New features in the catalytic cycle of cytochrome P450 during the formation of compound I from compound 0

Density functional theory (DFT) is applied to the dark section of the catalytic cycle of the enzyme cytochrome P450, namely, the formation of the active species, Compound I (Cpd I), from the ferric-hydroperoxide species (Cpd 0) by a protonation-assisted mechanism. The chosen 96-atom model includes the key functionalities deduced from experiment: Asp(251), Thr(252), Glu(366), and the water channels that relay the protons. The DFT model calculations show that (a) Cpd I is not formed spontaneously from Cpd 0 by direct protonation, nor is the process very exothermic. The process is virtually thermoneutral and involves a significant barrier such that formation of Cpd I is not facile on this route. (b) Along the protonation pathway, there exists an intermediate, a protonated Cpd 0, which is a potent oxidant since it is a ferric complex of water oxide. Preliminary quantum mechanical/molecular mechanical calculations confirm that Cpd 0 and Cpd I are of similar energy for the chosen model and that protonated Cpd 0 may exist as an unstable intermediate. The paper also addresses the essential role of Thr(252) as a hydrogen-bond acceptor (in accord with mutation studies of the OH group to OMe).     

Mechanisms of ATPases--a multi-disciplinary approach

ATPases are important molecular machines that convert the chemical energies stored in ATP to mechanical actions within the cell. ATPases are among the most abundant proteins with diverse functions involved in almost every cellular pathway. The well characterised ATPases include the various motor proteins responsible for cargo transfers, cell motilities, and muscle contractions; the protein degradation machinery - the proteasome; the ATP synthase, F-ATPase; and the chaperone systems. Other ATPases include DNA helicases and DNA replication complex; proteins responsible for protein/complex disassembly; and certain gene regulators. It is beyond the scope of this review to cover the complete range of ATPases. Instead, we will focus on a few representative ATPases, chosen based on their diverse mechanisms and properties. Furthermore, this review is by no means trying to cover comprehensively the literature for each ATPase nor the historical aspects in each field. We will focus on describing the various techniques being employed to derive the mechanisms and properties of the chosen ATPases. Among them, high and low resolution structural studies combined with biochemical assays seem to be the dominant technical advances adapted to reveal mechanisms for most of the ATPases except the bacterial sigma54 activators, whose mechanism of action is mostly derived from large amount of biochemical studies. A number of them, especially the F-ATPase and motor proteins, have been studied successfully by various single molecule and imaging techniques. We will therefore discuss them in greater details in order to describe the wide range techniques being utilised.     

Solid sampling technique for direct detection of condensed tannins in bark by matrix-assisted laser desorption/ionization mass spectrometry

A novel method for the direct analysis of condensed tannin components in bark was developed on the basis of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with a simple solid sampling technique. The MALDI mass spectra obtained from the wood (bark) powder sample clearly showed a series of peaks corresponding to the sodium ion adducts of condensed tannin oligomers up to around m/z 3000. The results indicate that the condensed tannins in the bark sample used in this work mostly consist of combinations of flavan-3-ol units such as profisetinidin (PF), prorobinetinidin (PR) and prodelphinidin (PD), at least up to 10-mers (m/z approximately 3000).     

CpRuIIPF6/quinaldic acid-catalyzed chemoselective allyl ether cleavage. A simple and practical method for hydroxyl deprotection

A cationic CpRu(II) complex in combination with quinaldic acid shows high reactivity and chemoselectivity for the catalytic deprotection of hydroxyl groups protected as allyl ethers. The catalyst operates in alcoholic solvents without the need for any additional nucleophiles, satisfying the practical requirements of operational simplicity, safety, and environmental friendliness. The wide applicability of this deprotection strategy to a variety of multifunctional molecules, including peptides and nucleosides, may provide new opportunities in protective group chemistry. [structure: see text]     

The counterion releasing effect and the partition coefficient of branched alkanols in ionic micellar solution

In the micellar solution of SDS, the partition coefficient (K_x) of following branched alkanols at infinite dilution was determined by applying a differential conductivity method: the alkanols used were i-C_mH_2m+1OH (m=4-9, i=1-5) in which the position of OH group (i) shifts from an end to the center of a hydrocarbon chain. The method provides two significant quantities, d!/dX_am and dC_sf/dC_af in addition to K_x. The following results have been obtained. (1) The dependence of K_x on i indicates that the hydrophobicity of alkanol is weakened with increasing i, whereas the increase in m strengthens the hydrophobicity. (2) The degree of counterion disossiation of micelles (!) is accelerated by the solubilized alkanols in micelles (mole fraction: X_am) and the acceleration rate, d!/dX_am (=0.17), depends on neither m nor i. (3) In the bulk water, the monomerically dissolved alkanols (concentration: C_af) depresses the concentration of free monomer surfactant (C_sf), and the depressing rate, dC_sf/dC_af, in micellar solution is identical with the corresponding quantity, ((CMC/(C_a)_o at CMC.     

