Artykuły w czasopismach: „Multi-protein assembly”

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Siggers, Trevor, i Raluca Gordân. "Protein–DNA binding: complexities and multi-protein codes". Nucleic Acids Research 42, nr 4 (16.11.2013): 2099–111. http://dx.doi.org/10.1093/nar/gkt1112.

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Abstract Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.

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Li, Mei, Erik Dujardin i Stephen Mann. "Programmed assembly of multi-layered protein/nanoparticle-carbon nanotube conjugates". Chemical Communications, nr 39 (2005): 4952. http://dx.doi.org/10.1039/b509109h.

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Tørresen, Ole K., Bastiaan Star, Pablo Mier, Miguel A. Andrade-Navarro, Alex Bateman, Patryk Jarnot, Aleksandra Gruca i in. "Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases". Nucleic Acids Research 47, nr 21 (4.10.2019): 10994–1006. http://dx.doi.org/10.1093/nar/gkz841.

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Abstract The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.

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Farrugia, Thomas, Adam W. Perriman, Kamendra P. Sharma i Stephen Mann. "Multi-enzyme cascade reactions using protein–polymer surfactant self-standing films". Chemical Communications 53, nr 13 (2017): 2094–97. http://dx.doi.org/10.1039/c6cc09809f.

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Venkatraman, Vishwesh, i David W. Ritchie. "Predicting Multi-Component Protein Assemblies Using an Ant Colony Approach". International Journal of Swarm Intelligence Research 3, nr 3 (lipiec 2012): 19–31. http://dx.doi.org/10.4018/jsir.2012070102.

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Many biological processes are governed by large assemblies of protein molecules. However, it is often very difficult to determine the three-dimensional structures of these assemblies using experimental biophysical techniques. Hence there is a need to develop computational approaches to fill this gap. This article presents an ant colony optimization approach to predict the structure of large multi-component protein complexes. Starting from pair-wise docking predictions, a multi-graph consisting of vertices representing the component proteins and edges representing candidate interactions is constructed. This allows the assembly problem to be expressed in terms of searching for a minimum weight spanning tree. However, because the problem remains highly combinatorial, the search space cannot be enumerated exhaustively and therefore heuristic optimisation techniques must be used. The utility of the ant colony based approach is demonstrated by re-assembling known protein complexes from the Protein Data Bank. The algorithm is able to identify near-native solutions for five of the six cases tested. This demonstrates that the ant colony approach provides a useful way to deal with the highly combinatorial multi-component protein assembly problem.

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Xian, Yuejiao, Chitra B. Karki, Sebastian Miki Silva, Lin Li i Chuan Xiao. "The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses". International Journal of Molecular Sciences 20, nr 8 (16.04.2019): 1876. http://dx.doi.org/10.3390/ijms20081876.

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In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures.

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Terzo, Esteban A., Shawn M. Lyons, John S. Poulton, Brenda R. S. Temple, William F. Marzluff i Robert J. Duronio. "Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body". Molecular Biology of the Cell 26, nr 8 (15.04.2015): 1559–74. http://dx.doi.org/10.1091/mbc.e14-10-1445.

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Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis.

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Mozdy, A. D., J. M. McCaffery i J. M. Shaw. "Dnm1p Gtpase-Mediated Mitochondrial Fission Is a Multi-Step Process Requiring the Novel Integral Membrane Component Fis1p". Journal of Cell Biology 151, nr 2 (16.10.2000): 367–80. http://dx.doi.org/10.1083/jcb.151.2.367.

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Yeast Dnm1p is a soluble, dynamin-related GTPase that assembles on the outer mitochondrial membrane at sites where organelle division occurs. Although these Dnm1p-containing complexes are thought to trigger constriction and fission, little is known about their composition and assembly, and molecules required for their membrane recruitment have not been isolated. Using a genetic approach, we identified two new genes in the fission pathway, FIS1 and FIS2. FIS1 encodes a novel, outer mitochondrial membrane protein with its amino terminus exposed to the cytoplasm. Fis1p is the first integral membrane protein shown to participate in a eukaryotic membrane fission event. In a related study (Tieu, Q., and J. Nunnari. 2000. J. Cell Biol. 151:353–365), it was shown that the FIS2 gene product (called Mdv1p) colocalizes with Dnm1p on mitochondria. Genetic and morphological evidence indicate that Fis1p, but not Mdv1p, function is required for the proper assembly and distribution of Dnm1p-containing fission complexes on mitochondrial tubules. We propose that mitochondrial fission in yeast is a multi-step process, and that membrane-bound Fis1p is required for the proper assembly, membrane distribution, and function of Dnm1p-containing complexes during fission.

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Guo, Zhen, Zhiwei Shen, Yujiao Wang, Tingyuan Tan i Yi Zhang. "Peptides Co-Assembling into Hydrangea-Like Microstructures". Journal of Nanoscience and Nanotechnology 20, nr 5 (1.05.2020): 3239–45. http://dx.doi.org/10.1166/jnn.2020.17393.

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Supramolecular assembly in vitro is a simple and effective way to produce multi-level biostructures to mimic the self-assembly of biomolecules in organisms. The study on peptide assembly behaviors would benefit a lot to understand what goes on in life, as well as in the construction of plenty of functional biomaterials that have potential applications in various fields. Since cellular microenvironments are crowded and contain various biomolecules, studying protein and peptide co-assembly is of great interest. Here, we introduced the co-assembly of 5-FAM-ELVFFAE-NH2 (EE-7) and (CY5)-KLVFFAK-NH2 (KK-7), which are sequences derived from the core of the amyloid β (Aβ) peptide, a key protein in Alzheimer’s diseases. Morphologic studies employing atomic force microscopy and scanning electron microscopy indicated that the co-assembled entities had a novel hydrangea-like microstructure, in contrast to micro-sheet structures formed from monocomponent EE-7 or KK-7, respectively. Fluorescence co-localization experiments confirmed that the hydrangealike microstructures were indeed made of both EE-7 and KK-7. We suggest that the formation of the hydrangea-like microstructures is driven by both the electrostatic and hydrophobic interactions between EE-7 and KK-7. A molecular mechanism has been provided to explain the formation of the hydrangea-like microstructures.

