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Journal articles on the topic 'Multi-protein assembly'

Author: Grafiati

Published: 6 September 2023

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1

Siggers, Trevor, and Raluca Gordân. "Protein–DNA binding: complexities and multi-protein codes." Nucleic Acids Research 42, no. 4 (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

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2

Li, Mei, Erik Dujardin, and Stephen Mann. "Programmed assembly of multi-layered protein/nanoparticle-carbon nanotube conjugates." Chemical Communications, no. 39 (2005): 4952. http://dx.doi.org/10.1039/b509109h.

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3

Tørresen, Ole K., Bastiaan Star, Pablo Mier, et al. "Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases." Nucleic Acids Research 47, no. 21 (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 t

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Farrugia, Thomas, Adam W. Perriman, Kamendra P. Sharma, and Stephen Mann. "Multi-enzyme cascade reactions using protein–polymer surfactant self-standing films." Chemical Communications 53, no. 13 (2017): 2094–97. http://dx.doi.org/10.1039/c6cc09809f.

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Venkatraman, Vishwesh, and David W. Ritchie. "Predicting Multi-Component Protein Assemblies Using an Ant Colony Approach." International Journal of Swarm Intelligence Research 3, no. 3 (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 cons

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Xian, Yuejiao, Chitra B. Karki, Sebastian Miki Silva, Lin Li, and Chuan Xiao. "The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses." International Journal of Molecular Sciences 20, no. 8 (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,

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Terzo, Esteban A., Shawn M. Lyons, John S. Poulton, Brenda R. S. Temple, William F. Marzluff, and 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, no. 8 (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 p

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Mozdy, A. D., J. M. McCaffery, and 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, no. 2 (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 membr

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Guo, Zhen, Zhiwei Shen, Yujiao Wang, Tingyuan Tan, and Yi Zhang. "Peptides Co-Assembling into Hydrangea-Like Microstructures." Journal of Nanoscience and Nanotechnology 20, no. 5 (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

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Tang, Jiakun, Ye Liu, Dongmei Qi, et al. "Nucleus‐Targeted Delivery of Multi‐Protein Self‐Assembly for Combined Anticancer Therapy." Small 17, no. 25 (2021): 2101219. http://dx.doi.org/10.1002/smll.202101219.

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11

Jayalath, Kumudie, Sean Frisbie, Minhchau To, and Sanjaya Abeysirigunawardena. "Pseudouridine Synthase RsuA Captures an Assembly Intermediate That Is Stabilized by Ribosomal Protein S17." Biomolecules 10, no. 6 (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-ter

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Chi, Wei, Jinfang Ma, and Lixin Zhang. "Regulatory factors for the assembly of thylakoid membrane protein complexes." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1608 (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

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Whitley, Paul, and Ismael Mingarro. "Stitching proteins into membranes, not sew simple." Biological Chemistry 395, no. 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 do

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14

Hahn, Hyunggu, Sang Ho Park, Hyun-Jung Kim, Sunghoon Kim, and Byung Woo Han. "The DRS–AIMP2–EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex." IUCrJ 6, no. 5 (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

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Bolanos-Garcia, Victor M., Qian Wu, Takashi Ochi, Dimitri Y. Chirgadze, Bancinyane Lynn Sibanda, and 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, no. 1969 (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

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Ribbe, Markus W., Kamil Górecki, Mario Grosch, et al. "Nitrogenase Fe Protein: A Multi-Tasking Player in Substrate Reduction and Metallocluster Assembly." Molecules 27, no. 19 (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 cataly

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17

Vonshak, Ohad, Yiftach Divon, Stefanie Förste, et al. "Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry." Nature Nanotechnology 15, no. 9 (2020): 783–91. http://dx.doi.org/10.1038/s41565-020-0720-7.

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18

van den Akker, Emile, Timothy J. Satchwell, Geoff Daniels, and Ashley M. Toye. "Mapping the Assembly of Band 3 and Rhesus Multi-Protein Complexes During Erythropoiesis." Blood 116, no. 21 (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

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Bergfort, Alexandra, Tarek Hilal, Benno Kuropka, et al. "The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling." Nucleic Acids Research 50, no. 5 (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 th

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20

Maghool, Shadi, N. Dinesha G. Cooray, David A. Stroud, David Aragão, Michael T. Ryan, and Megan J. Maher. "Structural and functional characterization of the mitochondrial complex IV assembly factor Coa6." Life Science Alliance 2, no. 5 (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 disulfid

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Gupta, Swati, Jyoti Chhibber-Goel, Manmohan Sharma, et al. "Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein." Acta Crystallographica Section D Structural Biology 76, no. 2 (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-termin

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22

Ortolan, Tatiana G., Prasad Tongaonkar, David Lambertson, Li Chen, Cherylene Schauber, and Kiran Madura. "The DNA repair protein Rad23 is a negative regulator of multi-ubiquitin chain assembly." Nature Cell Biology 2, no. 9 (2000): 601–8. http://dx.doi.org/10.1038/35023547.

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23

Uchida, Masaki, Ben LaFrance, Chris C. Broomell, Peter E. Prevelige, and Trevor Douglas. "Higher Order Assembly of Virus-like Particles (VLPs) Mediated by Multi-valent Protein Linkers." Small 11, no. 13 (2015): 1562–70. http://dx.doi.org/10.1002/smll.201402067.

