Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

The biological function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the pepsin-like fold. (i) We identify the set of conserved residues by using sequence-alignment techniques. These residues cluster in three distinct regions: near the cleavage-site cavity, in the four beta-sheets cross-linking the two lobes, and in a solvent-exposed region below the long beta-hairpin in the N-terminal lobe. (ii) We elucidate the role played by the conserved residues for the enzymatic functionality of one representative member of the fold family, the human beta-secretase, by means of classical molecular dynamics (MD). The conserved regions exhibit little overall mobility and yet are involved into the most important modes of structural fluctuations. These modes influence the substrate-catalytic aspartates distance through a relative rotation of the N- and C-terminal lobes. (iii) We investigate the effects of this modulation by estimating the reaction free energy at different representative substrate/enzyme conformations. The activation free energy is strongly affected by large-scale protein motions, similarly to what has been observed in the HIV-1 enzyme. (iv) We extend our findings to all other members of the two eukaryotic and retroviral fold families by recurring to a simple, topology-based, energy functional. This analysis reveals a sophisticated mechanism of enzymatic activity modulation common to all aspartic proteases. We suggest that aspartic proteases have been evolutionarily selected to possess similar functional motions despite the observed fold variations.     

Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment

Near-UV irradiation of structurally characterized [Re(I)(CO)3(1,10-phenanthroline)(Q107H)](W48F/Y72F/H83Q/Y108W)AzM(II) [Az = Pseudomonas aeruginosa azurin, M = Cu, Zn]/[Co(NH3)5Cl]Cl2 produces a tryptophan radical (W108*) with unprecedented kinetic stability. After rapid formation (k = 2.8 x 106 s-1), the radical persists for more than 5 h at room temperature in the folded ReAzM(II) structure. The absorption spectrum of ReAz(W108*)M(II) exhibits maxima at 512 and 536 nm. Oxidation of K4[Mo(CN)8] by ReAz(W108*)Zn(II) places the W108*/W108 reduction potential in the protein above 0.8 V vs NHE.     

On the efficiency of exchange in parallel tempering monte carlo simulations

We introduce the concept of effective fraction, defined as the expected probability that a configuration from the lowest index replica successfully reaches the highest index replica during a replica exchange Monte Carlo simulation. We then argue that the effective fraction represents an adequate measure of the quality of the sampling technique, as far as swapping is concerned. Under the hypothesis that the correlation between successive exchanges is negligible, we propose a technique for the computation of the effective fraction, a technique that relies solely on the values of the acceptance probabilities obtained at the end of the simulation. The effective fraction is then utilized for the study of the efficiency of a popular swapping scheme in the context of parallel tempering in the canonical ensemble. For large dimensional oscillators, we show that the swapping probability that minimizes the computational effort is 38.74%. By studying the parallel tempering swapping efficiency for a 13-atom Lennard-Jones cluster, we argue that the value of 38.74% remains roughly the optimal probability for most systems with continuous distributions that are likely to be encountered in practice.     

Dichloro and alkylchloro gallium derivatives of dichalcogenoimidodiphosphinate ligands: isolation of a spirogallium cation

Dichloro and chloromethyl Ga(III) complexes of general formulae [XClGa-eta2-{R2P(E)NP(E'R'2-E,E'}](X = Cl, R, R'= Ph, E, E'= O (1), S (2), Se (3); R = Ph, R'= OEt, E = O, E'= S (4); R = Me, R'= Ph, E, E'= S (5) and X = Me, E, E'= O (6), S (7), Se (8)) were synthesised by either metathesis reactions between GaCl3 and the potassium salt of the ligand (X = Cl) or by methane eliminations from in situ prepared GaMe2Cl and the protonated ligands LH (X = Me). Redistribution reaction of (3) in either CDCl3 or THF afforded the solvent-free tetracoordinate gallium spirocycle cation [Ga-{eta2-{Ph2P(Se)NP(Se)Ph2-Se,Se'})2]+ (9+). The molecular structures of complexes 2, 4, 5, 7 and 9(+) show non-planar gallacycle rings.     

HPLC monitored synthesis of R2NCH2 substituted benzene derivatives used as (C,N)-ligands for organometallic compounds

2-(Diethylaminomethyl)phenyl bromide and 1,3-bis(dimethylaminomethyl)-benzene, useful ligands for the synthesis of hypervalent organometallic compounds, were prepared and characterized by NMR (¹H, ¹³C, 2D experiments) spectroscopy. Their synthesis was monitored by the HPLC method. The compounds were eluted on a Nucleosil 120 Si column (5 μm, 25×0.4 cm) with n-hexane at room temperature using a 1.0 ml/min flow-rate. The maximum values of absorbance for the studied compounds, excepting the diethylamine, were located in a narrow range around 212 nm, the wavelength used for their UV detection. The diethylamine was detected at 190 nm. The calibration curves are straight lines with correlation factors r>0.995. The HPLC data are in good agreement with those provided by NMR spectroscopy.     

