Thermodynamic molecular switch in macromolecular interactions

It is known that most living systems can live and operate optimally only at a sharply defined temperature, or over a limited temperature range, at best, which implies that many basic biochemical interactions exhibit a well-defined Gibbs free energy minimum as a function of temperature. The Gibbs free energy change, deltaG(o) (T), for biological systems shows a complicated behavior, in which deltaG(o)(T) changes from positive to negative, then reaches a negative value of maximum magnitude (favorable), and finally becomes positive as temperature increases. The critical factor in this complicated thermodynamic behavior is a temperature-dependent heat capacity change (deltaCp(o)(T) of reaction, which is positive at low temperature, but switches to a negative value at a temperature well below the ambient range. Thus, the thermodynamic molecular switch determines the behavior patterns of the Gibbs free energy change, and hence a change in the equilibrium constant, Keq, and/or spontaneity. The subsequent, mathematically predictable changes in deltaH(o)(T), deltaS(o)(T), deltaW(o)(T), and deltaG(o)(T) give rise to the classically observed behavior patterns in biological reactivity, as demonstrated in three interacting protein systems: the acid dimerization reaction of alpha-chymotrypsin at low pH, interaction of chromogranin A with the intraluminal loop peptide of the inositol 1,4,5-triphosphate receptor at pH 5.5, and the binding of L-arabinose and D-galactose to the L-arabinose binding protein of Escherichia coli. In cases of protein unfolding of four mutants of phage T4 lysozyme, no thermodynamic molecular switch is observed.     

Temperature, stability, and the hydrophobic interaction

Changes in free energy are normally used to track the effect of temperature on the stability of proteins and hydrophobic interactions. Use of this procedure on the aqueous solubility of hydrocarbons, a standard representation of the hydrophobic effect, leads to the conclusion that the hydrophobic effect increases in strength as the temperature is raised to approximately 140 degrees C. Acceptance of this interpretation leads to a number of far-reaching conclusions that are at variance with the original conception of the hydrophobic effect and add considerably to the complexity of interpretation. There are two legitimate thermodynamic functions that can be used to look at stability as a function of temperature: the standard Gibbs free energy change, deltaG degrees, and deltaG degrees/T. The latter is proportional to the log of the equilibrium constant and is sometimes called the Massieu-Planck function. Arguments are presented for using deltaG degrees/T rather than deltaG degrees for variations in stability with temperature. This makes a considerable difference in the interpretation of the hydrophobic interaction, but makes little change in the stability profile of proteins. Protein unfolding and the aqueous solubility of benzene are given as examples. The contrast between protein unfolding and the hydration of nonpolar molecules provides a rough estimate of the contribution of other factors that stabilize and destabilize protein structure.     

Interaction of water vapour with twenty different poly-L-amino acids and their excess hydration in presence of sodium chloride

Using the isopiestic vapour pressure technique, the magnitudes of excess binding of water and NaCl per mole of twenty different poly-L-amino acid residues, respectively in the presence of different bulk molefractions (X2) of NaCl have been evaluated from the mathematical expressions for the Gibbs surface excesses. At certain high ranges of NaCl concentration, the plot of -Gamma1 (2) versus X1/X2 becomes linear, so that moles of water and NaCl, respectively bound per mole of amino acid residue can be evaluated. -Gamma(2)1 is the excess moles of H20 per mole of amino acid residue and X1 and X2 stand for mole fractions of the water and NaCl, respectively in the sample system. Also, using the integrated form of the Gibbs absorption equation, the values of standard free energy change (deltaG(0)) for the excess adsorption of NaCl per kg of poly-L-amino acids have been evaluated. These values are all positive as a result of positive excess hydration of polyamino acids. The standard free energy of excess hydration deltaG(0)hy (equal to -deltaG(0)) is negative due to spontaneous excess hydration of polyamino acid in the presence of a salt.     

