Towards an explanation of carboxylation/oxygenation bifunctionality in Rubisco. Transition structure for the carboxylation reaction of 2,3,4-pentanetriol

We construct a theoretical model of the transition structure for the carboxylation reaction of ribulose-1,5-biphosphate catalyzed by Rubisco. This is a first-order saddle point on the energy hypersurface for the nucleophilic attack of carbon dioxide on CH₃-(CHOH)₃-CH₃ at the C2 center.Ab initio analytical gradients methods at a 4-31G basis set level are used.The carbon framework and oxygens of the stationary structure superpose with the corresponding atoms of 2-carboxyarabinitol-1,5-biphosphate, which is a transition state analog that has recently been highly refined with X-ray methods. The hydroxyl group in C3 iscis to the C2 oxygen. The C3 center is somewhat pyramidized, the dienol O2-C2-C3-O3 is not planar.The geometry of the transition state allows for simple explanations of both the enolization of Rubisco's substrate ribulose-1,5-biphosphate, O₃PO-CH2-CO-(CHOH)₂-CH₂-OPO₃ and oxygenation reaction. The former is due to the pyramidal deformation at C3 and out of plane of O2-C2-C3-O3 framework: the enoliation is intramolecular and is probably enhanced by proton tunnelling. The latter is related with the fact that a rotation around an ethylene-like bond brings the triplet state down in energy. The reactive skeleton has a stationary geometry in the triplet state not very different from the one obtained in the global transition structure. There, the triplet is only 9 kcal/mol above the singlet. The spin densities at C2 and C3 centers clearly indicate the place where oxygenation will take place.     

In vivo pH measurement in the xylem of broad-leaved trees using ion-sensitive field-effect transistors

Summary A new method of in vivo pH determination in the xylem of broad-leaved trees using ion-sensitive field effect transistors is developed and its suitability for use is studied. In the first few hours after the sensor had been implanted in the xylem signals could be detected which were generated in response to mechanical damage; particularly strong signal changes are detectable in Populus balsamifera L., Tilia cordata Mill, and Aesculus hippocastanum L. The pH values of the xylem sap extracted from branches corresponded to the values measured by the in vivo method only at certain times. Due to sensor drift the measuring accuracy of long-term experiments lasting up to 3 weeks is restricted. The in vivo measurement of pH in the xylem of poplar branches revealed the ability of the living xylem to buffer the pH of the sap to its own characteristic value.Dedicated to Prof. Dr. O. L. Lange to his 65th birthday     

Use of the Golden Section search method to estimate the parameters of the Monod model employing spread-sheets

An alternative procedure to obtain the parameters of Monod's growth model in batch culture is presented. It is based on the integral kinetic analysis methodology, employs a one-dimensional Golden Section search optimization method and is implemented on a spread-sheet programme. The procedure is discussed in detail and is illustrated by analysis of batch substrate consumption data by an aerobic bacterial consortium.     

Effect of pH on lipid accumulation by an oleaginous yeast:Rhodotorula glutinis IIP-30

Maximum lipid production (66% w/w dry wt) inRhodotorula glutinis IIP-30 utilizing glucose in a fed-batch fermentation under N-limiting conditions at 30°C, was at pH 4. At pH 3, 5 and 6, the lipid contents were 12%, 48% and 44%, respectively. There was only a small change in the fatty acid profile over the pH range examined, although the ergosterol content decreased by a third as the pH increased.     

Cellulase production and activity in a species ofCladosporium

ACladosporium species produced large amounts of cellulase enzyme components when grown in shake-culture with medium containing carboxymethylcellulose. There was significantly less activity when Avicel, filter paper or cotton were used as substrates. KNO₃ was better than NH₄Cl or urea for the production of cellulase. Tween 80 at 0.1% (w/v) increased the production of cellulase by 1.5 to 4.5-fold. All the cellulase components were optimally active in the assay at pH 5.0 and 60°C.     

Measurements of transmembrane pH differences of low extents in bacterial chromatophores

In chromatophores from photosynthetic bacteria the interaction of the fluorescent monoamine, 9-amino, 6-chloro, 2-methoxyacridine (ACMA), with the membrane is evaluated and described by an S-shaped adsorption isotherm. This phenomenon is hysteretic, as indicated by the difference between the adsorption and desorption branches of the binding isotherm. Maximal saturation of adsorption is reached at one ACMA per one to four lipid molecules, indicating that the probe binds in its neutral form. Adsorption of the probe on the membrane causes a large quenching of its fluorescence, which is explaind as being due to hypochromic effects following stacking and aggregation in a medium of low dielectric constant. A further quenching of fluorescence is brought about by imposing artificially induced transmembrane pH's. This latter phenomenon titrates in at increasing pH values and approaches saturation when pH is 2. The dependence of pH on the observed quenching of fluorescence is predicted by considering a model based on the equilibrium distribution of the amine between two phases at different pH's, in which adsorption of the probe on the membrane is used to evaluate its free concentration in the inner and outer compartments of the chromatophore vesicle. It is proposed that the equation thus obtained should be used to measure pH from the quenching of ACMA fluorescence.Abbreviations pH transmembrane pH difference between the inner and outer compartments - Q quenching of fluorescence - BChl Bacteriochlorophyll - ACMA 9-amino-6-chloro-2-methoxyacridine - 9AA 9-aminoacridine - Tricine N-tris-(hydroxymethyl)methylglycine - MES 2-morpholinoethanesulfonic acid - FCCP carbonylcyanide-p-trifluoro-methoxy-phenylhydrazone - CCCP carbonylcyanide-m-chloro-phenylhydrazone     

