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Molecular Conformation (4):
Recent article
Molecular Conformation
Abstract
A structure-activity relationship (QSAR) analysis of 19 thiazole derivatives with H1-antihistamine activity was carried out. The semi-empirical method AMI was employed to calculate a set of physicochemical parameters for investigated compounds. The principal component analysis (PCA), discriminant fun...
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PMID: 21928712
PDF is available here.
PDF is available here.
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Abstract
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
Our calculations suggest that, in the most kinetically favorable pathway for the titled hydrolysis, three water molecules are directly participating in the hydrogen transfer via an eight-membered cyclic transition state, while the other four water molecules catalyze the hydrolysis of HN = C =...
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PMID: 21161555
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.
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.
Ukrainskij biokhimicheskij zhurnal/Ukrayins'kij biokhimichnij zhurnal/Ukrainian biochemical journal (82)6 2011
Abstract
The conformational analysis of the DNA structural unit--the nucleotide with thymine base and electroneutral phosphate group at 5'-position-has been carried out with the applied quantum mechanics methods at the MP2/6-311++G(d,p) // B3LYP/6-31G(d,p) theory level. As many as 660 conformations with relat...
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PMID: 21805865
PDF is available here.
PDF is available here.
Abstract
We report the synthesis and optical characterization of a series of aryl- and diaryl-2(1H)-pyrimidones. The electronic transitions of these chromophores are modulated by the extent of conjugation between the pendant phenyl ring and the pyrimidone core as well as the presence of electron-donating aux...
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PMID: 21790121
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
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
A new method was developed to assign the absolute configuration of molecules using kinetic resolution catalysts. Secondary alcohols were acylated in the presence of Birman's S-HBTM and R-HBTM catalysts, and the fast-reacting catalyst was identified by NMR analysis of the reaction mix...
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PMID: 21776975
PDF is available here.
PDF is available here.
Abstract
Glycosyltransferases are ubiquitous in nature. They catalyze a glycosidic bond formation between sugar donors and sugar or nonsugar acceptors to produce oligo/polysaccharides, glycoproteins, glycolipids, glycosylated natural products, and other sugar-containing entities. However, a t...
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PMID: 21766819
PDF is available here.
PDF is available here.
Abstract
Conformationally restricted naphthalene peri-diselenides function as glutathione peroxidase mimetics with superior catalytic activity to that displayed by typical acyclic diaryl diselenides. Their activity was increased by electron-donating methoxy substituents, while a further 100-f...
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PMID: 21739953
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
We report a new technique for determining the rate of copper catalyzed activation (kact) using cyclic voltammetry coupled with electrochemical simulation. This method is applied to measuring kact for one of the most active catalysts [CuI(Me6tren)]+ (Me6tren = N,N,N-tris-(2-dimethylaminoethyl)amine)...
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PMID: 21744867
PDF is available here.
PDF is available here.
Abstract
We report a new strategy in which the fluorophore is generated in situ through an intramolecular tetrazole-alkene cycloaddition reaction ("photoclick chemistry"). By conjugating a specific microtubule-binding taxoid core to the tetrazole/alkene pre-fluorophores, robust photoactivatable fluorescent p...
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PMID: 21736329
PDF is available here.
PDF is available here.
Abstract
We report a solid-state photochemical rearrangement reaction by which aromatic N-chloroamides exposed to UV light or sunlight are rapidly and efficiently converted to chloroaromatic amides. The course, the intermediate (nascent chlorine vs dichlorine) and the outcome of the reaction depend on the exc...
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PMID: 21612242
PDF is available here.
PDF is available here.
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
We have developed a new class of plasmonic vesicular nanostructures assembled from amphiphilic gold na-nocrystals with mixed polymer brushes coatings. One major finding is that the integration of gold nanocrystals (nanoparticles and nanorods) with two types of chemically distinct polymer grafts, whi...
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PMID: 21699155
PDF is available here.
PDF is available here.
