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Academic literature on the topic 'N-terminal or C-terminal swapped dimer of RNase A'
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Journal articles on the topic "N-terminal or C-terminal swapped dimer of RNase A"
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Fagagnini, Andrea, Andrea Pica, Sabrina Fasoli, Riccardo Montioli, Massimo Donadelli, Marco Cordani, Elena Butturini, Laura Acquasaliente, Delia Picone, and Giovanni Gotte. "Onconase dimerization through 3D domain swapping: structural investigations and increase in the apoptotic effect in cancer cells*." Biochemical Journal 474, no. 22 (November 6, 2017): 3767–81. http://dx.doi.org/10.1042/bcj20170541.
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Onconase® (ONC), a protein extracted from the oocytes of the Rana pipiens frog, is a monomeric member of the secretory ‘pancreatic-type’ RNase superfamily. Interestingly, ONC is the only monomeric ribonuclease endowed with a high cytotoxic activity. In contrast with other monomeric RNases, ONC displays a high cytotoxic activity. In this work, we found that ONC spontaneously forms dimeric traces and that the dimer amount increases about four times after lyophilization from acetic acid solutions. Differently from RNase A (bovine pancreatic ribonuclease) and the bovine seminal ribonuclease, which produce N- and C-terminal domain-swapped conformers, ONC forms only one dimer, here named ONC-D. Cross-linking with divinylsulfone reveals that this dimer forms through the three-dimensional domain swapping of its N-termini, being the C-terminus blocked by a disulfide bond. Also, a homology model is proposed for ONC-D, starting from the well-known structure of RNase A N-swapped dimer and taking into account the results obtained from spectroscopic and stability analyses. Finally, we show that ONC is more cytotoxic and exerts a higher apoptotic effect in its dimeric rather than in its monomeric form, either when administered alone or when accompanied by the chemotherapeutic drug gemcitabine. These results suggest new promising implications in cancer treatment.
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Pica, Andrea, Antonello Merlino, Alexander K. Buell, Tuomas P. J. Knowles, Elio Pizzo, Giuseppe D'Alessio, Filomena Sica, and Lelio Mazzarella. "Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase." Acta Crystallographica Section D Biological Crystallography 69, no. 10 (September 20, 2013): 2116–23. http://dx.doi.org/10.1107/s0907444913020507.
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The deletion of five residues in the loop connecting the N-terminal helix to the core of monomeric human pancreatic ribonuclease leads to the formation of an enzymatically active domain-swapped dimer (desHP). The crystal structure of desHP reveals the generation of an intriguing fibril-like aggregate of desHP molecules that extends along theccrystallographic axis. Dimers are formed by three-dimensional domain swapping. Tetramers are formed by the aggregation of swapped dimers with slightly different quaternary structures. The tetramers interact in such a way as to form an infinite rod-like structure that propagates throughout the crystal. The observed supramolecular assembly captured in the crystal predicts that desHP fibrils could form in solution; this has been confirmed by atomic force microscopy. These results provide new evidence that three-dimensional domain swapping can be a mechanism for the formation of elaborate large assemblies in which the protein, apart from the swapping, retains its original fold.
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Montioli, Riccardo, Rachele Campagnari, Sabrina Fasoli, Andrea Fagagnini, Andra Caloiu, Marcello Smania, Marta Menegazzi, and Giovanni Gotte. "RNase A Domain-Swapped Dimers Produced Through Different Methods: Structure–Catalytic Properties and Antitumor Activity." Life 11, no. 2 (February 21, 2021): 168. http://dx.doi.org/10.3390/life11020168.
