Handedness control of peptide helices by amino acid side-chain chirality: Ile/aIle peptides

A set of four hexapeptide sequences, each characterized by four strongly helicogenic Aib residues and all combinations of two isomeric Ile/aIle residues at positions 2 and 5, was synthesized by solution methods and fully characterized. A detailed solution (by FT-IR absorption, NMR, and CD techniques) and solid/crystalline state (by X-ray diffraction) conformational investigation allowed us to validate our assumption that all four peptides are folded in well-developed 3(10)-helical structures. However, the most relevant conformational conclusion extracted from the present 3D-analysis is that the handedness of the 3(10)-helical structures formed does not seem to be sensitive to the configurational change at the beta-carbon atom of the constituent Ile versus the diastereomeric aIle residues (in other words, the dominant control on this important structural parameter appears to be exerted by the chirality of the amino acid alpha-carbon atom). These results complement published findings on the diverging relative stabilities of the intermolecularly H-bonded beta-sheet structures generated by Ile versus aIle homo-oligopeptides.     

Effects of temperature on lactose hydrolysis by immobilized beta-galactosidase in plug-flow reactor

The hydrolysis of lactose using immobilized beta-galactosidase (from Aspergillus niger) on phenol-formaldehyde resin was studied at temperatures between 8 and 60 degrees C and initial lactose concentrations ranging from 2.5 to 20.0%. A model involving enzyme-galactose complex similar to Michaelis-Menten kinetics with competitive product (galactose) inhibition is suitable to describe the lactose hydrolysis reaction. A small degree of lack of fit between the model and the data was found to be due to the formation of oligosaccharides. Thermal deactivation of lactase follows first-order reaction mechanism. The effect of temperature on the reaction and the deactivation rate constants follows the Arrhenius relationship. The Oligosaccharide formation was not significantly affected by the temperature when the initial lactose concentration was 5%. A design equation for the plug-flow immobilized lactase reactor was developed from the reaction and the deactivation kinetics and was used to find the optimal operating temperature. The optimal temperature was found to be dependent on the operating time but not on the lactose concentration or the conversion. The optimal operating temperature is 60 degrees C when operating time is short but is close to 35 degrees C for a long operating time. A preliminary economic analysis indicates that the optimal operating temperature is 43, 38.5, and 33 degrees C when the operating time is 300 days, 1000 days, and infinity, respectively.     

Engineering increased stability in the antimicrobial peptide pediocin PA-1

Pediocin PA-1 is a food grade antimicrobial peptide that has been used as a food preservative. Upon storage at 4 degrees C or room temperature, pediocin PA-1 looses activity, and there is a concomitant 16-Da increase in the molecular mass. It is shown that the loss of activity follows first-order kinetics and that the instability can be prevented by replacing the single methionine residue (Met31) in pediocin PA-1. Replacing Met by Ala, Ile, or Leu protected the peptide from oxidation and had only minor effects on bacteriocin activity (for most indicator strains 100% activity was maintained). Replacement of Met by Asp was highly deleterious for bacteriocin activity.     

Hydrolysis kinetics of trisaccharides consisting of glucose, galactose, and fructose residues in subcritical water

The hydrolysis kinetics of trisaccharides consisting of glucose, galactose, and fructose residues with different glycosidic bonds, 1-kestose, d-melezitose, d-raffinose, and lactosucrose, in subcritical water were conducted over the temperature range of 150-230 degrees C and at a constant pressure of 10 MPa. The hydrolysis of trisaccharides in subcritical water proceeded consecutively, i.e., one cleavage of the two bonds antedated the other. The preceding cleavage was not expressed by the first-order kinetics, but by the kinetics considering the concentration of the acidic compounds, which were produced by the degradation of the constituent monosaccharides. The hydrolysis of the constituent disaccharides, except sucrose composed of the alpha-Glc-(1-->2)-beta-Fru bond, obeyed first-order kinetics. All of the rate constants of the hydrolytic kinetics were determined, and the values were found to depend on the type of bond.     

