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Journal articles on the topic 'GYF domain'

Author: Grafiati

Published: 15 June 2024

Last updated: 31 July 2025

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1

Kofler, Michael M., and Christian Freund. "The GYF domain." FEBS Journal 273, no. 2 (2006): 245–56. http://dx.doi.org/10.1111/j.1742-4658.2005.05078.x.

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2

Zhang, Xiaobo, Lei Qin, Junxing Lu, et al. "Genome-Wide Identification of GYF-Domain Encoding Genes in Three Brassica Species and Their Expression Responding to Sclerotinia sclerotiorum in Brassica napus." Genes 14, no. 1 (2023): 224. http://dx.doi.org/10.3390/genes14010224.

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GYF (glycine-tyrosine-phenylalanine)-domain-containing proteins, which were reported to participate in many aspects of biological processes in yeast and animals, are highly conserved adaptor proteins existing in almost all eukaryotes. Our previous study revealed that GYF protein MUSE11/EXA1 is involved in nucleotide-binding leucine-rich repeat (NLR) receptor-mediated defense in Arabidopsis thaliana. However, the GYF-domain encoding homologous genes are still not clear in other plants. Here, we performed genome-wide identification of GYF-domain encoding genes (GYFs) from Brassica napus and its

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3

Mayya, Vinay K., Mathieu N. Flamand, Alice M. Lambert, et al. "microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development." Nucleic Acids Research 49, no. 9 (2021): 4803–15. http://dx.doi.org/10.1093/nar/gkab162.

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Abstract microRNA (miRNA)-mediated gene silencing is enacted through the recruitment of effector proteins that direct translational repression or degradation of mRNA targets, but the relative importance of their activities for animal development remains unknown. Our concerted proteomic surveys identified the uncharacterized GYF-domain encoding protein GYF-1 and its direct interaction with IFE-4, the ortholog of the mammalian translation repressor 4EHP, as key miRNA effector proteins in Caenorhabditis elegans. Recruitment of GYF-1 protein to mRNA reporters in vitro or in vivo leads to potent tr

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Kofler, Michael, Kathrin Motzny, Michael Beyermann, and Christian Freund. "Novel Interaction Partners of the CD2BP2-GYF Domain." Journal of Biological Chemistry 280, no. 39 (2005): 33397–402. http://dx.doi.org/10.1074/jbc.m503989200.

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Mansour, Hala, Alejandro Cabezas-Cruz, Véronique Peucelle, et al. "Characterization of GEXP15 as a Potential Regulator of Protein Phosphatase 1 in Plasmodium falciparum." International Journal of Molecular Sciences 24, no. 16 (2023): 12647. http://dx.doi.org/10.3390/ijms241612647.

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The Protein Phosphatase type 1 catalytic subunit (PP1c) (PF3D7_1414400) operates in combination with various regulatory proteins to specifically direct and control its phosphatase activity. However, there is little information about this phosphatase and its regulators in the human malaria parasite, Plasmodium falciparum. To address this knowledge gap, we conducted a comprehensive investigation into the structural and functional characteristics of a conserved Plasmodium-specific regulator called Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Through in silico analysis, we identified th

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Opitz, Robert, Matthias Müller, Cédric Reuter, et al. "A modular toolkit to inhibit proline-rich motif–mediated protein–protein interactions." Proceedings of the National Academy of Sciences 112, no. 16 (2015): 5011–16. http://dx.doi.org/10.1073/pnas.1422054112.

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Small-molecule competitors of protein–protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains. Here, we present a modular strategy to obtain an extendable toolkit of chemical fragments (ProMs) designed to replace pairs of conserved prolines in recognition motifs. As proof-of-principl

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Kofler, Michael, Kathrin Motzny, and Christian Freund. "GYF Domain Proteomics Reveals Interaction Sites in Known and Novel Target Proteins." Molecular & Cellular Proteomics 4, no. 11 (2005): 1797–811. http://dx.doi.org/10.1074/mcp.m500129-mcp200.

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8

Albert, Gesa I., Christoph Schell, Karin M. Kirschner, et al. "The GYF domain protein CD2BP2 is critical for embryogenesis and podocyte function." Journal of Molecular Cell Biology 7, no. 5 (2015): 402–14. http://dx.doi.org/10.1093/jmcb/mjv039.