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Upon oligomerization, RNase A can acquire important properties, such as cytotoxicity against leukemic cells. When lyophilized from 40% acetic acid solutions, the enzyme self-associates through the so-called three-dimensional domain swapping (3D-DS) mechanism involving both N- and/or C-terminals. The same species are formed if the enzyme is subjected to thermal incubation in various solvents, especially in 40% ethanol. We evaluated here if significant structural modifications might occur in RNase A N- or C-swapped dimers and/or in the residual monomer(s), as a function of the oligomerization protocol applied. We detected that the monomer activity vs. ss-RNA was partly affected by both protocols, although the protein does not suffer spectroscopic alterations. Instead, the two N-swapped dimers showed differences in the fluorescence emission spectra but almost identical enzymatic activities, while the C-swapped dimers displayed slightly different activities vs. both ss- or ds-RNA substrates together with not negligible fluorescence emission alterations within each other. Besides these results, we also discuss the reasons justifying the different relative enzymatic activities displayed by the N-dimers and C-dimers. Last, similarly with data previously registered in a mouse model, we found that both dimeric species significantly decrease human melanoma A375 cell viability, while only N-dimers reduce human melanoma MeWo cell growth.
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Hallin, Erik I., Sigurbjörn Markússon, Lev Böttger, Andrew E. Torda, Clive R. Bramham, and Petri Kursula. "Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc." PLOS ONE 16, no. 5 (May 14, 2021): e0251459. http://dx.doi.org/10.1371/journal.pone.0251459.
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Synaptic plasticity is vital for brain function and memory formation. One of the key proteins in long-term synaptic plasticity and memory is the activity-regulated cytoskeleton-associated protein (Arc). Mammalian Arc forms virus-like capsid structures in a process requiring the N-terminal domain and contains two C-terminal lobes that are structural homologues to retroviral capsids. Drosophila has two isoforms of Arc, dArc1 and dArc2, with low sequence similarity to mammalian Arc, but lacking a large N-terminal domain. Both dArc isoforms are related to the Ty3/gypsy retrotransposon capsid, consisting of N- and C-terminal lobes. Structures of dArc1, as well as capsids formed by both dArc isoforms, have been recently determined. We carried out structural characterization of the four individual dArc lobe domains. As opposed to the corresponding mammalian Arc lobe domains, which are monomeric, the dArc lobes were all oligomeric in solution, indicating a strong propensity for homophilic interactions. A truncated N-lobe from dArc2 formed a domain-swapped dimer in the crystal structure, resulting in a novel dimer interaction that could be relevant for capsid assembly or other dArc functions. This domain-swapped structure resembles the dimeric protein C of flavivirus capsids, as well as the structure of histones dimers, domain-swapped transcription factors, and membrane-interacting BAK domains. The strong oligomerization properties of the isolated dArc lobe domains explain the ability of dArc to form capsids in the absence of any large N-terminal domain, in contrast to the mammalian protein.
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Morellet, Nelly, Pierre Hardouin, Nadine Assrir, Carine van Heijenoort, and Béatrice Golinelli-Pimpaneau. "Structural Insights into the Dimeric Form of Bacillus subtilis RNase Y Using NMR and AlphaFold." Biomolecules 12, no. 12 (December 1, 2022): 1798. http://dx.doi.org/10.3390/biom12121798.
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RNase Y is a crucial component of genetic translation, acting as the key enzyme initiating mRNA decay in many Gram-positive bacteria. The N-terminal domain of Bacillus subtilis RNase Y (Nter-BsRNaseY) is thought to interact with various protein partners within a degradosome complex. Bioinformatics and biophysical analysis have previously shown that Nter-BsRNaseY, which is in equilibrium between a monomeric and a dimeric form, displays an elongated fold with a high content of α-helices. Using multidimensional heteronuclear NMR and AlphaFold models, here, we show that the Nter-BsRNaseY dimer is constituted of a long N-terminal parallel coiled-coil structure, linked by a turn to a C-terminal region composed of helices that display either a straight or bent conformation. The structural organization of the N-terminal domain is maintained within the AlphaFold model of the full-length RNase Y, with the turn allowing flexibility between the N- and C-terminal domains. The catalytic domain is globular, with two helices linking the KH and HD modules, followed by the C-terminal region. This latter region, with no function assigned up to now, is most likely involved in the dimerization of B. subtilis RNase Y together with the N-terminal coiled-coil structure.
