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Bound Ligands (bound + ligand)
Selected AbstractsThe atomic resolution structure of human aldose reductase reveals that rearrangement of a bound ligand allows the opening of the safety-belt loopACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2007Marianna Biadene The crystal structure of human aldose reductase in complex with citrate has been determined to a resolution of 0.82,Å. The difference electron density for H atoms unequivocally shows that the cofactor is in the oxidized state corresponding to the situation after the catalytic event has occurred. A citrate molecule bound to the active site has been modelled in two different conformations. These two conformations correlate with a fully closed and a partially open conformation of the so-called safety-belt loop (Gly213,Ser226). The open conformation is observed for the first time with the cofactor bound to the protein and may be related to the initial phase of the opening of the safety belt. The structure suggests that after the catalytic event, a rearrangement of a bound ligand can trigger the opening of the safety-belt loop, thus initiating the release of the oxidized cofactor. [source] High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5,AMPACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001Pascal Retailleau Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS,adenylate product (TAM) complex to a resolution limit of 1.7,Å. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS combinations with native data. Hendrickson,Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9,Å structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25,Å and from the native model by 0.38,Å, but all have r.m.s. deviations of ,1.0,Å from the 2.9,Å model. Difference Fourier calculations between amplitudes from the 300,K experiment and the new amplitudes at 100,K using 1.7,Å model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria. [source] Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complexACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Andrey M. Grishin The Escherichia coli paa operon encodes enzymes of the phenylacetic acid-utilization pathway that metabolizes phenylacetate in the form of a coenzyme A (CoA) derivative. The phenylacetyl-coenzyme A oxygenase complex, which has been postulated to contain five components designated PaaABCDE, catalyzes ring hydroxylation of phenylacetyl-CoA. The PaaAC subcomplex shows low sequence similarity to other bacterial multicomponent monooxygenases (BMMs) and forms a separate branch on the phylogenetic tree. PaaAC, which catalyzes the hydroxylation reaction, was purified and crystallized in the absence of a bound ligand as well as in complexes with CoA, 3-hydroxybutyryl-CoA, benzoyl-CoA and the true substrate phenylacetyl-CoA. Crystals of the ligand-free enzyme belonged to space group P212121 and diffracted to 2.65,Å resolution, whereas complexes with CoA and its derivatives crystallized in space group P41212 and diffracted to ,2.0,Å resolution. PaaAC represents the first crystallized BMM hydroxylase that utilizes a CoA-linked substrate. [source] Variability in the Structures of Luminescent [2-(Aminomethyl)pyridine]silver(I) Complexes: Effect of Ligand Ratio, Anion, Hydrogen Bonding, and ,-StackingEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2005Rodney P. Feazell Abstract The reaction of 2-(aminomethyl)pyridine (2-amp) with silver(I) salts of triflate (OTf,), trifluoroacetate (tfa,), and tetrafluoroborate (BF4,) produce monomeric, dimeric, bridged, and polymeric structural motifs. The structural characteristics are dependent upon the ratio of ligand/metal in the structure as well as the ability of the anion to coordinate to the metal centers and form hydrogen bonds to the bound ligands. The silver coordination environment takes on several geometries including near linear (6), trigonal (4), tetrahedral (1), and both trigonal-bipyramidal and square-based pyramidal in a single structure (2). Structures 2, 3, and 5 also display short Ag,Ag contacts ranging from 2.8958(3) to 3.0305(4) Å. The species with metal,metal interactions, which are connectively very similar to their metal-isolated counterparts of 1, 4, and 6, are held together only by weak ,-stacking interactions or hydrogen bonds to their respective anions. Low-temperature luminescence spectra were collected for all compounds and are compared. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Monitoring of the internalization of neuropeptide Y on neuroblastoma cell line SK-N-MCFEBS JOURNAL, Issue 17 2000Marlies Fabry Neuropeptide Y (NPY) is an important neuromodulator in the central and peripheral nervous system. The peptide acts through different NPY receptor subtypes (Y1,Y5, y6) that belong to the family of G protein-coupled receptors. In general, cellular responses to prolonged exposure to agonists of G protein-coupled receptors are attenuated, often through internalization of the receptors and their bound ligands. In this study, a fluorescent labeled NPY derivative was synthesized and characterized to investigate the internalization of NPY in the human neuroblastoma cell line SK-N-MC. Internalization was proven by binding experiments and subsequent acidic washing as well as by direct visualization by means of confocal laser scanning microscopy. Approximately 20,30% of the fluorescent labeled NPY and a tritium-marked NPY were resistant to acid removal of cell surface-bound ligands indicating internalization. Extracellular fluorescent labeled NPY was found to be distributed heterogeneously in a clustered pattern, which suggests that the ligand-receptor complex is collected in pits and caveolae followed by endocytosis. [source] Glyconanomaterials: Synthesis, Characterization, and Ligand PresentationADVANCED MATERIALS, Issue 17 2010Xin Wang Abstract Glyconanomaterials, nanomaterials carrying surface-tethered carbohydrate ligands, have emerged and demonstrated increasing potential in biomedical imaging, therapeutics, and diagnostics. These materials combine the unique properties of nanometer-scale objects with the ability to present multiple copies of carbohydrate ligands, greatly enhancing the weak affinity of individual ligands to their binding partners. Critical to the performance of glyconanomaterials is the proper display of carbohydrate ligands, taking into consideration of the coupling chemistry, the type and length of the spacer linkage, and the ligand density. This article provides an overview of the coupling chemistry for attaching carbohydrate ligands to nanomaterials, and discusses the need for thorough characterization of glyconanomaterials, especially quantitative analyses of the ligand density and binding affinities. Using glyconanoparticles synthesized by a versatile photocoupling chemistry, methods for determining the ligand density by colorimetry and the binding affinity with lectins by a fluorescence competition assay are determined. The results show that the multivalent presentation of carbohydrate ligands significantly enhances the binding affinity by several orders of magnitude in comparison to the free ligands in solution. The effect is sizeable even at low surface ligand density. The type and length of the spacer linkage also affect the binding affinity, with the longer linkage promoting the association of bound ligands with the corresponding lectins. [source] Connectivity and binding-site recognition: Applications relevant to drug designJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2010Christopher J. R. Illingworth Abstract Here, we describe a family of methods based on residue,residue connectivity for characterizing binding sites and apply variants of the method to various types of protein,ligand complexes including proteases, allosteric-binding sites, correctly and incorrectly docked poses, and inhibitors of protein,protein interactions. Residues within ligand-binding sites have about 25% more contact neighbors than surface residues in general; high-connectivity residues are found in contact with the ligand in 84% of all complexes studied. In addition, a k-means algorithm was developed that may be useful for identifying potential binding sites with no obvious geometric or connectivity features. The analysis was primarily carried out on 61 protein,ligand structures from the MEROPS protease database, 250 protein,ligand structures from the PDBSelect (25%), and 30 protein,protein complexes. Analysis of four proteases with crystal structures for multiple bound ligands has shown that residues with high connectivity tend to have less variable side-chain conformation. The relevance to drug design is discussed in terms of identifying allosteric-binding sites, distinguishing between alternative docked poses and designing protein interface inhibitors. Taken together, this data indicate that residue,residue connectivity is highly relevant to medicinal chemistry. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibilityJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2009Garrett M. Morris Abstract We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Three-Dimensional Protein,Ligand Interaction Scaling of Two-Dimensional FingerprintsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2009Lu Tan We introduce a computational scaling methodology that utilizes protein,ligand interaction information extracted from complex crystal structures to enrich similarity searching using structural fingerprints with compound class-specific information. Scaling factors are derived to emphasize fingerprint bit positions that result from interacting fragments of bound ligands and correspond to frequently occurring structural features. Through interaction-based scaling, this information is transferred to standard fingerprints of multiple reference compounds. In systematic search calculations, fingerprints scaled on the basis of three-dimensional information are found to produce higher recall rates of active compounds than alternative types of scaled and non-scaled fingerprints. [source] | ||||||||||