Effects of temperature on the hydrolysis of lactose by immobilized beta-galactosidase in a capillary bed reactor

The effects of temperature on the hydrolysis of lactose by immobilized beta-galactosidase were studied in a continuous flow capillary bed reactor. Temperature affects the rates of enzymatic reactions in two ways. Higher temperatures increase the rate of the hydrolysis reaction, but also increase the rate of thermal deactivation of the enzyme. The effect of temperature on the kinetic parameters was studied by performing lactose hydrolysis experiments at 15, 20, 25, 30, and 40 degrees C. The kinetic parameters were observed to follow an Arrhenius-type temperature dependence. Galactose mutarotation has a significant impact on the overall rate of lactose hydrolysis. The temperature dependence of the mutarotation of galactose was effectively modelled by first-order reversible kinetics. The thermal deactivation characteristics of the immobilized enzyme reactor were investigated by performing lactose hydrolysis experiments at 52, 56, 60, and 64 degrees C. The thermal deactivation was modelled effectively as a first order decay process. Based on the estimated thermal deactivation rate constants, at an operating temperature of 40 degrees C, 10% of the enzyme activity would be lost in one year.     

Thermodynamics of interactions between amino acid side chains: experimental differentiation of aromatic-aromatic, aromatic-aliphatic, and aliphatic-aliphatic side-chain interactions in water

A stationary phase for high-pressure liquid chromatography has been prepared by derivatizing microparticulate silica gel with functionality mimicking the side chain of isoleucine. The chromatographic retentions of a series of hydrophobic and amphiphilic amino acid analytes on this stationary phase (Ile MSP) using an aqueous mobile phase were measured as a function of temperature from 273 K to 323 K. Observed temperature dependencies are consistent with a constant change in heat capacity, DeltaC degrees P, upon binding of the analyte to the stationary phase. The curvatures of plots of retention data versus temperature (related to the magnitude of DeltaC degrees P) are distinctly different for retention of aromatic and aliphatic analytes, with retention of aliphatic analytes Val, Ile, and Leu exhibiting the characteristic signature of the hydrophobic effect, i.e., a large negative DeltaC degrees P upon desolvation from water and a maximum of retention around room temperature. Retention of aromatic analytes (Trp, Phe, and Tyr) involves smaller heat capacity changes and pronounced negative enthalpies of interaction with the stationary phase. Estimates of DeltaC degrees P for the interactions of analyte side chains with the Ile side chain were obtained by fitting the temperature dependence of retention to an expression derived from thermodynamic considerations and chromatographic theory. Similar estimates were made for interactions with the Phe side chain, using previously published data for a phenylalanine mimic stationary phase (Phe MSP) (. Protein Sci. 1:786-795). As with the Ile MSP, the retentions of aliphatic analytes show temperature dependencies markedly different from those of aromatic analytes. Data from both phases indicate that a realistic differentiation can be made between the interactions of various types of amino acid side chains tested (i.e., aliphatic/aliphatic, aliphatic/aromatic, and aromatic/aromatic) by comparison of the corresponding thermodynamic functions for pairwise interactions. The retention of leucine on the Phe MSP and that of phenylalanine on the Ile MSP showed similar DeltaC degrees P values, suggesting that the aromatic-aliphatic interaction is reasonably independent of the residue attached to the stationary phase. This result is consistent with a one-to-one interaction and suggests a simple way to estimate the column-dependent phase factor, making it possible to compare entropies and free energies of interaction obtained using different MSPs. The possibilities for using MSP-derived interaction potentials in folding simulations are discussed.     

Nutrition and carbon metabolism of Methanococcus voltae.

Methanococcus voltae is a heterotrophic, H2-oxidizing methanogenic bacterium. In complex medium, this bacterium has a doubling time of 1.2 h at its temperature optimum of 38 degrees C. In defined medium, optimal growth is obtained with 0.75 mM isoleucine, 0.75 mM leucine, 2.5 mM acetate, 5 mM NH4Cl, 84 mM MgSO4, 0.4 M NaCl, 1 mM CaCl2, 10 microM Fe2O3, and 0.2 microM NiCl2. In addition, pantothenate, sodium selenate, and cobalt stimulate growth. Optimal growth is obtained between pH 6.0 and 7.0 with either H2 or formate as the electron donor. The volatile fatty acids 2-methylbutyrate and isovalerate can substitute for isoleucine and leucine, respectively. Cellular carbon is derived from acetate (31%), isoleucine (22%), leucine (25%), and carbon dioxide (23%). The amino acids and fatty acids are incorporated almost exclusively into protein. A comparison of the incorporation of U-14C-amino acids and 1-14C-fatty acids indicated that the fatty acids are degraded during incorporation into cell protein. The distribution of carbon from the amino acids suggests that acetyl coenzyme A is not a major intermediate in the degradation of these compounds. Thus, M. voltae may convert isoleucine and leucine to other amino acids by a unique mechanism. The lipid carbon is derived largely from acetate. Thus, the isoprenoid lipids are synthesized de novo from acetate rather than by degradation of leucine. The carbon in the nucleic acids is derived from carbon dioxide (45%), the C-1 of acetate (25%), the C-2 of acetate (22%), and isoleucine and leucine (7%). This labeling pattern is consistent with known biochemical pathways.     

