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Complex assembly

Ann M Dixon, Syamal Roy
Class II Major Histocompatibility complex (MHC-II) is a polymorphic heterodimer that binds antigen-derived peptides and presents them on the surface of antigen presenting cells. This mechanism of antigen presentation leads to recognition by CD4 T-cells and T-cell activation, making it a critical element of adaptive immune response. For this reason, the structural determinants of MHC-II function have been of great interest for the past 30 years, resulting in a robust structural understanding of the extracellular regions of the complex...
August 10, 2018: Human Immunology
Lorenzo Calisti, Matilde Cardoso Trabuco, Alberto Boffi, Claudia Testi, Linda Celeste Montemiglio, Amédée des Georges, Irene Benni, Andrea Ilari, Bartłomiej Taciak, Maciej Białasek, Tomasz Rygiel, Magdalena Król, Paola Baiocco, Alessandra Bonamore
Ferritin H-homopolymers have been extensively used as nanocarriers for diverse applications in the targeted delivery of drugs and imaging agents, due to their unique ability to bind the transferrin receptor (CD71), highly overexpressed in most tumor cells. In order to incorporate novel fluorescence imaging properties, we have fused a lanthanide binding tag (LBT) to the C-terminal end of mouse H-chain ferritin, HFt. The HFt-LBT possesses one high affinity Terbium binding site per each of the 24 subunits provided by six coordinating aminoacid side chains and a tryptophan residue in its close proximity and is thus endowed with strong FRET sensitization properties...
2018: PloS One
Buddhini C N Vithanage, Joanna Xiuzhu Xu, Dongmao Zhang
With their unique photochemical properties, porphyrins have remained for decades the most interesting chemicals as photonic materials for applications ranging from chemistry, biology, medicine, to photovoltaic. Porphyrins can self-assemble into higher-order structures. However, information has been scant on the kinetics and structural evolution during porphyrin assembly and disassembly. Furthermore, quantitative understanding of the porphyrin optical activities is complicated by the complex interplay of photon absorption, scattering, and fluorescence emission that can concurrently occur in porphyrin samples...
August 13, 2018: Journal of Physical Chemistry. B
Stefan Dannenmaier, Sebastian B Stiller, Marcel Morgenstern, Philipp Lübbert, Silke Oeljeklaus, Nils Wiedemann, Bettina Warscheid
Knowledge about the functions of individual proteins on a systems-wide level is crucial to fully understand molecular mechanisms underlying cellular processes. A considerable part of the proteome across all organisms is still poorly characterized. Mass spectrometry is an efficient technology for the global study of proteins. One of the most prominent methods for accurate proteome-wide comparative quantification is stable isotope labeling by amino acids in cell culture (SILAC). However, application of SILAC to prototrophic organisms such as Saccharomyces cerevisiae, also known as baker's yeast, is compromised since they are able to synthesize all amino acids on their own...
August 13, 2018: Analytical Chemistry
Dermot M Gillen, Chris S Hawes, Thorfinnur Gunnlaugsson
meta-Phenylene bis(phenylurea) receptors 1-4 were designed and synthesized to investigate the association between receptor shape and anion-selective binding and anion-directed self-assembly processes. Solution studies, performed through 1H NMR titrations with a variety of tetra-N-butylammonium (TBA) salts, demonstrated strong binding of two equivalents of H2PO4-, AcO-, BzO- anions and comparatively weak binding of Cl-, HSO4- and SO42- anions. Binding modes and stability constants (logβ) were determined by regression analysis of the obtained 1H NMR titration data in DMSO-d6, and the cooperativities of the binding interactions probed...
August 13, 2018: Journal of Organic Chemistry
Dzmitry Melnikau, Saioa Elcoroaristizabal, Alan George Ryder
The accurate fluorescence analysis of complex, multi-fluorophore containing proteins requires the use of multi-dimensional measurement techniques. For the measurement of intrinsic fluorescence from tyrosine (Tyr) and tryptophan (Trp) one needs tunable UV excitation and for steady-state measurements like Excitation Emission Matrix (EEM) simple pulsed Xe lamps are commonly used. Unfortunately, simultaneous multi-dimensional wavelength and time resolved measurement of intrinsic protein fluorescence in the 260 to 400 nm spectral range are challenging and typically required the use of very complex tunable laser systems or multiple single excitation wavelength sources...
