Deamidation of glutaminyl residues: dependence on pH, temperature, and ionic strength

We have shown the dependence of the deamidation half-times of the peptides, GlyLeuGlnAlaGly and GlyArgGlnAlaGly upon pH, temperature, and ionic strength. Increase in temperature or ionic strength, variation of pH to pH′s higher or lower than pH 6, and the use of phosphate buffer rather than Tris buffer at high pH all decrease the half-time of dcamidation. Temperature increase of 20°C or pH change of 2 pH units decreases the half-time about fivefold, while increase of one ionic strength unit decreases the half-time about twofold. In pH 7.4, I = 0.2, 37.0°C phosphate buffer, the deamidation half-times are 663 ± 74 and 389 ± 56 days respectively for the two peptides, GlyLeuGlnAlaGly and GlyArgGlnAlaGly.These experiments should serve as a warning to peptide and protein experimenters that even the more stable glutaminyl residues are unstable with respect to deamidation in certain solvent conditions. These experiments also provide, along with previously reported experiments on asparaginyl peptides (7), some quantitative data to help with the extrapolation of in vitro deamidation experiments to in vivo deamidation conditions.     

Direct calorimetric analysis of the enzymatic activity of yeast cytochrome c oxidase.

The kinetic and thermodynamic parameters associated with the enzymatic reaction of yeast cytochrome c oxidase with its biological substrate, ferrocytochrome c, have been measured by using a titration microcalorimeter to monitor directly the rate of heat production or absorption as a function of time. This technique has allowed determination of both the energetics and the kinetics of the reaction under a variety of conditions within a single experiment. Experiments performed in buffer systems of varying ionization enthalpies allow determination of the net number of protons absorbed or released during the course of the reaction. For cytochrome c oxidase the intrinsic enthalpy of reaction was determined to be -16.5 kcal/mol with one (0.96) proton consumed for each ferrocytochrome c molecule oxidized. Activity measurements at salt concentrations ranging from 0 to 200 mM KCl in the presence of 10 mM potassium phosphate, pH 7.40, and 0.5 mM EDTA display a biphasic dependence of the electron transferase activity upon ionic strength with a peak activity observed near 50 mM KCl. The ionic strength dependence was similar for both detergent-solubilized and membrane-reconstituted cytochrome c oxidase. Despite the large ionic strength dependence of the kinetic parameters, the enthalpy measured for the reaction was found to be independent of ionic strength. Additional experiments involving direct transfer of the enzyme from low to high salt conditions produced negligible enthalpy changes that remained constant within experimental error throughout the salt concentrations studied (0-200 mM KCl). These results indicate that the salt effect on the enzyme activity is of entropic origin and further suggest the absence of a major conformational change in the enzyme due to changes in ionic strength.(ABSTRACT TRUNCATED AT 250 WORDS)     

Modeling and artificial intelligence approaches to enzyme systems

Modeling is a means of formulating and testing complex hypotheses. Useful modeling is now possible with biological laboratory microcomputers with which experimenters feel comfortable. Artificial intelligence (AI) is sufficiently similar to modeling that AI techniques, now becoming usable on microcomputers, are applicable to modeling. Microcomputer and AI applications to physiological system studies with multienzyme models and with kinetic models of isolated enzymes are described. Using an IBM PC microcomputer, we have been able to fit kinetic enzyme models; to extend this process to design kinetic experiments by determining the optimal conditions; and to construct an enzyme (hexokinase) kinetics data base. We have also used a PC to do most of the constructing of complex multienzyme models, initially with small simple BASIC programs; alternative methods with standard spreadsheet or data base programs have been defined. Formulating and solving differential equations in appropriate representational languages, and sensitivity analysis, are soon likely to be feasible with PCs. Much of the modeling process can be stated in terms of AI expert systems, using sets of rules for fitting and evaluating models and designing further experiments. AI techniques also permit critiquing and evaluating the data, experiments, and hypotheses being modeled, and can be extended to supervise the calculations involved.     

Evidence for the interaction between the calcium indicator 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid and calcium-binding proteins

Stopped-flow and static difference spectroscopy experiments have shown that the calcium indicator 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA) interacts with several different calcium-binding proteins (beta-trypsin, parvalbumin, and calmodulin) and with serum albumin under experimental conditions commonly used in biophysical studies. The interaction decreases at high ionic strength. EDTA competes with BAPTA in the interaction with the proteins.     

Quasi-elastic light scattering studies of hyaluronic acid solutions

Autocorrelation functions for the intensity of laser light scattered from solutions of hyaluronic acid have been measured under a variety of experimental conditions. The form of these functions is consistent with the large amount of long-range intra- and intermolecular interactions characteristic of polyelectrolyte solutions. Further experiments have been performed in order to study the effect of hyaluronic acid on the Brownian diffusion of polystyrene spheres. Using several different sphere sizes as solution probes, the importance of the ionic environment in determining hyaluronic confirmation has been demonstrated.     