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Tang, Jiakun, Ye Liu, Dongmei Qi, Lan Yang, Hui Chen, Chenhui Wang i Xuli Feng. "Nucleus‐Targeted Delivery of Multi‐Protein Self‐Assembly for Combined Anticancer Therapy". Small 17, nr 25 (24.05.2021): 2101219. http://dx.doi.org/10.1002/smll.202101219.

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Jayalath, Kumudie, Sean Frisbie, Minhchau To i Sanjaya Abeysirigunawardena. "Pseudouridine Synthase RsuA Captures an Assembly Intermediate That Is Stabilized by Ribosomal Protein S17". Biomolecules 10, nr 6 (30.05.2020): 841. http://dx.doi.org/10.3390/biom10060841.

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The ribosome is a large ribonucleoprotein complex that synthesizes protein in all living organisms. Ribosome biogenesis is a complex process that requires synchronization of various cellular events, including ribosomal RNA (rRNA) transcription, ribosome assembly, and processing and post-transcriptional modification of rRNA. Ribosome biogenesis is fine-tuned with various assembly factors, possibly including nucleotide modification enzymes. Ribosomal small subunit pseudouridine synthase A (RsuA) pseudouridylates U516 of 16S helix 18. Protein RsuA is a multi-domain protein that contains the N-terminal peripheral domain, which is structurally similar to the ribosomal protein S4. Our study shows RsuA preferably binds and pseudouridylates an assembly intermediate that is stabilized by ribosomal protein S17 over the native-like complex. In addition, the N-terminal domain truncated RsuA showed that the presence of the S4-like domain is important for RsuA substrate recognition.

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Chi, Wei, Jinfang Ma i Lixin Zhang. "Regulatory factors for the assembly of thylakoid membrane protein complexes". Philosophical Transactions of the Royal Society B: Biological Sciences 367, nr 1608 (19.12.2012): 3420–29. http://dx.doi.org/10.1098/rstb.2012.0065.

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Major multi-protein photosynthetic complexes, located in thylakoid membranes, are responsible for the capture of light and its conversion into chemical energy in oxygenic photosynthetic organisms. Although the structures and functions of these photosynthetic complexes have been explored, the molecular mechanisms underlying their assembly remain elusive. In this review, we summarize current knowledge of the regulatory components involved in the assembly of thylakoid membrane protein complexes in photosynthetic organisms. Many of the known regulatory factors are conserved between prokaryotes and eukaryotes, whereas others appear to be newly evolved or to have expanded predominantly in eukaryotes. Their specific features and fundamental differences in cyanobacteria, green algae and land plants are discussed.

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Whitley, Paul, i Ismael Mingarro. "Stitching proteins into membranes, not sew simple". Biological Chemistry 395, nr 12 (1.12.2014): 1417–24. http://dx.doi.org/10.1515/hsz-2014-0205.

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Abstract Most integral membrane proteins located within the endomembrane system of eukaryotic cells are first assembled co-translationally into the endoplasmic reticulum (ER) before being sorted and trafficked to other organelles. The assembly of membrane proteins is mediated by the ER translocon, which allows passage of lumenal domains through and lateral integration of transmembrane (TM) domains into the ER membrane. It may be convenient to imagine multi-TM domain containing membrane proteins being assembled by inserting their first TM domain in the correct orientation, with subsequent TM domains inserting with alternating orientations. However a simple threading model of assembly, with sequential insertion of one TM domain into the membrane after another, does not universally stand up to scrutiny. In this article we review some of the literature illustrating the complexities of membrane protein assembly. We also present our own thoughts on aspects that we feel are poorly understood. In short we hope to convince the readers that threading of membrane proteins into membranes is ‘not sew simple’ and a topic that requires further investigation.

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Hahn, Hyunggu, Sang Ho Park, Hyun-Jung Kim, Sunghoon Kim i Byung Woo Han. "The DRS–AIMP2–EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex". IUCrJ 6, nr 5 (24.08.2019): 958–67. http://dx.doi.org/10.1107/s2052252519010790.

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Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S-transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2GST and EPRSGST, respectively). While AIMP2GST and EPRSGST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2GST via hydrogen bonds between the α7–β9 loop of DRS and the β2–α2 loop of AIMP2GST, where Ser156 of AIMP2GST is essential for the assembly. Structural analyses of DRS–AIMP2GST–EPRSGST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC.

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Bolanos-Garcia, Victor M., Qian Wu, Takashi Ochi, Dimitri Y. Chirgadze, Bancinyane Lynn Sibanda i Tom L. Blundell. "Spatial and temporal organization of multi-protein assemblies: achieving sensitive control in information-rich cell-regulatory systems". Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 370, nr 1969 (28.06.2012): 3023–39. http://dx.doi.org/10.1098/rsta.2011.0268.

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The regulation of cellular processes in living organisms requires signalling systems that have a high signal-to-noise ratio. This is usually achieved by transient, multi-protein complexes that assemble cooperatively. Even in the crowded environment of the cell, such assemblies are unlikely to form by chance, thereby providing a sensitive regulation of cellular processes. Furthermore, selectivity and sensitivity may be achieved by the requirement for concerted folding and binding of previously unfolded components. We illustrate these features by focusing on two essential signalling pathways of eukaryotic cells: first, the monitoring and repair of DNA damage by non-homologous end joining, and second, the mitotic spindle assembly checkpoint, which detects and corrects defective attachments of chromosomes to the kinetochore. We show that multi-protein assemblies moderate the full range of functional complexity and diversity in the two signalling systems. Deciphering the nature of the interactions is central to understanding the mechanisms that control the flow of information in cell signalling and regulation.

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Ribbe, Markus W., Kamil Górecki, Mario Grosch, Joseph B. Solomon, Robert Quechol, Yiling A. Liu, Chi Chung Lee i Yilin Hu. "Nitrogenase Fe Protein: A Multi-Tasking Player in Substrate Reduction and Metallocluster Assembly". Molecules 27, nr 19 (10.10.2022): 6743. http://dx.doi.org/10.3390/molecules27196743.

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The Fe protein of nitrogenase plays multiple roles in substrate reduction and metallocluster assembly. Best known for its function to transfer electrons to its catalytic partner during nitrogenase catalysis, the Fe protein is also a key player in the biosynthesis of the complex metalloclusters of nitrogenase. In addition, it can function as a reductase on its own and affect the ambient reduction of CO2 or CO to hydrocarbons. This review will provide an overview of the properties and functions of the Fe protein, highlighting the relevance of this unique FeS enzyme to areas related to the catalysis, biosynthesis, and applications of the fascinating nitrogenase system.