A Gaussian statistical mechanical model for the equilibrium thermodynamics of barnase folding

Given an all non-hydrogen-atom potential function that implicitly includes solvation effects, it is possible to adjust its parameters to favor the correct native structure for several proteins over decoys produced by ungapped threading. It is also possible to further train it to reproduce the experimental free energy of unfolding in aqueous solution at 298 K for wild-type barnase and 66 mutants. For this, the native state is represented by the crystal structure at a single energy level with a calculated low degeneracy; the denatured state is represented by the extended conformation and a high calculated degeneracy. The same two-state model can be extended to account for the stability of all 67 sequences toward urea denaturation at 298 K by building in a solvation term that depends on urea concentration. With the addition of one more parameter set to give the correct heat capacity of unfolded barnase in solution, it is possible to approximate the experimental thermodynamics of barnase thermal denaturation: melting temperature, width of thermal transition, deltaG, deltaH, deltaS, and deltaCp. This requires a novel sort of statistical mechanical model where the two states each have a Gaussian density of microscopic state distribution as a function of energy.     

Stability of proteins in the presence of polyols estimated from their guanidinium chloride-induced transition curves at different pH values and 25 degrees C

We have recently concluded from the heat-induced denaturation studies that polyols do not affect deltaG(D) degrees (the Gibbs free energy change (deltaG(D)) at 25 degrees C) of ribonuclease-A and lysozyme at physiological pH and temperature, and their stabilizing effect increases with decrease in pH. Since the estimation of deltaG(D) degrees of proteins from heat-induced denaturation curves requires a large extrapolation, the reliability of this procedure for the estimation of deltaG(D) degrees is always questionable, and so are conclusions drawn from such studies. This led us to measure deltaG(D) degrees of ribonuclease-A and lysozyme using a more accurate method, i.e., from their isothermal (25 degrees C) guanidinium chloride (GdmCl)-induced denaturations. We show that our earlier conclusions drawn from heat-induced denaturation studies are correct. Since the extent of unfolding of heat- and GdmCl-induced denatured states of these proteins is not identical, the extent of stabilization of the proteins by polyols against heat and GdmCl denaturations may also differ. We report that in spite of the differences in the structural nature of the heat- and GdmCl-denatured states of each protein, the extent of stabilization by a polyol is same. We also report that the functional dependence of deltaG(D) of proteins in the presence of polyols on denaturant concentration is linear through the full denaturant concentration range. Furthermore, polyols do not affect the secondary and tertiary structures of the native and GdmCl-denatured states.     

Analysis of ligand binding curves on basis of mean intrinsic thermodynamic quantities

The mean intrinsic thermodynamic quantity can be defined by considering the relative population of complex species in the solution and the value of intrinsic thermodynamic quantity corresponds to each step of ligation. In the present study a new method is introduced for analysis of experimental ligand binding data on basis of mean intrinsic thermodynamic quantities. In this regard, a deviation parameter was defined by comparing the non-interacting system with the cooperative interactive one. This parameter can be calculated just by estimation of the first binding constant. A set of relations between this deviation parameter and other binding characteristics, such as mean intrinsic Gibbs free energy of binding and mean Gibbs free energy of site-site interaction, have been developed. This model presents binding mechanism in a unified way that is simple, yet stringent, more straightforward, more reliable and informative. This analyzing method has been successfully applied for evaluation of various systems such as oxygen binding to hemoglobin, laurate and warfarin binding to human serum albumin, and reveals some new biological features of these binding systems.     

The sarcosine effect on protein stability: A case of nonadditivity?

We have used differential scanning calorimetry to determine the effect of low concentrations (C = 0-2 M) of the osmolyte sarcosine on the Gibbs energy changes (deltaG) for the unfolding of hen-egg-white lysozyme, ribonuclease A, and ubiquitin, under the same buffer and pH conditions. We have also computed this effect on the basis of the additivity assumption and using published values of the transfer Gibbs energies for the amino acid side chains and the peptide backbone unit. The values thus predicted for the slope delta deltaG/deltaC agree with the experimental ones, but only if the unfolded state is assumed to be compact (that is, if the accessibility to solvent of the unfolded state is modeled using segments excised from native structures). The additivity-based calculations predict similar delta deltaG/deltaC values for the three proteins studied. We point out that, to the extent that this approximate constancy of delta deltaG/deltaC holds, osmolyte-induced increases in denaturation temperature will be larger for proteins with low unfolding enthalpy (small proteins that bury a large proportion of apolar surface). The experimental results reported here are consistent with this hypothesis.     