Synthesis and structure of the incomplete cuboidal clusters [W3Se4H3(dmpe)3]+, [W3Se4H(3-x)(OH)x(dmpe)3]+ and [W3Se4(OH)3(dmpe)3]+, and the mechanism of the acid-assisted substitution of the coordinated hydrides

The novel incomplete cuboidal cluster [W3Se4H3(dmpe)3](PF6), [1](PF6), has been prepared by reduction of [W3Se4Br3(dmpe)3](PF6) with LiBH4 in THF solution. The trihydroxo complex [W3Se4(OH)3(dmpe)3](PF6), [2](PF6), was obtained by reacting [W3Se4Br3(dmpe)3](PF6) with NaOH in MeCN-H2O solution. The complexes [1](PF6) and [2](PF6) were converted to their BPh4- salts by treatment with NaBPh4. Recrystallisation of [1](BPh4) in the presence of traces of water affords the mixed dihydride hydroxo complex [W3Se4H2(OH)(dmpe)3](BPh4). The crystal structures of [1](BPh4), [2](BPh4) and [W3Se4H2(OH)(dmpe)3](BPh4) have been resolved. Although the [1]+ trihydride does not react with an excess of halide salts, reaction with HX leads to [W3Se4X3(dmpe)3]+ (X = Cl, Br). The kinetics of this reaction has been studied at 25 degrees C in MeCN-H2O solution (1:1, v/v) and found to occur with two consecutive kinetic steps. The first step is independent of the nature and concentration of the X(-) anion but shows a first order dependence on the concentration of acid (k1 = 12.0 mol(-1) dm(3) s(-1)), whereas the second one is independent of the nature and concentration of both the acid and added salts (k2 = 0.024 s(-1)). In contrast, the reaction of [2]+ with acids occurs in a single step with kobs = 0.63 s(-1)(HCl) and 0.17 s(-1)(HBr). These kinetic results are discussed on the basis of the mechanism previously proposed for the reactions of the analogous [W3S4H3(dmpe)3]+ cluster, with special emphasis on the effects caused by the change of S by Se on the rate constants for the different processes involved.     

Synthesis of chiral β-3-amino-2-hydroxyalkanoates and 3-alkyl-3-hydroxy-β-lactams by double asymmetric induction

Reactions of chiral (2S)-enolates of dioxolan-4-ones, derived from lactic, mandelic, and phenyllactic acids, with aliphatic (S_S)- and (S_R)-tert-butylsulfinyl aldimines afforded conformationally restrained C2-disubstituted N,O-orthogonally protected 3-amino-2-hydroxyalkanoates in the form of N-sulfinyl protected 1′-aminodioxolan-4-ones. The product distribution showed that there is significant kinetic selectivity, due to the presence of ‘matched’ and ‘mismatched’ components, between the (S)- or (R)-tert-butylsulfinyl aldimines and the (2S)-enolates of the 1,3-dioxolan-4-ones. Selective methoxide-induced removal of the acetal group of the N-sulfinyl-1′-aminodioxolanones yielded the corresponding N-sulfinyl protected methyl alkanoates. In addition, the selective acid-induced removal of the sulfinyl group of the N-sulfinyl-1′-aminodioxolanones provided the corresponding N-unprotected 1′-aminodioxolanones, whose base-induced cyclization afforded the corresponding β-lactams.     

Transition Metal-Promoted Reactions in Aqueous Media and Biological Settings

During the last decade, there has been a tremendous interest for developing non-natural biocompatible transformations in biologically relevant media. Among the different encountered strategies, the use of transition metal complexes offers unique possibilities due to their high transformative power. However, translating the potential of metal catalysts to biological settings, including living cells or small-animal models such as mice or zebrafish, poses numerous challenges associated to their biocompatibility, and their stability and reactivity in crowded aqueous environments. Herein, we describe the most relevant advances in this direction, with a particular emphasis on the systems’ structure, their mode of action and the mechanistic bases of each transformation. Thus, the key challenges from an organometallic perspective might be more easily identified.     

Micro-composites based on polylactic acid with kaolinite or rice husk particles and their performance on water vapor permeability

In this work, the effect of addition of kaolinite and rice husk microparticles on the water vapor permeability of polylactic acid (PLA) was evaluated. The PLA-composites materials were characterized by X-ray diffraction, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and optical microscopy. For the composite preparation, an experimental design was established using two factors: additive type and concentration. When evaluating the water vapor permeability of the composites, it was found that the incorporation of kaolinite at 1% and 5% reduced the permeability coefficient of PLA. Furthermore, the inclusion of 5% kaolinite showed an increase on the tensile strength of the material. By contrast, the addition of rice husk produced an increase on water vapor permeability of the material and a decrease of both the tensile strength and ductility (percent of elongation at fracture). The higher dispersion and more regular morphology of the kaolinite particles could explain the enhancement of the gas barrier. A similar thermal behavior was observed for both PLA and composite materials, confirming that no damage of these properties was caused with the incorporation of the filler particles.