Academic literature on the topic 'N-terminal domain (NTD)'
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Journal articles on the topic "N-terminal domain (NTD)"
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Makarov, Valentin V., Ekaterina N. Rybakova, Alexander V. Efimov, Eugene N. Dobrov, Marina V. Serebryakova, Andrey G. Solovyev, Igor V. Yaminsky, Michael E. Taliansky, Sergey Yu Morozov, and Natalia O. Kalinina. "Domain organization of the N-terminal portion of hordeivirus movement protein TGBp1." Journal of General Virology 90, no. 12 (December 1, 2009): 3022–32. http://dx.doi.org/10.1099/vir.0.013862-0.
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Three ‘triple gene block’ proteins known as TGBp1, TGBp2 and TGBp3 are required for cell-to-cell movement of plant viruses belonging to a number of genera including Hordeivirus. Hordeiviral TGBp1 interacts with viral genomic RNAs to form ribonucleoprotein (RNP) complexes competent for translocation between cells through plasmodesmata and over long distances via the phloem. Binding of hordeivirus TGBp1 to RNA involves two protein regions, the C-terminal NTPase/helicase domain and the N-terminal extension region. This study demonstrated that the extension region of hordeivirus TGBp1 consists of two structurally and functionally distinct domains called the N-terminal domain (NTD) and the internal domain (ID). In agreement with secondary structure predictions, analysis of circular dichroism spectra of the isolated NTD and ID demonstrated that the NTD represents a natively unfolded protein domain, whereas the ID has a pronounced secondary structure. Both the NTD and ID were able to bind ssRNA non-specifically. However, whilst the NTD interacted with ssRNA non-cooperatively, the ID bound ssRNA in a cooperative manner. Additionally, both domains bound dsRNA. The NTD and ID formed low-molecular-mass oligomers, whereas the ID also gave rise to high-molecular-mass complexes. The isolated ID was able to interact with both the NTD and the C-terminal NTPase/helicase domain in solution. These data demonstrate that the hordeivirus TGBp1 has three RNA-binding domains and that interaction between these structural units can provide a basis for remodelling of viral RNP complexes at different steps of cell-to-cell and long-distance transport of virus infection.
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Iino, Hitoshi, Kwang Kim, Atsuhiro Shimada, Ryoji Masui, Seiki Kuramitsu, and Kenji Fukui. "Characterization of C- and N-terminal domains of Aquifex aeolicus MutL endonuclease: N-terminal domain stimulates the endonuclease activity of C-terminal domain in a zinc-dependent manner." Bioscience Reports 31, no. 5 (April 21, 2011): 309–22. http://dx.doi.org/10.1042/bsr20100116.
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DNA MMR (mismatch repair) is an excision repair system that removes mismatched bases generated primarily by failure of the 3′–5′ proofreading activity associated with replicative DNA polymerases. MutL proteins homologous to human PMS2 are the endonucleases that introduce the entry point of the excision reaction. Deficiency in PMS2 function is one of the major etiologies of hereditary non-polyposis colorectal cancers in humans. Although recent studies revealed that the CTD (C-terminal domain) of MutL harbours weak endonuclease activity, the regulatory mechanism of this activity remains unknown. In this paper, we characterize in detail the CTD and NTD (N-terminal domain) of aqMutL (Aquifex aeolicus MutL). On the one hand, CTD existed as a dimer in solution and showed weak DNA-binding and Mn2+-dependent endonuclease activities. On the other hand, NTD was monomeric and exhibited a relatively strong DNA-binding activity. It was also clarified that NTD promotes the endonuclease activity of CTD. NTD-mediated activation of CTD was abolished by depletion of the zinc-ion from the reaction mixture or by the substitution of the zinc-binding cysteine residue in CTD with an alanine. On the basis of these results, we propose a model for the intramolecular regulatory mechanism of MutL endonuclease activity.
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Kumar, Raj, and E. Brad Thompson. "Transactivation Functions of the N-Terminal Domains of Nuclear Hormone Receptors: Protein Folding and Coactivator Interactions." Molecular Endocrinology 17, no. 1 (January 1, 2003): 1–10. http://dx.doi.org/10.1210/me.2002-0258.
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Abstract The N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.
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Rosenzweig, Rina, Patrick Farber, Algirdas Velyvis, Enrico Rennella, Michael P. Latham, and Lewis E. Kay. "ClpB N-terminal domain plays a regulatory role in protein disaggregation." Proceedings of the National Academy of Sciences 112, no. 50 (November 30, 2015): E6872—E6881. http://dx.doi.org/10.1073/pnas.1512783112.
