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Models, Molecular (0):
Recent article
Models, Molecular
Abstract
We summarize our current understanding of PD-1 and its ligands ranging from discovery to clinical significance....
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PMID: 21061197
PDF is available here.
PDF is available here.
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Abstract
We therefore developed an efficient bacterial expression system to produce a panel of π-TRTX-Pc1a mutants for probing structure-activity relationships as well as isotopically labeled toxin for determination of its solution structure and dynamics. We demonstrate that the toxin pharmacophore resides...
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PMID: 21825095
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)11 2011
Abstract
We have charted seven decades of research beginning with the discovery of CcP and leading to the latest functional and structural work, which has clarified the mechanism of the intermolecular ET, addressed the putative functional role of a low-affinity binding site, and identified lowly-populated in...
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PMID: 21820401
PDF is available here.
PDF is available here.
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.
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
Saccharopine dehydrogenase catalyzes the NAD-dependent oxidative deamination of saccharopine to l-lysine and α-ketoglutarate. Lysine 99 is within hydrogen-bond distance to the α-carboxylate of the lysine substrate and D319 is in the vicinity of the carboxamide side chain of NADH. Both are conserved...
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PMID: 21819960
PDF is available here.
PDF is available here.
FEBS Journal (278)19 2011
Abstract
Chromatin remodelling is the ATP-dependent change in nucleosome organisation driven by Snf2 family ATPases. The biochemistry of this process depends on the behaviours of ATP-dependent motor proteins and their dynamic nucleosome substrates, which brings significant technical and conce...
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PMID: 21810178
PDF is available here.
PDF is available here.
Abstract
We have thus performed experiments of NO uptake by erythrocytes and microparticles derived from erythrocytes and conducted simulations of these data as well as that of others. We have included extracellular diffusion (that is, diffusion of the NO to the membrane) and membrane permeability, in additi...
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PMID: 21808057
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 report that, although glycosome-resident enzyme T. brucei hexokinase 1 (TbHK1) protein levels are maintained during pexophagy, acidification inactivates the activity. Glycerol 3-phosphate, which is produced in vivo by a glycosome-resident glycerol kinase, mitigated acid inactivation of lysate-der...
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PMID: 21813651
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
We show that labile S4 complexes rearrange into stable complexes within a few minutes at 42 °C, with longer coincubation leading to an increased population of stable complexes. In contrast, prefolding the rRNA has a smaller effect on stable S4 binding. Experiments with minimal rRNA fragments show...
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PMID: 21821049
PDF is available here.
PDF is available here.
Abstract
We show that C0 and C1 can each bind to the same two distinctly different positions on F-actin. One position aligns well with the previously reported binding site that clashes with the binding of myosin to actin, but would force tropomyosin into an "on" position that exposes myosin binding sites alo...
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PMID: 21821050
PDF is available here.
PDF is available here.
Abstract
Two series of 2-phenyl-4(3H) quinazolinone derivatives have been synthesized. Most of the tested quinazolinone derivatives showed considerable potent anti-inflammatory and analgesic activity of superior GIT safety profile in experimental rats in comparing to indomethacin as reference drug. Compounds...
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PMID: 21928711
PDF is available here.
PDF is available here.
Abstract
We use cryo-electron microscopy to determine the subnanometre structures of Cascade before and after binding to a target sequence. These structures reveal a sea-horse-shaped architecture in which the crRNA is displayed along a helical arrangement of protein subunits that protect the crRNA from degra...
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PMID: 21938068
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
9-Substituted 6,6-dimethyl-11-oxo-6,11-dihydro-5H-benzo[b]carbazoles were discovered as highly selective and potent anaplastic lymphoma kinase (ALK) inhibitors by structure-based drug design. The high target selectivity was achieved by introducing a substituent close to the E(0) regi...
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PMID: 21823617
PDF is available here.
PDF is available here.
Molecular Cell (43)6 2011
Abstract
RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory...
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PMID: 21925380
PDF is available here.
PDF is available here.
Abstract
We study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere, by molecular dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3), derived from quantum mechanical data at the MP2/aug-cc-pVTZ(-hp) level augmented by CCSD(T). QMPFF3 cal...
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PMID: 21844369
PDF is available here.
PDF is available here.
Abstract
We summarize the structure-activity relationship obtained from the reported Tdp1 inhibitors. Better understanding of Top1cc repair in vivo coupled with detailed structural studies on Tdp1-inhibitor interaction will be crucial in guiding the rational design of Tdp1 inhibitors....
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PMID: 21843105
PDF is available here.
PDF is available here.
Abstract
We determined the structure of Phytophthora capsici AVR3a4, a close homolog of P. infestans AVR3a. Our structural and functional analyses reveal that the effector domain of AVR3a contains a conserved, positively charged patch and that this region, rather than the RXLR domain, is required for binding...
