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).     

Reaction of tetraazathiapentalene and thiadiazolopyrimidine derivatives with heterocumulenes: Cycloaddition and elimination reactions via hypervalent sulfur intermediates

Tetraazathiapentalene derivative 1 reacts with heterocumulenes such as diphenylketene (2) and 2‐pyridylisothiocyanate (5) to give heterocycles 3, 6 and 7 with elimination of methylisothiocyanate. The reactions of thiadiazolopyrimidine derivatives 8a‐b with ethoxycarbonyl isothiocyanate (9) and carbon disulfide (11) gives heterocycles 10 and 12 via thermal decomposition of 1:1 cycloadducts C and D which have a hypervalent sulfur. The mechanistic and reactivity features of these reactions are described.     

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.     

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.     

Remote substituent effect favoring the formation of syn-adducts in the chelation controlled radical reactions of γ-benzyloxy-α-methylenecarboxylic acid esters

The chelation controlled radical reactions of ethyl γ-benzyloxy-α-methylenecarboxylates bearing a bulky γ-substituent, such as CHMe₂, CHPh₂, c-C₆H₁₁ and CH(Ph)OTBDMS, with alkyl iodides gave the syn-adducts with high diastereoselectivities. However, the diastereoselectivity for the substrates bearing a γ-substituent CH(i-Pr)OTBDMS depended critically on the configuration of the substituent; the substrate bearing the OTBDMS group anti to the γ-benzyloxy group showed poor diastereoselectivity, but its diastereomer gave syn-adduct exclusively. The high syn-selectivitiy is referred to the H-atom transfer to the outside face of radical center in the sharply folded seven-membered chelate intermediate bearing the ethoxy group with Z-geometry. The corner flapping of the radical center atom of the global minimum energy conformer generates a local minimum conformer and the H-atom transfer to the outside face of the radical center of the newly formed structure gives the anti-adduct. The poor diastereoselectivity is due to the very small energy difference between the two conformers and consequently both the syn- and anti-adducts are yielded in nearly equal amounts.     

Free-radical-induced polymerization of epoxides in the presence of maleic anhydride

The free-radical-induced reactions of cyclohexene oxide in the presence of maleic anhydride have been found to lead to polyether in presence of AIBN and to a mixture of polyether, ester, and maleic anhydride adduct of polyether with di-tert-butyl peroxide (DTBP), the amounts of the mixture components depending on the concentration of DTBP and the temperature. Analogous reactions in the presence of succinic anhydride lead to no polyether. The obtained polyether has no hydroxyl group. The reaction appears to consist of three different steps, radical initiation, cationic propagation, and radical termination.     

Determination of phosphorus in biological material using electrothermal atomisation atomic absorption spectrometry with a molybdenum tube atomiser

Phosphorus has been determined by electrothermal atomisation atomic absorption spectrometry with a molybdenum tube atomiser. The effects of interferents on the phosphorus signal have been investigated. Chemical interferences were eliminated by high-temperature pyrolysis. The detection limit for the molybdenum tube system was 2.3 ng (corresponding to 2.3 micrograms ml-1 when 1 microliter was injected into the atomiser) and the characteristic mass was 1.9 ng of phosphorus. A calibration graph method combined with high-temperature pyrolysis has been evaluated through the determination of phosphorus in biological materials. The sensitivity, accuracy and precision of the method were superior to or nearly equal to those of graphite furnace atomic absorption spectrometry. The advantages of the high-temperature pyrolysis method are its simplicity and low cost.     

Significant differences in site of protonation and extent of fragmentations in chemical ionization and fast atom bombardment mass spectrometry of simple bifunctional compounds. A mechanistic implication for formation of protonated molecules

Chemical ionization (CI) and fast atom bombardment (FAB) mass spectra of simple bifunctional aromatic compounds were compared. Some significant differences were revealed with respect to the site of protonation and extent of fragmentations. Unlike conventional CI ionization, the protonated molecule formation by FAB could not be accounted for by ordinary proton transfer reactions in the gas phase. The observed ions under FAB conditions appear to be regulated by proton exchange reactions through frequent collisions in some particular region between the matrix and the gas phase.