Search results for "Models"
showing 10 items of 8211 documents
Mapping protein matrix cavities in human cytoglobin through Xe atom binding
2004
Abstract Cytoglobin is the fourth recognized globin type, almost ubiquitously distributed in human tissues; its function is still poorly understood. Cytoglobin displays a core region of about 150 residues, structurally related to hemoglobin and myoglobin, and two extra segments, about 20 residues each, at the N- and C-termini. The core region hosts a large apolar cavity, held to provide a ligand diffusion pathway to/from the heme, and/or ligand temporary docking sites. Here we report the crystal structure (2.4 A resolution, R -factor 19.1%) of a human cytoglobin mutant bearing the CysB2(38) → Ser and CysE9(83) → Ser substitutions (CYGB*), treated under pressurized xenon. Three Xe atoms bind…
Investigation of the phase transitions occurring during and after the dehydration of xylazine hydrochloride monohydrate.
2014
This paper reports an investigation of a complex solid state phase transition where two inter-converting polymorphs (X and A) of the pharmaceutical molecule xylazine hydrochloride formed and transformed during and after the dehydration of its monohydrate (H). The crystal structures of all three forms were compared. During the investigation of this solid state phase transition it was determined that the dehydration of H produced either a pure X form, or a mixture of the X and A forms. The phase composition depended on the sample preparation procedure and the experimental conditions. It was found that grinding of the hydrate enhanced the formation of polymorph X as a product of dehydration, w…
A Molecular Electron Density Theory Study of the Chemoselectivity, Regioselectivity, and Diastereofacial Selectivity in the Synthesis of an Anticance…
2019
The [3 + 2] cycloaddition (32CA) reaction of an &alpha
A Molecular Electron Density Theory Study of the Synthesis of Spirobipyrazolines through the Domino Reaction of Nitrilimines with Allenoates
2019
The reaction of diphenyl nitrilimine (NI) with methyl 1-methyl-allenoate yielding a spirobipyrazoline has been studied within molecular electron density theory (MEDT) at the MPWB1K/6-311G(d) computational level in dichloromethane. This reaction is a domino process that comprises two consecutive 32CA reactions with the formation of a pyrazoline intermediate. Analysis of the relative Gibbs free energies indicates that both 32CA reactions are highly regioselective, the first one being also completely chemoselective, in agreement with the experimental outcomes. The geometries of the TSs indicate that they are associated to asynchronous bond formation processes in which the shorter distance invo…
Enthalpy/entropy compensation effects from cavity desolvation underpin broad ligand binding selectivity for rat odorant binding protein 3
2014
Evolution has produced proteins with exquisite ligand binding specificity, and manipulating this effect has been the basis for much of modern rational drug design. However, there are general classes of proteins with broader ligand selectivity linked to function, the origin of which is poorly understood. The odorant binding proteins (OBPs) sequester volatile molecules for transportation to the olfactory receptors. Rat OBP3, which we characterize by X-ray crystallography and NMR, binds a homologous series of aliphatic gamma-lactones within its aromatic-rich hydrophobic pocket with remarkably little variation in affinity but extensive enthalpy/entropy compensation effects. We show that the bin…
Cluster organization and pore structure of ion channels formed by beticolin 3, a nonpeptidic fungal toxin
1999
Beticolin 3 (B3) belongs to a family of nonpeptidic phytotoxins produced by the fungus Cercospora beticola, which present a broad spectrum of cytotoxic effects. We report here that, at cytotoxic concentration (10 microM), B3 formed voltage-independent, weakly selective ion channels with multiple conductance levels in planar lipid bilayers. In symmetrical standard solutions, conductance values of the first levels were, respectively, 16 +/- 1 pS, 32 +/- 2 pS, and 57 +/- 2 pS (n = 4) and so on, any conductance level being roughly twice the lower one. Whether a cluster organization of elementary channels or different channel structures underlies this particular property was addressed by investi…
Substituted phosphonic analogues of phenylglycine as inhibitors of phenylalanine ammonia lyase from potatoes.
2018
A series of phosphonic acid analogues of phenylglycine variously substituted in phenyl ring have been synthesized and evaluated for their inhibitory activity towards potato l-phenylalanine ammonia lyase. Most of the compounds appeared to act as moderate (micromolar) inhibitors of the enzyme. Analysis of their binding performed using molecular modeling have shown that they might be bound either in active site of the enzyme or in the non-physiologic site. The latter one is located in adjoining deep site nearby the to the entrance channel for substrate into active site.
Structure of the human filamin A actin-binding domain.
2009
Filamin A (FLNa) is a large dimeric protein that binds to actin filaments via its actin-binding domain (ABD). The crystal structure of this domain was solved at 3.2 A resolution. The domain adopts a closed conformation typical of other ABDs, but also forms a dimer both in crystallization conditions and in solution. The structure shows the localization of the residues mutated in patients with periventricular nodular heterotopia or otopalatodigital syndrome. Structural analysis predicts that mutations in both types of disorder may affect actin binding.
Pentamethylcyclopentadienyl-rhodium and iridium complexes containing (N^N and N^O) bound chloroquine analogue ligands: synthesis, characterization an…
2016
The synthesis and characterization of twenty new pentamethylcyclopentadienyl-rhodium and iridium complexes containing N^N and N^O-chelating chloroquine analogue ligands are described. The in vitro antimalarial activity of the new ligands as well as the complexes was evaluated against the chloroquine sensitive (CQS) NF54 and the chloroquine resistant (CQR) Dd2 strains of Plasmodium falciparum. The antimalarial activity was found to be good to moderate; although all complexes are less active than artesunate, some of the ligands and complexes showed better activity than chloroquine (CQ). In particular, rhodium complexes were found to be considerably more active than iridium complexes against t…
Abyssomicin E, a highly functionalized polycyclic metabolite from Streptomyces species.
2007
Abyssomicin E (1), a new polycyclic metabolite with a C19 skeleton, was isolated from Streptomyces sp. (HKI0381). Its chemical structure was determined by comprehensive NMR and MS spectroscopic analyses. For the first time in this recently discovered class of compounds, the absolute stereochemistry was directly established by subsequent single-crystal X-ray diffraction study using anomalous dispersion with copper radiation.