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PMID: 21821794
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 found that RNF4 bound ubiquitin-charged UbcH5a tightly but free UbcH5a weakly. To provide insight into the mechanism of RING-mediated ubiquitylation, we docked the UbcH5~ubiquitin thioester onto the RNF4 RING structure. This revealed that with E2 bound to one monomer of RNF4, the thioester-linked...
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PMID: 21857666
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.
Biochimica et Biophysica Acta (1812)9 2011
Abstract
We determined if wild type (WT) lens ultrastructure and fiber cell adhesion are different in AQP0(-/-), and TgAQP1(+/+)/AQP0(-/-) mice that transgenically express AQP1 (TgAQP1) in fiber cells without AQP0 (AQP0(-/-)). In WT, lenses were transparent with 'Y' sutures. Fibers contained opposite end cur...
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PMID: 21511033
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron...
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PMID: 21756874
PDF is available here.
PDF is available here.
Abstract
We have undertaken an extensive structural analysis of proteins containing CUG-encoded residues and solved the crystal structures of the two natural isoforms of Candida albicans seryl-tRNA synthetase. We show that codon reassignment resulted in a nonrandom genome-wide CUG redistribution tailored to...
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PMID: 21825144
PDF is available here.
PDF is available here.
Abstract
We recently introduced the enhanced aromatic sequon as a family of portable structural motifs that are stabilized upon glycosylation in specific reverse turn contexts: a five-residue type I β-turn harboring a G1 β-bulge (using a Phe-Yyy-Asn-Xxx-Thr sequon) and a type II β-turn within a six-residu...
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PMID: 21825145
PDF is available here.
PDF is available here.
Abstract
We use Φ-value and double mutant analyses to probe the folding transition state of the membrane protein bacteriorhodopsin. We focus on the final C-terminal helix, helix G, of this seven transmembrane helical protein. Φ-values could be derived for 12 amino acid residues in helix G, most of which ha...
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PMID: 21831834
PDF is available here.
PDF is available here.
Abstract
We show that enzymes can also be extremely efficient electrocatalysts (catalysts of redox reactions at electrodes). Despite being large and electronically insulating through most of their volume, some enzymes, when attached to an electrode, catalyze electrochemical reactions that are otherwise extre...
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PMID: 21844379
PDF is available here.
PDF is available here.
Abstract
We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dy...
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PMID: 21831831
PDF is available here.
PDF is available here.
Abstract
We show here that DNA binding to the DNA-gate of gyrase and wrapping of DNA around the C-terminal domains of GyrA induces a narrowing of the N-gate. This half-closed state prepares capture of a T-segment in the upper cavity of gyrase. Subsequent N-gate closure upon binding of ATP then poises the rea...
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PMID: 21817063
PDF is available here.
PDF is available here.
Abstract
The static and dynamic features of magnetization have been investigated in terms of dc magnetization, ac susceptibility, and memory effects on single-layered perovskite La(0.7)Sr(1.3)CoO(4). The results indicate that short-range ferromagnetic clusters coexist with the glassy magnetic state, i.e., a c...
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PMID: 21811008
PDF is available here.
PDF is available here.
Abstract
Holes bound to acceptor defects in oxide materials usually need comparatively high energies, of the order of 0.5-1.0 eV, to be ionized thermally to the valence band maximum. It is discussed that this has to be attributed to the stabilization of such holes by mainly short range interactions with the s...
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PMID: 21813948
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
Our analysis demonstrated that dispersion was the largest correction term that influenced the magnitude of BDE. Previous studies have shown that B3LYP significantly underestimates BDE, whereas BP86 gives BDE values that are fairly close to the experimental values (36-37 kcal/mol). The same trend in...
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PMID: 21806069
PDF is available here.
PDF is available here.
Abstract
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
We created two mutant constructs with extended neck-linkers and measured their properties using single-molecule optical trapping and ensemble fluorescence techniques. Owing to a reduction in the inter-head tension, the constructs access an otherwise rarely populated conformational state in which bot...
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PMID: 21841789
PDF is available here.
PDF is available here.
Abstract
T cell immunoglobulin mucin-(TIM)-3 was first identified as a molecule specifically expressed on IFN-γ-secreting CD4(+) T helper 1 (Th1) and CD8(+) T cytotoxic (Tc1) cells in both mice and humans. TIM-3 acts as a negative regulator of Th1/Tc1 cell function by triggering cell death upon interaction w...
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PMID: 20700701
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
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
Abstract
We report here the rational synthesis of a [Mn(3)CaO(4)](6+) cubane that structurally models the trimanganese-calcium-cubane subsite of the OEC. Structural and electrochemical comparison between Mn(3)CaO(4) and a related Mn(4)O(4) cubane alongside characterization of an intermediate calcium-manganes...