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Vonshak, Ohad, Yiftach Divon, Stefanie Förste, David Garenne, Vincent Noireaux, Reinhard Lipowsky, Sophia Rudorf, Shirley S. Daube i Roy H. Bar-Ziv. "Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry". Nature Nanotechnology 15, nr 9 (20.07.2020): 783–91. http://dx.doi.org/10.1038/s41565-020-0720-7.

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van den Akker, Emile, Timothy J. Satchwell, Geoff Daniels i Ashley M. Toye. "Mapping the Assembly of Band 3 and Rhesus Multi-Protein Complexes During Erythropoiesis". Blood 116, nr 21 (19.11.2010): 812. http://dx.doi.org/10.1182/blood.v116.21.812.812.

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Abstract Abstract 812 Band 3 forms the core of a large multiprotein complex in the erythrocyte membrane, the Band 3 macrocomplex, which also includes proteins of the Rhesus complex (Rh and RhAG). Mutations in genes encoding proteins within this complex can result in hereditary spherocytosis with varying severity. The effect of distinct mutations and deficiencies in proteins of the Band 3 macrocomplex has been studied in detail in mature erythrocytes. This revealed important functional and structural properties of individual proteins and their relationships with other proteins within the Band 3 macrocomplex. Nevertheless, considerably less is know about the spatio-temporal mechanisms that direct the formation of the Band 3 macrocomplex, and that may explain the aberrations in the complex observed in spherocytosis. Therefore, we studied expression and mutual interactions of proteins of the band3 macrocomplex during development of proerythroblasts to reticulocytes. Using confocal microscopy and western blotting, significant pools of intracellular Band 3 and RhAG were found in the basophilic normoblast. These intracellular pools gradually decreased in the polychromatic normoblast and were absent or low in the orthochromatic normoblast and reticulocytes, while surface expression increased. We used pronase treatment of intact cells to remove extracellular epitopes of BRIC 6 (Band 3 antibody) and LA1818 (RhAG antibody) to study the mechanism by which the intracellular pool of Band 3 and RhAG contributes to formation of the Band 3 complex on the cell surface. Pronase treatment of cells incubated with cycloheximide to block protein synthesis resulted in a reduced but still significant reappearance of BRIC6 (Band 3) and LA1818 (RhAG) epitopes on the plasma membrane confirming the presence of intracellular Band 3 and RhAG pools. It also showed that the bulk of Band 3 and RhAG is synthesized and trafficked to the membrane between the early basophilic and polychromatic stage. Immuneprecipitation of Band 3 from cell lysates of pronase treated cells pre-treated with brefeldin A to collapse the Golgi showed no increase in co-immuneprecipitated protein 4.2 albeit an increase in intracellular Band 3 expression. This suggests that protein 4.2 and Band 3 interact in the first Golgi compartment or late ER. In addition, pre-treatment of cells with cycloheximide prior to pronase treatment resulted in depletion of the intracellular Band 3 and co-immuneprecipitated protein 4.2 pool indicating that Band 3 and protein 4.2 traffic as a complex to the plasma-membrane. We were unable to co-immuneprecipitate Rh or Band 3 with intracellular pools of RhAG, whereas Rh was co-immuneprecipitated with RhAG from the plasma-membrane and from total cell lysates. Knockdown of RhAG in differentiating erythroblasts revealed a concomitant drop in membrane expression of Rh, leaving Band 3 unaffected, indicating that plasma-membrane expression of Rh but not Band 3 is dependent on RhAG. In conclusion, despite the described association between the RhAG complex and the Band 3 complex in erythrocytes, the data suggest that the Band 3-protein 4.2 complex traffics and assembles independently from Rh and RhAG during erythroid differentiation. The experiments suggest that Rh and RhAG do not traffic as a complex to the plasma-membrane but probably assemble in the plasma-membrane. The RhAG knockdown experiments suggest that the dependency of Rh on RhAG as observed in Rhnull syndrome erythrocytes (“Rh regulator type”) originates early during erythropoiesis. Band3 surface expression was not affected upon RhAG knock down, which re-produced the unperturbed Band 3 levels seen in these patients. Disclosures: No relevant conflicts of interest to declare.

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Bergfort, Alexandra, Tarek Hilal, Benno Kuropka, İbrahim Avşar Ilik, Gert Weber, Tuğçe Aktaş, Christian Freund i Markus C. Wahl. "The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling". Nucleic Acids Research 50, nr 5 (21.02.2022): 2938–58. http://dx.doi.org/10.1093/nar/gkac087.

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Abstract Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4’s intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling.

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Maghool, Shadi, N. Dinesha G. Cooray, David A. Stroud, David Aragão, Michael T. Ryan i Megan J. Maher. "Structural and functional characterization of the mitochondrial complex IV assembly factor Coa6". Life Science Alliance 2, nr 5 (12.09.2019): e201900458. http://dx.doi.org/10.26508/lsa.201900458.

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Assembly factors play key roles in the biogenesis of many multi-subunit protein complexes regulating their stability, activity, and the incorporation of essential cofactors. The human assembly factor Coa6 participates in the biogenesis of the CuA site in complex IV (cytochrome c oxidase, COX). Patients with mutations in Coa6 suffer from mitochondrial disease due to complex IV deficiency. Here, we present the crystal structures of human Coa6 and the pathogenic W59CCoa6-mutant protein. These structures show that Coa6 has a 3-helical bundle structure, with the first 2 helices tethered by disulfide bonds, one of which likely provides the copper-binding site. Disulfide-mediated oligomerization of the W59CCoa6 protein provides a structural explanation for the loss-of-function mutation.

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Gupta, Swati, Jyoti Chhibber-Goel, Manmohan Sharma, Suhel Parvez, Karl Harlos, Amit Sharma i Manickam Yogavel. "Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein". Acta Crystallographica Section D Structural Biology 76, nr 2 (30.01.2020): 135–46. http://dx.doi.org/10.1107/s2059798319016413.

