[A simple temperature range method in the seconds to hours range and the reversible denaturation of chymotrypsin]

Uses of enthalpy-entropy compensation in protein research

Cooperative systems of proteins and small molecules form most of biology but are so weakly linked that conventional mass-law formalism requiring exact stoichiometry is inapplicable. The weaknesses cannot be eliminated but using selected families of reactions useful fragmentation of those quantities is often possible. Extra-thermodynamic treatments based on linear-free-energy relationships (LFE) are developed to utilize enthalpy, entropy and volume information not otherwise reliable Linkage systems build around mesophilic proteins are well suited to enforced marriage of linear equations and scaled molecule detail because the ratio of substructure sizes on which folded stability depends is independent of total number of amino-acid residues. Conformational changes in physiological function usually no greater than 0.5 A closely scale to linear thermodynamic changes. The formalisms for use of LFE and compensation relationships are modified to eliminate complications that have previously arisen from incorrect inclusion of the thermal parts of enthalpy and entropy changes in free energy changes. The results are used to remove current confusion about the basis of folded stability in proteins and to minimize the quantitative errors arising from classical treatments of denaturation data. The enthalpy to entropy ratio given by the slope of a compensation plot (its 'compensation temperature') is used to characterize protein construction and function so as to extract machine descriptions of protein linkage systems. In this way the 'fragile' nature of the free-energy surfaces of the myoglobin proteins and the 'strong' character of those surfaces of most other mesophiles can be deduced very simply from the Debye-Waller factors obtained in diffraction studies. The major evolutionary achievement in making proteins big is their crystallike phase behavior. That makes entropy exactly as important as enthalpy so the scalar quantities of small-molecule chemistry can be replaced by the vector quantities that appear necessary to make biology possible.

Protein substructures and folded stability

Protein substructures detected in proton-exchange experiments can be described in quantitative detail with the Debye-Waller temperature factors from diffraction studies. The smallest substructures, in mesophilic proteins approximately 12% of the total residues, determine thermodynamic as well as kinetic stability by electrostatic synergism of a few tightly packed clusters about central peptide-peptide hydrogen bonds. Fixed positions of the clusters establish genetic stability of a protein family. The normal product of thermal denaturation above 280 K in dilute buffers, a compact but motile bubble, is formed with positive free-energy change in step from native state the single transition state and smaller negative change in the step from transition state to product. The largest substructures, approximately 80% of the residues, undergo changes in atom free volumes in function that are small relative to coordinate errors in protein diffraction studies but nevertheless describe the most important conformation changes. The criterion of precision in protein construction is approximately 0.05 A and may be found to be smaller when precision in X-ray diffraction improves. The ratio of residues in the two substructures is fixed in mesophiles.

pH dependence of the activation parameters for chymopapain unfolding: influence of ion pairs on the kinetic stability of proteins

We studied the irreversible thermal denaturation of chymopapain, a papain-related cysteine proteinase. It was found that this process follows simple first-order kinetics under all conditions tested. Rate constants determined by monitoring ellipticity changes at 220 or 279 nm are essentially identical, indicating that denaturation involves global unfolding of the protein. Enthalpies (DeltaH(double dagger)) and entropies (DeltaS(double dagger)) of activation for unfolding were determined at various pH values from the temperature dependence of the rate constant. In the pH range 1.1-3.0, a large variation of both DeltaH(double dagger) and DeltaS(double dagger) was observed. For the few proteins studied so far (lysozyme, trypsin, barnase) it is known that activation parameters for unfolding vary little with pH. It is proposed that this contrasting behavior of chymopapain originates from the numerous ion pairs - especially those with low solvent accessibilities - present in its molecular structure. In contrast, fewer, more exposed ion pairs are present in the other proteins mentioned above. Our results were analyzed in terms of differences in the protonation behavior of carboxylic groups between the transition (TS) and native (N) states of the protein. For this purpose, a model of independently titrating sites was assumed, which explained reasonably well the pH dependence of activation parameters, as well as the protonation properties of native chymopapain. According to these calculations, pK values of carboxyls in TS are shifted 0.6-0.9 units upwards with respect to those in N. In addition, some groups in TS appear to be protonated with unusually large enthalpy changes.

