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Academic literature on the topic 'Arginine anchor motif'
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Journal articles on the topic "Arginine anchor motif"
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Banroques, Josette, Olivier Cordin, Monique Doère, Patrick Linder, and N. Kyle Tanner. "A Conserved Phenylalanine of Motif IV in Superfamily 2 Helicases Is Required for Cooperative, ATP-Dependent Binding of RNA Substrates in DEAD-Box Proteins." Molecular and Cellular Biology 28, no. 10 (March 10, 2008): 3359–71. http://dx.doi.org/10.1128/mcb.01555-07.
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ABSTRACT We have identified a highly conserved phenylalanine in motif IV of the DEAD-box helicases that is important for their enzymatic activities. In vivo analyses of essential proteins in yeast showed that mutants of this residue had severe growth phenotypes. Most of the mutants also were temperature sensitive, which suggested that the mutations altered the conformational stability. Intragenic suppressors of the F405L mutation in yeast Ded1 mapped close to regions of the protein involved in ATP or RNA binding in DEAD-box crystal structures, which implicated a defect at this level. In vitro experiments showed that these mutations affected ATP binding and hydrolysis as well as strand displacement activity. However, the most pronounced effect was the loss of the ATP-dependent cooperative binding of the RNA substrates. Sequence analyses and an examination of the Protein Data Bank showed that the motif IV phenylalanine is conserved among superfamily 2 helicases. The phenylalanine appears to be an anchor that maintains the rigidity of the RecA-like domain. For DEAD-box proteins, the phenylalanine also aligns a highly conserved arginine of motif VI through van der Waals and cation-π interactions, thereby helping to maintain the network of interactions that exist between the different motifs involved in ATP and RNA binding.
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Tang, Shuiquan, and Elizabeth A. Edwards. "Identification of Dehalobacter reductive dehalogenases that catalyse dechlorination of chloroform, 1,1,1-trichloroethane and 1,1-dichloroethane." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1616 (April 19, 2013): 20120318. http://dx.doi.org/10.1098/rstb.2012.0318.
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Two novel reductive dehalogenases (RDases) that are highly similar to each other but catalyse distinct dechlorination reactions were identified from Dehalobacter -containing mixed cultures. These two RDases were partially purified from crude protein extracts of anaerobic dechlorinating enrichment cultures using blue native polyacrylamide gel electrophoresis. Gel slices were assayed for dechlorinating activity, and associated proteins were identified using liquid chromatography tandem mass spectrometry with the metagenome of the parent culture as the reference database. The two RDases identified, annotated as CfrA and DcrA, share an amino acid identity of 95.2 per cent, but use different substrates: CfrA dechlorinates chloroform (CF) and 1,1,1-trichloroethane (1,1,1-TCA), but not 1,1-dichloroethane; DcrA dechlorinates 1,1-dichloroethane, but not CF or 1,1,1-TCA. These two novel RDases share no more than 40 per cent amino acid identity to any other known or putative RDases, but both have a twin-arginine motif and two iron–sulfur binding motifs conserved in most RDases. Peptides specific to two putative membrane anchor proteins, annotated as CfrB and DcrB, were also detected in gel slices.
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James, Eddie A., Antonis K. Moustakas, John Bui, George K. Papadopoulos, and William W. Kwok. "DR1001 presents ‘altered-self’ peptides by accepting citrulline in its binding pockets (49.20)." Journal of Immunology 182, no. 1_Supplement (April 1, 2009): 49.20. http://dx.doi.org/10.4049/jimmunol.182.supp.49.20.
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Abstract HLA-DRB1*1001 (DR1001) is associated with rheumatoid arthritis, containing the shared epitope (residues 70-74) within its third hypervariable region. It has been suggested that shared epitope alleles bias T cell selection and amplification, perhaps favoring the recognition of common self-peptides. However, the binding motif of DR1001 and its epitopes remain relatively uncharacterized. One recent paper inferred a binding motif for DR1001 by aligning the sequences of eluted peptides, but only two epitopes were available to validate these findings. The objective of this study was to assess the capacity of DR1001 to present RA associated self-peptides. This was accomplished by defining high affinity non-self epitopes, characterizing amino acids (including citrulline) that can bind at DR1001 anchor positions and using this information to predict putative citrullinated epitopes within RA associated proteins. We identified 15 novel DR1001 restricted epitopes using class II tetramers. Using two of these as a template, we defined the amino acid preferences for each peptide binding pocket. Citrulline was accepted at positions 4, 7 and 9. Based on the observed binding preferences we identified several arginine containing sequences from within RA associated proteins that would be expected to bind after citrullination. For 12 of these, we synthesized unmodified and citrullinated versions and measured their binding to DR1001. Five sequences bound to DR1001, implicating these as potential 'altered-self' epitopes.