Abstract
A divergent synthesis of (-)-4-epi-shikimic acid was developed. This route features a one-pot zinc-mediated reductive ring opening of an arabinofuranose followed by a Barbier reaction and culminates in a ring-closing metathesis. Functionalization of (-)-4-epi-shikimic acid via conjug...
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PMID: 21711006
PDF is available here.
PDF is available here.
Abstract
The synthesis of a cavitand featuring thiourea hydrogen bonding sites and its dimerization in the presence of suitable guests are reported. Dimerization creates wider capsule host than the corre-sponding urea or imide structures and longer alkanes can be accommodated. Specifically, n...
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PMID: 21692514
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 demonstrate that the hexagonal prisms can be functionalized without disrupting the prismatic cores, enabling the incorporation of new functionalities under mild conditions....
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PMID: 21671637
PDF is available here.
PDF is available here.
Abstract
ABSTRACT. The biosynthesis of the fungal metabolite tenellin from Beauveria bassiana CBS110.25 was investigated in the presence of the epigenetic modifiers 5-azacytidine and suberoyl bis-hydroxamic acid and under conditions where individual genes from the tenellin biosynthetic gene c...
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PMID: 21675761
PDF is available here.
PDF is available here.
Abstract
The metal-organic host material [{CoIII2(bpbp)(O2)}2bdc](PF6)4 (1·2O2; bpbp- = 2,6-bis(N,N-bis(2-pyridylmethyl)aminomethyl)-4-tert-butylphenolato; bdc2- = 1,4-benz...
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PMID: 21639095
PDF is available here.
PDF is available here.
Abstract
The microwave spectrum of 1-vinylimidazole has been investigated in the 21-80 GHz spectral region. The spectra of two conformers have been assigned. One of these forms is planar, while the other is nonplanar with the imidazole ring and the vinyl group forming an angle of 15(4)° from coplanarity. The...
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PMID: 21648385
PDF is available here.
PDF is available here.
Biophysics (40)1 2011
Abstract
We provide a brief historical account of how the overriding perception regarding aspects of nucleosome structure has changed over the past thirty years. We discuss recent technical advances regarding nucleosome structure and its physical characterization and review the evidence for alternative nucle...
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PMID: 21332355
PDF is available here.
PDF is available here.
Abstract
We show that the single-shot approach, although experimentally more challenging, is always superior in this respect. In fact, for 3D structure determination a constraint counting argument shows that the cross-correlation scheme suffers from data deficiency....
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PMID: 21093151
PDF is available here.
PDF is available here.
Abstract
We know. Therefore, we decide to give a review to comprehensively summarize research progress on it. This review highlights the diverse topologies for RNA quadruplex structure and its effect factors; outlines the current knowledge of RNA quadruplex's physiological functions in biological systems, es...
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PMID: 21749296
PDF is available here.
PDF is available here.
Abstract
The mechanism of phenylselenoetherification of pent-4-en-1-ol using some bases (pyridine, triethylamine, quinoline, 2,2'-bipyridine) as catalyst was examined through studies of kinetics of the cyclization, by UV-VIS spectrophotometry. It was demonstrated that the intramolecular cycli...
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PMID: 20711793
PDF is available here.
PDF is available here.
Abstract
This study analyzes the aromatic nature of cyanuric acid (hexahydrotriazine) and some of its derivatives, in terms of aromatic stabilization energy (ASE) and electronic behavior. The simplest molecule (C(3)N(3)O(3)H(3)) is the most aromatic item out of the entire set, but some of the...
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PMID: 20820829
PDF is available here.
PDF is available here.
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis of large, flexible molecules, such as the dopamine reuptake inhibitor GBR 12909 (1), is complicated by the fact that they can take on a wide range of closely-related conformations. The first step in the...
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PMID: 20839021
PDF is available here.
PDF is available here.
Abstract
We have characterized the binding properties between sialic acid, methyl 3'sialyllactoside, methyl 6'sialyllactoside and the H5N1 influenza virus neuraminidase using molecular docking and molecular dynamics simulations. Obtained molecular dynamics trajectories were analyzed in terms of ligand confor...