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PMID: 21817047
PDF is available here.
PDF is available here.
Molecular Cell (43)3 2011
Abstract
We have biochemically reconstituted two distinct populations of nucleosomes containing Saccharomyces cerevisiae CenH3 (Cse4). Reconstitution of octameric nucleosomes containing histones Cse4/H4/H2A/H2B is robust on noncentromere DNA, but inefficient on AT-rich centromere DNA. However, nonhistone Scm...
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PMID: 21816344
PDF is available here.
PDF is available here.
Molecular Cell (43)3 2011
Abstract
We show that CUL4B, but not its paralog, CUL4A, targets WDR5, a core subunit of histone H3 lysine 4 (H3K4) methyltransferase complexes, for ubiquitylation and degradation in the nucleus. Knocking down CUL4B increases WDR5 and trimethylated H3K4 (H3K4me3) on the neuronal gene promoters and induces th...
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PMID: 21816345
PDF is available here.
PDF is available here.
Abstract
CCL5 (RANTES) is a proinflammatory chemokine known to activate leukocytes through its receptor, CCR5. Although the monomeric form of CCL5 is sufficient to cause cell migration in vitro, CCL5's propensity for aggregation is essential for migration in vivo, T cell activation and apo...
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PMID: 21827949
PDF is available here.
PDF is available here.
Abstract
We identified indole derivatives that have anti-HBV activities. In this study, we optimize a series of 5-hydroxy-1H-indole-3-carboxylates, which exhibited potent anti-HBV activities, using three-dimensional quantitative structure-activity relationship (3D QSAR) studies with comparative molecular fie...
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PMID: 21053034
PDF is available here.
PDF is available here.
Abstract
We used the docking method to explore possible binding modes of an entry inhibitor (maraviroc) and non-nucleoside reverse transcriptase inhibitors (delavirdine, efavirenz and etravirine) to cytochrome P450 3A4 (CYP3A4). In addition, docking results were compared with the binding conformations of HIV...
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PMID: 21080015
PDF is available here.
PDF is available here.
Abstract
We evaluated four docking tools-MOE2009, Glide 5.5, QXP-Flo+0802, and Autodock 4.0-for their ability to simulate complexes between these enzymes and RNA oligomers. To validate our results, we analyzed the docking results with respect to the known key interactions between the protein and the nucleoti...
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PMID: 21120556
PDF is available here.
PDF is available here.
Abstract
The partial modification of carboxylic acid terminated polyamidoamine (PAMAM) dendrimers with glucosamine has been reported to give dendrimer glucosamine conjugates novel immuno-modulatory and anti-angiogenic properties. Experimental analysis of these glycosylated dendrimers showed t...
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PMID: 21161557
PDF is available here.
PDF is available here.
Abstract
Seventy-five 1,5,6,7-tetrahydro-pyrrolo[3,2-C]pyridinone derivatives displaying potent activities against Cdc7 kinase were selected to establish 3D-QSAR models using CoMFA and CoMSIA methods. Internal and external cross-validation techniques were investigated as well as some measures...
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PMID: 21416222
PDF is available here.
PDF is available here.
Abstract
We identified AKR1C2 mutations with sex-limited recessive inheritance in four 46,XY individuals with disordered sexual development (DSD). Analysis of the inheritance of microsatellite markers excluded other candidate loci. Affected individuals had moderate to severe undervirilization at birth; when...
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PMID: 21802064
PDF is available here.
PDF is available here.
Ukrainskij biokhimicheskij zhurnal/Ukrayins'kij biokhimichnij zhurnal/Ukrainian biochemical journal (82)6 2011
Abstract
It has been shown that calix[4]arene C-99 inhibited myosin subfragment-1 ATPase of myometrium. This inhibition is noncompetitive as to ATP and Mg2+. At the same time, this compound reduces the seeming enzymatic hydrolysis maximum rate of nucleoside triphosphate with respect to ATP and Mg2+. With the...
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PMID: 21805859
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.
Abstract
Traditionally, G protein-coupled receptors (GPCRs) were thought to function as monomeric units activating linear signaling pathways to reach a single functional response. However, it is now recognized that GPCRs can exist as higher order structures, such as homomers or heteromers. Th...
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PMID: 21764024
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1812)8 2011
Abstract
We review key molecular aspects of transactivation by NRs with special emphasis on the recent advances in the molecular mechanisms responsible for receptor- and gene-specific transcriptional activation. This article is part of a Special Issue entitled: Translating nuclear receptors from health to di...
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PMID: 21193032
PDF is available here.
PDF is available here.