The further crystallographic refinement of trichosanthin at 2.7A resolution and the comparison among the three molecular structures in two crystal forms

The three-dimensional structure of trichosanthin at 2.7A resolution has been improved further, by refitting one of the C-terminal tails, adjusting 16 residues in the molecular surface regions, discarding some water molecules with high B values, and adjusting weights during the further refinement. The R-factor has been reduced to 18.5% and the r.m.s deviations from ideal geometry are also improved. The structures of the two molecules in the monoclinic asymmetric unit and the only molecule in the orthorhombic asymmetric unit are compared with one another. The main-chain structures for most of the residues in the three molecules are substantially the same. However, the courses of the three C-terminal tails are completely different, and the intermolecular interactions resulting from the particular packing of the molecules in the crystals account for the differences. The strand Be-2 and the preceding B-turn in small domain show large r.m.s. deviations among the three molecules and they are also involved in i     

A multivariate statistical analysis approach to highlight molecular processes in plant cell walls through ATR FT-IR microspectroscopy: The role of the α-expansin PhEXPA1 in Petunia hybrida

Mid-infrared ATR FT-IR microspectroscopy is applied in conjunction with multivariate statistical analysis on petal samples of Petunia hybrida from wild-type and from two transgenic lines in which the PhEXPA1 expansin gene expression was down-regulated and up-regulated, respectively. New insights are given on the role of expansin in the rearrangement of the cell wall polymer network. Measurements are done without any previous sample treatment to preserve the native cell wall structure and natural biological variability. An original combination of data analysis techniques is proposed to highlight molecular processes in plant cells, based on an automated spectra selection procedure, Principal Component Analysis, Wilcoxon rank sum test and heat map data representation.     

Chemical composition of the essential oil from basil (Ocimum basilicum Linn.) and its in vitro cytotoxicity against HeLa and HEp-2 human cancer cell lines and NIH 3T3 mouse embryonic fibroblasts

This study examines the chemical composition and in?vitro anticancer activity of the essential oil from Ocimum basilicum Linn. (Lamiaceae), cultivated in the Western Ghats of South India. The chemical compositions of basil fresh leaves were identified by GC-MS: 11 components were identified. The major constituents were found to be methyl cinnamate (70.1%), linalool (17.5%), β-elemene (2.6%) and camphor (1.52%). The results revealed that this plant may belong to the methyl cinnamate and linalool chemotype. A methyl thiazol tetrazolium assay was used for in?vitro cytotoxicity screening against the human cervical cancer cell line (HeLa), human laryngeal epithelial carcinoma cell line (HEp-2) and NIH 3T3 mouse embryonic fibroblasts. The IC(50) values obtained were 90.5 and 96.3?μg?mL(-1), respectively, and the results revealed that basil oil has potent cytotoxicity.     

How do rotameric conformations influence the time-resolved fluorescence of tryptophan in proteins? A perspective based on molecular modeling and quantum chemistry

We discuss the dynamics of tryptophan rotamers in the context of the non-exponential fluorescence decay in proteins. The central question is: how does the ground-state conformational heterogeneity influence the time evolution of tryptophan fluorescence? This problem is examined here from the theoretical perspective. Three methods at different levels of theory, and with different scopes and computational requirements are reviewed. The Dead-end elimination method is limited to side-chain dynamics and provides an efficient way to detect the stable tryptophan rotamers in a protein. Its application to the study of heterogeneous emission characteristics is illustrated. Molecular dynamics is aimed at the full phase space of the macromolecule in solution, but must rely on classical force fields and laws of evolution. We examine to what extent the molecular mechanics paradigm yields sufficiently accurate thermodynamic results, and what are the possible kinetic implications. Finally Quantum Chemistry is the only theoretical method that allows a direct assessment of the excited states. It is necessarily restricted to small molecular systems, and thus must be used in a hybrid combination with classical methods and electrostatic models. So far understanding of the emitting state has greatly progressed as a result of these calculations, but the actual treatment of the photophysical decay processes at the quantum level has not yet really started.     

The influence of molecular interaction on polymerization—11: A study of the influence of the solvent on the tacticities of poly(2-naphthyl methacrylated) and poly(cumylphenyl methacrylate) obtained in various solvents

Polymerizations of 2-naphthyl methacrylate and 4(1-methylphenethyl)phenyl methacrylate (cumylphenyl methacrylate) have been carried out in solvents with different dielectric constants and donor numbers (DN). By means of ¹H-NMR and fluorescence spectroscopy, the tacticities of the polymers were studied. It was found that the structures of the polymers depend on the dielectric constant of the solvent and not on its donor number. In solvents with high dielectric constant, the contents of isotactic triads are higher than for solvents with low dielectric constants.     