Discriminatory interaction of purified eukaryotic initiation factors 4F plus 4A with the 5' ends of reovirus messenger RNAs

The interaction of several reovirus mRNAs with cap-binding initiation factors has been investigated. Two quantitative experimental techniques have been applied to this question: (a) the rates of reaction of different mRNAs with tobacco acid pyrophosphatase and (b) the extent of cross-linking of different mRNAs to initiation factors in the presence and absence of ATP. The effects of ionic strength on these reactions have also been investigated. Our results demonstrate for the first time that the purified initiation factors interact differentially with purified reovirus mRNAs under competitive conditions and thus confirm earlier interpretations based on kinetic data. Comparison of the data from these studies with the translational behavior of the reovirus mRNAs, both in vitro and in vivo, has also led to specific predictions about features of these mRNAs that determine their competitive efficiencies. 1) Under ordinary ionic conditions, the steric accessibility of the m7G cap moiety of a reovirus mRNA appears to be a major determinant of its translation rate. 2) When the ionic strength is increased to supranormal levels, an additional feature, which may simply be the amount of secondary structure formed by sequences proximal to the cap, can become rate-limiting for several, but not all, of these mRNAs.     

Initiation of Bacillus subtilis Ribonucleic Acid Polymerase on Deoxyribonucleic Acid from Bacteriophages 2C, φ29, T4, and Lambda

Ribonucleic acid (RNA) synthesis primed by bacteriophage T4 or lambda deoxyribonucleic acid (DNA) with Bacillus subtilis RNA polymerase is severely inhibited by high ionic strength. In contrast, RNA synthesis on B. subtilis bacteriophage 2C, SPO1, or phi29 DNA is only moderately affected under similar conditions. The basis of this inhibition lies in the inability of the enzyme to initiate RNA chains with adenosine triphosphate or guanosine triphosphate (ATP, GTP). Binding to templates and the rate of catalysis in high salt after initiation do not seem to be affected. Incorporation of gamma-(32)P-ATP and GTP under a variety of conditions suggests that the specificity of B. subtilis RNA polymerase is different from that of the Escherichia coli enzyme and that it recognizes few promoters on T4 and lambda DNA. Although B. subtilis RNA polymerase initiates RNA chains primarily with ATP or GTP, initiations with pyrimidines can occur on DNA molecules in which hydroxymethyluracil replaces thymine. RNA synthesis on denatured DNA does not seem to be inhibited by high ionic strength, and on native T4 or lambda DNA the inhibition of initiation at constant ionic strength is inversely but not linearly proportional to the ionic radii of cations used to stabilize bihelical DNA to denaturation.     

Neuronal activity: from in vitro preparation to behaving animals.

The knowledge of the mechanisms regulating electric neuronal activity is fragmented by the wide variety of techniques and experimental models currently used in neurophysiological research. The interest and importance of the results obtained in any research is improved when interpreted in the perspective of the organism functioning as a whole in physiological conditions. Such interpretation, freed of the constraints imposed by the different techniques and experimental conditions used, is especially important when discussing together results obtained at the behavioral, cellular, and molecular level. This article outlines some of the key factors to consider when experiments from different models are interpreted together.     

Rotational dynamics of transfer ribonucleic acid: effect of ionic strength and concentration

We have investigated the influence of ionic strength and nucleic acid concentration on the rotational Brownian motion of Escherichia coli tRNA1Val by studying the decay of the fluorescence polarization anisotropy (FPA) of intercalated ethidium on a nanosecond time scale. The rotational relaxation time tau R remains essentially constant as the ionic strength is varied from 2 to 100 mM at a tRNA concentration of 54 mg/mL. tau R also remains practically unchanged as the tRNA concentration is varied from 0.3 to 54 mg/mL at an ionic strength of 130 mM. Present hydrodynamic theories generally predict a more pronounced concentration dependence for rotational diffusion than we observe. This disagreement may result from a nonrandom distribution of the tRNA molecules in solution due to electrostatic interactions. By combining independent data from time-resolved nuclear Overhauser effect (NOE) cross-relaxation experiments and FPA experiments on the same tRNA, we are able to estimate the interproton spacing for the guanine N1-H and the uracil N3-H of the GU-50 base pair in E. coli tRNA1Val. This distance is 0.272 nm.     