Methanolysis of sphingomyelin. Toward an epimerization-free methodology for the preparation of D-erythro-sphingosylphosphocholine

It is well known that acid hydrolysis of natural sphingomyelin in aqueous methanol or 1-butanol at refluxing temperature is accompanied by epimerization at the C-3 position of the long-chain base. An improved procedure for the hydrolysis of commercially available, naturally occurring sphingomyelin is described. Prolonged exposure (3;-4 days) of sphingomyelin to freshly prepared 0.5 M anhydrous methanolic hydrogen chloride (generated by trapping the gas evolved from the reaction of concentrated sulfuric acid with solid sodium chloride in anhydrous methanol) at 50 degrees C resulted in cleavage of the amide side chain. The extent of epimerization of the allylic alcohol stereocenter was quantified by integration of the C-5 signal of the (13)C nuclear magnetic resonance spectrum of lysosphingomyelin.The method described here is superior to the traditional acid hydrolysis methods because it provides the product as a approximately 10:1 ratio of d-erythro/l-threo epimers; in contrast, a ratio of approximately 1. 3:1 was obtained by the previous methods. We also report that use of dichloromethane as a cosolvent with N,N-dimethylformamide in the reaction of lysosphingomyelin with an activated fatty acid reduced the time required for completion of the N-acylation reaction.     

Glial Metabolism of Isoleucine

Isoleucine, together with leucine and valine, constitutes the group of branched-chain amino acids (BCAAs). BCAAs are transported from the blood into the brain parenchyma, where they can serve several distinct functions. Since brain tissue is known to oxidatively metabolize BCAAs to CO₂, they are considered as fuel material in brain energy metabolism. Also, in the case of leucine, cultured astrocytes have been reported to be able to completely oxidize BCAA. While the metabolism of leucine by astroglia-rich primary culture (APC) has already been studied in detail, the metabolic fates of isoleucine and valine in these cells remained to be identified. Therefore, in the present study an NMR analysis was performed of ¹³C-labelled metabolites generated in the catabolism of [U-¹³C]Ile by astrocytes and released by them into the incubation medium. APC potently removed isoleucine from the medium and metabolized it. The major isoleucine metabolites released from APC are 2-oxo-3-methylvalerate, 2-methylbutyrate, 3-hydroxy-2-methylbutyrate and propionate. To a lesser extent, APC generate and release also [2,3-¹³C]glutamine, [4,5-¹³C]glutamine and ¹³C-labelled isotopomers of lactate and citrate. These results show that APC can release into the extracellular milieu catabolites and several TCA cycle dependent metabolites resulting from the degradation of isoleucine. Special issue article in honor of Dr. George DeVries.     

Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution.

We improved the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by an in vivo evolutionary technique using an extreme thermophile, Thermus thermophilus, as a host cell. The leuB gene encoding B. subtilis 3-isopropylmalate dehydrogenase was integrated into the chromosome of a leuB-deficient strain of T. thermophilus. The resulting transformant showed a leucine-autotrophy at 56 degrees C but not at 61 degrees C and above. Phenotypically thermostabilized strains that can grow at 61 degrees C without leucine were isolated from spontaneous mutants. Screening temperature was stepwise increased from 61 to 66 and then to 70 degrees C and mutants that showed a leucine-autotrophic growth at 70 degrees C were obtained. DNA sequence analyses of the leuB genes from the mutant strains revealed three stepwise amino acid replacements, threonine-308 to isoleucine, isoleucine-95 to leucine, and methionine-292 to isoleucine. The mutant enzymes with these amino acid replacements were more stable against heat treatment than the wild-type enzyme. Furthermore, the triple-mutant enzyme showed significantly higher specific activity than that of the wild-type enzyme.     

Kinetic modeling of the enzymatic hydrolysis of pretreated cellulose

The production of sugars by the enzymatic hydrolysis of cellulose is a two-step process that includes conversion of the intermediate cellobiose to glucose by beta-glucosidase. The hydrolysis was followed by analyzing the two sugar products (cellobiose and glucose). The enzyme showed maximum activity at pH 4.8. Thermal deactivation was significant at temperatures above 45 degrees C. At 50 degrees C (optimum temperature) thermal deactivation was found to follow first-order kinetics. Several models were tested by modeling the kinetics of the reaction. Their parameter values were determined by numerical optimization, including temperature dependence. The best fitting model was a competitive product inhibition for the two reactions in the operational range.     