A vibrational molecular force field of model compounds with biological interest—III. Harmonic dynamics of α- and β-d-galactose in the crystalline state

The infrared spectra of α- and β-d-galactose were recorded, both in the mid-IR range (4000-500 cm⁻¹) and in the far-IR (500-50 cm⁻¹). The Raman spectra were also obtained. These spectra constitute the basis of a crystalline-state force field established for these two molecules through a normal coordinate analysis. A modified Urey—Bradley—Shimanouchi force field was combined with an intermolecular potential energy function which includes van der Waals interactions, electrostatic terms and an explicit hydrogen bond function. The force constants were varied, so as to obtain an agreement between the observed vibrational frequencies and the calculated ones of α-d-galactose. The force field obtained was then applied to α-d-galactose O-d5 and β-d-galactose, in order to test its transferability. The computed potential energy distribution was found to be compatible with previous assignments for d-glucose, particularly for the modes involving C6 and COH groups. For β-d-galactose the same force field was used with changing the force constants due to the C1 and C6 groups.     

Physico-chemical comparison of betulinic acid, betulin and birch bark extract and in vitro investigation of their cytotoxic effects towards skin epidermoid carcinoma (A431), breast carcinoma (MCF7) and cervix adenocarcinoma (HeLa) cell lines

Betulin and betulinic acid are pentacyclic triterpenes present in the bark of the birch tree and other vegetal sources. Quantitatively, in birch bark betulin is more significant than betulinic acid; therefore, birch can be a large and feasible source of raw material for betulin extraction. Betulin can be used as extracted or, after chemical modification, as a starting compound for its acid, betulinic acid, with both substances possessing various interesting pharmacological properties. The purpose of this study is to analyse the betulin and betulinic acid content of a birch tree bark extract, as well as its cytotoxic activity. The extraction was done using a Soxhlet extractor and chloroform/dichlormethane/methanol (1?:?1?:?1) as solvent. The betulin and betulinic acid content of the extract was estimated using standards of pure betulin and betulinic acid, by thermal analysis as opposed to pure substance (thermogravimetric and differential thermal analysis). The extract and the main compounds were also analysed by NMR. The results indicated a high amount of betulin in the final extract (up to 50%), and an important quantity of betulinic acid: over 3%. The cytotoxic activity indicated a high proliferation inhibition for the birch tree extract but was still comparable with betulinic acid and betulin.     

Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations,binding free energy calculations and weak interactions analysis

Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU–tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA–tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug–tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.     

Preparation and reactions of palladium(II) complexes with C2-bonded heteroaromatic ligands trans[PdCl(RN)(PPh3)2] (RN = 2-pyridyl, 2-pirazyl, 2-pyrimidyl group). A new reaction pathway in the insertion of isocyanides into the Pdc bond of trans-[PdXR(L)2] compounds

The complexes trans-[PdCl(R_N)(PPh₃)₂] (I) [R_N = 2-pyridyl (2-Py), 2-pyrazyl (2-pyz), 2-pyrimidyl (2-pym) group] have been prepared in high yield by deprotonation with NEt₃ of the corresponding cationic compounds trans[PdCl(R_NH) (PPh₃)₂]⁺ (R_NH = N-protonated C²-heteroaromatic ligand) in the presence of an excess of PPh₃. In chlorinated solvents, complexes I undergo a slow reversible dimerization into the binuclear derivatives [PdCl(μ-R_N)(PPh₃)]₂ (II) (μ-R_N = C²,N¹-bridging ligand). From the ³¹P NMR spectra in 1,2-dichloroethane the following dissociation constants were obtained: 1.9 mol 1⁻¹ (R_N= 2-py), 5.1 × 10⁻² (2-pym), 6.6 × 10⁻³ (2-pyz). The dimerization becomes fast and quantitative if the PPh₃, involved in the equilibrium is removed by oxidation or by reaction with [PdCl(η³-2-MeC₃H₄)]₂. Only the 2-pyridyl complex Ia reacts (slowly) with CO yielding the migratory insertion product trans-[PdCl{C(2-py)O}(PPh₃)₂], together with the dimer IIa. All the complexes I undergo migratory insertion of t-butylisocyanide with formation of trans-[PdCl{C(R_N) = NCMe₃}(PPh₃)₂]] at rates which depend on the heterocyclic group (R_N = 2-py > 2-pyz ⪢ 2-pym). The reaction of the 2-pyrazyl complex Ib with CNCMe₃ has been studied in detail by conductivity measurements and by IR and ³¹P NMR spectroscopy. The data suggest a complex mechanism in which insertion occurs through rearrangement of a four-coordinate intermediate [PdCl(2-pyz)(CNCMe₃)(PPh₃)], and through interaction of a cationic intermediate trans-[Pd(2-pyz)(CNCMe₃)(PPh₃)₂]⁺ (Vb) with Cl⁻ and with the free isocyanide of the initial equilibria. The occurrence of the latter reactions is confirmed by independent experiments in which the cationic complex Vb (isolated as perchlorate salt) is treated with an equimolar amount of [AsPh₄]Cl or CNCMe₃. The isocyanide-promoted insertion step represents a new mechanistic pathway for isocyanide insertion into the PdC bond of trans-[PdXR(L)₂] complexes.