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24

Burkinshaw, Brianne J., Sergio A. Souza, and Natalie C. J. Strynadka. "Structural analysis of SepL, an enteropathogenicEscherichia colitype III secretion-system gatekeeper protein." Acta Crystallographica Section F Structural Biology Communications 71, no. 10 (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 struc

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Tieu, Quinton, and 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, no. 2 (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-m

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Sokolik, Chana G., Nasrin Qassem, and Jordan H. Chill. "The Disordered Cellular Multi-Tasker WIP and Its Protein–Protein Interactions: A Structural View." Biomolecules 10, no. 7 (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 f

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Lecomte, F. J. L., N. Ismail, and S. High. "Making membrane proteins at the mammalian endoplasmic reticulum." Biochemical Society Transactions 31, no. 6 (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 speci

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Cherak, Stephana J., and Raymond J. Turner. "Assembly pathway of a bacterial complex iron sulfur molybdoenzyme." Biomolecular Concepts 8, no. 3-4 (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

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Swapna, Lakshmipuram Seshadri, Nambudiry Rekha, and Narayanaswamy Srinivasan. "Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly." Bioinformation 8, no. 1 (2012): 6–12. http://dx.doi.org/10.6026/97320630008006.

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Maeda, Yoshiaki, and Hiroshi Matsui. "Genetically engineered protein nanowires: unique features in site-specific functionalization and multi-dimensional self-assembly." Soft Matter 8, no. 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, and Mark Evan Graham. "The interaction of assembly protein AP180 and clathrin is inhibited by multi-site phospho-mimetics." Neurochemistry International 129 (October 2019): 104474. http://dx.doi.org/10.1016/j.neuint.2019.104474.

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Srour, Batoul, Sylvain Gervason, Beata Monfort, and Benoit D’Autréaux. "Mechanism of Iron–Sulfur Cluster Assembly: In the Intimacy of Iron and Sulfur Encounter." Inorganics 8, no. 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 controve

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Kim, Hye-Youn, and Suntaek Hong. "Multi-Faceted Roles of DNAJB Protein in Cancer Metastasis and Clinical Implications." International Journal of Molecular Sciences 23, no. 23 (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

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Zechner, Ellen L., Silvia Lang, and Joel F. Schildbach. "Assembly and mechanisms of bacterial type IV secretion machines." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1592 (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 b

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Spalinger, Marianne R., Marlene Schwarzfischer, and Michael Scharl. "The Role of Protein Tyrosine Phosphatases in Inflammasome Activation." International Journal of Molecular Sciences 21, no. 15 (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 o

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GROEMPING, Yvonne, and Katrin RITTINGER. "Activation and assembly of the NADPH oxidase: a structural perspective." Biochemical Journal 386, no. 3 (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

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Zhao, Ting, Liying Guan, Xuehua Ma, Baohui Chen, Mei Ding, and Wei Zou. "The cell cortex-localized protein CHDP-1 is required for dendritic development and transport in C. elegans neurons." PLOS Genetics 18, no. 9 (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 stage

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GORDON, Donna M., Jing WANG, Boominathan AMUTHA, and 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, no. 1 (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 effic

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Henderson, Richard, and Samar Hasnain. "`Cryo-EM': electron cryomicroscopy, cryo electron microscopy or something else?" IUCrJ 10, no. 5 (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

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Larsson, Daniel S. D., Sandesh Kanchugal Kanchugal P, and Maria Selmer. "Structural Consequences of Deproteinating the 50S Ribosome." Biomolecules 12, no. 11 (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 inter

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Bergdahl, Roland, Christin Grundström, Patrik Storm, Wolfgang Schröder, and Uwe Sauer. "Photosystem II assembly factor HCF136 from A. thaliana at 1.67 Å resolution." Acta Crystallographica Section A Foundations and Advances 70, a1 (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

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Guarneri, Flavia, Matteo Tonni, Giuseppe Sarli, et al. "Non-Assembled ORF2 Capsid Protein of Porcine Circovirus 2b Does Not Confer Protective Immunity." Pathogens 10, no. 9 (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

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Le, Sarah N., Christopher R. Brown, Stacy Harvey, Hinrich Boeger, Hans Elmlund, and Dominika Elmlund. "The TAFs of TFIID Bind and Rearrange the Topology of the TATA-Less RPS5 Promoter." International Journal of Molecular Sciences 20, no. 13 (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 pro

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

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Heyd, Jochen, and Stefan Birmanns. "Solving Complex Puzzles: Automated Protein Complex Assembly From Cryo-Electron Microscopy Data Via Multi-Resolution Modeling." Biophysical Journal 96, no. 3 (2009): 412a. http://dx.doi.org/10.1016/j.bpj.2008.12.2101.

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Brodehl, Andreas, Stephanie Holler, Jan Gummert, and 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, no. 23 (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 a

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Pazour, Gregory J., Bethany L. Dickert, Yvonne Vucica, et al. "Chlamydomonas IFT88 and Its Mouse Homologue, Polycystic Kidney Disease Gene Tg737, Are Required for Assembly of Cilia and Flagella." Journal of Cell Biology 151, no. 3 (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 prim

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Bryan, Nicole B., Andrea Dorfleutner, Yon Rojanasakul, and 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, no. 1_Supplement (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 locali

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Zhang, Shiyong, Jia Li, Qin Qin, et al. "Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes." Toxins 10, no. 12 (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

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Lone, Moien, Qulsum Akhter, Mithilesh Kumar, et al. "ROLE OF R2TP COMPLEX IN LYMPHOMA AND ITS THERAPEUTIC POTENTIAL." International Journal of Advanced Research 8, no. 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, mito

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