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9

Gu, Wei, Michael Kofler, Iris Antes, Christian Freund, and Volkhard Helms. "Alternative Binding Modes of Proline-Rich Peptides Binding to the GYF Domain†." Biochemistry 44, no. 17 (2005): 6404–15. http://dx.doi.org/10.1021/bi0479914.

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10

Choi, Jung-Hyun, Israel Shpilman, Niaz Mahmood, et al. "No evidence that human GIGYF2 interacts with GRB10: implications for human disease." Life Science Alliance 8, no. 9 (2025): e202503334. https://doi.org/10.26508/lsa.202503334.

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GIGYF2 (growth factor receptor–bound protein 10 [GRB10]-interacting GYF [glycine–tyrosine–phenylalanine] protein 2) reduces mRNA stability and translation via microRNAs, ribosome quality control, and several RNA-binding proteins. GIGYF2 was first identified in mouse cell lines as an interacting partner with GRB10, which binds to the insulin receptor and the insulin-like growth factor receptor 1. Mutations in the humanGIGYF2gene were reported in autism. In mouse models,Gigyf2mutations engender several diseases. It was therefore thought that the GIGYF2-associated disease in humans is caused by d

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11

Kofler, Michael, Katja Heuer, Tobias Zech, and Christian Freund. "Recognition Sequences for the GYF Domain Reveal a Possible Spliceosomal Function of CD2BP2." Journal of Biological Chemistry 279, no. 27 (2004): 28292–97. http://dx.doi.org/10.1074/jbc.m402008200.

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12

Andujar-Sanchez, Montserrat, Eva S. Cobos, Irene Luque, and Jose C. Martinez. "Thermodynamic Impact of Embedded Water Molecules in the Unfolding of Human CD2BP2-GYF Domain." Journal of Physical Chemistry B 116, no. 24 (2012): 7168–75. http://dx.doi.org/10.1021/jp303495b.

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13

Matsui, Hidenori, Yuko Nomura, Mayumi Egusa, et al. "The GYF domain protein PSIG1 dampens the induction of cell death during plant-pathogen interactions." PLOS Genetics 13, no. 10 (2017): e1007037. http://dx.doi.org/10.1371/journal.pgen.1007037.

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14

Freund, Christian, Ronald Kühne, Hailin Yang, Sunghyouk Park, Ellis L. Reinherz, and Gerhard Wagner. "Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules." EMBO Journal 21, no. 22 (2002): 5985–95. http://dx.doi.org/10.1093/emboj/cdf602.

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15

Hashimoto, Masayoshi, Yutaro Neriya, Takuya Keima, et al. "EXA1, a GYF domain protein, is responsible for loss-of-susceptibility to plantago asiatica mosaic virus in Arabidopsis thaliana." Plant Journal 88, no. 1 (2016): 120–31. http://dx.doi.org/10.1111/tpj.13265.

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16

Meirson, Tomer, David Bomze, Gal Markel та Abraham O. Samson. "κ-helix and the helical lock and key model: a pivotal way of looking at polyproline II". Bioinformatics 36, № 12 (2020): 3726–32. http://dx.doi.org/10.1093/bioinformatics/btaa186.

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Abstract Motivation Polyproline II (PPII) is a common conformation, comparable to α-helix and β-sheet. PPII, recently termed with a more generic name—κ-helix, adopts a left-handed structure with 3-fold rotational symmetry. Lately, a new type of binding mechanism—the helical lock and key model was introduced in SH3-domain complexes, where the interaction is characterized by a sliding helical pattern. However, whether this binding mechanism is unique only to SH3 domains is unreported. Results Here, we show that the helical binding pattern is a universal feature of the κ-helix conformation, prese

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17

Ruscica, Vincenzo, Praveen Bawankar, Daniel Peter, Sigrun Helms, Cátia Igreja, and Elisa Izaurralde. "Direct role for the Drosophila GIGYF protein in 4EHP-mediated mRNA repression." Nucleic Acids Research 47, no. 13 (2019): 7035–48. http://dx.doi.org/10.1093/nar/gkz429.

