Temperature dependence of histidine ionization constants in myoglobin

The standard enthalpy of ionization of six titratable histidines in horse metaquomyoglobin was determined by repeating proton NMR titrations as a function of temperature and using the van't Hoff relationship. It was found that deltaH degrees varies between 16 and 37 kJ mol(-1) in the protein, compared with a value of 29 kJ mol(-1) in free histidine. The standard entropy change was evaluated by combining the enthalpy and free energy changes derived from the pKa values. Although the entropy change could not be precisely and accurately obtained by this method, it could be established that it spans a wide range, from -60 to 0 J K(-1) mol(-1), about the value of -23 J K(-1) mol(-1) for the free histidine. The entropy change was used within the framework of enthalpy-entropy compensation to partition the solvation component from the standard thermodynamic quantities for each of the titrating residues. It was shown that the partitioning of the values in the protein is not readily understood in terms of solvent accessibility or electrostatic interactions. The contribution of solvation effects to the temperature response appeared to be significant only in the case of His-119 and His-48. The standard quantities were also used to explore the energetics of proton binding in the native state at temperatures below the onset of thermal denaturation.     

Ionization constants of weak acids and bases in organic solvents

A discussion of the influence of organic solvents on pKa values is presented. Enthalpy and entropy of ionization in organic solvents are compared with aqueous systems. The impact of the solvent on the ionization constants is interpreted based on the free energy of transfer applied to all particles involved in the ionization reaction of acids and bases, and the concept of the 'medium effect' on these species. The limitation of Born's approach (which takes into account only electrostatic effects on the ionization equilibrium) is demonstrated and the importance of solute-solvent interactions on the change of the pKa values emphasized.     

Universality of thermodynamic constants governing biological growth rates

Background

Mathematical models exist that quantify the effect of temperature on poikilotherm growth rate. One family of such models assumes a single rate-limiting ‘master reaction’ using terms describing the temperature-dependent denaturation of the reaction''s enzyme. We consider whether such a model can describe growth in each domain of life.

Methodology/Principal Findings

A new model based on this assumption and using a hierarchical Bayesian approach fits simultaneously 95 data sets for temperature-related growth rates of diverse microorganisms from all three domains of life, Bacteria, Archaea and Eukarya. Remarkably, the model produces credible estimates of fundamental thermodynamic parameters describing protein thermal stability predicted over 20 years ago.

Conclusions/Significance

The analysis lends support to the concept of universal thermodynamic limits to microbial growth rate dictated by protein thermal stability that in turn govern biological rates. This suggests that the thermal stability of proteins is a unifying property in the evolution and adaptation of life on earth. The fundamental nature of this conclusion has importance for many fields of study including microbiology, protein chemistry, thermal biology, and ecological theory including, for example, the influence of the vast microbial biomass and activity in the biosphere that is poorly described in current climate models.     

Kinetic and thermodynamic parameters for Schiff base formation of vitamin B6 derivatives with amino acids

Thermodynamic and kinetic parameters for Schiff base formation of pyridoxal 5'-phosphate and pyridoxal with epsilon-aminocaproic acid as well as of pyridoxal 5'-phosphate with L-serine were obtained in 0.1 M sodium pyrophosphate buffer as a function of temperature. Changes in enthalpy, which were determined by direct microcalorimetry, were small at 25 degrees C, but varied strongly with pH for the reaction of pyridoxal 5'-phosphate with the amino acids. In contrast to the fast Schiff base formation of pyridoxal 5'-phosphate, a very slow reaction was found for pyridoxal and epsilon-aminocaproic acid concomitant with a larger change in enthalpy. By preventing hemiacetal formation the phosphate moiety plays a crucial role.     