Translocation of amino acyl residues from the membrane interface to the hydrophobic core: thermodynamic model and experimental analysis using ATR-FTIR spectroscopy

The interactions of a series of histidine-containing peptides with biological model membranes have been investigated by attenuated total reflection Fourier transform infra red (ATR-FTIR) spectroscopy. Related peptides have previously been shown to exhibit antibiotic and DNA transfection activities. The 26-residue LAH4X4 peptides were designed in such a manner to form amphipathic helical structures in membrane environments. Four histidines and four variable amino acids X constitute one face of the helix whereas leucines and alanines characterize the opposite hydrophobic surface. The dichroic ratio of ATR-FTIR spectra has been used to follow the pH-dependent transition from in-plane to transmembrane alignments upon increase in pH. A theoretical model of the topological modulations is presented and the experimental transition curves analysed in order to reveal the Gibbs free energy of transition. The novel concept provides access to the free energy changes associated with the amino acids X incorporated into an extended alpha-helix and in the context of phospholipid bilayers. For the peptides of the series the Gibbs free energies associated with the transition from the membrane interface to the bilayer interior follow the sequence of amino acids: L   

Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges

Thirty-four RNA duplexes containing single nucleotide bulges were optically melted, and the thermodynamic parameters deltaH degrees, deltaS degrees, deltaG degrees (37), and T(M) for each sequence were determined. Data from this study were combined with data from previous thermodynamic data [Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Biochemistry 29, 278-85] to develop a model that will more accurately predict the free energy of an RNA duplex containing a single nucleotide bulge. Differences between purine and pyrimidine bulges as well as differences between Group I duplexes, those in which the bulge is not identical to either neighboring nucleotide, and Group II duplexes, those in which the bulge is identical to at least one neighboring nucleotide, were considered. The length of the duplex, non-nearest-neighbor effects, and bulge location were also examined. A model was developed which divides sequences into two groups: those with pyrimidine bulges and those with purine bulges. The proposed model for pyrimidine bulges predicts deltaG degrees (37,bulge) = 3.9 kcal/mol + 0.10deltaG degrees (37,nn) + beta, while the model for purine bulges predicts deltaG degrees (37,bulge) = 3.3 kcal/mol - 0.30deltaG degrees (37,nn) + beta, where beta has a value of 0.0 and -0.8 kcal/mol for Group I and Group II sequences, respectively, and deltaG degrees (37,nn) is the nearest-neighbor free energy of the base pairs surrounding the bulge. The conformation of bulge loops present in rRNA was examined. Three distinct families of structures were identified. The bulge loop was either extrahelical, intercalated, or in a "side-step" conformation.     

Reduction of intrinsic kinetic and thermodynamic barriers for enzyme-catalysed proton transfers from carbon acid substrates

Many enzymes catalyse the heterolytic abstraction of the alpha-proton from a carbon acid substrate. Gerlt and Gassman have applied Marcus formalism to such proton transfer reactions to argue that transition states for concerted general acid-general base catalysed enolization at enzyme active sites occur late on the reaction coordinate (J. Am. Chem. Soc. 115 (1993) 11552). We postulate that as an enzyme evolves, it may decrease deltaG++ for a proton transfer step associated with substrate enolization by following the path of steepest descent on the two-dimensional surface corresponding to deltaG++, as defined by Marcus formalism. We show that for an enzyme that has decreased deltaG++ following the path of steepest descent, the values of the intrinsic kinetic (deltaG++(int,E)) and thermodynamic (deltaG(E)0) barriers for proton transfer reactions on the enzyme may be predicted from the known values of deltaG++(int,N) and deltaG(N)0 for the corresponding non-enzymic reaction and the free energy of activation on the enzyme (deltaG++(E)). In addition, the enzymic transition state will occur later on the reaction coordinate than the corresponding non-enzymic transition state (i.e. x++(E)>x++(N)) if the condition (6 - square root 2)/82deltaG++(int,N).     