Neuronal activity: from in vitro preparation to behaving animals

The knowledge of the mechanisms regulating electric neuronal activity is fragmented by the wide variety of techniques and experimental models currently used in neurophysiological research. The interest and importance of the results obtained in any research is improved when interpreted in the perspective of the organism functioning as a whole in physiological conditions. Such interpretation, freed of the constraints imposed by the different techniques and experimental conditions used, is especially important when discussing together results obtained at the behavioral, cellular, and molecular level. This article outlines some of the key factors to consider when experiments from different models are interpreted together.     

Neuronal activity

The knowledge of the mechanisms regulating electric neuronal activity is fragmented by the wide variety of techniques and experimental models currently used in neurophysiological research. The interest and importance of the results obtained in any research is improved when interpreted in the perspective of the organism functioning as a whole in physiological conditions. Such interpretation, freed of the constraints imposed by the different techniques and experimental conditions used, is especially important when discussing together results obtained at the behavioral, cellular, and molecular level. This article outlines some of the key factors to consider when experiments from different models are interpreted together.     

Changes in the quaternary structure of phosphoenolpyruvate carboxylase induced by ionic strength affect its catalytic activity

Phosphoenolpyruvate carboxylase from maize leaves dissociated into dimers and/or monomers when exposed to increasing ionic strength (e.g. 200-400 mM NaCl) as indicated by gel filtration experiments. Changes in the oligomerization state were dependent on pH, time of preincubation with salt and protein concentration. A dissociation into dimers and monomers was observed at pH 8, while at pH 7 dissociation into the dimeric form only was observed. Exposure of the enzyme to higher ionic strength decreased the activity in a time-dependent manner. Turnover conditions and glucose 6-phosphate protected the carboxylase from the decay in activity, which was faster at pH 7 than at pH 8. The results suggest that changes in activity of the enzyme, following exposure to high ionic strength, are the consequence of dissociation. Tetrameric and dimeric forms of the phosphoenolpyruvate carboxylase seemingly reveal different catalytic properties. We suggest that the distinct catalytic properties of the different oligomeric species of phosphoenolpyruvate carboxylase and changes in the equilibrium between them could be the molecular basis for an effective regulation of metabolite levels by this key enzyme of C4 plants.     

Flavobacterium meningosepticum peptide:N-glycosidase: influence of ionic strength on enzymatic activity.

Flavobacterium meningosepticum peptide:N-glycosidase-mediated deglycosylation of N-linked glycan strands of glycoproteins has been found to be strongly influenced by the ionic strength of the assay medium. By use of a modification of a previously published assay procedure for quantitative analysis of glycan release we have been able to improve reproducibility and thus to compare the extent of deglycosylation achieved under a variety of conditions of ionic strength. We have observed that enzyme activity is adversely affected by high ionic strength buffers such as those recommended for deglycosylation of various glycoproteins and recommend the use of low ionic strength buffers for routine use.     

Multiple Forms of Choline Acetyltransferase from Rat Brain

WE have found that several different forms of choline acetyl-transferase (ChAc) from rat brain can be separated by isoelectric focusing. Such heterogeneity of ChAc is of particular interest in the context of its ultrastructural localization. Subcellular fractionation^1–4 and histochemistry⁵ have shown that the enzyme in rat, in conditions of low ionic strength and pH, adhered to several different membranous structures.     

W-reactivation of phage lambda in recF, recL, uvrA, and uvrB mutants of E. coli K-12.

Summary Assay conditions are described which permit detection of cryptic temperature sensitive RNA polymerases in vitro. RNA polymerase was prepared from fifteen different temperature sensitive mutants of Salmonella typhimurium chosen at random from a larger group isolated by localized mutagenesis and uridine suicide techniques. The dependence of enzyme activity on temperature, ionic strength and pH was studied in vitro. Assays at higher ionic strength (0.23 M) and temperature (50°C) distinguish three classes of mutants (Table 2). Activity of seven mutant RNA polymerases (called Class 1) under these conditions was 1% to 5% that of the parental RNA polymerase. Five mutant RNA polymerases (called Class 2) had 18% to 64% of the parental activity and three were not distinguishable from the parental enzyme under these conditions. Mixing experiments showed that the defect in Class 1 mutant enzymes is a property of the enzymes and not due to a diffusible inhibitor. In one case the lesion was shown to reside in the core enzyme. Class 1 mutant RNA polymerases were shown to be irreversibly inactivated during the assay at higher temperature and ionic strength. This suggests that the Class 1 enzymes may be more thermolabile than the wild type enzyme or may fail to be protected from thermal denaturation by formation of a ternary complex with template and product. We conclude that the method used to isolate these mutants (Young et al., 1976) and the assay described here (Table 2) are efficient ways to isolate and detect temperature sensitive RNA polymerase mutants of Salmonella typhimurium.     