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ClpB/Hsp100 is an ATP-dependent disaggregase that solubilizes and reactivates protein aggregates in cooperation with the DnaK/Hsp70 chaperone system. The ClpB–substrate interaction is mediated by conserved tyrosine residues located in flexible loops in nucleotide-binding domain-1 that extend into the ClpB central pore. In addition to the tyrosines, the ClpB N-terminal domain (NTD) was suggested to provide a second substrate-binding site; however, the manner in which the NTD recognizes and binds substrate proteins has remained elusive. Herein, we present an NMR spectroscopy study to structurally characterize the NTD–substrate interaction. We show that the NTD includes a substrate-binding groove that specifically recognizes exposed hydrophobic stretches in unfolded or aggregated client proteins. Using an optimized segmental labeling technique in combination with methyl-transverse relaxation optimized spectroscopy (TROSY) NMR, the interaction of client proteins with both the NTD and the pore-loop tyrosines in the 580-kDa ClpB hexamer has been characterized. Unlike contacts with the tyrosines, the NTD–substrate interaction is independent of the ClpB nucleotide state and protein conformational changes that result from ATP hydrolysis. The NTD interaction destabilizes client proteins, priming them for subsequent unfolding and translocation. Mutations in the NTD substrate-binding groove are shown to have a dramatic effect on protein translocation through the ClpB central pore, suggesting that, before their interaction with substrates, the NTDs block the translocation channel. Together, our findings provide both a detailed characterization of the NTD–substrate complex and insight into the functional regulatory role of the ClpB NTD in protein disaggregation.
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Cohn, Marianne T., Peter Kjelgaard, Dorte Frees, José R. Penadés, and Hanne Ingmer. "Clp-dependent proteolysis of the LexA N-terminal domain in Staphylococcus aureus." Microbiology 157, no. 3 (March 1, 2011): 677–84. http://dx.doi.org/10.1099/mic.0.043794-0.
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The SOS response is governed by the transcriptional regulator LexA and is elicited in many bacterial species in response to DNA damaging conditions. Induction of the SOS response is mediated by autocleavage of the LexA repressor resulting in a C-terminal dimerization domain (CTD) and an N-terminal DNA-binding domain (NTD) known to retain some DNA-binding activity. The proteases responsible for degrading the LexA domains have been identified in Escherichia coli as ClpXP and Lon. Here, we show that in the human and animal pathogen Staphylococcus aureus, the ClpXP and ClpCP proteases contribute to degradation of the NTD and to a lesser degree the CTD. In the absence of the proteolytic subunit, ClpP, or one or both of the Clp ATPases, ClpX and ClpC, the LexA domains were stabilized after autocleavage. Production of a stabilized variant of the NTD interfered with mitomycin-mediated induction of sosA expression while leaving lexA unaffected, and also significantly reduced SOS-induced mutagenesis. Our results show that sequential proteolysis of LexA is conserved in S. aureus and that the NTD may differentially regulate a subset of genes in the SOS regulon.
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Rowley, Paul A., and Margaret C. M. Smith. "Role of the N-Terminal Domain of φC31 Integrase in attB-attP Synapsis." Journal of Bacteriology 190, no. 20 (August 8, 2008): 6918–21. http://dx.doi.org/10.1128/jb.00612-08.
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ABSTRACT φC31 integrase is a serine recombinase containing an N-terminal domain (NTD) that provides catalytic activity and a large C-terminal domain that controls which pair of DNA substrates is able to synapse. We show here that substitutions in amino acid V129 in the NTD can lead to defects in synapsis and DNA cleavage, indicating that the NTD also has an important role in synapsis.
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Hu, Tiancen, Jennifer E. Yeh, Luca Pinello, Jaison Jacob, Srinivas Chakravarthy, Guo-Cheng Yuan, Rajiv Chopra, and David A. Frank. "Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity." Molecular and Cellular Biology 35, no. 19 (July 13, 2015): 3284–300. http://dx.doi.org/10.1128/mcb.00060-15.
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The transcription factor STAT3 is constitutively active in many cancers, where it mediates important biological effects, including cell proliferation, differentiation, survival, and angiogenesis. The N-terminal domain (NTD) of STAT3 performs multiple functions, such as cooperative DNA binding, nuclear translocation, and protein-protein interactions. However, it is unclear which subsets of STAT3 target genes depend on the NTD for transcriptional regulation. To identify such genes, we compared gene expression inSTAT3-null mouse embryonic fibroblasts (MEFs) stably expressing wild-type STAT3 or STAT3 from which NTD was deleted. NTD deletion reduced the cytokine-induced expression of specific STAT3 target genes by decreasing STAT3 binding to their regulatory regions. To better understand the potential mechanisms of this effect, we determined the crystal structure of the STAT3 NTD and identified a dimer interface responsible for cooperative DNA bindingin vitro. We also observed an Ni2+-mediated oligomer with an as yet unknown biological function. Mutations on both dimer and Ni2+-mediated interfaces affected the cytokine induction of STAT3 target genes. These studies shed light on the role of the NTD in transcriptional regulation by STAT3 and provide a structural template with which to design STAT3 NTD inhibitors with potential therapeutic value.
