binding sites of template. To this end, NSiteMatch identifies more templates than traditional template-based predictors. The NSiteMatch predictor is compared with three representative methods, Findsite, Q-SiteFinder, and MetaPocket. An extensive evaluation demonstrates that NSiteMatch achieves higher success rates than Findsite, Q-SiteFinder, and MetaPocket, in prediction of binding sites of ATP, ADP, and AMP.

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48

Naber, Nariman, Roger Cooke, and Edward Pate. "Conformational changes at the nucleotide pocket of motor proteins monitored by electron paramagnetic resonance spectroscopy." Pure and Applied Chemistry 83, no. 9 (May 16, 2011): 1675–84. http://dx.doi.org/10.1351/pac-con-10-12-08.

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A fundamental goal in the field of motor proteins is to identify the conformational changes associated with the hydrolysis of the physiological substrate, ATP, and to define how these conformational changes are modulated by binding to the polymer track and translated into biologically useful movement. We have used electron paramagnetic resonance (EPR) spectroscopy to monitor conformational changes at the nucleotide-binding site of myosin- and kinesin-family motors. A novel set of nucleotide-analog EPR spin probes were synthesized and used to localize a spin moiety at the nucleotide site. This allows a reporter group to be placed with high specificity at the ATP binding site. Our results indicate that the nucleotide-binding site of myosin motors opens when the motor binds to its polymer roadway, actin, while that of kinesin closes on binding to microtubules (MTs). However, the transition is not all-or-none. There is instead an equilibrium between open and closed conformations. The different conformational changes in the two motor families can be correlated with differences in their biochemical cycles. Thus, we can now define the relationship between nucleotide-site structure, biochemistry and polymer binding for the two motors.

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49

Maruta, Natsumi, Yuri Trusov, David Chakravorty, Daisuke Urano, Sarah M. Assmann, and Jose R. Botella. "Nucleotide exchange–dependent and nucleotide exchange–independent functions of plant heterotrimeric GTP-binding proteins." Science Signaling 12, no. 606 (November 5, 2019): eaav9526. http://dx.doi.org/10.1126/scisignal.aav9526.

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Heterotrimeric guanine nucleotide–binding proteins (G proteins), which are composed of α, β, and γ subunits, are versatile, guanine nucleotide–dependent, molecular on-off switches. In animals and fungi, the exchange of GDP for GTP on Gα controls G protein activation and is crucial for normal cellular responses to diverse extracellular signals. The model plant Arabidopsis thaliana has a single canonical Gα subunit, AtGPA1. We found that, in planta, the constitutively active, GTP-bound AtGPA1(Q222L) mutant and the nucleotide-free AtGPA1(S52C) mutant interacted with Gβγ1 and Gβγ2 dimers with similar affinities, suggesting that G protein heterotrimer formation occurred independently of nucleotide exchange. In contrast, AtGPA1(Q222L) had a greater affinity than that of AtGPA1(S52C) for Gβγ3, suggesting that the GTP-bound conformation of AtGPA1(Q222L) is distinct and tightly associated with Gβγ3. Functional analysis of transgenic lines expressing either AtGPA1(S52C) or AtGPA1(Q222L) in the gpa1-null mutant background revealed various mutant phenotypes that were complemented by either AtGPA1(S52C) or AtGPA1(Q222L). We conclude that, in addition to the canonical GDP-GTP exchange–dependent mechanism, plant G proteins can function independently of nucleotide exchange.

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50

Liu, Xiaofei, and Arne Stenlund. "Mutations in Sensor 1 and Walker B in the Bovine Papillomavirus E1 Initiator Protein Mimic the Nucleotide-Bound State." Journal of Virology 84, no. 4 (November 25, 2009): 1912–19. http://dx.doi.org/10.1128/jvi.01756-09.

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ABSTRACT Viral replication initiator proteins are multifunctional proteins that utilize ATP binding and hydrolysis by their AAA+ modules for multiple functions in the replication of their viral genomes. These proteins are therefore of particular interest for understanding how AAA+ proteins carry out multiple ATP driven functions. We have performed a comprehensive mutational analysis of the residues involved in ATP binding and hydrolysis in the papillomavirus E1 initiator protein based on the recent structural data. Ten of the eleven residues that were targeted were defective for ATP hydrolysis, and seven of these were also defective for ATP binding. The three mutants that could still bind nucleotide represent the Walker B motif (D478 and D479) and Sensor 1 (N523), three residues that are in close proximity to each other and generally are considered to be involved in ATP hydrolysis. Surprisingly, however, two of these mutants, D478A and N523A, mimicked the nucleotide bound state and were capable of binding DNA in the absence of nucleotide. However, these mutants could not form the E1 double trimer in the absence of nucleotide, demonstrating that there are two qualitatively different consequences of ATP binding by E1, one that can be mimicked by D478A and N523A and one which cannot.

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