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Wentzel, Alexander, Andreas Christmann, Thorsten Adams, and Harald Kolmar. "Display of Passenger Proteins on the Surface ofEscherichia coli K-12 by the Enterohemorrhagic E. coli Intimin EaeA." Journal of Bacteriology 183, no. 24 (December 15, 2001): 7273–84. http://dx.doi.org/10.1128/jb.183.24.7273-7284.2001.
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ABSTRACT Intimins are members of a family of bacterial adhesins from pathogenic Escherichia coli which specifically interact with diverse eukaryotic cell surface receptors. The EaeA intimin from enterohemorrhagic E. coli O157:H7 contains an N-terminal transporter domain, which resides in the bacterial outer membrane and promotes the translocation of four C-terminally attached passenger domains across the bacterial cell envelope. We investigated whether truncated EaeA intimin lacking two carboxy-terminal domains could be used as a translocator for heterologous passenger proteins. We found that a variant of the trypsin inhibitor Ecballium elaterium trypsin inhibitor II (EETI-II), interleukin 4, and the Bence-Jones protein REIv were displayed on the surface of E. coli K-12 via fusion to truncated intimin. Fusion protein net accumulation in the outer membrane could be regulated over a broad range by varying the cellular amount of suppressor tRNA that is necessary for translational readthrough at an ambercodon residing within the truncated eaeA gene. Intimin-mediated adhesion of the bacterial cells to eukaryotic target cells could be mimicked by surface display of a short fibrinogen receptor binding peptide containing an arginine-glycine-aspartic acid sequence motif, which promoted binding of E. coli K-12 to human platelets. Cells displaying a particular epitope sequence fused to truncated intimin could be enriched 200,000-fold by immunofluorescence staining and fluorescence-activated cell sorting in three sorting rounds. These results demonstrate that truncated intimin can be used as an anchor protein that mediates the translocation of various passenger proteins through the cytoplasmic and outer membranes of E. coli and their exposure on the cell surface. Intimin display may prove a useful tool for future protein translocation studies with interesting biological and biotechnological ramifications.
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Safrit, J. T., A. Y. Lee, C. A. Andrews, and R. A. Koup. "A region of the third variable loop of HIV-1 gp120 is recognized by HLA-B7-restricted CTLs from two acute seroconversion patients." Journal of Immunology 153, no. 8 (October 15, 1994): 3822–30. http://dx.doi.org/10.4049/jimmunol.153.8.3822.
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Abstract HIV-1 envelope-specific CTL clones were isolated from the peripheral blood of two patients from within weeks of seroconversion. These clones were CD8+ and restricted by the HLA-B7 molecule. The minimum epitope recognized by the clones was determined to be the 30-amino acid (aa) sequence RPNNNTRKSI within the third variable (V3) loop of the envelope glycoprotein gp120. The aa sequence of this epitope is consistent with the motif found in naturally processed peptides eluted from HLA-B7 molecules. This region of the V3 loop is reasonably well conserved among clade B and some nonclade B isolates of HIV-1, especially at the anchor residues that determine binding to the HLA-B7 molecule. Using peptides based upon virus sequences present within each patient, we determined that autologous viruses were recognized by the clones, and we detected no escape variants from the initial clonal response during the acute phase of infection. Interestingly, a serine to arginine change at position 9 of the epitope abrogated clone recognition in one of the patients. This aa change is one factor that has been associated with a change from a nonsyncytium-inducing to a syncytium-inducing phenotype of HIV-1, raising the possibility that in HLA-B7-expressing patients, escape from this clonal CTL response and a change in viral phenotype may be linked. This study demonstrates that human CTL can be generated against sequences within the third variable loop of HIV-1 gp120. Because multiple vaccine strategies are based upon the V3 loop of HIV-1 gp120, this defined epitope can be exploited in determining the ability of certain vaccines to stimulate a CTL response in a select population of individuals.
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Yue, Ling, Liang Shang, and Eric Hunter. "Truncation of the Membrane-Spanning Domain of Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Defines Elements Required for Fusion, Incorporation, and Infectivity." Journal of Virology 83, no. 22 (September 2, 2009): 11588–98. http://dx.doi.org/10.1128/jvi.00914-09.