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Scaffold modules known as aminoacyl-tRNA synthetase (aaRS)-interacting multifunctional proteins (AIMPs), such as AIMP1/p43, AIMP2/p38 and AIMP3/p18, are important in driving the assembly of multi-aaRS (MARS) complexes in eukaryotes. Often, AIMPs contain an N-terminal glutathione S-transferase (GST)-like domain and a C-terminal OB-fold tRNA-binding domain. Recently, the apicomplexan-specific Plasmodium falciparum p43 protein (Pfp43) has been annotated as an AIMP and its tRNA binding, tRNA import and membrane association have been characterized. The crystal structures of both the N- and C-terminal domains of the Plasmodium vivax p43 protein (Pvp43), which is an ortholog of Pfp43, have been resolved. Analyses reveal the overall oligomeric structure of Pvp43 and highlight several notable features that show Pvp43 to be a soluble, cytosolic protein. The dimeric assembly of the N-terminal GST-like domain of Pvp43 differs significantly from canonical GST dimers, and it is tied to the C-terminal tRNA-binding domain via a linker region. This work therefore establishes a framework for dissecting the additional roles of p43 orthologs in eukaryotic multi-protein MARS complexes.

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Ortolan, Tatiana G., Prasad Tongaonkar, David Lambertson, Li Chen, Cherylene Schauber i Kiran Madura. "The DNA repair protein Rad23 is a negative regulator of multi-ubiquitin chain assembly". Nature Cell Biology 2, nr 9 (17.08.2000): 601–8. http://dx.doi.org/10.1038/35023547.

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Uchida, Masaki, Ben LaFrance, Chris C. Broomell, Peter E. Prevelige i Trevor Douglas. "Higher Order Assembly of Virus-like Particles (VLPs) Mediated by Multi-valent Protein Linkers". Small 11, nr 13 (12.01.2015): 1562–70. http://dx.doi.org/10.1002/smll.201402067.

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Burkinshaw, Brianne J., Sergio A. Souza i Natalie C. J. Strynadka. "Structural analysis of SepL, an enteropathogenicEscherichia colitype III secretion-system gatekeeper protein". Acta Crystallographica Section F Structural Biology Communications 71, nr 10 (23.09.2015): 1300–1308. http://dx.doi.org/10.1107/s2053230x15016064.

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During infection, enteropathogenicEscherichia coliassembles a complex multi-protein type III secretion system that traverses the bacterial membranes and targets the host cell membrane to directly deliver virulence or effector proteins to the host cytoplasm. As this secretion system is composed of more than 20 proteins, many of which form oligomeric associations, its assembly must be tightly regulated. A protein called the gatekeeper, or SepL, ensures that the secretion of the translocon component, which inserts into the host membrane, occurs before the secretion of effectors. The crystal structure of the gatekeeper SepL was determined and compared with the structures of SepL homologues from other bacterial pathogens in order to identify SepL residues that may be critical for its role in type III secretion-system assembly.

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Tieu, Quinton, i Jodi Nunnari. "Mdv1p Is a Wd Repeat Protein That Interacts with the Dynamin-Related Gtpase, Dnm1p, to Trigger Mitochondrial Division". Journal of Cell Biology 151, nr 2 (16.10.2000): 353–66. http://dx.doi.org/10.1083/jcb.151.2.353.

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Mitochondrial fission is mediated by the dynamin-related GTPase, Dnm1p, which assembles on the mitochondrial outer membrane into punctate structures associated with sites of membrane constriction and fission. We have identified additional nuclear genes required for mitochondrial fission, termed MDV (for mitochondrial division). MDV1 encodes a predicted soluble protein, containing a coiled-coil motif and seven COOH-terminal WD repeats. Genetic and two-hybrid analyses indicate that Mdv1p interacts with Dnm1p to mediate mitochondrial fission. In addition, Mdv1p colocalizes with Dnm1p in fission-mediating punctate structures on the mitochondrial outer membrane. Whereas localization of Mdv1p to these structures requires Dnm1p, localization of Mdv1p to mitochondrial membranes does not. This indicates that Mdv1p possesses a Dnm1p-independent mitochondrial targeting signal. Dnm1p-independent targeting of Mdv1p to mitochondria requires MDV2. Our data indicate that MDV2 also functions separately to regulate the assembly of Dnm1p into punctate structures. In contrast, Mdv1p is not required for the assembly of Dnm1p, but Dnm1p-containing punctate structures lacking Mdv1p are not able to complete division. Our studies suggest that mitochondrial fission is a multi-step process in which Mdv2p regulates the assembly of Dnm1p into punctate structures and together with Mdv1p functions later during fission to facilitate Dnm1p-dependent mitochondrial membrane constriction and/or division.

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Sokolik, Chana G., Nasrin Qassem i Jordan H. Chill. "The Disordered Cellular Multi-Tasker WIP and Its Protein–Protein Interactions: A Structural View". Biomolecules 10, nr 7 (21.07.2020): 1084. http://dx.doi.org/10.3390/biom10071084.

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WASp-interacting protein (WIP), a regulator of actin cytoskeleton assembly and remodeling, is a cellular multi-tasker and a key member of a network of protein–protein interactions, with significant impact on health and disease. Here, we attempt to complement the well-established understanding of WIP function from cell biology studies, summarized in several reviews, with a structural description of WIP interactions, highlighting works that present a molecular view of WIP’s protein–protein interactions. This provides a deeper understanding of the mechanisms by which WIP mediates its biological functions. The fully disordered WIP also serves as an intriguing example of how intrinsically disordered proteins (IDPs) exert their function. WIP consists of consecutive small functional domains and motifs that interact with a host of cellular partners, with a striking preponderance of proline-rich motif capable of interactions with several well-recognized binding partners; indeed, over 30% of the WIP primary structure are proline residues. We focus on the binding motifs and binding interfaces of three important WIP segments, the actin-binding N-terminal domain, the central domain that binds SH3 domains of various interaction partners, and the WASp-binding C-terminal domain. Beyond the obvious importance of a more fundamental understanding of the biology of this central cellular player, this approach carries an immediate and highly beneficial effect on drug-design efforts targeting WIP and its binding partners. These factors make the value of such structural studies, challenging as they are, readily apparent.

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Lecomte, F. J. L., N. Ismail i S. High. "Making membrane proteins at the mammalian endoplasmic reticulum". Biochemical Society Transactions 31, nr 6 (1.12.2003): 1248–52. http://dx.doi.org/10.1042/bst0311248.