August 13, 2018: Methods and Applications in Fluorescence
Jorge Cruz-Reyes, Blaine H M Mooers, Pawan K Doharey, Joshua Meehan, Shelly Gulati
RNA editing causes massive remodeling of the mitochondrial mRNA transcriptome in trypanosomes and related kinetoplastid protozoa. This type of editing involves the specific insertion or deletion of uridylates (U) directed by small noncoding guide RNAs (gRNAs). Because U-insertion exceeds U-deletion by a factor of 10, editing increases the nascent mRNA size by up to 55%. In Trypanosoma brucei, the editing apparatus uses ~40 proteins and >1,200 gRNAs to create the functional open reading frame in 12 mRNAs...
August 12, 2018: Wiley Interdisciplinary Reviews. RNA
Xuefeng Li, Rongzhe Li, Zuifang Liu, Xiang Gao, Shijun Long, Gaowen Zhang
With the deepening of research on high-strength hydrogels, the multi-functional study of hydrogels has become a hot spot. In this paper, a dual cross-linked physical high-strength hydrogels is prepared by a relatively simple method. 2-Vinyl- 4,6-Diamino-2-vinyl-1,3,5-triazine (VDT) induces the formation of the first cross-linking points through the interaction of hydrogen bonds with poly(acrylamide-co-acrylic acid) (PAm-co-Ac) chains, then the secondary physical cross-linkers Fe3+ that introduce ionic coordinates between Fe3+ and -COO- groups...
August 12, 2018: Macromolecular Rapid Communications
Britto Sandanaraj, Mohan Reddy, Pavankumar Bhandari, Sugam Kumar, Vinod Aswal
Self-assembly of proteins into higher order super-structures is ubiquitous in biological systems. Genetic methods comprising both computational and rational design strategies are emerging as powerful methods for design of synthetic protein complexes with high accuracy and fidelity. Although useful, most of the reported protein complexes lack dynamic behavior that may limit their potential applications. On the contrary, protein engineering using chemical strategiesoffers excellent possibilities for the design of protein complexes with stimuli-responsive functions and adaptive behavior...
August 12, 2018: Chemistry: a European Journal
Franklin Delehelle, Sylvain Cussat-Blanc, Jean-Marc Alliot, Hervé Luga, Patricia Balaresque
Motivation: Segmental Duplications (SDs) are DNA fragments longer than 1 kbp, distributed within and between chromosomes and sharing more than 90% identity. Although they hold a significant role in genomic fluidity and adaptability, many key questions about their intrinsic characteristics and mutability remain unsolved due to the persistent difficulty of sequencing highly duplicated genomic regions. The recent development of long and linked-read NGS technologies will increase the need to search for SDs in genomes newly sequenced with these technics...
August 15, 2018: Bioinformatics
Julian Michael Rocha, Charles Joseph Richardson, Mingxing Zhang, Caroline Maureen Darch, Eugene Cai, Andreas Diepold, Andreas Gahlmann
In bacterial type 3 secretion, substrate proteins are actively transported from the bacterial cytoplasm into the host cell cytoplasm by a large membrane-embedded machinery called the injectisome. Injectisomes transport secretion substrates in response to specific environmental signals, but the molecular details by which the cytosolic secretion substrates are selected and transported through the type 3 secretion pathway remain unclear. Secretion activity and substrate selectivity are thought to be controlled by a sorting platform consisting of the proteins SctK, SctQ, SctL, and SctN, which together localize to the cytoplasmic side of membrane-embedded injectisomes...
August 13, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Elif Eren, Norman R Watts, Altaira D Dearborn, Ira W Palmer, Joshua D Kaufman, Alasdair C Steven, Paul T Wingfield
Hepatitis B virus (HBV) is the leading cause of liver disease worldwide. While an adequate vaccine is available, current treatment options are limited, not highly effective, and associated with adverse effects, encouraging the development of alternative therapeutics. The HBV core gene encodes two different proteins: core, which forms the viral nucleocapsid, and pre-core, which serves as an immune modulator with multiple points of action. The two proteins mostly have the same sequence, although they differ at their N and C termini and in their dimeric arrangements...