A thermodynamic comparison of HPr proteins from extremophilic organisms

A thermodynamic stability study of five histidine-containing phosphocarrier protein (HPr) homologues derived from organisms inhabiting diverse environments is described. These HPr homologues are from Bacillus subtilis (Bs), Streptococcus thermophilus (St), Bacillus staerothermophilus (Bst), Bacillus halodurans (Bh), and Oceanobacillus iheyensis (Oi). Analyses of solvent and thermal denaturation experiments provide the cardinal thermodynamic parameters, like deltaG, deltaH, deltaS, T(m), and deltaC(p), that characterize the conformational stability for each homologue. The homologue from Bacillus staerothermophilus (BstHPr) was established as the most thermostable homologue and also the homologue with highest deltaG at all temperatures. A good correlation between habitat temperature of the organism and thermal stability of the protein is also seen. Stability curves (deltaG vs T) for every homologue are also reported; these reveal very similar deltaC(p) and temperature of maximum stability (T(S)) values for all HPr homologues. Stability curves show that the higher thermal stability of some homologues is not a result of change in curvature of the curve or a shift to higher temperature, but rather a displacement of the stability curves to higher deltaG values. Stability curves also allowed estimation of deltaG at habitat temperature of the organisms, and we find good agreement between homologues. Electrostatic contributions to stability of each homologue were investigated by measuring stability as a function of varying pH and NaCl concentration, and our results suggest that most HPr homologues share similar electrostatic contributions to stability.     

Thermodynamic analysis of trinitrotoluene biodegradation and mineralization pathways

Biodegradation of 2,4,6-trinitrotoluene (TNT) proceeds through several different metabolic pathways. However, the reaction steps which are considered rate-controlling have not been fully determined. Glycolysis and other biological pathways contain biochemical reactions which are acutely rate-limiting due to enzyme control. These rate-limiting steps also have large negative Gibbs free energy changes. Because xenobiotic compounds such as TNT can be used by biological systems as nitrogen, carbon, and energy sources, it is likely that their degradation pathways also contain acutely rate-limiting steps. Identification of these rate-controlling reactions will enhance and better direct genetic engineering techniques to increase specific enzyme levels.This article identifies likely rate-controlling steps (or sets of steps) in reported TNT biodegradation pathways by estimating the Gibbs free energy change for each step and for the overall pathways. The biological standard Gibbs free energy change of reaction was calculated for each pathway step using a group contribution method specifically tailored for biomolecules. The method was also applied to hypothetical "pathways" constructed to mineralize TNT using several different microorganisms. Pathways steps that have large negative Gibbs free energy changes are postulated to be potentially rate-controlling. The microorganisms which utilize degradation pathways with the largest overall (from TNT to citrate) negatiave Gibbs free energy changes were also determined. Such microorganisms can extract more energy from the starting substrate and are thus assumed to have a competitive advantage over other microorganisms. Results from this modeling-based research are consistent with much experimental work available in the literature. (c) 1996 John Wiley & Sons, Inc.     

Gibbs adsorption isotherm combined with Monte Carlo sampling to see action of cosolutes on protein folding

Driven by conditions set by smaller solutes, proteins fold and unfold. Experimentally, these conditions are stated as intensive variables--pH and other chemical potentials--as though small solutes were infinite resources that come at an externally varied free energy cost. Computationally, the finite spaces of simulation allow only fixed numbers of these solutes. By combining the analytic Gibbs adsorption isotherm with the computational Monte Carlo sampling of polymer configurations, we have been able to overcome an inherent limitation of computer simulation. The idea is to compute analytically the free energy changes wrought by solutes on each particular configuration. Then numerical computation is needed only to sample the set of configurations as efficiently as when no bathing solute is present. For illustration, the procedure is applied to an idealized two-dimensional heteropolymer to yield lessons about the effect of cosolutes on protein stability.     

