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Crystallography, X-Ray (0):
Recent article
Crystallography, X-Ray
Abstract
We present an application of in silico quantitative structure-activity relationship (QSAR) models to establish a new ligand-based computational approach for generating virtual libraries. The Free-Wilson methodology was applied to extract rules from two data sets containing compounds which were scree...
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PMID: 20981520
PDF is available here.
PDF is available here.
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Abstract
We determined the high-resolution crystal structures of the EV71 3C(pro)/rupintrivir complex, showing that although rupintrivir interacts with EV71 3C(pro) similarly to HRV 3C(pro), the C terminus of the inhibitor cannot accommodate the leaving-group pockets of EV71 3C(pro). Our structures reveal th...
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PMID: 21813612
PDF is available here.
PDF is available here.
Abstract
Two new crystal structures, calcium bis(hydrogen methylphosphonate), Ca(CH(3)PO(3)H)(2), and lithium hydrogen methylphosphonate, Li(CH(3)PO(3)H), have been obtained, and the experimental and theoretical charge densities, as well as their topological properties, are reported. Both compounds display la...
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PMID: 21931209
PDF is available here.
PDF is available here.
Abstract
The combined study of electron-density features in three substituted hydropyrimidines of the Biginelli compound family has been fulfilled. Results of the low-temperature X-ray diffraction measurements and density functional theory (DFT) B3LYP/6-311++G** calculations of these compounds are described....
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PMID: 21931212
PDF is available here.
PDF is available here.
Abstract
We determined the crystal structure of the catalytic domain of MMP-2 in complex with APP-IP. We found that APP-IP in the complex is indeed embedded into the substrate-binding cleft of the catalytic domain in the N to C direction opposite that of substrate. With the crystal structure, it was first cl...
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PMID: 21813640
PDF is available here.
PDF is available here.
Abstract
We answer this question by showing the oxygen equilibrium curves of single crystals of human hemoglobin in the R and R2 state. In this study, we have used a naturally occurring mutant hemoglobin C (β6 Glu→Lys) to stabilize the R and R2 crystals. Additionally, we have refined the x-ray crystal str...
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PMID: 21816820
PDF is available here.
PDF is available here.
Abstract
Abstract
We used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed hea...
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PMID: 21835983
PDF is available here.
PDF is available here.
Abstract
We review evidence that the lipid-exposed surfaces of membrane proteins have generally evolved to maintain correct structure and function in the face of major changes in lipid composition. Such tolerance has allowed evolution to extensively remodel membrane lipid compositions during the emergence of...
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PMID: 21848311
PDF is available here.
PDF is available here.
Biochemistry (Washington) (50)37 2011
Abstract
We benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of...
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PMID: 21842868
PDF is available here.
PDF is available here.
Abstract
Abstract
We show that molecular interactions, e.g., protein-DNA interactions, can be analyzed in a directly analogous manner and with similarly remarkable results. Specifically, mesoscopic molecular interactions act as incoherent sensors that measure the energies of microscopic interactions between atoms. We...
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PMID: 21825146
PDF is available here.
PDF is available here.
Abstract
One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure--function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions....
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PMID: 21823653
PDF is available here.
PDF is available here.
Abstract
We obtained an all-atom model structure for the high-affinity form of MTBD bound to MT by an anisotropic network model, protein-protein docking, and molecular dynamics simulations. We observe that the magnitude of the coiled-coil helix sliding is dramatically reduced near the two prolines that form...
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PMID: 21809817
PDF is available here.
PDF is available here.
Abstract
We conducted kinetic, mutagenic, and structural studies. The kinetic parameters for TomN, and four alanine mutants, P1A, R11A, R39A, and R61A, were determined using 2-hydroxymuconate, the substrate for 4-OT. The TomN-catalyzed reaction using this substrate compares favorably to that of 4-OT. In addi...
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PMID: 21809870
PDF is available here.
PDF is available here.
Abstract
Six new secondary metabolites including two aphidicolin analogues, inflatins A (1) and B (2), and four chlamydosporol derivatives, inflatins C-F (3-6), have been isolated from the crude extract of Tolypocladium inflatum. The structures of 1-6 were determined mainly by NMR experiments, and 4 and 5 wer...
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PMID: 21812410
PDF is available here.
PDF is available here.