July 17, 2018: Structure
Rakhi Bajaj, Mathieu Bollen, Wolfgang Peti, Rebecca Page
The kinetochore scaffold 1 (KNL1) protein coordinates the spindle assembly checkpoint (SAC), a signaling pathway that delays chromosome segregation until all sister chromatids are properly attached to spindle microtubules. Recently, microtubules and protein phosphatase 1 (PP1), which both bind the N-terminal domain of KNL1, have emerged as regulators of the SAC; however, how these proteins interact to contribute to SAC signaling is unknown. Here, we use X-ray crystallography, nuclear magnetic resonance spectroscopy, and biochemical assays to show how KNL1 binds both PP1 and microtubules...
July 13, 2018: Structure
Qianhui Qu, Yoh-Hei Takahashi, Yidai Yang, Hongli Hu, Yan Zhang, Joseph S Brunzelle, Jean-Francois Couture, Ali Shilatifard, Georgios Skiniotis
The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics...
August 3, 2018: Cell
Peter L Hsu, Heng Li, Ho-Tak Lau, Calvin Leonen, Abhinav Dhall, Shao-En Ong, Champak Chatterjee, Ning Zheng
The SET1/MLL family of histone methyltransferases is conserved in eukaryotes and regulates transcription by catalyzing histone H3K4 mono-, di-, and tri-methylation. These enzymes form a common five-subunit catalytic core whose assembly is critical for their basal and regulated enzymatic activities through unknown mechanisms. Here, we present the crystal structure of the intact yeast COMPASS histone methyltransferase catalytic module consisting of Swd1, Swd3, Bre2, Sdc1, and Set1. The complex is organized by Swd1, whose conserved C-terminal tail not only nucleates Swd3 and a Bre2-Sdc1 subcomplex, but also joins Set1 to construct a regulatory pocket next to the catalytic site...
July 25, 2018: Cell
Homa Papoli Yazdi, Hans Ellegren
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae...
August 7, 2018: Genome Biology and Evolution
Gianpiero Lazzari, Valerie Nicolas, Michiya Matsusaki, Mitsuru Akashi, Patrick Couvreur, Simona Mura
The preclinical drug screening of pancreatic cancer treatments suffers from the absence of appropriate models capable to reproduce in vitro the heterogeneous tumor microenvironment and its stiff desmoplasia. Driven by this pressing need, we describe in this paper the conception and the characterization of a novel 3D tumor model, consisting of a triple co-culture of pancreatic cancer cells (PANC-1), fibroblasts (MRC-5) and endothelial cells (HUVEC), which assembled to form a hetero-type multicellular tumor spheroid (MCTS)...
August 9, 2018: Acta Biomaterialia
Mohammadreza Sadeghi, Eda Altan, Xutao Deng, Christopher M Barker, Ying Fang, Lark L Coffey, Eric Delwart
Metagenomic analysis of whole mosquitoes allows the genetic characterization of all associated viruses, including arboviruses and insect-specific viruses, plus those in their diet or infecting their parasites. We describe here the virome in mosquitoes, primarily Culex pipiens complex, Cx. tarsalis and Cx. erythrothorax, collected in 2016 from 31 counties in California, USA. The nearly complete genomes of 56 viruses, including 32 novel genomes, some from potentially novel RNA and DNA viral families or genera, were assembled and phylogenetically analyzed, significantly expanding the known Culex-associated virome...
August 8, 2018: Virology
A Diaconu, L E Nita, A P Chiriac, M Butnaru
The study presents a novel strategy for obtaining highly ordered interpolymeric complexes based on a protein, bovine serum albumin and a synthetic polymer, poly(aspartic acid). In this approach, experimental tests were carried out in the presence of a magnetic field of different intensities, namely 0.11 T and 0.3 T produced by permanent magnets. The influence of the magnetic force on the complexation process and the resulted self-assembled structures were studied by means of FTIR spectroscopy, X-ray diffraction, DLS, SEM microscopy and in vitro assay...
August 8, 2018: International Journal of Biological Macromolecules
Pablo Palazon-Riquelme, Gloria Lopez-Castejon
Due to its strategic location, the epithelium is constantly exposed to a wide variety of pathogen and danger signals. Traditionally the epithelium has been perceived as a defensive but passive barrier, however it has now become evident that the epithelium senses and actively responds to these signals in order to maintain barrier homeostasis and contribute to the inflammatory response. One way it does this, is by producing pro-inflammatory cytokines including IL-1β and IL-18. These two cytokines are synthesized as inactive precursors, which maturation is mediated by pro-inflammatory caspases after the activation and assembly of macromolecular complexes called inflammasomes...
August 11, 2018: Immunology
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