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ABSTRACT The membrane-spanning domain (MSD) of the envelope (Env) glycoprotein from human (HIV) and simian immunodeficiency viruses plays a key role in anchoring the Env complex into the viral membrane but also contributes to its biological function in fusion and virus entry. In HIV type 1 (HIV-1), it has been predicted to span 27 amino acids, from lysine residue 681 to arginine 707, and encompasses an internal arginine at residue 694. By examining a series of C-terminal-truncation mutants of the HIV-1 gp41 glycoprotein that substituted termination codons for amino acids 682 to 708, we show that this entire region is required for efficient viral infection of target cells. Truncation to the arginine at residue 694 resulted in an Env complex that was secreted from the cells. In contrast, a region from residues 681 to 698, which contains highly conserved hydrophobic residues and glycine motifs and extends 4 amino acids beyond 694R, can effectively anchor the protein in the membrane, allow efficient transport to the plasma membrane, and mediate wild-type levels of cell-cell fusion. However, these fusogenic truncated Env mutants are inefficiently incorporated into budding virions. Based on the analysis of these mutants, a “snorkeling” model, in which the flanking charged amino acid residues at 681 and 694 are buried in the lipid while their side chains interact with polar head groups, is proposed for the HIV-1 MSD.
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Ali, Hashim, David Noyvert, Jacqueline Hankinson, Gemma Lindsey, Aleksei Lulla, and Valeria Lulla. "The astrovirus N-terminal nonstructural protein anchors replication complexes to the perinuclear ER membranes." PLOS Pathogens 20, no. 7 (July 15, 2024): e1011959. http://dx.doi.org/10.1371/journal.ppat.1011959.
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An essential aspect of positive-sense RNA virus replication is anchoring the replication complex (RC) to cellular membranes. Positive-sense RNA viruses employ diverse strategies, including co-translational membrane targeting through signal peptides and co-opting cellular membrane trafficking components. Often, N-terminal nonstructural proteins play a crucial role in linking the RC to membranes, facilitating the early association of the replication machinery. Astroviruses utilize a polyprotein strategy to synthesize nonstructural proteins, relying on subsequent processing to form replication-competent complexes. This study provides evidence for the perinuclear ER membrane association of RCs in five distinct human astrovirus strains. Using tagged recombinant classical human astrovirus 1 and neurotropic MLB2 strains, we establish that the N-terminal domain guides the ER membrane association. We identified di-arginine motifs responsible for the perinuclear ER retention and formation of functional RCs through mutational analysis of the N-terminal domain in replicon and reverse genetics systems. In addition, we demonstrate the association of key components of the astrovirus replication complex: double-stranded RNA, RNA-dependent RNA polymerase, protease, and N-terminal protein. Our findings highlight the intricate virus-ER interaction mechanism employed by astroviruses, potentially leading to the development of novel antiviral intervention strategies.
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Wang, Li, Kangjing Chen, and Zhucheng Chen. "Structural basis of ALC1/CHD1L autoinhibition and the mechanism of activation by the nucleosome." Nature Communications 12, no. 1 (July 1, 2021). http://dx.doi.org/10.1038/s41467-021-24320-4.
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AbstractChromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is regulated remain unclear. Here we report the crystal structure of human ALC1 and the cryoEM structure bound to the nucleosome. The structure shows the macro domain of ALC1 binds to lobe 2 of the ATPase motor, sequestering two elements for nucleosome recognition, explaining the autoinhibition mechanism of the enzyme. The H4 tail competes with the macro domain for lobe 2-binding, explaining the requirement for this nucleosomal epitope for ALC1 activation. A dual-arginine-anchor motif of ALC1 recognizes the acidic pocket of the nucleosome, which is critical for chromatin remodeling in vitro. Together, our findings illustrate the structures of ALC1 and shed light on its regulation mechanisms, paving the way for the discovery of drugs targeting ALC1 for the treatment of cancer.
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Hsu, Sheng-Chieh, Ching-Yu Lin, Yen-Yi Lin, Colin C. Collins, Chia-Lin Chen, and Hsing-Jien Kung. "TEAD4 as an Oncogene and a Mitochondrial Modulator." Frontiers in Cell and Developmental Biology 10 (May 5, 2022). http://dx.doi.org/10.3389/fcell.2022.890419.
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TEAD4 (TEA Domain Transcription Factor 4) is well recognized as the DNA-anchor protein of YAP transcription complex, which is modulated by Hippo, a highly conserved pathway in Metazoa that controls organ size through regulating cell proliferation and apoptosis. To acquire full transcriptional activity, TEAD4 requires co-activator, YAP (Yes-associated protein) or its homolog TAZ (transcriptional coactivator with PDZ-binding motif) the signaling hub that relays the extracellular stimuli to the transcription of target genes. Growing evidence suggests that TEAD4 also exerts its function in a YAP-independent manner through other signal pathways. Although TEAD4 plays an essential role in determining that differentiation fate of the blastocyst, it also promotes tumorigenesis by enhancing metastasis, cancer stemness, and drug resistance. Upregulation of TEAD4 has been reported in several cancers, including colon cancer, gastric cancer, breast cancer, and prostate cancer and serves as a valuable prognostic marker. Recent studies show that TEAD4, but not other members of the TEAD family, engages in regulating mitochondrial dynamics and cell metabolism by modulating the expression of mitochondrial- and nuclear-encoded electron transport chain genes. TEAD4’s functions including oncogenic activities are tightly controlled by its subcellular localization. As a predominantly nuclear protein, its cytoplasmic translocation is triggered by several signals, such as osmotic stress, cell confluency, and arginine availability. Intriguingly, TEAD4 is also localized in mitochondria, although the translocation mechanism remains unclear. In this report, we describe the current understanding of TEAD4 as an oncogene, epigenetic regulator and mitochondrial modulator. The contributing mechanisms will be discussed.