Cooperative and thermodynamic parameters for oligoinosinate-polycytidylate complexes

The cooperative nature of the binding between polycytidylate and the oligoinosinates I(pI)_5–10 has been determined. Using the data of Tazawa, Tazawa, and Ts'o, it is shown that knowledge of the slope of the adsorption isothern allows one to determine the oligomer-polymer binidng constant, the oligomer–oligomer interaction constant, and the average degree of association (cooperative clustering) of the oligomers on the polymer. Knowledge of the above equilibrium constants as a function of temperature yields the respective thermodynamic parameters; no assumptions need to be made about the nature of the equilibrium constants or the thermodynamic parameters. For very long chains of polycytidylate, simple, explicit relations are given for the determination of the equilibrium constants involved. For finite chains of polycytidylate, the calculation of a single graph for each oligomer and polymer size allows the equilibrium constants to be determined for all experimental conditions of temperature and concentration. We find that the enthalpy and entropy of binding an oligomer n, bases to be δH_n = ±13.7 ? n(6.65) and δS_n = +32.5 ? n(18.8) given, respectively, in kcal/mole and e.u.; these parameters predict a melting temperature of 81°C for the poly(I)·poly(C) complex compared with the experimental value of 75°C. If the enthalpy is interpreted as arising from a sum of hydrogen bonding and stacking interactions, then the enthalpy of stacking is ?13.7 kcal/mole while the enthalpy of hydrogen bonding is +7 ± 4 kcal/mole; the positive enthalpy of hydrogen bonding presumably is a result of the fact that in the inosine-cytosine base pair, only two of the three sites on cytosine can hydrogen bond, the third being blocked from hydrogen bonding with water. The enthalpy of interaction between neighboring bound oligomers is found to be ?10.4 kcal/mole while the corresponding entropy is ?26.1 e.u. The binding is bound to be cooperative, though the extent of clustering varies markedly with temperature; the average number of oligomers in a cluster on the polymer is found to about five at a melting temperature of 25°C. The approach and equations given have generally applicability to oligomer-polymer associations.     

Ionization constants and solubility of compounds involved in enzymatic synthesis of aminopenicillins and aminocephalosporins

The article deals with experimental determination of ionization constants and solubility for the compounds (target products, initial β-lactams, acylating agents and by-products) involved in enzymatic synthesis of some therapeutically used aminopenicillins and aminocephalosporins, namely ampicillin, amoxicillin, cephalexin, cephadroxil, cephaloglycin, cefaclor, cefprozil, cefatrizine. Methodology of investigations and the evaluation of experimental data for the determination of ionization constants and solubility of the different type electrolytes are presented. Applications of the methods based on acid–base potentiometric titration and on determination of solubility–pH dependence of assayed substances are discussed. The original data on ionization constants and solubility of amoxicillin, cefprozil, cefatrizine, cephadroxil and initial β-lactams for production of cefaclor, cefprozil and cefatrizine, as well as solubility of by-product d-(−)-p-hydroxyphenylglycine are presented. Experimentally determined parameters and constants available in the literature for all abovementioned aminopenicillins and aminocephalosporins are collected. These data might be used for choice of the conditions of both processes: the enzymatic synthesis and the isolation of the product from reaction mixture.     

Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence

Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R² = 0.9427) between our calculations and the pK_a values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R² > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pK_a values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.     

Size and structure of antigen-antibody complexes: thermodynamic parameters

The role of antigen-antibody (Ag-Ab) complexes in the immune response depends, in part, on the size of the complexes. Previously, we combined electron microscopy with classical and quasi-elastic light scattering to characterize the molecular weight distribution and the conformation of Ag-Ab complexes made from bovine serum albumin (BSA) and pairs of anti-BSA monoclonal antibodies at a single concentration and Ag:Ab molar ratio. In this report, the molecular weight distribution of Ag-Ab complexes was determined by classical light scattering at a single Ag:Ab ratio and over a range of concentrations, and binding of BSA to pairs of MAb was determined by radioimmunoassay at several Ag:Ab molar ratios. A thermodynamic model was developed for the equilibrium size distribution of Ag-Ab complexes formed between a pair of MAb, each with unique affinity and specificity, and an Ag containing a single epitope for each of the pair of MAb. The combined experimental data were used in conjunction with the model to determine the values of cyclization and polymerization constants. Successful determination of the parameters required data from both classical light scattering and electron microscopy. Cyclization constants were lower than those reported in other studies of Ag-Ab complexes; this may be attributable to our use of a protein Ag, as compared to a divalent hapten. In two out of three cases, cyclization constants increased with increasing number of Ab in the complex, in contrast to previous assumptions. The validity of the thermodynamic model was further shown by its ability, in combination with conformational and hydrodynamic model, to predict the hydrodynamic radius of the complexes over a wide range of experimental conditions.