Abstract
We have solved the crystal structure of the RNA recognition and leucine-rich repeat motifs of TAP bound to one symmetrical half of the CTE RNA. L-shaped conformations of protein and RNA are involved in a mutual molecular embrace on complex formation. We have monitored the impact of structure-guided...
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PMID: 21822283
PDF is available here.
PDF is available here.
Abstract
We describe crystallographic and biochemical analyses of filament nucleation by VopL. The WH2 element of VopL does not nucleate on its own and requires the VCD for activity. The VCD forms a U-shaped dimer in the crystal, stabilized by a terminal coiled coil. Dimerization of the WH2 motifs contribute...
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PMID: 21873984
PDF is available here.
PDF is available here.
Abstract
The LINE-1 (L1) retrotransposon emerges as a major source of human interindividual genetic variation, with important implications for evolution and disease. L1 retrotransposition is poorly understood at the molecular level, and the mechanistic details and evolutionary origin of the L1-encoded L1ORF1...
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PMID: 21822284
PDF is available here.
PDF is available here.
Abstract
We determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-l...
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PMID: 21822288
PDF is available here.
PDF is available here.
Abstract
We report 3.15-Å crystal structures of this ligase trapped in catalytically viable preligation states, with the 3'-hydroxyl nucleophile positioned for in-line attack on the 5'-triphosphate. Guided by metal- and solvent-mediated interactions, the 5'-triphosphate hooks into the major groove of the ad...
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PMID: 21857665
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition....
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PMID: 21836017
PDF is available here.
PDF is available here.
Abstract
These results identify the MinD-dependent conformational changes in MinE that convert it from a latent to an active form and lead to a model of how MinE persists at the MinD-membrane surface. PAPERFLICK:...
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PMID: 21816275
PDF is available here.
PDF is available here.
Abstract
We report the design and synthesis of two compounds named pitstops that selectively block endocytic ligand association with the clathrin TD as confirmed by X-ray crystallography. Pitstop-induced inhibition of clathrin TD function acutely interferes with receptor-mediated endocytosis, entry of HIV, a...
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PMID: 21816279
PDF is available here.
PDF is available here.
Abstract
We describe the 2.5 Å crystal structure of Gemin2 bound to SmD1/D2/F/E/G pentamer and SMN's Gemin2-binding domain, a key assembly intermediate. Remarkably, through its extended conformation, Gemin2 wraps around the crescent-shaped pentamer, interacting with all five Sm proteins, and gripping its b...
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PMID: 21816274
PDF is available here.
PDF is available here.
Abstract
Stacking interactions of phenanthroline square-planar complexes in crystal structures were studied by analyzing data from the Cambridge Structural Database. In most of the crystal structures, two phenanthroline complexes were oriented "head to tail." Phenanthroline complexes show a w...
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PMID: 21161558
PDF is available here.
PDF is available here.
Abstract
We report three-dimensional structures of individual SipD, SipD in fusion with the needle subunit PrgI, and of SipD:PrgI in complex with the bile salt, deoxycholate. Assembly of the complex involves major conformational changes in both SipD and PrgI. This rearrangement is mediated via a π bulge in...
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PMID: 21829362
PDF is available here.
PDF is available here.
Crystal structure of reovirus attachment protein sigma1 in complex with sialylated oligosaccharides.
Abstract
We determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structu...
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PMID: 21829363
PDF is available here.
PDF is available here.
Abstract
Yeast tRNA-thiouridine modification protein 1 (Tum1p), a crucial component of the Urm1 system, is believed to play important roles in protein urmylation and tRNA-thiouridine modification. Previous studies have demonstrated that the conserved residue Cys259 in the C-terminal rhodanese...
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PMID: 21821903
PDF is available here.
PDF is available here.
Abstract
We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane...
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PMID: 21743456
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)8 2011
Abstract
We summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of t...
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PMID: 20934540
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)11 2011
Abstract
The cytochrome bc(1) complex is a key component in several respiratory pathways. One of the characteristics of the eukaryotic complex is the presence of a small acidic subunit, which is thought to guide the interaction of the complex with its electron acceptor and facilitate electron transfer. Paraco...
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PMID: 21856278
PDF is available here.
PDF is available here.
Abstract
A series of conformationally flexible bicyclic N-arylimides were employed as molecular balances to study the weak aliphatic CH-π interaction between alkyl and arene groups. The formation of intramolecular CH-π interactions in the folded conformers was characterized by X-ray crystal...