Thermodynamic studies of binding proteins: effects of temperature variations on substrate binding and conformation of the leucine-isoleucine-valine binding protein of Escherichia coli

The behaviour of the Leucine isoleucine Valine binding protein of Escherichia coli as a function of temperature has been examined. Substrate binding measurements showed a temperature dependence of the leucine-isoleucine-valine binding protein leucine complex formation constants. The protein-substrate complex was completely dissociated beyond 70 degrees C. In the range 5-65 degrees C the protein remained active but Van't Hoff's plots indicated changes of the reaction thermodynamic parameters. Large negative delta Cp values (--2.25 kJ mole-1 K-1 between 5 and 40 degrees C and--9.40 above 40 degrees C) indicate important substrate induced modifications of the protein conformation. Scanning calorimetry of the leucine isoleucine valine binding protein before and after addition of leucine was also performed. Two thermal events were recorded when the protein was substratefree and only one, at a higher temperature and more important, when the substrate was added. The results of these two approaches were in agreement in that both methods suggested a binding dependent conformational change of the protein which resulted in a greater stability of its structure.     

The kinetics of pancreatic ribonuclease reaction with alkaline and acidic forms of poly A

Summary The RNase hydrolysis of random-coil (alkaline form) poly A follows biphasic kinetics at low salt concentrations. However, its resistance to RNase increases with the ionic strength. Helical (acidic form) poly A is also susceptible to RNase but its hydrolysis follows first-order kinetics, and its resistance increases as the pH is lowered. These conformation-dependent kinetics of poly A hydrolysis are similar to those obtained in the hydrolysis of cellular RNA and reovirus double-stranded RNA.     

Isoleucine hydroxamate, an isoleucine antagonist

Isoleucine hydroxamate (Ile.Hdx) was found to inhibit the growth of Serratia marcescens and to antagonize isoleucine. At a low concentration of Ile.Hdx, at which the growth of the wild strain was completely inhibited, the growth of an isoleucine auxotroph was not inhibited in the medium containing a limiting amount of d-threonine as the isoleucine source. At a higher concentration, this antagonist exhibited a considerable inhibitory effect on the growth of the auxotroph. Ile.Hdx showed the same inhibitory effect as isoleucine on l-threonine dehydratase activity at the concentrations 10 times those of isoleucine. Ile.Hdx caused also derepression of isoleucine-valine biosynthetic enzymes and the derepression was overcome by isoleucine. These results indicate the Ile.Hdx causes growth inhibition by its effects on isoleucine metabolism.     

Thermal-alkaline solubilization of waste activated sludge as a pre-treatment stage for anaerobic digestion

This work studied the hydrolysis kinetics and the solubilization of waste activated sludge under a medium range temperature (50-90 degrees C) and pH in the alkaline region (8-11), as a pretreatment stage for anaerobic digestion. The hydrolysis rate for the solubilization of volatile suspended solids (VSS) followed a first-order rate. A linear polynomial hydrolysis model was derived from the experimental results leading to a satisfactory correlation between the hydrolysis rate coefficient, pH, and temperature. At pH 11 and a temperature of 90 degrees C the concentration of the VSS was 6.82%, the VSS reduction reached 45% within ten hours and at the same time the soluble COD was 70.000 mg/l and the total efficiency for methane production 0.28 l of CH4 per g of VSS loading.     

Agonistic activities of isoleucine8-angiotensin II in man

In order to clarify the importance of C-terminal phenylalanine in angiotensin II (ANG II) molecule, agonistic activities of a C-terminal substituted peptide, isoleucine8-angiotensin II (Ile8-ANG II), were studied in comparison with those of sarcosine1-, isoleucine8-angiotensin II (Sar1-, Ile8-ANG II) and isoleucine5-angiotensin II (Ile5-ANG II) in 5 normal men. When infused iv at a rate of 600 pmol/kg X min for 30 min, Ile8-ANG II and Sar1-, Ile8-ANG II raised the blood pressure to the same extent (15/15 mmHg on the average), while the average blood pressure increase was 21/21 mmHg after an iv infusion of Ile5-ANG II at a rate of 5 pmol/kg X min for 30 min. Duration of the pressor action after the cessation of each infusion was 50-90, 90-120 and 10-25 min, respectively. In each case plasma renin activity (PRA) decreased and plasma aldosterone (PA) increased. When infused iv at a rate of 10 pmol/kg X min (maximum non-pressor dose) for 120 min, both Ile8-ANG II and Sar1-, Ile8-ANG II lowered PRA and increased PA gradually, but 100 mg oral captopril given immediately before these infusions caused no significant increase in PRA or no significant decrease in PA but again a decrease in PRA and an increase in PA.(ABSTRACT TRUNCATED AT 250 WORDS)     

Chemical stability of prostacyclin (PGI2) in aqueous solutions.