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Abstract The eIF4E-homologous protein (4EHP) is a translational repressor that competes with eIF4E for binding to the 5′-cap structure of specific mRNAs, to which it is recruited by protein factors such as the GRB10-interacting GYF (glycine-tyrosine-phenylalanine domain) proteins (GIGYF). Several experimental evidences suggest that GIGYF proteins are not merely facilitating 4EHP recruitment to transcripts but are actually required for the repressor activity of the complex. However, the underlying molecular mechanism is unknown. Here, we investigated the role of the uncharacterized Drosophila m

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18

Hale, Valerie A., Evan L. Guiney, Lindsey Y. Goldberg, et al. "Notch Signaling Is Antagonized by SAO-1, a Novel GYF-Domain Protein That Interacts with the E3 Ubiquitin Ligase SEL-10 in Caenorhabditis elegans." Genetics 190, no. 3 (2011): 1043–57. http://dx.doi.org/10.1534/genetics.111.136804.

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19

Khosravi-Far, R., M. Chrzanowska-Wodnicka, P. A. Solski, A. Eva, K. Burridge, and C. J. Der. "Dbl and Vav mediate transformation via mitogen-activated protein kinase pathways that are distinct from those activated by oncogenic Ras." Molecular and Cellular Biology 14, no. 10 (1994): 6848–57. http://dx.doi.org/10.1128/mcb.14.10.6848-6857.1994.

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Vav and Dbl are members of a novel class of oncogene proteins that share significant sequence identity in a approximately 250-amino-acid domain, designated the Dbl homology domain. Although Dbl functions as a guanine nucleotide exchange factor (GEF) and activator of Rho family proteins, recent evidence has demonstrated that Vav functions as a GEF for Ras proteins. Thus, transformation by Vav and Dbl may be a consequence of constitutive activation of Ras and Rho proteins, respectively. To address this possibility, we have compared the transforming activities of Vav and Dbl with that of the Ras

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20

Khosravi-Far, R., M. Chrzanowska-Wodnicka, P. A. Solski, A. Eva, K. Burridge, and C. J. Der. "Dbl and Vav mediate transformation via mitogen-activated protein kinase pathways that are distinct from those activated by oncogenic Ras." Molecular and Cellular Biology 14, no. 10 (1994): 6848–57. http://dx.doi.org/10.1128/mcb.14.10.6848.

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Vav and Dbl are members of a novel class of oncogene proteins that share significant sequence identity in a approximately 250-amino-acid domain, designated the Dbl homology domain. Although Dbl functions as a guanine nucleotide exchange factor (GEF) and activator of Rho family proteins, recent evidence has demonstrated that Vav functions as a GEF for Ras proteins. Thus, transformation by Vav and Dbl may be a consequence of constitutive activation of Ras and Rho proteins, respectively. To address this possibility, we have compared the transforming activities of Vav and Dbl with that of the Ras

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21

Koch, Daniel, Ay Lin Kho, Atsushi Fukuzawa, et al. "Obscurin Rho GEF domains are phosphorylated by MST-family kinases but do not exhibit nucleotide exchange factor activity towards Rho GTPases in vitro." PLOS ONE 18, no. 4 (2023): e0284453. http://dx.doi.org/10.1371/journal.pone.0284453.

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Obscurin is a giant muscle protein (>800 kDa) featuring multiple signalling domains, including an SH3-DH-PH domain triplet from the Trio-subfamily of guanosine nucleotide exchange factors (GEFs). While previous research suggests that these domains can activate the small GTPases RhoA and RhoQ in cells, in vitro characterization of these interactions using biophysical techniques has been hampered by the intrinsic instability of obscurin GEF domains. To study substrate specificity, mechanism and regulation of obscurin GEF function by individual domains, we successfully optimized recombinant pr

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22

Buchsbaum, R., J. B. Telliez, S. Goonesekera, and L. A. Feig. "The N-terminal pleckstrin, coiled-coil, and IQ domains of the exchange factor Ras-GRF act cooperatively to facilitate activation by calcium." Molecular and Cellular Biology 16, no. 9 (1996): 4888–96. http://dx.doi.org/10.1128/mcb.16.9.4888.