Proximity Effects in Acid and Base-Catalysed Ether Formation

When heated with sodium ethoxide in ethanol 7-methylidenebicyclo[3.3.1]nonan-3-endo-ol (endo- 1 ) is converted into 1-methyl-2-oxa-adamantane ( 3 ). This reaction involves nucleophilic addition of a hydroxy group to an unactivated olefinic bond. Formation of the cyclic ether 3 also takes place when endo- 1 is heated in aqueous ethanol. This electrophilic addition is strongly catalysed by weak acids and suppressed by weak bases. These unusual reactions proceed more slowly with 7-methylbicyclo[3.3.1]non-6-en-3-endo-ol (endo- 2 ) and can be ascribed to a proximity effect. This follows from the IR . and NMR . spectra of endo- 1 and endo- 2 which show strong intramolecular hydrogen (OH-π) bonding. The unsaturated endo- and exo-alcohols 1 and 2 , respectively, undergo only exo-complexation with silver ion.     

Interpretation of structure formation during the sol-gel transition of a resorcinol-formaldehyde solution by population balance

Growth of colloidal particles formed during the sol-gel transition of a resorcinol-formaldehyde (RF) solution was simulated based on the population balance equation by using the discrete-sectional model (DSM). During the early stage of the sol-gel transition, the transient change of sizes of colloidal particles estimated by this method agreed well with the previous experimental observation by dynamic light scattering (DLS), which confirmed the influence of the catalyst concentration of a starting RF solution on the growth rate of the particles. From the size distribution of colloidal particles predicted at the gelation time, the surface area of a RF hydrogel after the completion of the sol-gel transition was estimated, which coincided with the BET surface area of a RF aerogel because the porous structure of a hydrogel was maintained and few micropores were formed during supercritical drying.     

Comparison of the compact dry TC method with the standard pour plate method (AOAC official method 966.23) for determining aerobic colony counts in food samples: Performance-tested method

Compact Dry TC qualifies as a rapid method kit for determining aerobic colony counts in foods. The plates are presterilized and contain culture medium and a cold-soluble gelling agent. The medium is rehydrated by inoculating 1 mL diluted sample into the center of the self-diffusible medium and allowing the solution to diffuse by capillary action. The plates can then be incubated and the colonies counted without any additional steps. The Compact Dry TC method was validated with 5 different raw meats. The performance tests were conducted at 35 degrees and 30 degrees C. In all required performance studies, no apparent differences were observed between the Compact Dry TC method and the Standard Pour Plate method (AOAC Official Method 966.23) for the detection level of aerobic microorganisms. For the accuracy claim (n = 60), a correlation factor of r2(35) = 0.9977 (35 degrees C) and r2(30) = 0.9932 (30 degrees C) could be assigned, as stated in the application for "Performance Tested Method." Quality consistency and storage robustness studies, showed no significant variations in plate count results with different production lots or plates of diverse storage age.     

Formation and stabilization model of the 42-mer Abeta radical: implications for the long-lasting oxidative stress in Alzheimer's disease

Amyloid fibrils mainly consist of 40-mer and 42-mer peptides (Abeta40, Abeta42). Abeta42 is believed to play a crucial role in the pathogenesis of Alzheimer's disease because its aggregative ability and neurotoxicity are considerably greater than those of Abeta40. The neurotoxicity of Abeta peptides involving the generation of free radicals is closely related to the S-oxidized radical cation of Met-35. However, the cation's origin and mechanism of stabilization remain unclear. Recently, structural models of fibrillar Abeta42 and Abeta40 based on systematic proline replacement have been proposed by our group [Morimoto, A.; et al. J. Biol. Chem. 2004, 279, 52781] and Wetzel's group [Williams, A. D.; et al. J. Mol. Biol. 2004, 335, 833], respectively. A major difference between these models is that our model of Abeta42 has a C-terminal beta-sheet region. Our biophysical study on Abeta42 using electron spin resonance (ESR) suggests that the S-oxidized radical cation of Met-35 could be generated by the reduction of the tyrosyl radical at Tyr-10 through a turn structure at positions 22 and 23, and stabilized by a C-terminal carboxylate anion through an intramolecular beta-sheet at positions 35-37 and 40-42 to form a C-terminal core that would lead to aggregation. A time-course analysis of the generation of radicals using ESR suggests that stabilization of the radicals by aggregation might be a main reason for the long-lasting oxidative stress of Abeta42. In contrast, the S-oxidized radical cation of Abeta40 is too short-lived to induce potent neurotoxicity because no such stabilization of radicals occurs in Abeta40.     

Photoelectrochemistry of p-type Cu2O semiconductor electrode in ionic liquid

We investigated the photoelectrochemical characteristics and photo-stability of Cu₂O layered on a copper plate using a hydrophobic ionic liquid. Our findings revealed that Cu₂O is stable under white light irradiation, provided water is removed from the electrolyte. Methyl viologen derivative, a well-established electron acceptor, was introduced to the ionic liquid electrolyte, allowing the photo-induced electron transfer reaction at the Cu₂O/electrolyte interface to be characterized. The methyl viologen derivative exhibited two distinct redox reactions at −0.56 V and −0.98 V vs. Ag/AgCl, clearly indicating that no dimer formation or co-proportionation reaction occurred. The excessive photocurrents being continuously generated resulted from a viable photo-induced electron transfer reaction from the Cu₂O to the acceptor. However, in contrast, the reduction of the Cu₂O by water in the aqueous solution causes this electron transfer to be inhibited. We further demonstrate that these findings are vital to understanding the role of the Cu₂O and its photoelectrochemical applications.