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Barden, Stephan, Benjamin Schomburg, Jens Conradi, Steffen Backert, Norbert Sewald, and Hartmut H. Niemann. "Structure of a three-dimensional domain-swapped dimer of theHelicobacter pyloritype IV secretion system pilus protein CagL." Acta Crystallographica Section D Biological Crystallography 70, no. 5 (April 30, 2014): 1391–400. http://dx.doi.org/10.1107/s1399004714003150.
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A new crystal form of theHelicobacter pyloritype IV secretion system (T4SS) pilus protein CagL is described here. In contrast to two previously reported monomeric structures, CagL forms a three-dimensional domain-swapped dimer. CagL dimers can arise during refolding from inclusion bodies or can form spontaneously from purified monomeric CagL in the crystallization conditions. Monomeric CagL forms a three-helix bundle, with which the N-terminal helix is only loosely associated. In the new crystal form, the N-terminal helix is missing. The domain swap is owing to exchange of the C-terminal helix between the two protomers of a dimer. A loop-to-helix transition results in a long helix of 108 amino acids comprising the penultimate and the last helix of the monomer. The RGD motif of dimeric CagL adopts an α-helical conformation. In contrast to the previously reported structures, the conserved and functionally important C-terminal hexapeptide is resolved. It extends beyond the three-helix bundle as an exposed helical appendage. This new crystal form contributes to the molecular understanding of CagL by highlighting rigid and flexible regions in the protein and by providing the first view of the C-terminus. Based on the structural features, a previously unrecognized homology between CagL and CagI is discussed.
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Watkins, Harriet A., and Edward N. Baker. "Structural and Functional Characterization of an RNase HI Domain from the Bifunctional Protein Rv2228c from Mycobacterium tuberculosis." Journal of Bacteriology 192, no. 11 (April 2, 2010): 2878–86. http://dx.doi.org/10.1128/jb.01615-09.
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ABSTRACT The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with α-ribazole phosphatase (CobC). The N-terminal domain of Rv2228c (Rv2228c/N) and the full-length protein were expressed as fusions with maltose binding protein (MBP). Rv2228c/N was shown to have RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein was shown to have additional CobC activity. The crystal structure of the MBP-Rv2228c/N fusion protein was solved by molecular replacement and refined at 2.25-Å resolution (R = 0.182; R free = 0.238). The protein is monomeric in solution but associates in the crystal to form a dimer. The Rv2228c/N domain has the classic RNase H fold and catalytic machinery but lacks several surface features that play important roles in the cleavage of RNA/DNA hybrids by other RNases H. The absence of either the basic protrusion of some RNases H or the hybrid binding domain of others appears to be compensated by the C-terminal CobC domain in full-length Rv2228c. The double-stranded-RNase activity of Rv2228c/N contrasts with classical RNases H and is attributed to the absence in Rv2228c/N of a key phosphate binding pocket.
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Abbas, Yazan, Irene Yuning Xie, and Bhushan Nagar. "Crystal structure of N-terminal IFIT3 reveals domain-swapping dimerization." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1629. http://dx.doi.org/10.1107/s2053273314083703.