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We have recently shown that the neuronal exchange factor p140 Ras-GRF becomes activated in vivo in response to elevated calcium levels [C. L. Farnsworth, N. W. Freshney, L. B. Rosen, A. Ghosh, M. E. Greenberg, and L. A. Feig, Nature (London) 376:524-527, 1995]. Activation is mediated by calcium-induced calmodulin binding to an IQ domain near the N terminus of Ras-GRF. Here we show that the adjacent N-terminal pleckstrin homology (PH), coiled-coil, and IQ domains function cooperatively to allow Ras-GRF activation. Deletion of the N-terminal PH domain redistributes a large percentage of Ras-GRF

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23

Cann, M. J. "Sodium regulation of GAF domain function." Biochemical Society Transactions 35, no. 5 (2007): 1032–34. http://dx.doi.org/10.1042/bst0351032.

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Cyclic nucleotide PDEs (phosphodiesterases) regulate cellular levels of cAMP and cGMP by controlling the rate of degradation. Several mammalian PDE isoforms possess N-terminal GAF (found in cGMP PDEs, Anabaena adenylate cyclases and Escherichia coli FhlA; where FhlA is formate hydrogen lyase transcriptional activator) domains that bind cyclic nucleotides. Similarly, the CyaB1 and CyaB2 ACs (adenylate cyclases) of the cyanobacterium Anabaena PCC 7120 bind cAMP through one (CyaB1) or two (CyaB2) N-terminal GAF domains and mediate autoregulation of the AC domain. Sodium inhibits the activity of C

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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 (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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Díaz-Benjumea, Rocío, Sunil Laxman, Thomas R. Hinds, Joseph A. Beavo, and Ana Rascón. "Characterization of a novel cAMP-binding, cAMP-specific cyclic nucleotide phosphodiesterase (TcrPDEB1) from Trypanosoma cruzi." Biochemical Journal 399, no. 2 (2006): 305–14. http://dx.doi.org/10.1042/bj20060757.

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Trypanosoma cruzi, the causative agent of Chagas disease, encodes a number of different cAMP-specific PDE (phosphodiesterase) families. Here we report the identification and characterization of TcrPDEB1 and its comparison with the previously identified TcrPDEB2 (formerly known as TcPDE1). These are two different PDE enzymes of the TcrPDEB family, named in accordance with the recent recommendations of the Nomenclature Committee for Kinetoplast PDEs [Kunz, Beavo, D'Angelo, Flawia, Francis, Johner, Laxman, Oberholzer, Rascon, Shakur et al. (2006) Mol. Biochem. Parasitol. 145, 133–135]. Both enzym

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26

Long, Hou-Wan, On-In Ho, Qi-Qiao He, and Yain-Whar Si. "Transfer Learning in Financial Time Series with Gramian Angular Field (Student Abstract)." Proceedings of the AAAI Conference on Artificial Intelligence 39, no. 28 (2025): 29418–20. https://doi.org/10.1609/aaai.v39i28.35272.

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Transfer learning enhances model performance in financial time series by leveraging data from related domains. The selection of appropriate source domains is crucial to avoid negative transfer. We propose using Gramian Angular Field (GAF) transformations to improve time series similarity functions for better domain alignment. Extensive experiments with DNN and LSTM models show that GAF-based similarity functions, specifically Coral (GAF) for DNN and CMD (GAF) for LSTM, significantly reduce prediction errors, demonstrating their effectiveness in complex financial environments.

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Bowman, Amber L., Dawn H. Catino, John C. Strong, William R. Randall, Aikaterini Kontrogianni-Konstantopoulos, and Robert J. Bloch. "The Rho-Guanine Nucleotide Exchange Factor Domain of Obscurin Regulates Assembly of Titin at the Z-Disk through Interactions with Ran Binding Protein 9." Molecular Biology of the Cell 19, no. 9 (2008): 3782–92. http://dx.doi.org/10.1091/mbc.e08-03-0237.

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Obscurin is an ∼800-kDa protein composed of structural and signaling domains that organizes contractile structures in striated muscle. We have studied the Rho-GEF domain of obscurin to understand its roles in morphogenesis and signaling. We used adenoviral overexpression of this domain, together with ultrastructural and immunofluorescence methods, to examine its effect on maturing myofibrils. We report that overexpression of the Rho-GEF domain specifically inhibits the incorporation of titin into developing Z-disks and disrupts the structure of the Z-disk and Z/I junction, and alters features

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Meller, Nahum, M. Jody Westbrook, John D. Shannon, Chittibabu Guda, and Martin A. Schwartz. "Function of the N-terminus of zizimin1: autoinhibition and membrane targeting." Biochemical Journal 409, no. 2 (2007): 525–33. http://dx.doi.org/10.1042/bj20071263.