Folding of chymotrypsin inhibitor 2. 2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding

The refolding of chymotrypsin inhibitor 2 (CI2) is, at least, a triphasic process. The rate constants are 53 s-1 for the major phase (77% of the total amplitude) and 0.43 and 0.024 s-1 for the slower phases (23% of the total amplitude) at 25 degrees C and pH 6.3. The multiphase nature of the refolding reaction results from heterogeneity in the denatured state because of proline isomerization. The fast phase corresponds to the refolding of the fraction of protein that has all its prolines in a native trans conformation in the denatured state. It is not catalyzed by peptidyl-prolyl isomerase. The rate-limiting step of folding for the slower phases, however, is proline isomerization, and they are both catalyzed by peptidyl-prolyl isomerase. The slowest phase has properties consistent with a process involving proline isomerization in a denatured state. In particular, the activation enthalpy is large, 16 kcal mol-1 K-1, and the rate is independent of guanidinium chloride concentration ([GdnHCl]). In comparison, the intermediate phase shows properties consistent with a process involving proline isomerization in a partially structured state. The activation enthalpy is small, 8 kcal mol-1 K-1, and the rate has a strong dependence on [GdnHCl]. Temperature dependences of the rate constants for unfolding and for the fast refolding phase, both in the absence and in the presence of GdnHCl, were used to characterize the thermodynamic nature of the transition state and its relative exposure to solvent. The Eyring plot for unfolding is linear, indicating that there is relatively little change in heat capacity between native state and transition state.(ABSTRACT TRUNCATED AT 250 WORDS)

A "slow" temperature jump apparatus built from a stopped-flow machine

A simple modification to a standard thermostated stopped-flow machine is described which allows it to be used as a temperature jump machine. Temperature jumps larger than 10 degrees C can be achieved in less than 150 ms which makes it useful for the range of times where conventional rapid temperature jumps are not applicable. The apparatus has a sample size of 300 microliters and can produce temperature jumps both above and below the initial temperature.

Construction of up-and-down temperature-jump apparatus

A fast up-and-down temperature-jump apparatus whose dead time is about 60 ms was constructed. The principle of the method is to let the sample solution flow to the observation cell through a capillary in a heat-exchange chamber. Bubbling and cavitation effects in the observation cell at large up or down temperature jumps were eliminated by application of a nitrogen gas pressure of 2-5 bar. The down-temperature-jump method is especially effective for measuring temperature-induced conformational transitions of biopolymers and their assemblies.

Absolute measurement of enhanced fluctuations in assemblies of biomolecules by ultrasonic techniques

By expressing the fluctuation-dissipation theorem explicitly, equations are obtained for the ultrasonic relaxation amplitudes that contain one single molecular parameter, i.e., the fluctuation, or the sum of fluctuations. The absolute measurement of this parameter is therefore possible. The equations apply to a two-state system, to a multistate system and to a linear Ising chain as well. In an aqueous medium, where molar volume changes are important, the ultrasonic relaxation amplitudes are proportional to the volume fluctuations. For assemblies of biomolecules that exhibit enhanced ultrasonic absorption on assembly it is possible to measure the increase on assembly of the sum of fluctuations. In view of application to tobacco mosaic virus protein aggregates, examples are given in which the fluctuations associated with two normal modes of relaxation are equally enhanced when the difference of conformational stability of the states is reduced. The corresponding observable changes of the ultrasonic spectra are described.

A spectroscopic analysis of the thermally induced folding-unfolding transition of beta-trypsin

Absorption and fluorescence changes were used to monitor the thermally induced folding-unfolding transition of beta-trypsin. These parameters reflect changes in the microenvironment of different subsets of the four tryptophanyl residues of this protein. The thermal transition was found to be sequential.

Spurious conformational transitions in proteins?

Temperature-dependent dynamic processes in biological macromolecules can produce sharp and reversible transitions in spectroscopic properties that might be misinterpreted as evidence for thermally induced conformational changes. This provides a rational explanation for the paradoxical case of D-amino acid oxidase [D-amino-acid:oxygen oxidoreductase (deaminating), EC 1.4.3.3], for which a sharp fluorescence transition at 14 degrees C, not observed by sensitive calorimetry [Sturtevant, J. M. & Mateo, P. L. (1978) Proc. Natl. Acad. Sci. USA 75, 2584-2587], could be due to a dynamic quenching process of large activation energy, rather than a change in conformational state of the protein. Similar interpretations may be valid in other systems studied by experimental techniques that depend, directly or indirectly, on molecular relaxation processes.

Folding and association of oligomeric enzymes

The spontaneous structure formation of oligomeric enzymes consists of the consecutive 'folding' and association of the constituent polypeptide chains. Whether catalytic function is an intrinsic property of the folded monomers may be determined using kinetic reconstitution experiments. It is shown that full activity requires association; the correct assembly of subunits depends on their proper folding. The native structure is determined as the kinetically accessible state of lowest free energy.

Some aspects of protein folding

The mechanisms by which a polypeptide chain reaches the three dimensional structure which generates its functional properties are not yet totally understood. The great amount of data now available in the field of protein structure and the data already obtained on protein folding by in vitro experiments allow some schematic representation as, at least, a working hypothesis. In this respect the emphasis is put on the hierarchy in protein structure and the possibility of a folding by stages, some elements or "building blocks" being able to reach independently a native structure and to refine this structure by interacting with each other in the whole molecule.

