Searching the "biologically relevant"conformation of dopamine: a computational approach

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.     

Supramolecular networks through second-sphere coordination based on 1D metal-4,4′-dipyridyldisulfide coordination polymers and hydrogenfumarate or sulfonate anions

Four hydrogen-bonded assemblies of formula [M(dpds)₂(OH₂)₂]A₂·nH₂O (A = anion) are described. These assemblies result from the second-sphere coordination interactions between the 1D coordination polymers [M(dpds)₂(OH₂)₂]²⁺, M = Zn(II) and Cu(II), dpds = 4,4′-dipyridyldisulfide, and the pyridine-3-sulfonate (3pySO₃⁻) or hydrogenfumarate (Hfum⁻) anions. Significantly, supramolecular structural variations are observed depending on the presence of water lattice molecules, which formed discrete aggregates when the Hfum⁻ anion was used. The effects of geometrical variations in the building blocks are also evident on using Jahn-Teller-distorted divalent Cu(II) ions or regular octahedral species based on Zn(II) ions. The second-sphere effects on the stabilization of the compounds are illustrated by TGA experiments.     

Detection of migration of phthalates from agglomerated cork stoppers using HPLC-MS/MS

Agglomerated stoppers are manufactured from natural cork granules and adhesives. Esters, such as phthalates and adipates, are commonly used in adhesives at concentrations of typically 2-5%. Because of this, and regarding consumer safety, it is necessary to ensure that these compounds do not migrate into the beverage where the cork stopper is used. A reversed-phase high performance liquid chromatography method with tandem mass spectrometry detection is developed for the separation of nine phthalates into 12% ethanol, used as simulant of alcoholic beverages. The chromatographic separation was carried out with a Luna C18 (2) HSTcolumn (50 × 3.0 mm, 2.5 μm) with a gradient elution of water/methanol with 0.1% acetic acid at 300 μL min(-1). The method was validated for four selected phthalates: di-butylphthalate, di-isononylphthalate, di-isodecylphthalate, and butyl-benzyl phthalate, with recoveries ranging between 95% and 112% and intralaboratory precision (RSD) between 5 and 14%, depending on the phthalate. The lowest quantification limit, 0.15 mg kg(-1), was achieved for di-butylphthalate. Nevertheless, in all cases, the limits obtained guarantee the method utility if restriction limits set in Commission Regulation No 10/2011 for plastic materials are taken into account.     

Second campaign of microclimate monitoring in the carcer tullianum: temporal and spatial correlation and gradients evidenced by multivariate analysis

Background

This paper discusses results obtained in the second monitoring campaign of the Carcer Tullianum, a particular hypogeum environment located in the historical centre of Rome (Italy). In the first paper we stressed the need to apply chemometric tools to this kind of studies in order to obtain full and significant information; really information on sampling design, sensors (type, number, position) and instrument validation seems to be not easy to find in literature for researches dealing with monitoring of indoor environments. Also in this case three main parameters (temperature, humidity, illuminance) were monitored in the complex construction by an inexpensive self-assembled system along some horizontal and vertical vectors together with some measurements of oxygen, carbon dioxide and barometric pressure. With respect to the first campaign, we used a higher number of sensors to cover a new excavated zone; for the same reason, as well as to take into account the presence of visitors, a different experimental design was adopted.

Results

Different data treatments were applied to data coming from all the used sensors. A good view of the microclimate was obtained that also resulted coherent with the different position of the three rooms constituting the monitored site (Carcer, Tullianum, Convent). Classical time plots resulted useful to evidence the correlation of the main monitored parameters (T, RH% and illuminance) with macroclimate, as well as their delay in following macroclimate. Box-Whisker and Gain-Loss graphs evidenced at the best the microclimate differences between the three rooms; an almost hypogean microclimate was evidenced for the lower room (Tullianum) where humidity values range between 90 and 100% while lower values, but anyway higher than the external, and spread more widely were measured passing to Convent and Carcer with minimum values around 50% for the last. A scarce or very scarce correlation with macroclimate was evidenced for all the three main measured parameters. Lighting results mainly dependent on artificial light and only in few cases, but unfortunately in the most precious zone, illuminance exceeds values suggested by Normative.