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Rho family small GTPases are critical regulators of multiple cellular functions. Dbl-homology-domain-containing proteins are the classical GEFs (guanine nucleotide exchange factors) responsible for activation of Rho proteins. Zizimin1 is a Cdc42-specific GEF that belongs to a second family of mammalian Rho-GEFs, CZH [CDM (Ced-5/DOCK180/Myoblast city)-zizimin homology] proteins, which possess a novel type of GEF domain. CZH proteins can be divided into a subfamily related to DOCK 180 and a subfamily related to zizimin1. The two groups share two conserved regions named the CZH1 (or DHR1) domain

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Rodriguez, Alyssa A., Jessica L. Wojtaszek, Briana H. Greer, et al. "An autoinhibitory role for the GRF zinc finger domain of DNA glycosylase NEIL3." Journal of Biological Chemistry 295, no. 46 (2020): 15566–75. http://dx.doi.org/10.1074/jbc.ra120.015541.

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The NEIL3 DNA glycosylase maintains genome integrity during replication by excising oxidized bases from single-stranded DNA (ssDNA) and unhooking interstrand cross-links (ICLs) at fork structures. In addition to its N-terminal catalytic glycosylase domain, NEIL3 contains two tandem C-terminal GRF-type zinc fingers that are absent in the other NEIL paralogs. ssDNA binding by the GRF–ZF motifs helps recruit NEIL3 to replication forks converged at an ICL, but the nature of DNA binding and the effect of the GRF–ZF domain on catalysis of base excision and ICL unhooking is unknown. Here, we show tha

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Perrin, Marilyn H., Steve Sutton, Deborah L. Bain, W. Travis Berggren, and Wylie W. Vale. "The First Extracellular Domain of Corticotropin Releasing Factor-R1 Contains Major Binding Determinants for Urocortin and Astressin*." Endocrinology 139, no. 2 (1998): 566–70. http://dx.doi.org/10.1210/endo.139.2.5757.

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Abstract The CRF receptors are members of a 7-transmembrane receptor family that includes GH-releasing hormone (GRF), calcitonin, vasoactive intestinal peptide (VIP), secretin, and PTH receptors. To determine the structural features of the CRF receptor that may influence ligand recognition, a series of mutant receptors was analyzed for binding to astressin, a CRF antagonist, and to urocortin, a CRF agonist. Mutant receptors included chimeras between the CRF-R1 and GRF-R or Activin IIB-R, a single membrane spanning receptor serine/threonine kinase. Binding to the mutant receptors was assessed u

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Kalesnikoff, Janet, Eon J. Rios, Ching-Cheng Chen та ін. "Roles of RabGEF1/Rabex-5 domains in regulating FcϵRI surface expression and FcϵRI-dependent responses in mast cells". Blood 109, № 12 (2007): 5308–17. http://dx.doi.org/10.1182/blood-2007-01-067363.

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Abstract RabGEF1/Rabex-5, a guanine nucleotide exchange factor (GEF) for the endocytic pathway regulator, Rab5, contains a Vps9 domain, an A20-like zinc finger (ZnF) domain, and a coiled coil domain. To investigate the importance of these domains in regulating receptor internalization and cell activation, we lentivirally delivered RabGEF1 mutants into RabGEF1-deficient (−/−) mast cells and examined FcϵRI-dependent responses. Wild-type RabGEF1 expression corrected phenotypic abnormalities in −/− mast cells, including decreased basal FcϵRI expression, slowed FcϵRI internalization, elevated IgE +

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32

Nakashima, Kosuke, and Hideki Matsui. "A Novel Inhibition Modality for Phosphodiesterase 2A." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 5 (2020): 498–505. http://dx.doi.org/10.1177/2472555220913241.

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Phosphodiesterase type 2A (PDE2A) has received considerable interest as a molecular target for treating central nervous system diseases that affect memory, learning, and cognition. In this paper, the authors present the discovery of small molecules that have a novel modality of PDE2A inhibition. PDE2A possesses GAF-A and GAF-B domains and is a dual-substrate enzyme capable of hydrolyzing both cGMP and cAMP, and activation occurs through cGMP binding to the GAF-B domain. Thus, positive feedback of the catalytic activity to hydrolyze cyclic nucleotides occurs in the presence of appropriate conce

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Baumeister, Mark A., Kent L. Rossman, John Sondek, and Mark A. Lemmon. "The Dbs PH domain contributes independently to membrane targeting and regulation of guanine nucleotide-exchange activity." Biochemical Journal 400, no. 3 (2006): 563–72. http://dx.doi.org/10.1042/bj20061020.