Characterization of recombinant human renin: Kinetics,pH-stability, and peptidomimetic inhibitor binding

The kinetic behavior andpH-stability of recombinant human renin was analyzed using a new fluorogenic substrate based on the normal P₆-P₃ renin cleavage sequence in human angiotensinogen. The design of this fluorogenic substrate makes possible, for the first time, direct monitoring of the kinetics of proteolytic conversion of prorenin to renin. ThepH-stability profile for renin, measured with the substrate at 25°C, indicated a broad plateau of stability betweenpH 6.0 and 10.0. Analysis of thepH-activity profile of renin for the substrate indicated a minimumK _m (1.8 µM) atpH 7.4 and a maximumV _m betweenpH 7.4 and 8.0. The thermodynamics of the binding of a novel, soluble, peptidomimetic inhibitor to renin indicated it is possible to retain the tight-binding characteristics and enthalpy contributions to binding of larger peptide-derived inhibitors, while reducing inhibitor size and entropic contributions to binding. A novel derivative of the fluorogenic substrate, containing a 3-methyl histidine substitution at the P₂ site, was used to test the recent hypothesis that renin functions by virtue of substrate-directed catalysis.     

Expedient syntheses of neoglycoproteins using phase transfer catalysis and reductive amination as key reactions

Starting from peracetylated chloro- or bromo-glycosyl donors ofN-acetylneurmainic acid,N-acetylglucosamine, glucose and lactose, the correspondingp-formylphenyl glycosides were synthesized stereospecifically under phase transfer catalysed conditions at room temperature in yields of 38–67%. After Zemplén de-O-acetylation, the formyl groups were directly and chemoselectively coupled to the lysine residues of bovine serum albumin by reductive amination using sodium cyanoborohydride. The conjugation reactions were followed as a function of time and under a series of different molar ratios of the reactants to provide glycoconjugates of varying degree of antigenicities. Thus, carbohydrate protein conjugates were made readily available using essentially two key reactions.Presented in part at the 15th International Carbohydrate Symposium, Yokohama, Japan, August 12–17, 1990.     

Binding protein dependent transport of C4-dicarboxylates in Rhodobacter capsulatus

The characteristics of malate transport into aerobically grown cells of the purple photosynthetic bacterium Rhodobacter capsulatus were determined. A single transport system was distinguished kinetically which displayed a K_t value of 2.9 ± 1.2 μM and V_max of 43 ± 6 nmol · min^-1 · mg^-1 protein. Competition experiments indicated that the metabolically related C4-dicarboxylates succinate and fumarate are also transported by this system. Malate uptake was sensitive to osmotic shock and evidence from the binding of radiolabelled malate and succinate to periplasmic protein fractions indicated that transport is mediated by a dicarboxylate binding protein. The activity of the transport system was studied as a function of external and internal pH and it was found that a marked activation of uptake occurred at intracellular pH values greater than 7. The use of a high affinity binding protein dependent system to transport a major carbon and energy source suggests that Rhodobacter capsulatus would be capable of obtaining growth sustaining quantities of C4-dicarboxylates even if these were present at very low concentrations in the environment.     

Numerical simulation of thermal bone necrosis during cementation of femoral prostheses

The implant of a femoral prosthesis is a critical process because of the relatively high temperature values reached at the bone/cement interface during the cementation of the infibulum. In fact, the cement is actually a polymer that polymerizes in situ generating heat. Moreover, the conversion of monomer into polymer is never 100%; this is dangerous because of the toxicity of the monomer. In this paper, we present a 3-D axisymmetric mathematical model capable of taking into account both the geometry of the implant and the chemical/physical properties of the cement. This model, together with its numerical simulation, thus represents a useful tool to set up the optimal conditions for the new materials developed in this orthopaedic field. The real complex geometry is assumed to be a bone/cement/metallic system having cylindrical symmetry, thus allowing the model to be reduced to two space variables. The cementation process is described by the Fourier heat equation coupled with a suitable polymerization kinetics. The numerical approximation is accomplished by semi-implicit finite differences in time and finite elements in space with numerical quadrature. The full discrete scheme amounts to solve linear positive definite symmetric systems preceded by an elementwise algebraic computation. We present various numerical simulations which confirm some critical aspects of this orthopaedic fixing technique such as thermal bone necrosis and the presence of unreacted residual monomer.This work was partially supported by MURST (Fondi per la Ricerca Scientifica 40%) and CNR (IAN, Contract 880032601, and Progetto Finalizzato Sistemi Informatici e Calcolo Parallelo, Sottoprogetto Calcolo Scientifico per Grandi Sistemi) of Italy