General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation

A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin interactions responsible for spin relaxation. The covariance matrix, which is evaluated using a molecular dynamics (MD) simulation, is diagonalized yielding reorientational eigenmodes and amplitudes that reveal detailed information about correlated protein dynamics. The eigenvalue distribution allows one to quantitatively assess whether overall and internal motions are statistically separable. To each eigenmode belongs a correlation time that can be adjusted to optimally reproduce experimental relaxation parameters. A key feature of the method is that it does not require separability of overall tumbling and internal motions, which makes it applicable to a wide range of systems, such as folded, partially folded, and unfolded biomolecular systems and other macromolecules in solution. The approach was applied to NMR relaxation data of ubiquitin collected at multiple magnetic fields in the native form and in the partially folded A-state using MD trajectories with lengths of 6 and 70 ns. The relaxation data of native ubiquitin are well reproduced after adjustment of the correlation times of the 10 largest eigenmodes. For this state, a high degree of separability between internal and overall motions is present as is reflected in large amplitude and collectivity gaps between internal and overall reorientational modes. In contrast, no such separability exists for the A-state. Residual overall tumbling motion involving the N-terminal beta-sheet and the central helix is observed for two of the largest modes only. By adjusting the correlation times of the 10 largest modes, a high degree of consistency between the experimental relaxation data and the iRED model is reached for this highly flexible biomolecule.     

Synthèse de composés cyclopentaniques chiraux,di, tri et tétrasubstitués. Application à la synthèse de dérivés Oxa-13-prostanoïques

The cyclopentenecarbaldehyde 1a , acetals 2a , 2b and the cyclopentenone 2c have been transformed through regio and stereocontrolled reactions into a variety of enantiomerically pure substituted cyclopentanes. Using appropriately selected Wittig reagents, aldehyde 1a furnished the condensation products 3 , 4 , 5 . Michael addition of diethyl malonate on the α,β-unsaturated aldehyde 1a under phasetransfer conditions led efficiently to 7 . Reduction of the cyclopentenone 2c gave 21 in high yield. The cyclopentenes 2a , 2b and 23 , submitted to hydroboration-oxidation furnished the cyclopentanols 10 , 13 and 24 , respectively, in 30, 70 and 50% yields, reflecting the substitution pattern of the starting alkenes. The salient feature of these reactions is the stereospecificity due to the chiral centre of the molecules 1a , 2a , 2b and 2c , leading to compounds with two, three and four asymmetric centres. The straightforward synthesis of 11α-hydroxy-13-oxaprostanoic acid 20 is described and an approach towards the preparation of 9α, 11α-dihydroxy-13-oxaprostanoic acid 34 is also presented. The structure of these products has been determined by ¹H- and ¹³C-NMR spectroscopy.     

Morphology and surface heterogeneities in synthetic goethites

In the framework on a study of the acido-basic and sorption properties of iron oxides, a thorough characterization of two types of goethite powders was performed in several laboratories joined in a common project. Chemical analysis by ICPAES; high-resolution SEM, TEM, and AFM observations; XRD with line width analysis; and argon and nitrogen sorption isotherms were used for that purpose. The main crystallographic faces of goethite particles could be identified as {001}, {101}, and {121}, and their abundance correlated with the distribution of low-pressure argon adsorption local isotherms. These results will be very useful for further studies on the relationship between surface reactivity in aqueous solution and orientation of solid surfaces.     

Structural requirements in chiral diphosphine-rhodium complexes—XI: Asymmetric homogeneous hydrogenation of z-α-acylaminocinnamic acids and esters with (1s, 2s)-trans-1,2-bis(diphenylphosphinomethyl) cyclohexane/rhodium(i) complexes