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Marcianò, G., and D. T. Huang. "Structure of the human histone chaperone FACT Spt16 N-terminal domain." Acta Crystallographica Section F Structural Biology Communications 72, no. 2 (January 22, 2016): 121–28. http://dx.doi.org/10.1107/s2053230x15024565.
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The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of theSaccharomyces cerevisiaeandSchizosaccharomyces pombeSpt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.
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Wang, Yong-Sheng, Chung-ke Chang, and Ming-Hon Hou. "Crystallographic analysis of the N-terminal domain ofMiddle East respiratory syndrome coronavirusnucleocapsid protein." Acta Crystallographica Section F Structural Biology Communications 71, no. 8 (July 28, 2015): 977–80. http://dx.doi.org/10.1107/s2053230x15010146.
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The N-terminal domain of the nucleocapsid protein fromMiddle East respiratory syndrome coronavirus(MERS-CoV NP-NTD) contains many positively charged residues and has been identified to be responsible for RNA binding during ribonucleocapsid formation by the virus. In this study, the crystallization and crystallographic analysis of MERS-CoV NP-NTD (amino acids 39–165), with a molecular weight of 14.7 kDa, are reported. MERS-CoV NP-NTD was crystallized at 293 K using PEG 3350 as a precipitant and a 94.5% complete native data set was collected from a cooled crystal at 77 K to 2.63 Å resolution with an overallRmergeof 9.6%. The crystals were monoclinic and belonged to space groupP21, with unit-cell parametersa= 35.60,b= 109.64,c = 91.99 Å, β = 101.22°. The asymmetric unit contained four MERS-CoV NP-NTD molecules.
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Galaz-Davison, Pablo, Ernesto A. Román, and César A. Ramírez-Sarmiento. "The N-terminal domain of RfaH plays an active role in protein fold-switching." PLOS Computational Biology 17, no. 9 (September 3, 2021): e1008882. http://dx.doi.org/10.1371/journal.pcbi.1008882.
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The bacterial elongation factor RfaH promotes the expression of virulence factors by specifically binding to RNA polymerases (RNAP) paused at a DNA signal. This behavior is unlike that of its paralog NusG, the major representative of the protein family to which RfaH belongs. Both proteins have an N-terminal domain (NTD) bearing an RNAP binding site, yet NusG C-terminal domain (CTD) is folded as a β-barrel while RfaH CTD is forming an α-hairpin blocking such site. Upon recognition of the specific DNA exposed by RNAP, RfaH is activated via interdomain dissociation and complete CTD structural rearrangement into a β-barrel structurally identical to NusG CTD. Although RfaH transformation has been extensively characterized computationally, little attention has been given to the role of the NTD in the fold-switching process, as its structure remains unchanged. Here, we used Associative Water-mediated Structure and Energy Model (AWSEM) molecular dynamics to characterize the transformation of RfaH, spotlighting the sequence-dependent effects of NTD on CTD fold stabilization. Umbrella sampling simulations guided by native contacts recapitulate the thermodynamic equilibrium experimentally observed for RfaH and its isolated CTD. Temperature refolding simulations of full-length RfaH show a high success towards α-folded CTD, whereas the NTD interferes with βCTD folding, becoming trapped in a β-barrel intermediate. Meanwhile, NusG CTD refolding is unaffected by the presence of RfaH NTD, showing that these NTD-CTD interactions are encoded in RfaH sequence. Altogether, these results suggest that the NTD of RfaH favors the α-folded RfaH by specifically orienting the αCTD upon interdomain binding and by favoring β-barrel rupture into an intermediate from which fold-switching proceeds.
Dissertations / Theses on the topic "N-terminal domain (NTD)"
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Meyer, Sandra. "Caractérisation des domaines N-terminal et de liaison à l'ADN du récepteur des androgènes par des approches biophysiques." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAJ091/document.