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Whereas protein biogenesis at the endoplasmic reticulum is well understood in the case of secretory proteins and simple membrane proteins, much less is known about the synthesis of multi-spanning integral membrane proteins. While it is clear that the multiple membrane-spanning domains of these proteins must be inserted into the lipid bilayer during biosynthesis, the mechanism by which their integration is achieved and their subsequent folding/assembly are poorly defined. In this review, we summarize our current understanding of protein synthesis at the endoplasmic reticulum and highlight specific features that are relevant to the biogenesis of multi-spanning membrane proteins.

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Cherak, Stephana J., i Raymond J. Turner. "Assembly pathway of a bacterial complex iron sulfur molybdoenzyme". Biomolecular Concepts 8, nr 3-4 (26.09.2017): 155–67. http://dx.doi.org/10.1515/bmc-2017-0011.

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AbstractProtein folding and assembly into macromolecule complexes within the living cell are complex processes requiring intimate coordination. The biogenesis of complex iron sulfur molybdoenzymes (CISM) requires use of a system specific chaperone – a redox enzyme maturation protein (REMP) – to help mediate final folding and assembly. The CISM dimethyl sulfoxide (DMSO) reductase is a bacterial oxidoreductase that utilizes DMSO as a final electron acceptor for anaerobic respiration. The REMP DmsD strongly interacts with DMSO reductase to facilitate folding, cofactor-insertion, subunit assembly and targeting of the multi-subunit enzyme prior to membrane translocation and final assembly and maturation into a bioenergetic catalytic unit. In this article, we discuss the biogenesis of DMSO reductase as an example of the participant network for bacterial CISM maturation pathways.

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29

Swapna, Lakshmipuram Seshadri, Nambudiry Rekha i Narayanaswamy Srinivasan. "Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly". Bioinformation 8, nr 1 (6.01.2012): 6–12. http://dx.doi.org/10.6026/97320630008006.

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Maeda, Yoshiaki, i Hiroshi Matsui. "Genetically engineered protein nanowires: unique features in site-specific functionalization and multi-dimensional self-assembly". Soft Matter 8, nr 29 (2012): 7533. http://dx.doi.org/10.1039/c2sm25352f.

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Moshkanbaryans, Lia, Ling-Shan Chan, Kasper Engholm-Keller, Jesse Ray Wark, Phillip James Robinson i Mark Evan Graham. "The interaction of assembly protein AP180 and clathrin is inhibited by multi-site phospho-mimetics". Neurochemistry International 129 (październik 2019): 104474. http://dx.doi.org/10.1016/j.neuint.2019.104474.

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32

Srour, Batoul, Sylvain Gervason, Beata Monfort i Benoit D’Autréaux. "Mechanism of Iron–Sulfur Cluster Assembly: In the Intimacy of Iron and Sulfur Encounter". Inorganics 8, nr 10 (3.10.2020): 55. http://dx.doi.org/10.3390/inorganics8100055.

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Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.

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33

Kim, Hye-Youn, i Suntaek Hong. "Multi-Faceted Roles of DNAJB Protein in Cancer Metastasis and Clinical Implications". International Journal of Molecular Sciences 23, nr 23 (29.11.2022): 14970. http://dx.doi.org/10.3390/ijms232314970.

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Heat shock proteins (HSPs) are highly conserved molecular chaperones with diverse cellular activities, including protein folding, assembly or disassembly of protein complexes, and maturation process under diverse stress conditions. HSPs also play essential roles in tumorigenesis, metastasis, and therapeutic resistance across cancers. Among them, HSP40s are widely accepted as regulators of HSP70/HSP90 chaperones and an accumulating number of biological functions as molecular chaperones dependent or independent of either of these chaperones. Despite large numbers of HSP40s, little is known about their physiologic roles, specifically in cancer progression. This article summarizes the multi-faceted role of DNAJB proteins as one subclass of the HSP40 family in cancer development and metastasis. Regulation and deregulation of DNAJB proteins at transcriptional, post-transcriptional, and post-translational levels contribute to tumor progression, particularly cancer metastasis. Furthermore, understanding differences in function and regulating mechanism between DNAJB proteins offers a new perspective on tumorigenesis and metastasis to improve therapeutic opportunities for malignant diseases.

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34

Zechner, Ellen L., Silvia Lang i Joel F. Schildbach. "Assembly and mechanisms of bacterial type IV secretion machines". Philosophical Transactions of the Royal Society B: Biological Sciences 367, nr 1592 (19.04.2012): 1073–87. http://dx.doi.org/10.1098/rstb.2011.0207.

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Type IV secretion occurs across a wide range of prokaryotic cell envelopes: Gram-negative, Gram-positive, cell wall-less bacteria and some archaea. This diversity is reflected in the heterogeneity of components that constitute the secretion machines. Macromolecules are secreted in an ATP-dependent process using an envelope-spanning multi-protein channel. Similar to the type III systems, this apparatus extends beyond the cell surface as a pilus structure important for direct contact and penetration of the recipient cell surface. Type IV systems are remarkably versatile in that they mobilize a broad range of substrates, including single proteins, protein complexes, DNA and nucleoprotein complexes, across the cell envelope. These machines have broad clinical significance not only for delivering bacterial toxins or effector proteins directly into targeted host cells, but also for direct involvement in phenomena such as biofilm formation and the rapid horizontal spread of antibiotic resistance genes among the microbial community.

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35

Spalinger, Marianne R., Marlene Schwarzfischer i Michael Scharl. "The Role of Protein Tyrosine Phosphatases in Inflammasome Activation". International Journal of Molecular Sciences 21, nr 15 (31.07.2020): 5481. http://dx.doi.org/10.3390/ijms21155481.