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IFIT proteins are interferon-inducible, antiviral effectors that form a multiprotein complex with the ability to recognize markers of viral infection and subsequently restrict viruses. IFIT1, IFIT2 and IFIT3 are at the heart of the complex, interacting with each other and several host factors, forming what is known as the 'IFIT interactome'. Central to their ability to mediate complex formation is the tetratricopeptide repeat (TPR) motif, a general protein-protein interaction module comprising a pair of antiparallel alpha helices. Additionally The TPR motifs of IFIT proteins have the unique ability to recognize RNA. Whereas IFIT1 interacts with virus derived ssRNA, IFIT2 has been shown to interact with dsRNA; IFIT3 is not known to bind RNA. Importantly, structural information is available for the N-terminal domain of IFIT1 and full-length IFIT2, but not for IFIT3. To gain insight into the mechanisms regulating complex formation, we are targeting the structure of human IFIT3 before incorporation into the IFIT complex. To that end, we have determined a low resolution crystal structure of N-terminal IFIT3, which reveals a domain swapped dimer. Notably, IFIT3 dimerization is similar to IFIT2, but distinct from IFIT1, which dimerizes via its C-terminus. Sequence conservation and structural analysis suggest that IFIT2 and IFIT3 evolved a similar mechanism for domain swapping. We propose that IFIT2 and IFIT3 may interact by forming domain swapped heterodimers. Current work is aimed at investigating the mechanisms of domain swapping via mutational analysis, and determining the structure of C-terminal human IFIT3.
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Sakuma, Mayuko, Shoji Nishikawa, Satoshi Inaba, Takehiko Nishigaki, Seiji Kojima, Michio Homma, and Katsumi Imada. "Structure of the periplasmic domain of SflA involved in spatial regulation of the flagellar biogenesis of Vibrio reveals a TPR/SLR-like fold." Journal of Biochemistry 166, no. 2 (April 15, 2019): 197–204. http://dx.doi.org/10.1093/jb/mvz027.
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Abstract Bacteria have evolved various types of flagellum, an organella for bacterial motility, to adapt to their habitat environments. The number and the spatial arrangement of the flagellum are precisely controlled to optimize performance of each type of the flagellar system. Vibrio alginolyticus has a single sheathed flagellum at the cell pole for swimming. SflA is a regulator protein to prevent peritrichous formation of the sheathed flagellum, and consists of an N-terminal periplasmic region, a transmembrane helix, and a C-terminal cytoplasmic region. Whereas the cytoplasmic region has been characterized to be essential for inhibition of the peritrichous growth, the role of the N-terminal region is still unclear. We here determined the structure of the N-terminal periplasmic region of SflA (SflAN) at 1.9-Å resolution. The core of SflAN forms a domain-swapped dimer with tetratricopeptide repeat (TPR)/Sel1-like repeat (SLR) motif, which is often found in the domains responsible for protein–protein interaction in various proteins. The structural similarity and the following mutational analysis based on the structure suggest that SflA binds to unknown partner protein by SflAN and the binding signal is important for the precise control of the SflA function.
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Langedijk, J. P. M., P. A. van Veelen, W. M. M. Schaaper, A. H. de Ru, R. H. Meloen, and M. M. Hulst. "A Structural Model of Pestivirus Erns Based on Disulfide Bond Connectivity and Homology Modeling Reveals an Extremely Rare Vicinal Disulfide." Journal of Virology 76, no. 20 (October 15, 2002): 10383–92. http://dx.doi.org/10.1128/jvi.76.20.10383-10392.2002.
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ABSTRACT Erns is a pestivirus envelope glycoprotein and is the only known viral surface protein with RNase activity. Erns is a disulfide-linked homodimer of 100 kDa; it is found on the surface of pestivirus-infected cells and is secreted into the medium. In this study, the disulfide arrangement of the nine cysteines present in the mature dimer was established by analysis of the proteolytically cleaved protein. Fragments were obtained after digestion with multiple proteolytic enzymes and subsequently analyzed by liquid chromatography-electrospray ionization mass spectrometry. The analysis demonstrates which cysteine is involved in dimerization and reveals an extremely rare vicinal disulfide bridge of unknown function. With the assistance of the disulfide arrangement, a three-dimensional model was built by homology modeling based on the alignment with members of the Rh/T2/S RNase family. Compared to these other RNase family members, Erns shows an N-terminal truncation, a large insertion of a cystine-rich region, and a C-terminal extension responsible for membrane translocation. The homology to mammalian RNase 6 supports a possible role of Erns in B-cell depletion.