Mixture design as a first step for optimization of fermentation medium for cutinase production from <Emphasis Type="Italic">Colletotrichum lindemuthianum</Emphasis>

Cutinase enzymes from fungi have found diverse applications in industry. However, most of the available literature on cutinase production is related to the cultivation of genetically engineered bacteria or yeast cells. In the present study, we use mixture design experiments to evaluate the influence of six nutrient elements on production of cutinase from the fungus Colletotrichum lindemuthianum. The nutritional elements were starch, glucose, ammonium sulfate, yeast extract, magnesium sulfate, and potassium phosphate. In the experimental design, we imposed the constraints that exactly one factor must be omitted in each set of experiments and no factor can account for more than one third of the mixture. Thirty different sets of experiments were designed. Results obtained showed that while starch is found to have negative influence on the production of the enzyme, yeast extract and potassium phosphate have a strong positive influence. Magnesium sulfate, ammonium sulfate, and glucose have low positive influence on the enzyme production. Contour plots have also been created to obtain information concerning the interaction effects of the media components on enzyme production.     

A “parallel plate” electrostatic model for bimolecular rate constants applied to electron transfer proteins

A “parallel plate” model describing the electrostatic potential energy of protein-protein interactions is presented that provides an analytical representation of the effect of ionic strength on a bimolecular rate constant. The model takes into account the asymmetric distribution of charge on the surface of the protein and localized charges at the site of electron transfer that are modeled as elements of a parallel plate condenser. Both monopolar and dipolar interactions are included. Examples of simple (monophasic) and complex (biphasic) ionic strength dependencies obtained from experiments with several electron transfer protein systems are presented, all of which can be accommodated by the model. The simple cases do not require the use of both monopolar and dipolar terms (i.e., they can be fit well by either alone). The biphasic dependencies can be fit only by using dipolar and monopolar terms of opposite sign, which is physically unreasonable for the molecules considered. Alternatively, the high ionic strength portion of the complex dependencies can be fit using either the monopolar term alone or the complete equation; this assumes a model in which such behavior is a consequence of electron transfer mechanisms involving changes in orientation or site of reaction as the ionic strength is varied. Based on these analyses, we conclude that the principal applications of the model presented here are to provide information about the structural properties of intermediate electron transfer complexes and to quantify comparisons between related proteins or site-specific mutants. We also conclude that the relative contributions of monopolar and dipolar effects to protein electron transfer kinetics cannot be evaluated from experimental data by present approximations.     

Analysis of hSCOMT adsorption in bioaffinity chromatography with immobilized amino acids: the influence of pH and ionic strength

In the last years, chromatographic supports with amino acids as immobilized ligands (AAILs) were been used successfully for isolation of several biomolecules, such as proteins. In this context and based on specific properties of human soluble cathecol-O-methyltransferase (hSCOMT), we screened and analyzed the effect of experimental conditions, such as pH and ionic strength manipulation for hSCOMT adsorption, over six different AAIL commercial supports. Typically, the proteins adsorption on AAIL chromatographic supports is around their pI. While hSCOMT isoelectric point is around 5.5, this parameter leads us to design new adsorption strategies with several acid buffers for the chromatographic process. In terms of the ionic strength manipulation strategy, the results suggest that the AAILs-hSCOMT interaction is strongly affected by the intrinsic hSCOMT hydrophobic domains. On the other hand, the interaction mechanism of hSCOMT on amino acid resins appears to be highly dependent on the binding pH. Consequently the retention mechanism of the target enzyme on the AAILs can be as either in typical hydrophobic or ionic chromatographic supports, so long as selecting various mobile phases and separation conditions. In spite of these mixed-mode interactions and operation strategies, the elution of interferent's proteins from recombinant host can be achieved only with suitable adjusts in pH mobile phase set point. This lead to a new approach in biochromatographic COMT retention, while possess a higher specificity than other chromatographic methods reported in literature.     

Engineering of human lysozyme as a polyelectrolyte by the alteration of molecular surface charge

The surface positive charges of human lysozyme were either increased or decreased to alter the electrostatic interaction between enzyme and substrate in the lytic action of human lysozyme using site-directed mutagenesis. The amino acid substitutions accompanying either the addition or the removal of two units of positive charge have shifted the optimal ionic strength (NaCl concentration in 10 mM Mes buffer, pH 6.2) for the lysis of Micrococcus lysodeikticus cell from 0.04 M to 0.1 M and from 0.04 M to 0.02 M respectively. In addition to the change in ionic strength-activity profile, the pH-activity profile and the effect of a polycationic electrolyte, poly-L-Lys-HCl, on the lytic activity were significantly changed. Owing to the shifts in both ionic strength profiles and pH profiles the Arg74/Arg126 mutant has become a better catalyst than wild-type enzyme under the conditions of high ionic strength and high pH, and the Gln41/Ser101 mutant has become a better catalyst under the conditions of low ionic strength and low pH.