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Inflammasomes are multi-protein complexes that mediate the activation and secretion of the inflammatory cytokines IL-1β and IL-18. More than half a decade ago, it has been shown that the inflammasome adaptor molecule, ASC requires tyrosine phosphorylation to allow effective inflammasome assembly and sustained IL-1β/IL-18 release. This finding provided evidence that the tyrosine phosphorylation status of inflammasome components affects inflammasome assembly and that inflammasomes are subjected to regulation via kinases and phosphatases. In the subsequent years, it was reported that activation of the inflammasome receptor molecule, NLRP3, is modulated via tyrosine phosphorylation as well, and that NLRP3 de-phosphorylation at specific tyrosine residues was required for inflammasome assembly and sustained IL-1β/IL-18 release. These findings demonstrated the importance of tyrosine phosphorylation as a key modulator of inflammasome activity. Following these initial reports, additional work elucidated that the activity of several inflammasome components is dictated via their phosphorylation status. Particularly, the action of specific tyrosine kinases and phosphatases are of critical importance for the regulation of inflammasome assembly and activity. By summarizing the currently available literature on the interaction of tyrosine phosphatases with inflammasome components we here provide an overview how tyrosine phosphatases affect the activation status of inflammasomes.

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36

GROEMPING, Yvonne, i Katrin RITTINGER. "Activation and assembly of the NADPH oxidase: a structural perspective". Biochemical Journal 386, nr 3 (8.03.2005): 401–16. http://dx.doi.org/10.1042/bj20041835.

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The NADPH oxidase of professional phagocytes is a crucial component of the innate immune response due to its fundamental role in the production of reactive oxygen species that act as powerful microbicidal agents. The activity of this multi-protein enzyme is dependent on the regulated assembly of the six enzyme subunits at the membrane where oxygen is reduced to superoxide anions. In the resting state, four of the enzyme subunits are maintained in the cytosol, either through auto-inhibitory interactions or through complex formation with accessory proteins that are not part of the active enzyme complex. Multiple inputs are required to disrupt these inhibitory interactions and allow translocation to the membrane and association with the integral membrane components. Protein interaction modules are key regulators of NADPH oxidase assembly, and the protein–protein interactions mediated via these domains have been the target of numerous studies. Many models have been put forward to describe the intricate network of reversible protein interactions that regulate the activity of this enzyme, but an all-encompassing model has so far been elusive. An important step towards an understanding of the molecular basis of NADPH oxidase assembly and activity has been the recent solution of the three-dimensional structures of some of the oxidase components. We will discuss these structures in the present review and attempt to reconcile some of the conflicting models on the basis of the structural information available.

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37

Zhao, Ting, Liying Guan, Xuehua Ma, Baohui Chen, Mei Ding i Wei Zou. "The cell cortex-localized protein CHDP-1 is required for dendritic development and transport in C. elegans neurons". PLOS Genetics 18, nr 9 (20.09.2022): e1010381. http://dx.doi.org/10.1371/journal.pgen.1010381.

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Cortical actin, a thin layer of actin network underneath the plasma membranes, plays critical roles in numerous processes, such as cell morphogenesis and migration. Neurons often grow highly branched dendrite morphologies, which is crucial for neural circuit assembly. It is still poorly understood how cortical actin assembly is controlled in dendrites and whether it is critical for dendrite development, maintenance and function. In the present study, we find that knock-out of C. elegans chdp-1, which encodes a cell cortex-localized protein, causes dendrite formation defects in the larval stages and spontaneous dendrite degeneration in adults. Actin assembly in the dendritic growth cones is significantly reduced in the chdp-1 mutants. PVD neurons sense muscle contraction and act as proprioceptors. Loss of chdp-1 abolishes proprioception, which can be rescued by expressing CHDP-1 in the PVD neurons. In the high-ordered branches, loss of chdp-1 also severely affects the microtubule cytoskeleton assembly, intracellular organelle transport and neuropeptide secretion. Interestingly, knock-out of sax-1, which encodes an evolutionary conserved serine/threonine protein kinase, suppresses the defects mentioned above in chdp-1 mutants. Thus, our findings suggest that CHDP-1 and SAX-1 function in an opposing manner in the multi-dendritic neurons to modulate cortical actin assembly, which is critical for dendrite development, maintenance and function.

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38

GORDON, Donna M., Jing WANG, Boominathan AMUTHA i Debkumar PAIN. "Self-association and precursor protein binding of Saccharomyces cerevisiae Tom40p, the core component of the protein translocation channel of the mitochondrial outer membrane". Biochemical Journal 356, nr 1 (8.05.2001): 207–15. http://dx.doi.org/10.1042/bj3560207.

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The precursor protein translocase of the mitochondrial outer membrane (Tom) is a multi-subunit complex containing receptors and a general import channel, of which the core component is Tom40p. Nuclear-encoded mitochondrial precursor proteins are first recognized by surface receptors and then pass through the import channel. The Tom complex has been purified; however, the protein–protein interactions that drive its assembly and maintain its stability have been difficult to study. Here we show that Saccharomyces cerevisiae Tom40p expressed in bacteria and purified to homogeneity associates efficiently with itself. The self-association is very strong and can withstand up to 4M urea or 1M salt. The tight self-association does not require the N-terminal segment of Tom40p. Furthermore, purified Tom40p preferentially recognizes the targeting sequence of mitochondrial precursor proteins. Although the binding of the targeting sequence to Tom40p is inhibited by urea concentrations in excess of 1M, it is moderately resistant to 1M salt. Simultaneous self-assembly and precursor protein binding suggest that Tom40p contains at least two different domains mediating these processes. The experimental approach described here should be useful for analysing protein–protein interactions involving individual or groups of components of the mitochondrial import machinery.

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39

Henderson, Richard, i Samar Hasnain. "`Cryo-EM': electron cryomicroscopy, cryo electron microscopy or something else?" IUCrJ 10, nr 5 (1.09.2023): 519–20. http://dx.doi.org/10.1107/s2052252523006759.

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Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. During the last ten years, cryoEM has become widely available and has provided a major boost to structure determination of membrane proteins and large multi-protein complexes. Many of the structures have now been made available at resolutions around 2 Å, where fundamental questions regarding enzyme mechanisms can be addressed. Over the years, the abbreviation cryoEM has been understood to stand for different things. We wish the wider community to engage and clarify the definition of cryoEM so that the expanding literature involving cryoEM is unified.

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40

Larsson, Daniel S. D., Sandesh Kanchugal Kanchugal P i Maria Selmer. "Structural Consequences of Deproteinating the 50S Ribosome". Biomolecules 12, nr 11 (31.10.2022): 1605. http://dx.doi.org/10.3390/biom12111605.

