Kinetics of thermal unfolding of lysozyme

How to make big molecules fly out of liquid water: applications, features and physics of laser assisted liquid phase dispersion mass spectrometry

Applications, features, and mechanistic details of laser assisted liquid phase dispersion mass spectrometry are highlighted and discussed. It has been used in the past to directly isolate charged molecular aggregates from the liquid phase and to determine their molecular weight employing sensitive time-of-flight mass spectrometry. The liquid matrix in this MALDI (matrix assisted laser desorption and ionization) type approach consists of a 10 microm diameter free liquid filament in vacuum (or a free droplet) which is excited with a focused infrared laser pulse tuned to match the absorption frequency of the OH-stretch vibration of bulk water near 2.8 microm. Due to these features we will refer to the approach as free liquid matrix assisted laser dispersion of ions or ionic aggregates (IR-FL-MALDI), although also LILBID ("laser induced liquid beam (bead) desorption and ionization") has been proposed early as a descriptive acronym for the technique and may be used alternatively. Low-charge-state macromolecular adducts are isolated in the gas phase from solution via a yet poorly characterized mechanism which sensitively depends upon the laser intensity and wavelength, and after the gentle liquid-to-vacuum transfer the aggregates are analyzed via time-of-flight (TOF) mass spectrometry (MS). Possible mechanisms for the isolation and charging of biomolecules directly from liquid solution are discussed in the present contribution. Recent technical advances such as minimizing the sample consumption, strategies for high throughput mass spectrometry, and coupling of liquid beam MS with HPLC will be highlighted as well. An interesting feature of IR-FL-MALDI is what we call the linear response, i.e., a surprising linearity of the gas phase mass signal on the solution concentration over many orders of magnitude for a large number of biomolecular systems as well as ions. Due to these features the approach may be regarded as a true solution probing spectroscopy, which enables elegant biokinetic studies. Several experiments in which time resolved IR-FL-MALDI-MS has recently been employed successfully are given. A particular highlight is the possibility to quantitatively detect oxidation states in solution, which clearly distinguishes the present approach from other established MS source concepts. Due to the good matrix tolerance also proteins in complex mixtures can be monitored quantitatively.

Transition state characterization of the low- to physiological-temperature nondenaturational conformational change in bovine adenosine deaminase by slow scan rate differential scanning calorimetry

Bovine adenosine deaminase undergoes a nondenaturational conformational change at 29 degrees C upon heating which is characterized by a large increase in heat capacity. We have determined the transition state thermodynamics of the conformational change using a novel application of differential scanning calorimetry (DSC) which employs very slow scan rates. DSC scans at the conventional, and arbitrary, scan rate of 1 degree C/min show no evidence of the transition. Scan rates from 0.030 to 0.20 degrees C/min reveal the transition indicating it is under kinetic control. The transition temperature T(t) and the transition temperature interval deltaT increase with scan rate. A first order rate constant k1 is calculated at each T(t) from k1 = r(scan)/deltaT, where r(scan) is the scan rate, and an Arrhenius plot is constructed. Standard transition state analysis reveals an activation free energy deltaG(double dagger) of 88.1 kJ/mole and suggests that the conformational change has an unfolding quality that appears to be on the direct path to the physiological-temperature conformer.

Cooperative charge fluctuations by migrating protons in globular proteins

A review of the hydrogen bonded network on the protein surface shows the presence of a charged complex system with parallel and competitive interactions, including ionizable side-chains, migrating protons, bound water and nearby backbone peptides. This system displays cooperative effects of dynamical nature, reviewed for lysozyme as a case. By increasing the water coverage of the protein powder, the bound water cluster exhibits a percolative transition, detectable by the onset of large water-assisted displacements of migrating protons, with a parallel emergence of protein mobility and biological function. By lowering the temperature, migrating protons exhibit a glassy dielectric relaxation in the low frequency range, pointing to a frustration by competing interactions similar to that observed in spin glasses and fragile glass forming liquids. The observation of these dissipative processes implies the occurrence of spontaneous charge fluctuations. A simplified model of the protein surface, where conformational and ionizable side-chain fluctuations are averaged out, is used to discuss the statistical physics of these cooperative effects. Some biological implications of this dynamical cooperativity for enzymatic activity are briefly suggested at the end.

Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude

BACKGROUND

The dimeric four-helix-bundle protein Rop folds and unfolds extremely slowly. To understand the molecular basis for the slow kinetics, we have studied the folding and unfolding of wild-type Rop and a series of hydrophobic core mutants.

RESULTS

Mutation of the hydrophobic core creates stable, dimeric, and wild-type-like proteins with dramatically increased rates of both folding and unfolding. The increases in rates are dependent upon the number and position of repacked residues within the hydrophobic core.

CONCLUSIONS

Rop folds by a rapid collision of monomers to form a dimeric intermediate with substantial helical content, followed by a slow rearrangement to the final native structure. Rop unfolding is a single extremely slow kinetic phase. The slow steps of both folding and unfolding are dramatically increased by hydrophobic core replacements, suggesting that their main effect is to substantially decrease the energy of the transition state.

Comparative study of the stability of the folding intermediates of the calcium-binding lysozymes

Unfolding profiles of two calcium-binding lysozymes, equine milk lysozyme and pigeon egg-white lysozyme, were obtained by circular dichroism and proton NMR measurements. Equine lysozyme unfolds through a stable molten globule intermediate. The molten globule of equine lysozyme was characterized as more ordered than that of bovine alpha-lactalbumin. On the other hand, pigeon lysozyme unfolds by a two-state mechanism and the intermediate could not be observed in guanidine or thermal unfolding, the same as with conventional non-calcium-binding lysozymes. Thus, from the point of view of the unfolding profile, equine lysozyme belongs to the group of alpha-lactalbumin, but pigeon lysozyme belongs to the conventional lysozyme group.

Reversible denaturation of the gene V protein of bacteriophage f1

The guanidine hydrochloride (GuHCl)-induced denaturation of the gene V protein of bacteriophage f1 has been studied, using the chemical reactivity of a cysteine residue that is buried in the folded protein and the circular dichroism (CD) at 211 and 229 nm as measures of the fraction of polypeptide chains in the folded form. It is found that this dimeric protein unfolds in a single cooperative transition from a folded dimer to two unfolded monomers. A folded, monomeric form of the gene V protein was not detected at equilibrium. The kinetics of unfolding of the gene V protein in 3 M GuHCl and the refolding in 2 M GuHCl are also consistent with a transition between a folded dimer and two unfolded monomers. The GuHCl concentration dependence of the rates of folding and unfolding suggests that the transition state for folding is near the folded conformation.

Toward a better understanding of protein folding pathways

Experimental observations of how unfolded proteins refold to their native three-dimensional structures contrast with many popular theories of protein folding mechanisms. The available experimental evidence (ignoring slow cis-trans peptide bond isomerization) is largely consistent with the following general scheme: under folding conditions, unfolded protein molecules rapidly equilibrate between different conformations prior to complete refolding. This rapid prefolding equilibrium favors certain compact conformations that have somewhat lower free energies than the other unfolded conformations. Some of the favored conformations are important for productive folding. The rate-limiting step occurs late in the pathway and involves a high-energy, distorted form of the native conformation; there appears to be a single transition state through which essentially all molecules refold. Consequently, proteins are not assembled via a large number of independent pathways, nor is folding initiated by a nucleation event in the unfolded protein followed by rapid growth of the folded structure. The known folding pathways involving disulfide bond formation follow the same general principles. An exceptional folding mechanism for reduced ribonuclease A proposed by Scheraga et al. (Scheraga, H.A., Konishi, Y., Rothwarf, D.M. & Mui, P.W. (1987) Proc. Natl. Acad. Sci. USA 84, 5740-5744) is shown to result from experimental shortcomings, an incorrect kinetic analysis, and a failure to consider the kinetics of unfolding.