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Dbl family GEFs (guanine nucleotide-exchange factors) for the Rho GTPases almost invariably contain a PH (pleckstrin homology) domain adjacent to their DH (Dbl homology) domain. The DH domain is responsible for GEF activity, and the PH domain plays a regulatory role that remains poorly understood. We demonstrated previously that Dbl family PH domains bind phosphoinositides with low affinity and cannot function as independent membrane targeting modules. In the present study, we show that dimerization of a Dbs (Dbl's big sister) DH/PH domain fragment is sufficient to drive it to the plasma membr

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Lim, Christopher, Jason M. Berk, Alyssa Blaise, et al. "Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogenOrientia tsutsugamushi." Proceedings of the National Academy of Sciences 117, no. 48 (2020): 30380–90. http://dx.doi.org/10.1073/pnas.2018163117.

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Rho family GTPases regulate an array of cellular processes and are often modulated by pathogens to promote infection. Here, we identify a cryptic guanine nucleotide exchange factor (GEF) domain in the OtDUB protein encoded by the pathogenic bacteriumOrientia tsutsugamushi. A proteomics-based OtDUB interaction screen identified numerous potential host interactors, including the Rho GTPases Rac1 and Cdc42. We discovered a domain in OtDUB with Rac1/Cdc42 GEF activity (OtDUBGEF), with higher activity toward Rac1 in vitro. While this GEF bears no obvious sequence similarity to known GEFs, crystal s

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Wallace, Bret D., Zachary Berman, Geoffrey A. Mueller, et al. "APE2 Zf-GRF facilitates 3′-5′ resection of DNA damage following oxidative stress." Proceedings of the National Academy of Sciences 114, no. 2 (2016): 304–9. http://dx.doi.org/10.1073/pnas.1610011114.

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The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3′-5′ nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3α (TOP3α) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9. Biochemical and NMR results esta

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Stepanenko, Olga V., Irina M. Kuznetsova, Konstantin K. Turoverov, and Olesya V. Stepanenko. "Impact of Double Covalent Binding of BV in NIR FPs on Their Spectral and Physicochemical Properties." International Journal of Molecular Sciences 23, no. 13 (2022): 7347. http://dx.doi.org/10.3390/ijms23137347.

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Understanding the photophysical properties and stability of near-infrared fluorescent proteins (NIR FPs) based on bacterial phytochromes is of great importance for the design of efficient fluorescent probes for use in cells and in vivo. Previously, the natural ligand of NIR FPs biliverdin (BV) has been revealed to be capable of covalent binding to the inherent cysteine residue in the PAS domain (Cys15), and to the cysteine residue introduced into the GAF domain (Cys256), as well as simultaneously with these two residues. Here, based on the spectroscopic analysis of several NIR FPs with both cy

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Mishra, Vishnu Narayan, and Garima Tomar. "Existence of wandering and periodic domain in given angular region." Mathematica Slovaca 70, no. 4 (2020): 839–48. http://dx.doi.org/10.1515/ms-2017-0397.

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AbstractDynamics of composition of entire functions is well related to it's factors, as it is known that for entire functions f and g, fog has wandering domain if and only if gof has wandering domain. However the Fatou components may have different structures and properties. In this paper we have shown the existence of domains with all possibilities of wandering and periodic in given angular region θ.

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Wang, Yi-Chun, Shang-Hsuan Huang, Chien-Ping Chang, and Chuan Li. "Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program." Genes 14, no. 2 (2023): 330. http://dx.doi.org/10.3390/genes14020330.

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Glycine- and arginine-rich (GAR) motifs with different combinations of RG/RGG repeats are present in many proteins. The nucleolar rRNA 2′-O-methyltransferase fibrillarin (FBL) contains a conserved long N-terminal GAR domain with more than 10 RGG plus RG repeats separated by specific amino acids, mostly phenylanalines. We developed a GAR motif finder (GMF) program based on the features of the GAR domain of FBL. The G(0,3)-X(0,1)-R-G(1,2)-X(0,5)-G(0,2)-X(0,1)-R-G(1,2) pattern allows the accommodation of extra-long GAR motifs with continuous RG/RGG interrupted by polyglycine or other amino acids.