The rate constant for the hydrolysis of prostacyclin (PGI2) to 6-keto-PGF1alpha was measured by monitoring the UV spectral change, over a pH range 6 to 10 at 25 degrees C and the total ionic strength of 0.5 M. The first-order rate constant (kdegreesobs) extrapolated to zero buffer concentration follows an expression, kdegreesobs = kH+ (H+), where kH+ is a second-order rate constant for the specific acid catalyzed hydrolysis. The value of kH+ obtained (3.71 x 10(4) sec-1 M-1) Is estimated approximately 700-fold greater than a kH+ value expected from the hydrolysis of other vinyl ethers. Such an unusually high reactivity of PGI2 even for a vinyl ether is attributed to a possible ring strain release that would occur upon the rate controlling protonation of C5. A Br?nsted slope (alpha) of 0.71 was obtained for the acid (including H3O+) catalytic constants, from which a pH independent first-order rate constant for the spontaneous hydrolysis (catalyzed by H2O as a general acid) was estimated to be 1.3 x 10(-6) sec-1. An apparent activation energy (Ea) of 11.85 Kcal/mole was obtained for the hydrolysis at pH 7.48, from which a half-life of PGI2 at 4 degrees C was estimated to be approximately 14.5 min. when the total phosphate concentration is 0.165 M (cf. 3.5 min. at 25 degrees C).     

The effect of amino acids on the temperature sensitive phenotype of the mammalian leucyl-tRNA synthetase mutant tsHl and its revertants.

The temperature sensitive leucyl-tRNA synthetase mutant tsHl and two revertants have been compared to the parental Chinese hamster ovary cells with respect to the effects of amino acid concentrations in the medium on growth. Elevating the leucine concentration 30- or 100-fold allowed tsHl to grow exponentially at 38.5 degrees C, normally the nonpermissive temperature. Partial revertants that had recovered some enzyme activity required smaller supplements for growth. Measurements of the leucine pools indicated that they respond directly to the extracellular leucine concentration and may mediate the effect. Use of combinations of amino acids confirmed that isoleucine has a similar though weaker effect on tsHl and identified an even weaker protection by valine. The triple combination of leucine, isoleucine and valine was a much more efficient medium supplement and three times normal concentrations of these amino acids supported growth of tsHl at 38.5 degrees C. It is postulated that they are acting at their respective aminoacyl-tRNA synthetases to help stabilize a complex which also contains the mutant leucyl-tRNA synthetase. The pool size measurements also showed that the leucine pools of tsHl and a revertant increased 2-fold more in a response to increased temperature than those of WT. It is suggested that this is a regulatory response to low leucyl-tRNA synthetase activity and is important in determining growth phenotypes.     

Preferential acid-catalyzed hydrolysis of the formamide linkage of N'-formylkynurenine in frozen solution.

Acid-catalyzed hydrolysis of the formamide linkage of N-acetyl-N'-formyl-L-kynurenineamide in frozen dilute hydrochloric acid solution followed first-order kinetics, yielding N-acetyl-L-kynurenineamide as the sole reaction product. The maximum rate of reaction in the frozen solution was found at around -7.5 degrees and approximated that of the reaction in liquid solution at 40 degrees. By freezing the dilute acid solution at -8 degrees the reaction was accelerated by 60 times compared with that in super-cooled liquid solution at the same temperature.     

Carboxymethylation of an active site glutamic acid residue of ribonuclease F1 iodoacetate

Ribonuclease (RNase) F1 was inactivated by incubation with an excess amount of iodoacetate at pH 5.5, 37 degrees C according to pseudo first-order kinetics. It was protected to various degrees, from inactivation by nucleotides, among which guanosine 2'-phosphate was most effective. The pseudo first-order rate constant was proportional to the reagent concentration, indicating that the reaction in reality follows second-order kinetics. The second-order rate constant was determined to be 25 x 10(-4) M-1 s-1. The inactivation rate was maximal at pH 5.5-6.0. When iodo[2-14C]acetate was used as the reagent, the stoichiometry of incorporation was determined to be 1.1 mol carboxymethyl group per mol of RNase F1 and glutamic acid residue 58 was assigned as the site of modification.