Kinetics of the polymerization reaction of tobacco mosaic virus protein: transient-saturation type polymerization reaction

The kinetics of the endothermic polymerization reaction of tobacco mosaic virus protein in the mild acid region was studied by means of temperature-jump (rising time of 6 sec)-turbidimetry, electron microscopy, and computer simulation. The time course profile of the turbidity increase changed from a normal one to an anomalous one as the size of the temperature-jump was made greater. The anomalous type polymerization profile, which we named the "transient-saturation" type, could be characterized by a rapid increase of turbidity and its transient saturation, and a slow increase to the final level. At a higher concentration of the protein, this transient-saturation effect was more marked, whereas the slow turbidity in the second phase occurred with a higher rate. This transient-saturation type polymerization profile was observed also in a pH-induced polymerization reaction. It was not observed in the case of the N-bromosuccinimide modified tobacco mosaic virus protein under a similar environmental change. By an electron microscopic study and computer simulation, it was revealed that in the first phase, a large number of short polymers were formed, and the concentration of the polymerizing units was rapidly reduced to the equilibrium value, and the polymerization reaction stopped transiently. In the second phase, polymer-polymer associations took place slowly and longer polymers were formed. The revlevance of the present study to the polymerization reaction of actin, myosin, and to a transient-overshoot type polymerization are discussed.

Conformation of viroids

Viroids are uncoated infectious RNA molecules (MW 107 000-127 000) known as pathogens of certain higher plants. Thermodynamic and kinetic studies were carried out on highly purified viroid preparations by applying UV-absorption melting analysis and temperature jump methods. The thermal denaturation of viroids is characterized by high thermal stability, high cooperativity and a high degree of base pairing. Two relaxation processes could be resolved; a process in the sec range could be evaluated as an independent all-or-none-transition with the following properties: reaction enthalpy= 550 kcal/mol, activation enthalpy of the dissociation = 470 kcal/mol; G : C content = 72 %. These data indicate the existence of an uninterrupted double helix of 52 base pairs. A process in the msec range involves 15 - 25 base pairs which are most probably distributed over several short double helical stretches. A tentative model for the secondary structure of viroids isproposed and the possible functional implications of their physicochemical properties are discussed.

Properties of the refolding and unfolding reactions of ribonuclease A

Both the refolding kinetics and unfolding kinetics of ribonuclease A have been measured at the same final conditions, as a function of temperature at pH 3.9, by stopped-flow (pH-jump) experiments; absorbance changes at 240 and 286.5 nm were measured. Refolding follows first-order kinetics in the upper two-thirds of the thermal transition zone. Under the same conditions, the unfolding kinetics are biphasic; the terminal phase has the same rate constant as refolding. The biphasic kinetics of unfolding demonstrate the presence of intermediate states. Since both the refolding and unfolding kinetics are consistent with a simple sequential model, the intermediates satisfy kinetic criteria for being on the direct pathway of unfolding. At temperatures just above the transition zone, the fast phase of unfolding becomes the major kinetic phase. The rate of the slow unfolding reaction increases rapidly with temperature, and approaches the average rate of the fast phase at temperatures just above the transition zone. The entire set of kinetic results can be reproduced semiquantitatively by assignment of values to four parameters in a cooperative sequential model. However, reasons are given for the belief that this simple model will have to be generalized before it can give a realistic description of the kinetics of the unfolding reaction.

The sequential unfolding of ribonuclease A: detection of a fast initial phase in the kinetics of unfolding

Temperature-jump studies have been used to detect a rapid reaction in the thermal unfolding of ribonuclease A (RNase A). The fast reaction occurs over a wide range of pH, and the results of a detailed study at pH 1.3 are reported here. Although its amplitude is small, the reaction is easily measurable over the entire temperature range of thermal unfolding. It occurs in the millisecond time range, and is faster by 3-4 orders of magnitude than the slow unfolding reaction studied previously. Unfolding is measured here by the change in absorbance at 287 nm, which reflects the exposure to solvent of buried tyrosine groups. Since the fast reaction has a detectable amplitude only in the temperature range of unfolding, it apparently detects the presence of intermediate, partly-folded states. Previous equilibrium studies of the unfolding of RNase A in the pH range 1-2 have indicated that it is essentially a 2-state reaction, without detectable intermediates. The existence of a rapid transient phase in the unfolding of RNase A had been predicted previously from a model for this unfolding reaction, based on nucleation-dependent sequential folding. The model served to reconcile kinetic and equilibrium studies of the thermal unfolding reaction of RNase A at neutral pH. Kinetic studies had shown that the slow unfolding reaction, measured at 287 nm, could be represented as a single exponential process, as expected for a 2-state reaction. However, earlier equilibrium measurements, especially the calorimetric studies of Sturtevant and coworkers, had revealed significant deviations from the 2-state behavior at neutral pH. These conflicting observations are explained by the model, which satisfies closely many criteria for a 2-state unfolding, even when appreciable concentrations of partly folded molecules are present. In particular, it predicts that the final, and major, portion of the kinetic reaction will occur as a single process characterized by an exponential time course.