Thermal unfolding of an intermediate is associated with non-Arrhenius kinetics in the folding of hen lysozyme

Mass Spectrometric Approaches Using Electrospray Ionization Charge States and Hydrogen-Deuterium Exchange for Determining Protein Structures and Their Conformational Changes

Electrospray ionization (ESI) mass spectrometry (MS) is a powerful analytical tool for elucidating structural details of proteins in solution especially when coupled with amide hydrogen/deuterium (H/D) exchange analysis. ESI charge-state distributions and the envelopes of charges they form from proteins can provide an abundance of information on solution conformations that is not readily available through other biophysical techniques such as near ultraviolet circular dichroism (CD) and tryptophan fluorescence. The most compelling reason for the use of ESI-MS over nuclear magnetic resonance (NMR) for measuring H/D after exchange is that larger proteins and lesser amounts of samples can be studied. In addition, MS can provide structural details on transient or folding intermediates that may not be accessible by CD, fluorescence, and NMR because these techniques measure the average properties of large populations of proteins in solution. Correlations between measured H/D and calculated parameters that are often available from crystallographic data can be used to extend the range of structural details obtained on proteins. Molecular dynamics and energy minimization by simulation techniques such as assisted model building with energy refinement (AMBER) force field can be very useful in providing structural models of proteins that rationalize the experimental H/D exchange results. Charge-state envelopes and H/D exchange information from ESI-MS data used complementarily with NMR and CD data provides the most powerful approach available to understanding the structures and dynamics of proteins in solution.

Protein analysis by hydrogen exchange mass spectrometry

Mass spectrometry has provided a powerful method for monitoring hydrogen exchange of protein backbone amides with deuterium from solvent. In comparison to popular NMR approaches, mass spectrometry has the advantages of higher sensitivity, wider coverage of sequence, and the ability to analyze larger proteins. Proteolytic fragmentation of proteins following the exchange reaction provides moderate structural resolution, in some cases enabling measurements from single amides. The technique has provided new insight into protein-protein and protein-ligand interfaces, as well as conformational changes during protein folding or denaturation. In addition, recent studies illustrate the utility of hydrogen exchange mass spectrometry toward detecting protein motions relevant to allostery, covalent modifications, and enzyme function.

Hyperquenching and cold equilibration strategies for the study of liquid–liquid and protein folding transitions

In this paper we consider the extension of the recent quantitative studies of hyperquenched glassformers to include (1). systems that exhibit first order liquid-liquid phase transitions, and (2). systems that contain molecules, which, during normal cooling, undergo internal structural changes above the glass temperature. The general aim of these studies is to trap-in a high enthalpy, high entropy, state of the system and then observe it evolving in time at low temperatures during a controlled annealing procedure. In this manner events that normally occur during change of temperature may be observed occurring during passage of time, at much lower temperatures. At such low temperatures the smearing effects of vibrations are greatly reduced. While the case of most interest in the second class is the refolding of thermally denatured protein molecules, any reconstructive molecular or chemical exchange process is a potential subject for investigation. Processes that occur in stages can be studied in greater detail, and any stage of interest can be frozen when desired, by drop of temperature, for more detailed spectroscopic examination. We review an electrospray method for hyperquenching liquids at approximately 10(5) K/s, and discuss some results of such experiments in order to illustrate a calorimetric approach to exploiting the hyperquenching-and- cold-equilibration strategy. To apply the idea to the study of proteins, the following protein solvent requirements must be met: (1). the solvents must not crystallize ice on cooling or heating, yet must not denature the proteins; (2). the solvents must support thermally denatured molecules without permitting aggregation. We describe two solvent systems, the first of which meets the first requirement, but the second only partially. The second solvent system apparently meets both. Preliminary results, only at the proof of concept stage, are reported for cold refolding of lysozyme, which, it seems, can be trapped in our solvent in the unfolded but refoldable state, with only moderate (approx. 120 K/s) quenching rates.

Thermal dissociation of multimeric protein complexes by using nanoelectrospray mass spectrometry

The behavior of macromolecular systems at different temperatures is often crucial to their biological activity and function. While heat-induced changes of individual proteins are readily monitored by a number of spectroscopic methods, changes in noncovalent complexes of biomolecules are more challenging to interpret. Nanoelectrospray mass spectrometry is becoming increasingly powerful in the study of large noncovalent complexes, and here we describe the design, characterization, and application of a novel probe that allows the thermocontrol of the solution in the electrospray capillary. The transition temperature for the unfolding of the protein lysozyme is readily obtained and correlates closely with that measured by fluorescence spectroscopy, thereby demonstrating the validity of this approach. We apply this technique to the study of the 200-kDa complex of the small heat shock protein TaHSP16.9, revealing both its dissociation into suboligomeric species and an increase in its size and polydispersity at elevated temperatures. In contrast, gas-phase activation of this complex is also carried out and yields a dissociation pathway fundamentally different from that observed for thermal activation in solution. As such, this probe allows the study of the reversible heat-induced changes of noncovalent complexes in a biologically relevant manner.