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PMID: 21797218
PDF is available here.
PDF is available here.
Abstract
An efficient palladium(0)-catalyzed, Cu(I)-mediated synthetic route to trisubstituted olefins and conjugate dienes has been developed via oxo directing Liebeskind-Srogl cross-coupling reactions of gem-dihaloolefin-type α-oxo ketene dithioacetals with aryl and alkenylboronic acids. T...
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PMID: 21761823
PDF is available here.
PDF is available here.
Abstract
A facile in situ formed primary amine-imine organocatalyst was developed in the asymmetric Michael addition of substituted 4-hydroxycoumarins to cyclic enones. A series of optically active polycyclic coumarin derivatives were obtained in high yields with excellent enantioselectivitie...
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PMID: 21770363
PDF is available here.
PDF is available here.
Abstract
A neutral ferrocene-appended aryl triazole receptor 1 for phosphate anions has been synthesized and characterized by X-ray crystal analysis. Among various anions, 1 shows a distinct electrochemical recognition of phosphate anions by its multiple H-bonding (C-H···O) with a tetrahed...
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PMID: 21774510
PDF is available here.
PDF is available here.
Abstract
Through the design and synthesis of a new chiral phosphepine, the first catalytic asymmetric method for the [3 + 2] cycloaddition of allenes with olefins has been developed that generates cyclopentenes that bear nitrogen-, phosphorus-, oxygen-, and sulfur-substituted quaternary stere...
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PMID: 21766794
PDF is available here.
PDF is available here.
Abstract
We cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H...
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PMID: 21764753
PDF is available here.
PDF is available here.
Abstract
Tetraphenylethylene (TPE)-based glycoconjugates were easily synthesized by copper(I)-catalyzed "click reactions" between propargyl-attached TPE and azido-functionalized sugars. The TPE compound bearing lactosyl moieties (Lac-TPE) was found to be a fluorescence "turn-on" sensor for ch...
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PMID: 21748854
PDF is available here.
PDF is available here.
Abstract
Ion channels in cell membranes are targets for a multitude of ligands including naturally occurring toxins, illicit drugs, and medications used to manage pain and treat cardiovascular, neurological, autoimmune, and other health disorders. In the past decade, the x-ray crystallography...
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PMID: 21961291
PDF is available here.
PDF is available here.
Abstract
A unique approach to asymmetric synthesis of various optically pure multisubstituted 2,3-dihydropyrroles catalyzed by a novel rosin-derived tertiary amine-thiourea via a tandem Michael/cyclization sequence with high yield (up to 97%) and good to excellent enantioselectivities (up to...
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PMID: 21732616
PDF is available here.
PDF is available here.
Abstract
Mononuclear nonheme iron(IV)-oxo complexes with two different topologies, cis-α-[FeIV(O)(BQCN)]2+ and cis-β-[FeIV(O)(BQCN)]2+, were synthesized and characterized with various spectroscopic methods. The effect of ligand topology on the reactivities of nonheme iron(IV)-oxo complexes...
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PMID: 21736350
PDF is available here.
PDF is available here.
Abstract
We determined the crystal structures of the P domain protein of the first Lewis-binding norovirus (VA207, GII.9) that has a distinct binding property from those of Norwalk virus and VA387. Co-crystallization of the VA207 P dimer with Le(y) or sialyl Le(x) tetrasaccharides showed that VA207 interacts...
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PMID: 21811409
PDF is available here.
PDF is available here.
Abstract
Schicagenins A-C (1-3), three unprecedented nortriterpenoids characterized with a tetracyclic oxa-cage motif and C(9) side chain, were discovered from the leaves and stems of Schisandra chinensis. Their structures were determined on the basis of extensive spectroscopic analysis, and...
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PMID: 21714531
PDF is available here.
PDF is available here.
Abstract
Abstract
A tandem transformation that involves the formation of three bonds and two heterocyclic rings in a one-pot fashion through amino-alkylation of an ionic-liquid-immobilized diamine with keto acids followed by successive double intramolecular cyclizations to afford a tricyclic framework...
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PMID: 21721136
PDF is available here.
PDF is available here.
Abstract
Through the use of an amino acid based imidazole catalyst, a regiodivergent silylation of chiral diols in cases where there is not a significant steric and electronic difference between the regioisotopic hydroxyl groups has been developed. This transformation allows for the conversio...
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PMID: 21711005
PDF is available here.