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Reimels, Theresa A., Mia Steinberg, Hua Yan, et al. "Rabex-5 E3 and Rab5 GEF domains differ in their regulation of Ras, Notch, and PI3K signaling in Drosophila wing development." PLOS ONE 19, no. 10 (2024): e0312274. http://dx.doi.org/10.1371/journal.pone.0312274.

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Rabex-5 (also called RabGEF1), a protein originally characterized for its Rab5 GEF function, also has an A20-like E3 ubiquitin ligase domain. We and others reported that Rabex-5 E3 activity promotes Ras mono- and di-ubiquitination to inhibit Ras signaling in Drosophila and mammals. Subsequently, we reported that Rabex-5 inhibits Notch signaling in the Drosophila hematopoietic system. Here we report genetic interactions using Rabex-5 transgenes encoding domain-specific mutations that show that Rabex-5 requires an intact E3 domain to inhibit Notch signaling in the epithelial tissue of the develo

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Schormann, Norbert, Manisha Patel, Luke Thannickal, et al. "The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis." Acta Crystallographica Section F Structural Biology Communications 79, no. 5 (2023): 119–27. http://dx.doi.org/10.1107/s2053230x23003199.

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Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducin

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Firestein, Ron, and Michael L. Cleary. "Pseudo-phosphatase Sbf1 contains an N-terminal GEF homology domain that modulates its growth regulatory properties." Journal of Cell Science 114, no. 16 (2001): 2921–27. http://dx.doi.org/10.1242/jcs.114.16.2921.

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Sbf1 (SET binding factor 1) is a pseudo-phosphatase related to the myotubularin family of dual specificity phosphatases, some of which have been implicated in cellular growth and differentiation by virtue of their mutation in human genetic disorders. Sbf1 contains germline-encoded alterations of its myotubularin homology domain that render it non-functional as a phosphatase. We report here the complete structure of Sbf1 and further characterization of its growth regulatory properties. In addition to its similarity to myotubularin, the predicted full-length Sbf1 protein contains pleckstrin (PH)

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Xu, Qian-Zhao, Pavlo Bielytskyi, James Otis, et al. "MAS NMR on a Red/Far-Red Photochromic Cyanobacteriochrome All2699 from Nostoc." International Journal of Molecular Sciences 20, no. 15 (2019): 3656. http://dx.doi.org/10.3390/ijms20153656.

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Unlike canonical phytochromes, the GAF domain of cyanobacteriochromes (CBCRs) can bind bilins autonomously and is sufficient for functional photocycles. Despite the astonishing spectral diversity of CBCRs, the GAF1 domain of the three-GAF-domain photoreceptor all2699 from the cyanobacterium Nostoc 7120 is the only CBCR-GAF known that converts from a red-absorbing (Pr) dark state to a far-red-absorbing (Pfr) photoproduct, analogous to the more conservative phytochromes. Here we report a solid-state NMR spectroscopic study of all2699g1 in its Pr state. Conclusive NMR evidence unveils a particula

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Mizoguchi, Yoko, Miyuki Tsumura, Satoshi Okada, et al. "STAT1 Gain-of-Function in Patients with Chronic Mucocutaneous Candidiasis Can be Detected By the Excessive Phosphorylation of STAT1 in Peripheral Blood Monocytes." Blood 124, no. 21 (2014): 4111. http://dx.doi.org/10.1182/blood.v124.21.4111.4111.

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Abstract Chronic mucocutaneous candidiasis (CMCD) is a rare congenital disorder characterized by persistent or recurrent skin, nails and mucosal membranes infections caused by Candida albicans. Several studies suggest that impairment of development in Th17 linage and/or IL-17 signaling could be responsible for development of CMCD and seven responsible genes, CARD9, STAT3, IL12B, IL12RB1, IL17RA, IL17F, and AIRE have been identified. Recently, heterozygous mutations in coiled-coil domain (CCD) and DNA-binding domain (DBD) of STAT1 are identified in approximately 40% of patients with CMCD. Signa

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Galperin, Michael Y. "Structural Classification of Bacterial Response Regulators: Diversity of Output Domains and Domain Combinations." Journal of Bacteriology 188, no. 12 (2006): 4169–82. http://dx.doi.org/10.1128/jb.01887-05.

