Search results for "protein conformation"
showing 10 items of 515 documents
Mapping the tRNA binding site on the surface of human DNMT2 methyltransferase.
2012
The DNMT2 enzyme methylates tRNA-Asp at position C38. Because there is no tRNA–Dnmt2 cocrystal structure available, we have mapped the tRNA binding site of DNMT2 by systematically mutating surface-exposed lysine and arginine residues to alanine and studying the tRNA methylation activity and binding of the corresponding variants. After mutating 20 lysine and arginine residues, we identified eight of them that caused large (>4-fold) decreases in catalytic activity. These residues cluster within and next to a surface cleft in the protein, which is large enough to accommodate the tRNA anticodon loop and stem. This cleft is located next to the binding pocket for the cofactor S-adenosyl-l-methion…
Binding Properties of HABA-Type Azo Derivatives to Avidin and Avidin-Related Protein 4
2006
Summary The chicken genome encodes several biotin-binding proteins, including avidin and avidin-related protein 4 (AVR4). In addition to D -biotin, avidin binds an azo dye compound, 4-hydroxyazobenzene-2-carboxylic acid (HABA), but the HABA-binding properties of AVR4 are not yet known. Differential scanning calorimetry, UV/visible spectroscopy, and molecular modeling were used to analyze the binding of 15 azo molecules to avidin and AVR4. Significant differences are seen in azo compound preferences for the two proteins, emphasizing the importance of the loop between strands β3 and β4 for azo ligand recognition; information on these loops is provided by the high-resolution (1.5 A) X-ray stru…
Dopaminergic isoquinolines with hexahydrocyclopenta[ ij ]-isoquinolines as D 2 -like selective ligands
2016
Dopamine receptors (DR) ligands are potential drug candidates for treating neurological disorders including schizophrenia or Parkinson's disease. Three series of isoquinolines: (E)-1-styryl-1,2,3,4-tetrahydroisoquinolines (series 1), 7-phenyl-1,2,3,7,8,8a-hexahydrocyclopenta[ij]-IQs (HCPIQs) (series 2) and (E)-1-(prop-1-en-1-yl)-1,2,3,4- tetrahydroisoquinolines (series 3), were prepared to determine their affinity for both D1and D2-like DR. The effect of different substituents on the nitrogen atom (methyl or allyl), the dioxygenated function (methoxyl or catechol), the substituent at the β-position of the THIQ skeleton, and the presence or absence of the cyclopentane motif, were studied. We…
Nautilus pompilius Hemocyanin: 9 Å Cryo-EM Structure and Molecular Model Reveal the Subunit Pathway and the Interfaces between the 70 Functional Units
2007
Hemocyanins are giant extracellular oxygen carriers in the hemolymph of many molluscs. Nautilus pompilius (Cephalopoda) hemocyanin is a cylindrical decamer of a 350 kDa polypeptide subunit that in turn is a "pearl-chain" of seven different functional units (FU-a to FU-g). Each globular FU has a binuclear copper centre that reversibly binds one O(2) molecule, and the 70-FU decamer is a highly allosteric protein. Its primary structure and an 11 A cryo-electron microscopy (cryo-EM) structure have recently been determined, and the crystal structures of two related FU types are available in the databanks. However, in molluscan hemocyanin, the precise subunit pathway within the decamer, the inter…
Positional Isomers of Chromophore–Peptide Conjugates Self-Assemble into Different Morphologies
2018
Ordering π-systems into defined supramolecular structures is important for the development of organic functional materials. In recent years, peptides with defined secondary structures and/or self-assembly properties were introduced as powerful tools to order peptide-chromophore conjugates into different morphologies. This work explores whether or not the directionality of peptides can be used to control the self-assembly. The position of the π-system in conjugates between oligoprolines and perylene monoimide (PMI) chromophores was varied by attaching the PMI moiety to the second-to-last residue from the C- and N-termini, respectively. Microscopic and diffraction analysis revealed that the p…
Structure of rat odorant-binding protein OBP1 at 1.6 angstrom resolution
2009
The nasal mucosa is a specialist interfacial region sandwiched between the olfactory system and the gaseous chemical milieu. In mammals and insects, this region is rich in odorant-binding proteins that are thought to aid olfaction by assisting mass transfer of the many different organoleptic compounds that make up the olfactory landscape. However, in mammals at least, our grasp on the exact function of odorant-binding proteins is tentative and better insight into the role of these proteins is warranted, not least because of their apparent significance in the olfactory systems of insects. Here, the crystal structure of rat odorant-binding protein 1 is reported at 1.6 Å resolution. This prote…
Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder.
2014
Background: Mutations in phosphomannomutase2 cause glycosylation disorder, a disease without a cure that will largely benefit from accurate ligand-bound models. Results: We obtained two models of phospomannomutase2 bound to glucose 1,6-bisphosphate and validated them with limited proteolysis. Conclusion: Ligand binding induces a large conformational transition in PMM2. Significance: We produce and validate closed-form models of PMM2 that represent a starting point for rational drug discovery.
Structural Mechanism of SDS-Induced Enzyme Activity of Scorpion Hemocyanin Revealed by Electron Cryomicroscopy
2009
Summary Phenoloxidases (POs) occur in all organisms and are involved in skin and hair coloring in mammals, and initiating melanization in wound healing. Mutation or overexpression of PO can cause albinism or melanoma, respectively. SDS can convert inactive PO and the oxygen carrier hemocyanin (Hc) into enzymatically active PO. Here we present single-particle cryo-EM maps at subnanometer resolution and pseudoatomic models of the 24-oligomeric Hc from scorpion Pandinus imperator in resting and SDS-activated states. Our structural analyses led to a plausible mechanism of Hc enzyme PO activation: upon SDS activation, the intrinsically flexible Hc domain I twists away from domains II and III in …
Mediation of Elicitin Activity on Tobacco Is Assumed by Elicitin-Sterol Complexes
2001
Elicitins secreted by phytopathogenic Phytophthora spp. are proteinaceous elicitors of plant defense mechanisms and were demonstrated to load, carry, and transfer sterols between membranes. The link between elicitor and sterol-loading properties was assessed with the use of site-directed mutagenesis of the 47 and 87 cryptogein tyrosine residues, postulated to be involved in sterol binding. Mutated cryptogeins were tested for their ability to load sterols, bind to plasma membrane putative receptors, and trigger biological responses. For each mutated elicitin, the chemical characterization of the corresponding complexes with stigmasterol (1:1 stoichiometry) demonstrated their full functionali…
Double-Network-Structured Graphene Oxide-Containing Nanogels as Photothermal Agents for the Treatment of Colorectal Cancer.
2017
Here, we reported the production of hyaluronic acid/polyaspartamide-based double-network nanogels for the potential treatment of colorectal carcinoma. Graphene oxide, thanks to the huge aromatic surface area, allows to easily load high amount of irinotecan (33.0% w/w) and confers to the system hyperthermic properties when irradiated with a near-infrared (NIR) laser beam. We demonstrate that the release of antitumor drug is influenced both by the pH of the external medium and the NIR irradiation process. In vitro biological studies, conducted on human colon cancer cells (HCT 116), revealed that nanogels are uptaken by the cancer cells and, in the presence of the antitumor drug, can produce a…