Early stages in the trifluoroethanol-induced unfolding of hen egg-white lysozyme and its complex with (GlcNAc)3

The trifluoroethanol-induced unfolding of hen egg-white lysozyme was studied by circular dichroism. It was shown that if the H2O/trifluoroethanol ratio is above 10:1 (v/v), the unique three-dimensional structure of the protein is not affected, whereas within the ration 10:1-2.8:1 (v/v), this structure is partially unfolded. At the ratio 2.4:1 (v/v), the native conformation of lysozyme is completely disrupted and the conformational transition fits a two-state model. A similar effect was observed for the trifluoroethanol-induced unfolding of the lysozyme-(GlcNAc)3 complex. Within the H2O2 trifluoroethanol ratio 15:1-5.5:1 (v/v), the characteristic intensities of the Cotton effects which arise from the association of (GlcNAc)3 with the active site of lysozyme, diminished and approached those exhibited by lysozyme itself at the same H2O trifluoroethanol ratios. This shows that (GlcNAc)3 is released from the protein surface in early stages of the unfolding process. At the ratio 2.4:1 (v/v), the lysozyme-(GlcNAc)3 complex was completely disrupted and the protein unfolded. It is suggested that a considerable alteration in hydration of the lysozyme molecule caused by trifluoroethanol increases protein surface fluctuations, causing the release of (GlcNAc)3 from the active site of lysozyme.

Mechanisms of hydrogen exchange in proteins from nuclear magnetic resonance studies of individual tryptophan indole NH hydrogens in lysozyme

The individual rates of solvent exchange of the six tryptophan indole NH hydrogens of lysozyme in 2H2O have been measured over a wide range of temperatures by using 1H NMR. Two distinct mechanisms for exchange have been identified, one characterized by a high activation energy and the other by a much lower activation energy. The high-energy process has been shown to be associated directly with the cooperative thermal unfolding of the protein and is the dominant mechanism for exchange of the most slowly exchanging hydrogen even 15 degrees C below the denaturation temperature. Rate constants and activation for the folding and unfolding reactions were obtained from the experimental exchange rates. At low temperatures, a lower activation energy mechanism is dominant for all hydrogens, and this can be associated with local fluctuations in the protein structure which allows access of solvent. The relative exchange rates and activation energies can only qualitatively be related to the different environments of the residues in the crystal structure. There is provisional evidence that a mechanism intermediate between these two extremes may be significant for some hydrogens under restricted conditions.

Equilibrium and kinetics of the thermal unfolding of alpha-lactalbumin. The relation to its folding mechanism

The thermal unfolding of alpha-lactalbumin has been studied by equilibrium measurements of aromatic difference spectra, and by kinetic measurements of the Joule heating temperature-jump. The unfolding at neutral pH is a reversible two-state transition. The equilibrium transition curves are analyzed by the nonlinear squares method, which gives correct values of thermodynamic parameters based on the data in a wide range of temperature. The results are discussed in relation to the previous studies on the unfolding by guanidine hydrochloride or by acid. The thermally unfolded state, a partially unfolded species, is shown to be thermodynamically similar to but not identical with the acid state. The folding pathway deduced from the kinetic results is essentially consistent with the folding model of alpha-lactalbumin proposed previously. Large decreases in entropy and in heat capacity during the reversed activation suggest the packing of the folded segments by hydrophobic interactions, while the forward activation shows a marked temperature dependence, probably caused by the disruption of specific long-range interactions.

Equilibrium and kinetics of the unfolding of alpha-lactalbumin by guanidine hydrochloride (IV): dependence of the N equilibrium A transconformation on the temperature

The reversible unfolding from the native (N) state to the acid (A) state of alpha-lactalbumin by guanidine-HCl (0.8-2.0 M) was studied at 10-35 degrees C by means of difference spectra and pH-jump measurements. At each temperature, all points plotted as the logarithmic equilibrium constant log KNA of the N equilibrium A process against pH could fall on a curve independent of the denaturant concentration by shifting each point along the log KNA axis, where the shift factor f did not depend on temperature. Moreover, by shifting the points at each temperature along the log (KNA/f) axis, a master curve, independent of both temperature and the denaturant concentration, could be obtained for the pH-dependence of log KNA. From the dependence of the logarithmic rate constants on pH, master curves independent of both temperature and the denaturant concentration could also be made for the N leads to A and the A leads to A processes, where A mean the activated state. The results show the two-state character of the N equilibrium A process. The enthalpy changes and the differences in heat capacity for the N equilibrium A, N equilibrium A and A equilibrium A processes were determined from the accurate measurements of temperature dependence of the unfolding at pH 4.3 and 1.0 M guanidine-HCl. The results show that the disruption of hydrophobic interaction is caused mainly in the A leads to A process, while most of the changes in the pK values of the ionizing groups are caused in the N leads to A process.

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.