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PMID: 20853123
PDF is available here.
PDF is available here.
Abstract
A new charge distribution is proposed for the amino acids where each atom is associated with two point charges while each bond center is associated with one point charge. Centroids of charges arising due to atomic orbital hybridization called hybridization-displaced charges (HDC) and...
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PMID: 20853124
PDF is available here.
PDF is available here.
Abstract
We theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-...
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PMID: 20853125
PDF is available here.
PDF is available here.
Abstract
Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured (49)Ti NMR chemical shifts of anatase. Significant binding of arginine through el...
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PMID: 20853182
PDF is available here.
PDF is available here.
Abstract
We combined experimental data from a MB-SCL of bicyclic guanidines screened against the κ-opioid receptor and molecular similarity methods. The activity data and similarity analyses were integrated in a biometric analysis-similarity map. Such a map allows the molecules to be categorized as actives,...
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PMID: 20853183
PDF is available here.
PDF is available here.
Abstract
Phytochemical studies on the branches and leaves of Lyonia ovalifolia yielded a new grayanane diterpenoid, lyonin A (1), together with two known compounds, secorhodomollolides A and D (2 and 3, resp.). The structure of 1 was elucidated by combination of 1D- and 2D-NMR, and MS analyse...
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PMID: 21674790
PDF is available here.
PDF is available here.
Abstract
I is derived from a common substructure procedure which includes steric and electrostatic fields with the cross-validated q(2) and the non-cross-validated r(2) value of 0.86 and 0.97, respectively. The same for the CoMFA model II which is derived based on the bioactive conformation are 0.19 and 0.77...
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PMID: 21689378
PDF is available here.
PDF is available here.
Abstract
We show the first direct and quantitative experiments demonstrating the induction of phosphatidylserine asymmetry in a membrane by electrostatic association of poly-L-lysine in an attempt to elucidate the complex factors which govern the estab-lishment and maintenance of lipid compositional asymmetr...
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PMID: 21595482
PDF is available here.
PDF is available here.
Abstract
The uniquely functionalized steroid-based cyclodimers 4, cis-5, and trans-5 have been synthesized and fully characterized.The cyclodimer 5, with a cis-trans ratio of 3:1, is obtained by coupling the terminal alkenes of two 4-pentenoate groups on a cyclodimer 4 via Grubbs' intramolecu...
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PMID: 21591628
PDF is available here.
PDF is available here.
Abstract
Volvalerelactones A and B (1 and 2), two new sesquiterpenoid lactones with an unprecedented 3/7/6 tricyclic ring system, were isolated from the roots of Valeriana officinalis var. latifolia. Their structures and relative configurations were elucidated by spectroscopic data and single...
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PMID: 21591723
PDF is available here.
PDF is available here.
Abstract
Water-binding foldamers have been rarely studied. By orienting both H-bond donors and acceptors toward their interior, two pyridine-derived crescent-shaped folding oligoamides were found to be capable of trapping both conventional and unconventional water dimer clusters in their cavi...
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PMID: 21591725
PDF is available here.
PDF is available here.
Abstract
Two novel polyketides, simplextones A (1) and B (2), were isolated from the sponge Plakortis simplex. Their structures were established by spectroscopic methods. The absolute configurations were assigned by modified Mosher's method, X-ray crystallographic analysis, and quantum mechan...
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PMID: 21604759
PDF is available here.
PDF is available here.
Abstract
We revise the absolute stereochemistry of (-)-trigonoliimines A, B, and C....
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PMID: 21667943
PDF is available here.
PDF is available here.
Abstract
The movement of the small ribosomal subunit (30S) relative to the large ribosomal subunit (50S) during translation is widely known, but many molecular details and roles of rRNA and proteins in this process are still undefined, especially in solution models. The functional relationship of modified nuc...
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PMID: 21557607
PDF is available here.
PDF is available here.
Abstract
We have determined the value of the glass transition temperature (T_{g}) as well as the steepness index (m_{P}) at various T-P conditions....