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Ribosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were shown as competent for in vitro assembly into functional 50S subunits. Here, we used cryo-EM to determine the structures of such LiCl core particles derived from E. coli 50S subunits. A wide range of complexes with large variations in the extent of the ordered 23S rRNA and the occupancy of r-proteins were resolved to between 2.8 Å and 9 Å resolution. Many of these particles showed high similarity to in vivo and in vitro assembly intermediates, supporting the inherent stability or metastability of these states. Similar to states in early ribosome assembly, the main class showed an ordered density for the particle base around the exit tunnel, with domain V and the 3′-half of domain IV disordered. In addition, smaller core particles were discovered, where either domain II or IV was unfolded. Our data support a multi-pathway in vitro disassembly process, similar but reverse to assembly. Dependencies between complex tertiary RNA structures and RNA-protein interactions were observed, where protein extensions dissociated before the globular domains. We observed the formation of a non-native RNA structure upon protein dissociation, demonstrating that r-proteins stabilize native RNA structures and prevent non-native interactions also after folding.

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Bergdahl, Roland, Christin Grundström, Patrik Storm, Wolfgang Schröder i Uwe Sauer. "Photosystem II assembly factor HCF136 from A. thaliana at 1.67 Å resolution". Acta Crystallographica Section A Foundations and Advances 70, a1 (5.08.2014): C1170. http://dx.doi.org/10.1107/s2053273314088299.

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The High Chlorophyll Fluorescence 136 protein (HCF136) is essential for the assembly and repair of Photosystem II (PSII) and its central reaction centre (RC)[1]. HCF136 is an abundant protein in the thylakoid lumen and has been suggested to directly interact with subunits of the RC. The multi-subunit pigment-protein PSII complex is imbedded in the thylakoid membrane of the oxygenic photosynthetic organisms, and responsible for water splitting during oxygenic photosynthesis. PSII harbours more than 20 different integral and peripheral membrane proteins and its assembly requires a high level of coordination[2]. Two proteins D1 (psbA) and D2 (psbD) form the core of the complex and bind most of the redox-active co-factors. The PSII RC contains, in addition to D1 and D2, the intrinsic PsbI subunit and cytochrome b559. Light is a harmful substrate and subunits are damaged during the water-splitting reaction. The largest irreversible damage is experienced by the central D1 protein that has the highest turnover rate of all thylakoid proteins. Analysis of mutated A. thaliana has identified HCF136 as an essential factor for PSII RC assembly and RC turnover and repair[3]. In order to gain functional and structural insight in the way the HCF136 protein is involved in the PSII repair cycle, we have cloned, expressed, purified and crystallized the HCF136 protein from A. thaliana. Here we present the structure of this doughnut shaped WD40 domain family protein determined at 1.67 Å resolution. Biochemical and biophysical analysis of HCF136 and components of the PSII RC are under way.

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Guarneri, Flavia, Matteo Tonni, Giuseppe Sarli, Maria Beatrice Boniotti, Davide Lelli, Ilaria Barbieri, Giulia D'Annunzio, Giovanni Loris Alborali, Barbara Bacci i Massimo Amadori. "Non-Assembled ORF2 Capsid Protein of Porcine Circovirus 2b Does Not Confer Protective Immunity". Pathogens 10, nr 9 (9.09.2021): 1161. http://dx.doi.org/10.3390/pathogens10091161.

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Porcine Circovirus 2 (PCV2) vaccines are based on either inactivated whole virion, or recombinant ORF2 capsid protein assembled into Virus-like Particles (VLPs). No data are available about the immunizing properties of free, non-assembled capsid protein. To investigate this issue, ORF2 of a reference PCV2b strain was expressed in a Baculovirus-based expression system without assembly into VLPs. The free purified protein was formulated into an oil vaccine at three distinct Ag payloads: 10.8/3.6/1.2 micrograms/dose. Each dose was injected intramuscularly into five, 37-day old piglets, carefully matched for maternally-derived antibody. Five control piglets were injected with sterile PBS in oil adjuvant. Twenty-eight days later, all the pigs were challenged intranasally with 105.3 TCID50 of PCV2b strain DV6503. After challenge infection, all the pigs remained in good clinical conditions. The recombinant vaccine did not induce significant antibody and PCV2-specific IFN-γ responses. ELISPOT and lymphocyte proliferation data confirmed poor induction of cell-mediated immunity. In terms of PCV2 viremia, there was no significant difference between vaccinated and control animals. The histological data indicated the absence of a detectable viral load and of PCVAD lesions in both vaccinated and control animals, as well as of histiocytes and multi-nucleated giant cells. We conclude that free, non-assembled ORF2 capsid protein does not induce protective immunity.

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Le, Sarah N., Christopher R. Brown, Stacy Harvey, Hinrich Boeger, Hans Elmlund i Dominika Elmlund. "The TAFs of TFIID Bind and Rearrange the Topology of the TATA-Less RPS5 Promoter". International Journal of Molecular Sciences 20, nr 13 (4.07.2019): 3290. http://dx.doi.org/10.3390/ijms20133290.

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The general transcription factor TFIID is a core promoter selectivity factor that recognizes DNA sequence elements and nucleates the assembly of a pre-initiation complex (PIC). The mechanism by which TFIID recognizes the promoter is poorly understood. The TATA-box binding protein (TBP) is a subunit of the multi-protein TFIID complex believed to be key in this process. We reconstituted transcription from highly purified components on a ribosomal protein gene (RPS5) and discovered that TFIIDΔTBP binds and rearranges the promoter DNA topology independent of TBP. TFIIDΔTBP binds ~200 bp of the promoter and changes the DNA topology to a larger extent than the nucleosome core particle. We show that TBP inhibits the DNA binding activities of TFIIDΔTBP and conclude that the complete TFIID complex may represent an auto-inhibited state. Furthermore, we show that the DNA binding activities of TFIIDΔTBP are required for assembly of a PIC poised to select the correct transcription start site (TSS).

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44

Connelly, Rhykka Leanne, Kenneth Gasser i Daniel Traber. "O07. CCK and NO coordinate the assembly of a multi-protein complex leading to Erk activation". Nitric Oxide 14, nr 4 (czerwiec 2006): 2–3. http://dx.doi.org/10.1016/j.niox.2006.04.011.