Conclusions

Box-Whisker and Gain-Loss graphs allowed us to have the best view of the microclimate for all the monitored rooms. The influence of lighting by lamps on the other monitored parameters resulted overlapped and clearly topped the solar one. The worst situation was found in the Carcer, where the presence of the main chandelier worsens the state of the frescoed walls, already subjected to wide changes in temperature and humidity. Also the lighthouse located above the Convent provokes lighting exceeding values suggested by Normative while, as expected, LEDs resulted as suitable source of light from a conservation point of view. Susanne Heidi Plattner, Patrizia Fortini and Maria Pia Sammartino contributed equally to this work     

Actin filament guidance on a chip: toward high-throughput assays and lab-on-a-chip applications

Biological molecular motors that are constrained so that function is effectively limited to predefined nanosized tracks may be used as molecular shuttles in nanotechnological applications. For these applications and in high-throughput functional assays (e.g., drug screening), it is important that the motors propel their cytoskeletal filaments unidirectionally along the tracks with a minimal number of escape events. We here analyze the requirements for achieving this for actin filaments that are propelled by myosin II motor fragments (heavy meromyosin; HMM). First, we tested the guidance of HMM-propelled actin filaments along chemically defined borders. Here, trimethylchlorosilane (TMCS)-derivatized areas with high-quality HMM function were surrounded by SiO(2) domains where HMM did not bind actin. Guidance along the TMCS-SiO(2) border was almost 100% for filament approach angles between 0 and 20 degrees but only about 10% at approach angles near 90 degrees . A model (Clemmens, J.; Hess, H.; Lipscomb, R.; Hanein, Y.; Bohringer, K. F.; Matzke, C. M.; Bachand, G. D.; Bunker, B. C.; Vogel, V. Langmuir 2003, 19, 10967-10974) accounted for essential aspects of the data and also correctly predicted a more efficient guidance of actin filaments than previously shown for kinesin-propelled microtubules. Despite the efficient guidance at low approach angles, nanosized (<700 nm wide) TMCS tracks surrounded by SiO(2) were not effective in guiding actin filaments. Neither was there complete guidance along nanosized tracks that were surrounded by topographical barriers (walls and roof partially covering the track) unless there was also chemically based selectivity between the tracks and surroundings. In the latter case, with dually defined tracks, there was close to 100% guidance. A combined experimental and theoretical analysis, using tracks of the latter type, suggested that a track width of less than about 200-300 nm is sufficient at a high HMM surface density to achieve unidirectional sliding of actin filaments. In accord with these results, we demonstrate the long-term trapping of actin filaments on a closed-loop track (width < 250 nm). The results are discussed in relation to lab-on-a-chip applications and nanotechnology-assisted assays of actomyosin function.     

Directed mutagenesis alters the stereochemistry of catalysis by isolated ketoreductase domains from the erythromycin polyketide synthase

The ketoreductase (KR) domains eryKR(1) and eryKR(2) from the erythromycin-producing polyketide synthase (PKS) reduce 3-ketoacyl-thioester intermediates with opposite stereospecificity. Modeling of eryKR(1) and eryKR(2) showed that conserved amino acids previously correlated with production of alternative alcohol configurations lie in the active site. eryKR(1) domains mutated at these positions showed an altered stereochemical outcome in reduction of (2R, S)-2-methyl-3-oxopentanoic acid N-acetylcysteamine thioester. The wild-type eryKR(1) domain exclusively gave the (2S, 3R)-3-hydroxy-2-methylpentanoic acid N-acetylcysteamine thioester, while the double mutant (F141W, P144G) gave only the (2S, 3S) isomer, a switch of the alcohol stereochemistry. Mutation of the eryKR(2) domain, in contrast, greatly increased the proportion of the wild-type (2R, 3S)-alcohol product. These data confirm the role of key residues in stereocontrol and suggest an additional way to make rational alterations in polyketide antibiotic structure.     

Organische Chemie 2002

Die enantioselektive Synthese bleibt zentrales Thema in metallorganischen, metallfreien and bioorganischen Transformationen sowie in der industriellen organischen Chemie. Glanzpunkte zielmolekülorientierter Synthesechemie waren ein Zugang zu C₆₀, die Route zum Diazonamid A und die Totalsynthese von Vinblastin. Mit „Pyrrolysin”︁ wurde die 22. proteinogene Aminosäure entdeckt. Trotz der immer höheren Zahl an Testsubstanzen besteht in der medizinischen Chemie ein Engpass an klinisch erfolgreichen Wirkstoffen.