Z-α-acylaminocinnamate esters were hydrogenated with neutral rhodium(I) complexes containing (1S, 2S)-trans-1,2-bis(diphenylphosphinomethyl)cyclohexane. Increasing the steric bulk of the alcohol moiety of the ester function results in increased enantioface differentiation in favor of the re-si prochiral face to yield an excess of the S-amino acid derivatives. In the series of N-acetylphenylalanine ester products (resulting from hydrogenation of Z-α-acetamidocinnamate esters) the optical purity increased from 1% ee-(R) [Me]; 20% ee-(S) [Et]; 47% ee-(S) [i-Pr]; to 58% ee-(S) [t-Bu]. Increasing the steric bulk of the acyl function (NHCOR, where R is an alkyl moiety) favors the reduction of the si-re prochiral face [in the methyl ester substrates] to yield an excess of the R-amino acid derivatives. In the series of N-acylphenylalanine methyl ester products (resulting from hydrogenation of Z-methyl α-acylaminocinnamates) the optical purity increased from 1% ee-(R) [Me]; 13% ee-(R) [i-Pr]; to 15% ee-(R) [t-Bu and 1-adamantyl]. The α-formamido and α-benzamido substrates gave hydrogenation products having 22% ee-(R) [H] and 35% ee-(R) [Ph]. In the corresponding free acids, increasing the steric bulk of the acyl function (NHCOR, where R is an alkyl moiety) results in almost no change in the optical purity of the reduction products. In the series of N-acylphenyl-alanine products (resulting from hydrogenation of Z-α-acylaminocinnamic acids) the optical purity was 35% ee-(S) [Me]; 31% ee-(S) [i-Pr]; 33% ee-(S) [t-Bu]; and 35% ee-(S) [1-adamantyl]. The α-benzamido substrate gave a hydrogenation product having 8% ee-(S).     

Selenourea-Ca2+ reactions in gas phase. Similarities and dissimilarities with urea and thiourea

The gas-phase reactions between Ca(2+) and selenourea were investigated by means of electrospray/tandem mass spectrometry techniques. The MS/MS spectra of [Ca(selenourea)](2+) complexes show intense peaks at m/z 43, 121, 124, and 146 and assigned to monocations produced in different coulomb explosion processes. The structures and bonding characteristics of the stationary points of the [Ca(selenourea)](2+) potential energy surface (PES) were theoretically studied by DFT calculations carried out at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level. The analysis of the topology of this PES allows identification of H(2)NCNH(+), CaSeH(+), selenourea(+). and CaNCSe(+) ion peaks at m/z 43, 121, 124, and 146, respectively. The reactivity of selenourea and the topology of the corresponding potential energy surface mimic that of thiourea. However, significant dissimilarities are found with respect to urea. The dissociative electron-transfer processes, not observed for urea, is one of the dominant fragmentations for selenourea, reflecting its much lower ionization energy. Similarly, the coulomb explosions yielding CaXH(+) + H(2)NCNH(+) (X = O or Se), which for urea are not observed, are very favorable for selenourea. Finally, while in urea the loss of NH(3) competes with the formation of NH(4+), for selenourea the latter process is clearly dominant.     

Determination of citric acid in soft drinks using flow injection with potentiometric detection

A flow injection analysis (FIA) system with potentiometric detection has been developed for the determination of citric acid in commercial fruit juices using a copper-selective tubular electrode. It consists of the complexation of citrate ion with copper (II) ion, monitoring the free copper (II) concentration. Linear relationships between the potential and log concentrations of citric acid in the range of 1 × 10^–3 mol/L – 1 × 10^–2 mol/L were attained with samples injected in the system without prior treatment. Repeatability was determined by assessing the relative standard deviation for ten replicate injections of different juice samples which varied from 1.2% to 3.0%. The results provided by the automated system were compared with those of an enzymatic conventional method used for the analysis of citric acid in food and a relative deviation of less than 4.0% was found. Recovery trials resulted in values from 97.0% to 101.0%. The system allows a sampling frequency of 60 samples/h. Received: 22 October 1998 / Revised: 14 December 1998 / Accepted: 16 December 1998     

Synthesis of Dienedioic and Tetraenedioic Acids by Oxidative Coupling of Unsaturated Carboxylic Acid Dienediolates by 1,2-Diiodoethane

Acyclic and cyclic unsaturated carboxylic acids 1 to 4 are most easily converted to unsaturated dicarboxylic acids 5 to 8 by oxidative coupling of their diene- or triene-diolates by 1,2-diiodoethane. This procedure improves formerly reported oxidations by iodine or silver salts.     

Polyenolates of Unsaturated Carboxylic Acids in Synthesis. Synthesis of Unsaturated α-Amino Acids and β-Hydrazing Acids

Regioselective reaction of lithium diene-and triene-diolates 1 and 2 with O-diphenylphosphinyl hydroxylamine affords unsaturated α-amino acids 3 and 4. Addition to DEAD leads selectively to γ-hydrazino unsaturated acids 5 and 6.