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Gallego-Parrilla, José Jesús, Emmanuele Severi, Govind Chandra, and Tracy Palmer. "Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase." Microbiology 170, no. 2 (February 16, 2024). http://dx.doi.org/10.1099/mic.0.001431.
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The twin-arginine protein transport (Tat) system exports folded proteins across the cytoplasmic membranes of prokaryotes and the energy transducing-membranes of plant thylakoids and mitochondria. Proteins are targeted to the Tat machinery by N-terminal signal peptides with a conserved twin-arginine motif, and some substrates are exported as heterodimers where the signal peptide is present on one of the partner proteins. A subset of Tat substrates is found in the membrane. Tat-dependent membrane proteins usually have large globular domains and a single transmembrane helix present at the N- or C-terminus. Five Tat substrates that have C-terminal transmembrane helices have previously been characterized in the model bacterium Escherichia coli. Each of these is an iron–sulfur cluster-containing protein involved in electron transfer from hydrogen or formate. Here we have undertaken a bioinformatic search to identify further tail-anchored Tat substrates encoded in bacterial genomes. Our analysis has revealed additional tail-anchored iron–sulfur proteins associated in modules with either a b-type cytochrome or a quinol oxidase. We also identified further candidate tail-anchored Tat substrates, particularly among members of the actinobacterial phylum, that are not predicted to contain cofactors. Using reporter assays, we show experimentally that six of these have both N-terminal Tat signal peptides and C-terminal transmembrane helices. The newly identified proteins include a carboxypeptidase and a predicted protease, and four sortase substrates for which membrane integration is a prerequisite for covalent attachment to the cell wall.
Dissertations / Theses on the topic "Arginine anchor motif"
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Martin, Franck. "Structural and functional studies of chromatin remodeling complex mamalian SWI / SNF." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAJ044.
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La chromatine est une structure dynamique régulée par différents mécanismes épigénétiques parmi lesquels le remodelage de la chromatine dépendant de l’ATP comme le SWI/SNF. Leur importance est telle que les mutations des protéines de remodelage de la chromatine sont fortement associées à plusieurs maladies dont le cancer. Par exemple les protéines BCL7, qui sont de nouvelles sous unité centrales récemment identifié du complexe SWI/SNF des mammifère, sont associées à différents types de cancers comme dans le Diffuse Large B-cell Lymphoma (DLBCL). Les informations sur les protéines BCL7 sont à ce jour très limitées. En utilisant des approches biochimiques et structurelles, ce projet vise à mieux comprendre la structure et la fonction de ces sous unités auxiliaires. Nous rapportons ici que les protéines se lient à l’acidique patch du nucleosome avec sa regions N-terminal qui comprend un motif d’ancrage arginines et que la mutation de l’une de ces arginines impacte directement la liaison au nucleosome. Nous apportons aussi une hypothèse sur la position au sein du complexe SWI/SNF de BCL7 qui interagit avec le module ARP et plus particulièrement avec ACTB par l'intermédiaire d'un motif 2W, et qu’elles sont directement des partenaires de liaisons avec BAF47. Nous avons aussi pu identifier qu’une fois sur les nucléosomes c’est BAF47 qui prend place sur l’acidique patch et l’hélice de BCL7A est déplacéChromatin is a dynamic structure regulated by various epigenetic mechanisms, including ATP-dependent chromatin remodeling such as SWI/SNF. Their importance is such that mutations in chromatin remodeling proteins are strongly associated with several diseases, including cancer. For example, BCL7 proteins, which are newly identified core subunits of the mammalian SWI/SNF complex, are associated with different types of cancer, such as Diffuse Large B-cell Lymphoma (DLBCL). To date, information on BCL7 proteins is very limited. Using biochemical and structural approaches, this project aims to better understand the structure and function of these auxiliary subunits. We report here that the proteins bind to the nucleosome with its N-terminal regions, which include an arginine anchoring motif, and that mutation of one of these arginines directly impacts binding to the nucleosome. We also hypothesize that the position within the SWI/SNF complex of BCL7, which interacts with the ARP module and more specifically with ACTB via a 2W motif, is directly linked to BAF47. We were also able to identify that once on the nucleosomes, BAF47 takes its place on the acidic patch and the BCL7A helix is displaced