Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

High precision delta(17)O isotope measurements of oxygen from silicates and other oxides: method and applications

The use of infrared laser-assisted fluorination to release oxygen from milligram quantities of silicates or other oxide mineral grains is a well-established technique. However, relatively few studies have reported the optimisation of this procedure for oxygen-17 isotope measurements. We describe here details of an analytical system using infrared (10 μm) laser-assisted fluorination, in conjunction with a dual inlet mass spectrometer of high resolving power ( approximately 250) to provide (17)O and (18)O oxygen isotope measurements from 0.5-2 mg of silicates or other oxide mineral grains. Respective precisions (1) of typically 0.08 and 0.04 per thousand are obtained for the complete analytical procedure. Departures from the mass-dependent oxygen isotope fractionation line are quantified by Delta(17)O; our precision (1) of such measurements on individual samples is shown to be +/-0.024 per thousand. In turn, this permits the offset between parallel, mass-dependent fractionation lines to be characterised to substantially greater precision than has been possible hitherto. Application of this system to investigate the (17)O versus (18)O relationship for numerous terrestrial whole-rock and mineral samples, of diverse geological origins and age, indicates that the complete data set may be described by a single, mass-dependent fractionation line of slope 0.5244+/- 0.00038 (standard error). Copyright 1999 John Wiley & Sons, Ltd.     

Fractal aspects of calcium binding protein structures

The structures of EF-hand calcium binding proteins may be classified into two distinct groups: extended and compact structures. In this paper we studied 20 different structures of calcium binding proteins using the fractal analysis. Nine structures show extended shapes, one is semi-compact and the other 10 have compact shapes. Our study reveals different fractal characteristics for protein backbones belonging to different structural classes and these observations may be correlated to the physicochemical forces governing the protein folding.     

A NEW FINITE ELEMENT APPROXIMATION OF A STATE-CONSTRAINED OPTIMAL CONTROL PROBLEM

In this paper, we study numerical methods for an optimal control problem with pointwise state constraints. The traditional approaches often need to deal with the deltasingularity in the dual equation, which causes many difficulties in its theoretical analysis and numerical approximation. In our new approach we reformulate the state-constrained optimal control as a constrained minimization problems only involving the state, whose optimality condition is characterized by a fourth order elliptic variational inequality. Then direct numerical algorithms （nonconforming finite element approximation） are proposed for the inequality, and error estimates of the finite element approximation are derived. Numerical experiments illustrate the effectiveness of the new approach.     

Total synthesis of Cinncassin A1

In this communication, we report the first total synthesis of the phenolic natural product Cinncassin A₁, which was recently isolated from the twigs of the cinnamon plant (Cinnamomum cassia). The novel and concise synthesis strategy involves a highly diastereoselective titanium enolate homocoupling and a permanganate-mediated oxidative lactonization reaction as key steps. The structure of the compound was verified by single-crystal X-ray crystallography.     

Polyoxometalate binding to human serum albumin: a thermodynamic and spectroscopic approach

The molecular recognition of polyoxometalates by human serum albumin is studied using two different polyoxometalates (POMs) at pH 7.5. The results are compared with those obtained at pH 3.5 and 9.0. At pH 7.5, both POMs strongly interact with the protein with different binding behaviors. The Keggin shaped POM, [H(2)W(12)O(40)](6-) (H2W12), specifically binds the protein, forming a complex with a 1:1 stoichiometry with Ka = 2.9 x 10(6) M(-1). The binding constant decreased dramatically with the increase of the ionic strength, thus indicating a mostly electrostatic binding process. Isothermal titration calorimetry (ITC) experiments show that the binding is an enthalpically driven exothermic process. For the wheel shaped POM [NaP(5)W(30)O(110)](14-) (P5W30), there are up to five binding sites on the protein. Increasing the ionic strength changes the binding behavior significantly, leading to a simple exothermic process, with several binding sites. Competitive binding experiments indicate that the two POMs share one common binding site. In addition, they show the existence of another important binding site for P5W30. The two POMs exhibit different binding dependences on the pH. The combination of the experimental results with the knowledge of the surface map of the protein in its N-B conformation transition domain leads to the proposal for the probable binding site of POMs. The present work reveals a protein conformation change upon P5W30 binding, a new feature not explicitly documented in previous studies.     

Molecular interaction and energy transfer between human serum albumin and polyoxometalates

As a step toward the elucidation of the mechanistic pathways governing the known bioactivity of polyoxometalates (POMs), two representative molecules of this class of chemicals, the wheel-shaped [NaP(5)W(30)O(110)]14- (P(5)W(30)) and the Keggin-type anion [H(2)W(12)O(40)]6- (H(2)W(12)), are shown, by two independent techniques, to interact with the fatty-acid-free human serum albumin (HSA). The excited-state lifetime of the single tryptophan molecule of this protein is dramatically decreased by the binding. The quenching mechanism is found to constitute the first example of energy transfer between HSA and POMs. Such molecular recognition is believed to be a key step for subsequent evolution of the systems. Circular dichroism (CD) was used to assess the structural effects of POM binding on HSA and to confirm the interaction revealed by fluorescence studies. CD experiments showed that the two POMs have different effects on the secondary structure of the protein. Binding P(5)W(30) partially unfolds the protein whereas H(2)W(12) has no remarkable effect on the structure of the protein.