PDF is available here.
Abstract
A series of naphthalenyl-substituted arenediynes were prepared to examine photochemical reactivity. For naphthalen-1-ylethynyl arenediyne, 350 nm photolysis resulted in a tandem [2 + 2] photocycloaddition to afford cyclobutene adducts. For naphthalen-2-ylethynyl derivatives, electron...
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PMID: 21667926
PDF is available here.
PDF is available here.
Abstract
A reliable, facile, high overall yielding and diastereoselective synthesis of ketoheptoses was developed and applied for preparation of the two most diabetogenic ketoheptoses as well as in a modified version for the synthesis of kamusol.
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PMID: 21671612
PDF is available here.
PDF is available here.
Abstract
We describe riboneogenesis, a thermodynamically driven pathway that converts glycolytic intermediates into ribose-5-phosphate without production of NADPH. Riboneogenesis begins with synthesis, by the combined action of transketolase and aldolase, of the seven-carbon bisphosphorylated sugar sedoheptu...
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PMID: 21663798
PDF is available here.
PDF is available here.
Abstract
Abstract
We show that FrsA converts pyruvate to acetaldehyde and carbon dioxide in a cofactor-independent manner and that its pyruvate decarboxylation activity is enhanced by the dephosphorylated form of IIA(Glc) (d-IIA(Glc)). Crystal structures of FrsA and its complex with d-IIA(Glc) revealed residues requi...
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PMID: 21623357
PDF is available here.
PDF is available here.
Abstract
Magnesium dimers play important roles in inorganic and organometallic chemistry. This study evaluates the inherent bridging ability of a range of different ligands in magnesium dimers. In the first part, the Cambridge Structural Database is interrogated to establish the frequency of...
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PMID: 20820825
PDF is available here.
PDF is available here.
Abstract
We report the isolation of N-aryl peptoid oligomers that adopt chiral folds, despite the absence of chiral centers. Peptoid monomers incorporating ortho-substituted N-aryl side chains are identified that exhibit axial chirality. We observe significant energy barriers to rotation about the stereogeni...
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PMID: 21634437
PDF is available here.
PDF is available here.
Abstract
We describe structural and functional analyses of the Thermus thermophilus CRISPR Cse3 endonuclease. High-resolution X-ray structures of Cse3 bound to repeat RNAs model both the pre- and post-cleavage complexes associated with processing the pre-crRNA. These structures establish the molecular basis...
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PMID: 21572444
PDF is available here.
PDF is available here.
Abstract
We show that Cse3 type CRISPR-specific endoRNases bind a hairpin structure and residues downstream of the cleavage site within the repetitive segment of cognate CRISPR RNA. Cocrystal structures of Cse3-RNA complexes reveal an RNA-induced conformational change in the enzyme active site that aligns th...
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PMID: 21572442
PDF is available here.
PDF is available here.
Abstract
Seventeen new lathyrane diterpenoids (1-17) and two known analogues have been isolated from an ethanolic extract of Euphorbia micractina roots. Their structures including absolute configurations were determined by spectroscopic data interpretation and single-crystal X-ray crystallography. Compound 10...
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PMID: 21534583
PDF is available here.
PDF is available here.
Abstract
Three new limonoids, chisomicines A-C (1-3), have been isolated from the bark of Chisocheton ceramicus. Their structures were determined by 2D NMR, CD spectroscopic methods, and X-ray analysis. Chisomicine A (1) exhibited NO production inhibitory activity in J774.1 cells stimulated by LPS dose-depend...
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PMID: 21428417
PDF is available here.
PDF is available here.
Abstract
Eight secondary metabolites, including three new azaphilones (chermesinones A-C, 1-3), three new p-terphenyls (6'-O-desmethylterphenyllin, 4; 3-hydroxy-6'-O-desmethylterphenyllin, 5; 3''-deoxy-6'-O-desmethylcandidusin B, 7), and two known p-terphenyls (6, 8), were isolated from the culture of the man...
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PMID: 21510637
PDF is available here.
PDF is available here.
Abstract
Three new dimeric prenylated C6-C3 compounds, namely, illicidiones A (1), B (2), and C (3), were isolated from the stem bark of Illicium oligandrum. The structure and absolute configuration of these compounds were determined by extensive spectroscopic and chemical analyses, including NMR, modified Mo...
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PMID: 21524101
PDF is available here.
PDF is available here.