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PMID: 21728535
PDF is available here.
PDF is available here.
Abstract
We perform a molecular dynamics simulation study of the behavior of a lipid coating layer on an oscillating bubble surface. Micrometer sized bubbles, stabilized with a lipid monolayer coating, are used in acoustic imaging as a contrast agent. The coating layer is expected to be strongly influenced b...
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PMID: 21728546
PDF is available here.
PDF is available here.
Abstract
We investigated membrane-like polymer structures of fractal connectivity such as Sierpinski gaskets and Sierpinski carpets applying the bond fluctuation model in three dimensions. Without excluded volume (phantom), both polymeric fractals obey Gaussian elasticity on larger scales determined by their...
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PMID: 21728562
PDF is available here.
PDF is available here.
Abstract
The binding interactions of two antitumour agents that target the paclitaxel site, docetaxel and discodermolide, to unassembled -tubulin heterodimers and microtubules have been studied using biochemical and NMR techniques. The use of discodermolide as a water-soluble paclita...
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PMID: 21539341
PDF is available here.
PDF is available here.
Abstract
The polymorphic and pseudopolymorphic forms of CG-400549, a novel FabI inhibitor with potent in vivo activity were prepared and characterized by differential scanning calorimetry (DSC), powder X-ray diffractometry (PXRD) and thermogravimetric analysis (TG). Seven crystal forms of CG-400549, one anhyd...
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PMID: 21656363
PDF is available here.
PDF is available here.
Abstract
Abstract
(1R,2R,6S)-3-Methyl-6-(prop-1-en-2-yl)cyclohex-3-ene-1,2-diol 1 possesses potent antiparkinsonian activity in both MPTP and haloperidol animal models. The use of compound 1 resulted in nearly full recovery of the locomotor and exploratory activities and was as effective as the comparator agent (levod...
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PMID: 21534547
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)9 2011
Abstract
We iteratively performed atomistic molecular dynamics simulations and biophysical measurements to probe the interaction of a cyclic antimicrobial peptide and its inactive linear analogue with model membranes. We establish that, relative to the linear peptide, the cyclic one binds stronger to negativ...
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PMID: 21586269
PDF is available here.
PDF is available here.
Abstract
GPR40, a G-protein-coupled receptor has been well established to play a crucial role in regulating blood glucose levels. Hence, GPR40 is a potential target for future antidiabetic agents. The present 3D QSAR study is aimed at delineating structural parameters governing GPR40 agonisti...
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PMID: 21352503
PDF is available here.
PDF is available here.
Abstract
The effects of chloride and sulfate salts of tetrapropylammonium (TPA(+)) and guanidinium (Gdm(+)) on the conformational stabilities of tryptophan zipper (trpzip) and α-helical (alahel) peptides were measured by circular dichroism spectroscopy. Like Gdm(+), TPA(+) interacts with the planar tryptopha...
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PMID: 21520945
PDF is available here.
PDF is available here.
Abstract
Our systematic study reveals that nano-confinement is affected both by pore radius and length and that the conformations of the polymer chains strongly depend on their grafting position along the nanopore and on quality of solvent. In poor solvent, polymer chains can collapse to the walls, form a co...
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PMID: 21524134
PDF is available here.
PDF is available here.
Abstract
A novel, sensible, and specific fluorescent biosensor of human calmodulin (hCaM), namely hCaM L39C-mBBr/V91C-mBBr, was constructed. The biosensor was useful for detecting ligands with opposing fluorescent signals, calcium ions (Ca(2+)) and CaM inhibitors in solution. Thus, the device was successfully...
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PMID: 21495717
PDF is available here.
PDF is available here.
Mutation Research (722)1 2011
Abstract
We analysed the effect of ELF-MF on chromatin conformation in E. coli GE499 cells by the anomalous viscosity time-dependence (AVTD) technique. Possible genotoxic effects of the specific combination of static and ELF-MF, which has been proven to affect chromatin conformation, were investigated by a c...
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PMID: 21497670
PDF is available here.
PDF is available here.