Protein Thermostability Calculations Using Alchemical Free Energy Simulations

Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design.     

Secondary structure of prothymosin alpha evidenced for conformational transitions induced by changes in temperature and concentration of n-dodecyltrimethylammonium bromide

Conformational changes of prothymosin alpha (ProTalpha) induced by changes in temperature and concentration of the denaturant n-dodecyltrimethylammonium bromide (C12TAB) were studied by difference spectroscopy. The conformational transition of ProTalpha by C12TAB was followed as a function of denaturant concentration by absorbance measurements at 230 nm and the data were analyzed to obtain the Gibbs energy of the transition in water (deltaG0(w)) and in a hydrophobic environment (deltaG0(hc)) for saturated protein-surfactant complexes. The value of deltaG0(w) was 6.38 kJ mol(-1) and that for deltaG0(hc), which is not affected by temperature, was -18.62 kJ mol(-1). Changes of absorbance at 230 nm of ProTalpha with temperature can be assumed to resemble a transition in the secondary structure. The parameters characterizing the thermodynamics of unfolding, melting temperature (Tm), enthalpy (deltaHm), entropy (deltaSm) and heat capacity (deltaCp) were determined. The values obtained for Tm, deltaHm, and deltaSm are smaller that those found for other globular proteins; deltaCp was found to be much smaller. These results suggest that ProTalpha exhibits some type of secondary structure under these conditions (10 mM glycine buffer, pH 2.4).     

Carnosine promotes the heat denaturation of glycated protein

Glycation alters protein structure and decreases biological activity. Glycated proteins, which accumulate in affected tissue, are reliable markers of disease. Carnosine, which prevents glycation, may also play a role in the disposal of glycated protein. Carnosinylation tags glycated proteins for cell removal. Since thermostability determines cell turnover of proteins, the present study examined carnosine's effect on thermal denaturation of glycated protein using cytosolic aspartate aminotransferase (cAAT). Glycated cAAT (500 microM glyceraldehyde for 72h at 37 degrees C) increased the T(0.5) (temperature at which 50% denaturation occurs) and the Gibbs free energy barrier (DeltaG) for denaturation. The enthalpy of denaturation (DeltaH) for glycated cAAT was also higher than that for unmodified cAAT, suggesting that glycation changes the water accessible surface. Carnosine enhanced the thermal unfolding of glycated cAAT as evidenced by a decreased T(0.5) and a lowered Gibbs free energy barrier. Additionally, carnosine decreased the enthalpy of denaturation, suggesting that carnosine may promote hydration during heat denaturation of glycated protein.     

Kinetic analysis of enhanced thermal stability of an alkaline protease with engineered twin disulfide bridges and calcium-dependent stability

The thermal stability of a cysteine-free alkaline protease (Alp) secreted by the eukaryote Aspergillus oryzae was improved both by the introduction of engineered twin disulfide bridges (Cys-69/Cys-101 and Cys-169/Cys-200), newly constructed as part of this study, and by the addition of calcium ions. We performed an extensive kinetic analysis of the increased thermal stability of the mutants as well as the role of calcium dependence. The thermodynamic activation parameters for irreversible thermal inactivation, the activation free energy (deltaG), the activation enthalpy (deltaH), and the activation entropy (deltaS) were determined from absolute reaction rate theory. The values of deltaH and deltaS were significantly and concomitantly increased as a result of introducing the twin disulfide bridges, for which the increase in the value of deltaH outweighed that of deltaS, resulting in significant increases in the value of deltaG. The enhancement of the thermal stability obtained by introducing the twin disulfide bridges is an example of the so-called low-temperature stabilization of enzymes. The stabilizing effect of calcium ions on wild-type Alp is similar to the results we obtained by introducing the engineered twin disulfide bridges.