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ABSTRACT CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators wit

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ERCAN, Altan. "Sex effect on the correlation of immunoglobulin G glycosylation with rheumatoid arthritis disease activity." TURKISH JOURNAL OF BIOLOGY 44, no. 6 (2020): 406–16. http://dx.doi.org/10.3906/biy-2005-7.

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Rheumatoid arthritis (RA) is a chronic autoimmune disease which affects females more than males with a presence of auto-antibodies. Immunoglobulin G (IgG) produced by adaptive arm has 2 functional domains, Fc and Fab. The Fc domain binds Fc gamma receptors and C1q proteins of the innate arm. Therefore, the IgG Fc domain serves as a bridge between the innate and adaptive arms and is regulated by an evolutionarily conserved N-glycosylation with variable structures. These glycans are classified as agalactosylated G0, monogalactosylated G1, and digalactosylated G2, which are further modified by co

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Lee, Jin-Mok, Ha Yeon Cho, Hyo Je Cho, et al. "O2- and NO-Sensing Mechanism through the DevSR Two-Component System in Mycobacterium smegmatis." Journal of Bacteriology 190, no. 20 (2008): 6795–804. http://dx.doi.org/10.1128/jb.00401-08.

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ABSTRACT The DevS histidine kinase of Mycobacterium smegmatis contains tandem GAF domains (GAF-A and GAF-B) in its N-terminal sensory domain. The heme iron of DevS is in the ferrous state when purified and is resistant to autooxidation from a ferrous to a ferric state in the presence of O2. The redox property of the heme and the results of sequence comparison analysis indicate that DevS of M. smegmatis is more closely related to DosT of Mycobacterium tuberculosis than DevS of M. tuberculosis. The binding of O2 to the deoxyferrous heme led to a decrease in the autokinase activity of DevS, where

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Schultz, Joachim E., Sandra Bruder, Anita Schultz, Sergio E. Martinez, Ning Zheng, and Joseph A. Beavo. "Bacterial GAF domains." BMC Pharmacology 5, Suppl 1 (2005): S17. http://dx.doi.org/10.1186/1471-2210-5-s1-s17.

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Blangy, A., E. Vignal, S. Schmidt, A. Debant, C. Gauthier-Rouviere, and P. Fort. "TrioGEF1 controls Rac- and Cdc42-dependent cell structures through the direct activation of rhoG." Journal of Cell Science 113, no. 4 (2000): 729–39. http://dx.doi.org/10.1242/jcs.113.4.729.

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Rho GTPases regulate the morphology of cells stimulated by extracellular ligands. Their activation is controlled by guanine exchange factors (GEF) that catalyze their binding to GTP. The multidomain Trio protein represents an emerging class of Ρ regulators that contain two GEF domains of distinct specificities. We report here the characterization of Rho signaling pathways activated by the N-terminal GEF domain of Trio (TrioD1). In fibroblasts, TrioD1 triggers the formation of particular cell structures, similar to those elicited by RhoG, a GTPase known to activate both Rac1 and Cdc42Hs. In add

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Marlaire, Simon, and Christoph Dehio. "Bartonella effector protein C mediates actin stress fiber formation via recruitment of GEF-H1 to the plasma membrane." PLOS Pathogens 17, no. 1 (2021): e1008548. http://dx.doi.org/10.1371/journal.ppat.1008548.

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Bartonellae are Gram-negative facultative-intracellular pathogens that use a type-IV-secretion system (T4SS) to translocate a cocktail of Bartonella effector proteins (Beps) into host cells to modulate diverse cellular functions. BepC was initially reported to act in concert with BepF in triggering major actin cytoskeletal rearrangements that result in the internalization of a large bacterial aggregate by the so-called ‘invasome’. Later, infection studies with bepC deletion mutants and ectopic expression of BepC have implicated this effector in triggering an actin-dependent cell contractility

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Braga, Vania M. M. "GEF without a Dbl domain?" Nature Cell Biology 4, no. 8 (2002): E188—E190. http://dx.doi.org/10.1038/ncb0802-e188.

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