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Cette thèse se situe à l’interface entre la biologie et la biophysique. Les méthodologies utilisées recouvrent principalement la résonance magnétique nucléaire (RMN), la diffusion des rayons X aux petits angles (SAXS), le dichroïsme circulaire (CD) et la spectroscopie de fluorescence. Une première partie vise à étudier le domaine de liaison à l’ADN (DBD) du récepteur des androgènes (AR) et les déterminants de l’interaction avec l’ADN. Une mutation faux-sens dans le DBD altère la spécificité de reconnaissance de l’ADN du récepteur bien que la structure tridimensionnelle soit identique au DBD sauvage. Les résultats montrent un changement dans la dynamique du récepteur mutant entrainant une déstabilisation de l’homo-dimère.La seconde partie de ma thèse consiste à établir un lien séquence/fonction au niveau du domaine N terminal (NTD) de AR. D’après la littérature, cette région joue un rôle important pour l’activité du récepteur, et elle est également décrite comme étant intrinsèquement désordonnée. Les résultats révèlent que cette région établit des contacts transitoires avec le DBD. Ceci suggère l’existence d'un couplage allostérique entre le DBD et les résidus adjacents sur le NTD.Ce couplage modifie l'ensemble conformationnel accessible au NTD en favorisant une conformation en hélice-αMy PhD project is at the boundary between biology and biophysic. Methods used include nuclear magnetic resonance (NMR), small ange X-ray scattering (SAXS), circular dichroïsm (CD) and fluorescence spectroscopy. The androgen receptor (AR) DNA binding domain (DBD) and its interaction with DNA was studied in a first part. A mutation in the DBD leads to a modified DNA recognition by the mutant compared to the wild-type. Our results indicate changes in dynamic of the mutant receptor that leads to the homodimer destabilisation.The second part of my project aim to establish a link between sequence and function of the AR N terminal domain (NTD).As described in literature, this region is involved in the activity of the receptor and is also an intrinsically disordered protein (IDP). The results obtained during my thesis indicate that this region is involved in transient contact with the DBD. This suggest an allosteric coupling between the DBD and the neighboring residues on the NTD.This coupling modifies the conformational ensemble accessible to the NTD by stabilizing a α-helix conformation
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Teska, Mikoláš. "Vlastnosti DNA vazebných mutant proteinů CSL." Master's thesis, 2012. http://www.nusl.cz/ntk/nusl-306654.
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Notch pathway plays a critical role during the development and life of metazoan organisms. CSL proteins are the component of the Notch pathway that mediates the regulation of target genes. The discovery of CSL-like proteins in yeast raised the question of their function in unicellular organisms which did not utilize the canonical Notch pathway. CSL-homologues in yeast are conserved in parts that are important for DNA binding and for fission yeast proteins it was shown that they bind to CSL recognition elements in vitro. In fission yeast, CSL paralogues Cbf11 and Cbf12 play antagonistic roles in cell adhesion and the coordination of cell and nuclear division. Yeast CSL proteins have long and intrinsically unstructured N- terminal domains compared to metazoan CSL proteins. In this study, we investigated the functional significance of these extended N-termini of CSL proteins by their complete removal. For newly constructed truncated variants of proteins Cbf11 and Cbf12 in Schizosaccharomyces pombe we observed the lack of ability to bind CSL recognition RBP probe. The removal of N-terminal parts of CSL proteins in fission yeast led to the change in their cellular localization. Once strongly preferred nuclear localization changed by the removal of N-terminal domains to cytoplasmic localization with a...
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Dolečková, Denisa. "Interaktom N-terminální domény IL-1α." Master's thesis, 2011. http://www.nusl.cz/ntk/nusl-313299.
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Interactome of IL-1α N-terminal domain Cytokines are highly effective mediators produced by various cell types within and outside of the immune system with the aim to influence the orientation, intensity, and duration of the immune response and inflammatory process. Their biological effects mediated through binding the high-affinity membrane receptors and triggering the signal transduction pathway are usually well defined. However, as it is more and more frequently observed, in addition to the exocrine function, some cytokines may show intracrine effects. For this type of cytokines, the term "dual function cytokines" has been adopted. One of these cytokines is Interleukin-1α, in which the recent research has concentrated on determining its intracellular functions. The intracellular function of interleukin-1α has not been clearly defined so far. However, apart from the absence of the conventional hydrophobic sequence, its existence is supported by the fact that the N-terminal peptide included in its precursor is highly conserved and contains nuclear localization signal. The aim of this work is to define the conditions of localization of the interleukin-1α N- terminal domain in different cellular compartments and to study proteins potentially interacting with it using fluorescent microscopy. Key words:...
Conference papers on the topic "N-terminal domain (NTD)"
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Wu, Jian Hui. "Abstract 3652: Development of novel chemical inhibitors targeting the N-terminal domain (NTD) of androgen receptor variants as anti-prostate cancer agents." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-3652.
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