Dissertations / Theses on the topic "N-terminal or C-terminal swapped dimer of RNase A"
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VOTTARIELLO, FRANCESCA. "OLIGOMERIZATION OF RNase A:a) A STUDY OF THE INFLUENCE OF SERINE 80 RESIDUE ON THE 3D DOMAIN SWAPPING MECHANISMb) “ZERO-LENGTH” DIMERS OF RNase A AND THEIR CATIONIZATION WITH PEI." Doctoral thesis, 2010. http://hdl.handle.net/11562/344075.
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"Zero-length" dimers of ribonuclease A, a novel type of dimers formed by two RNase A molecules bound to each other through a zero-length amide bond [Simons, B.L. et al. (2007) Proteins 66, 183-195], were analyzed, and tested for their possible in vitro cytotoxic activity. Results: (i) Besides dimers, also trimers and higher oligomers can be identified among the products of the covalently linking reaction. (ii) The "zero-length" dimers prepared by us appear not to be a unique species, as was instead reported by Simons et al. The product is heterogeneous, as shown by the involvement in the amide bond of amino and carboxyl groups others than only those belonging to Lys66 and Glu9. This is demonstrated by results obtained with two RNase A mutants, E9A and K66A. (iii) The "zero-length" dimers degrade poly(A).poly(U) (dsRNA) and yeast RNA (ssRNA): while the activity against poly(A).poly(U) increases with the increase of the oligomer's basicity, the activity towards yeast RNA decreases with the increase of oligomers' basicity, in agreement with many previous data, but in contrast with the results reported by Simons et al. (iv) No cytotoxicity against various tumor cells lines could be evidenced in RNase A "zero-length" dimers. (v) They instead become cytotoxic if cationized by conjugation with polyethylenimine [Futami, J. et al. (2005) J. Biosci. Bioengin. 99, 95-103]. However, polyethylenimine derivatives of RNase A "zero-length" dimers and native, monomeric RNase A are equally cytotoxic. In other words, protein "dimericity" does not play any role in this case. Moreover, (vi) cytotoxicity seems not to be specific for tumor cells: polyethylenimine-cationized native RNase A is also cytotoxic towards human monocytes."Zero-length" dimers of ribonuclease A, a novel type of dimers formed by two RNase A molecules bound to each other through a zero-length amide bond [Simons, B.L. et al. (2007) Proteins 66, 183-195], were analyzed, and tested for their possible in vitro cytotoxic activity. Results: (i) Besides dimers, also trimers and higher oligomers can be identified among the products of the covalently linking reaction. (ii) The "zero-length" dimers prepared by us appear not to be a unique species, as was instead reported by Simons et al. The product is heterogeneous, as shown by the involvement in the amide bond of amino and carboxyl groups others than only those belonging to Lys66 and Glu9. This is demonstrated by results obtained with two RNase A mutants, E9A and K66A. (iii) The "zero-length" dimers degrade poly(A).poly(U) (dsRNA) and yeast RNA (ssRNA): while the activity against poly(A).poly(U) increases with the increase of the oligomer's basicity, the activity towards yeast RNA decreases with the increase of oligomers' basicity, in agreement with many previous data, but in contrast with the results reported by Simons et al. (iv) No cytotoxicity against various tumor cells lines could be evidenced in RNase A "zero-length" dimers. (v) They instead become cytotoxic if cationized by conjugation with polyethylenimine [Futami, J. et al. (2005) J. Biosci. Bioengin. 99, 95-103]. However, polyethylenimine derivatives of RNase A "zero-length" dimers and native, monomeric RNase A are equally cytotoxic. In other words, protein "dimericity" does not play any role in this case. Moreover, (vi) cytotoxicity seems not to be specific for tumor cells: polyethylenimine-cationized native RNase A is also cytotoxic towards human monocytes.