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Heyd, Jochen, i Stefan Birmanns. "Solving Complex Puzzles: Automated Protein Complex Assembly From Cryo-Electron Microscopy Data Via Multi-Resolution Modeling". Biophysical Journal 96, nr 3 (luty 2009): 412a. http://dx.doi.org/10.1016/j.bpj.2008.12.2101.

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Brodehl, Andreas, Stephanie Holler, Jan Gummert i Hendrik Milting. "The N-Terminal Part of the 1A Domain of Desmin Is a Hot Spot Region for Putative Pathogenic DES Mutations Affecting Filament Assembly". Cells 11, nr 23 (2.12.2022): 3906. http://dx.doi.org/10.3390/cells11233906.

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Desmin is the major intermediate filament protein of all three muscle cell types, and connects different cell organelles and multi-protein complexes such as the cardiac desmosomes. Several pathogenic mutations in the DES gene cause different skeletal and cardiac myopathies. However, the significance of the majority of DES missense variants is currently unknown, since functional data are lacking. To determine whether desmin missense mutations within the highly conserved 1A coil domain cause a filament assembly defect, we generated a set of variants with unknown significance and systematically analyzed the filament assembly using confocal microscopy in transfected SW-13, H9c2 cells and cardiomyocytes derived from induced pluripotent stem cells. We found that mutations in the N-terminal part of the 1A coil domain affect filament assembly, leading to cytoplasmic desmin aggregation. In contrast, mutant desmin in the C-terminal part of the 1A coil domain forms filamentous structures comparable to wild-type desmin. Our findings suggest that the N-terminal part of the 1A coil domain is a hot spot for pathogenic desmin mutations, which affect desmin filament assembly. This study may have relevance for the genetic counselling of patients carrying variants in the 1A coil domain of the DES gene.

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Pazour, Gregory J., Bethany L. Dickert, Yvonne Vucica, E. Scott Seeley, Joel L. Rosenbaum, George B. Witman i Douglas G. Cole. "Chlamydomonas IFT88 and Its Mouse Homologue, Polycystic Kidney Disease Gene Tg737, Are Required for Assembly of Cilia and Flagella". Journal of Cell Biology 151, nr 3 (30.10.2000): 709–18. http://dx.doi.org/10.1083/jcb.151.3.709.

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Intraflagellar transport (IFT) is a rapid movement of multi-subunit protein particles along flagellar microtubules and is required for assembly and maintenance of eukaryotic flagella. We cloned and sequenced a Chlamydomonas cDNA encoding the IFT88 subunit of the IFT particle and identified a Chlamydomonas insertional mutant that is missing this gene. The phenotype of this mutant is normal except for the complete absence of flagella. IFT88 is homologous to mouse and human genes called Tg737. Mice with defects in Tg737 die shortly after birth from polycystic kidney disease. We show that the primary cilia in the kidney of Tg737 mutant mice are shorter than normal. This indicates that IFT is important for primary cilia assembly in mammals. It is likely that primary cilia have an important function in the kidney and that defects in their assembly can lead to polycystic kidney disease.

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Bryan, Nicole B., Andrea Dorfleutner, Yon Rojanasakul i Christian Stehlik. "Pathogen-induced activation of inflammasomes requires intracellular redistribution of the apoptosis associated speck-like protein containing a caspase recruitment domain (ASC) (135.70)". Journal of Immunology 182, nr 1_Supplement (1.04.2009): 135.70. http://dx.doi.org/10.4049/jimmunol.182.supp.135.70.

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Abstract Activation of caspase-1, which is necessary for the maturation and secretion of the pro-inflammatory cytokines IL-1β and IL-18, occurs upon assembly of multi-protein complexes known as inflammasomes. Apoptosis associated speck-like protein containing a caspase recruitment domain (ASC) is an adaptor protein, which is essential for the recruitment of caspase-1 into inflammasomes. However, distribution of endogenous ASC has not been thoroughly examined. In the current study, we used laser scanning confocal microscopy and subcellular fractionation to demonstrate that endogenous ASC localized primarily to the nucleus in resting human macrophages. Upon pathogenic stimulation, ASC rapidly redistributed to the cytosol, and subsequently formed a characteristic perinuclear aggregate. These aggregates were found to incorporate other key inflammasome proteins including NLRP3 and caspase-1. Furthermore, sequestering ASC to the nucleus impaired formation of the inflammasome and abolished caspase-1 activation, as measured by IL-1β secretion. Our results indicate that the redistribution of ASC from the nucleus to the cytosol represents a novel and essential mechanism that regulates inflammasome assembly and activation.

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Zhang, Shiyong, Jia Li, Qin Qin, Wei Liu, Chao Bian, Yunhai Yi, Minghua Wang i in. "Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes". Toxins 10, nr 12 (23.11.2018): 488. http://dx.doi.org/10.3390/toxins10120488.

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Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

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Lone, Moien, Qulsum Akhter, Mithilesh Kumar, Umar Maqbool, Mahaiwon Shadang, Shyam S. Chauhan i Riyaz A. Mir. "ROLE OF R2TP COMPLEX IN LYMPHOMA AND ITS THERAPEUTIC POTENTIAL". International Journal of Advanced Research 8, nr 11 (30.11.2020): 300–303. http://dx.doi.org/10.21474/ijar01/12010.

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The R2TP complex which comprises of RUVBL1, RUVBL2, PIH1D1 and RPAP3 in humans is known to be a specialized Co-chaperone of Hsp-90 protein. This multimeric-protein complex is involved in the assembly and maturation of several multi-subunit complexes including RNA polymerase II, small nucleolar ribonucleoproteins, and complexes containing phosphatidylinositol-3-kinase-like kinases. Since their discovery as a co-chaperone of Hsp90, the R2TP complex is involved in multitude of cellular processes including, chromatin remodelling, transcription regulation, ribonucleoprotein complex biogenesis, mitotic assembly, telomerase complex assembly, and apoptosis. Lymphoma arises from the abnormal proliferation of B-cells and the R2TP complex have been reported to play an important role in the activation of p53 and RB. Therefore, the inactivation in any of the tumor suppressor pathways can drive cells to malignancy.However, there are multiple factors which may contribute towards malignancy but the folding defects in these tumor suppressor pathways could be one of the reasons. R2TP is tightly linked with oncogenesis and its inhibition can decrease the proliferation activity of cancer cells. So, the multisubunit chaperone complex as well as its components could be promising candidates for cancer chemotherapy.

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