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

Do two-state proteins fold by pathways or funnels? Native-state hydrogen exchange experiments show discrete nonnative structures in equilibrium with the native state. These could be called hidden intermediates (HI) because their populations are small at equilibrium, and they are not detected in kinetic experiments. HIs have been invoked as disproof of funnel models, because funnel pictures appear to indicate (1) no specific sequences of events in folding; (2) a continuum, rather than a discrete ladder, of structures; and (3) smooth landscapes. In the present study, we solve the exact dynamics of a simple model. We find, instead, that the present microscopic model is indeed consistent with HIs and transition states, but such states occur in parallel, rather than along the single pathway predicted by the sequential stabilization model. At the microscopic level, we observe a huge multiplicity of trajectories. But at the macroscopic level, we observe two pathways of specific sequences of events that are relatively traditional except that they are in parallel, so there is not a single reaction coordinate. Using singular value decomposition, we show an accurate representation of the shapes of the model energy landscapes. They are highly complex funnels.

Weak temperature dependence of the free energy surface and folding pathways of structured peptides

The thermodynamics and energetics of a 20-residue synthetic peptide with a stable three-stranded antiparallel beta-sheet fold are investigated by implicit solvent molecular dynamics (MD) at 330 K (slightly above the melting temperature in the model) and compared with previous simulation results at 360 K. At both temperature values, the peptide folds reversibly to the NMR solution conformation, irrespective of the starting conformation. The sampling of the conformational space (2.3 micros and 25 folding events at 330 K, and 3 micros and 50 folding events at 360 K) is sufficient to obtain a thermodynamic description of minima and transition states on the free energy surface, which is determined near equilibrium by counting populations. The free energy surface, plotted as a function of two-order parameters that monitor formation of either of the beta-hairpins, is similar at both temperature values. The statistically predominant folding pathway and its frequency (about two-thirds of the folding events) are the same at 330 K and 360 K. Furthermore, the main unfolding route is the reverse of the predominant folding pathway. The effective energy and its electrostatic and van der Waals contributions show a downhill profile at both temperatures, implying that the free energy barrier is of entropic origin and corresponds to the freezing of about two-thirds of the chain into a beta-hairpin conformation. The average folding rate is nearly the same at 330 K and 360 K, while the unfolding rate is about four times slower at 330 K than at 360 K. Taken together with previous MD analysis of alpha-helices and beta-hairpins, the present simulation results indicate that the free energy surface and folding mechanism of structured peptides have a weak temperature dependence.

Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization

Pectate lyase C (pelC) is a member of the class of proteins that possess a parallel beta-helix folding motif. A study of the kinetic folding mechanism is presented in this report. Kinetic circular dichroism (CD) and fluorescence have been used to observe changes in the structure of pelC as a function of time upon folding and unfolding. Three folding phases are observed with far-UV CD and four phases are observed with near-UV CD. The two slowest phases have relaxation times on the order of 21 and 46 s in aqueous buffer. Double-jump refolding assays and the measured activation enthalpies (16.0 and 21.2 kcal/mol for the respective slow phases) suggest that these two phases are the result of the slow cis-trans isomerization of prolyl-peptide bonds. We have determined that the earliest observed folding phase involves the formation of most, if not all, of the secondary structure with a relaxation time of 0.25 s. We also observed a phase by near-UV CD on the order of 0.25 s. This suggests that along with the appearance of secondary structure, some tertiary contacts are made. There is one kinetic phase observed in the near-UV CD and fluorescence that has no corresponding far-UV CD phase. This occurs with a relaxation time of 1.1 s. The temperature dependence of the natural log of the folding rate constant suggests that folding occurs via a sequential mechanism in which an on-pathway intermediate in rapid equilibrium with the unfolded protein is present. Semiempirical CD calculations support the idea that the beta-helix region of pelC forms in the fast kinetic phase, yielding near-native secondary and tertiary structures in that region. This is followed by the slower formation of the loop regions connecting individual strands of the beta-helix.

A solid-state NMR study of protein mobility in lyophilized protein-sugar powders

The molecular mobility of protein in lyophilized lysozyme-sugar systems stored at different relative humidities was studied using solid-state NMR. Relaxation measurements, T(1) of high-frequency (MHz), and T(1rho), of low-frequency (kHz) motions, were performed on lysozyme lyophilized with lactose and trehalose. Molecular aggregation and enzymatic activity of the protein were determined using HPLC and bioassays. An increase in hydration had little effect on the T(1rho) values of pure lysozyme, trehalose, lactose, trehalose-lysozyme, and lysozyme at low lactose concentrations. The T(1) values of pure sugar increased as moisture content increased. The presence of both sugars led to increased T(1) values of the lysozyme but increasing hydration gradually reduced T(1) values. When a larger amount of lactose was lyophilized with lysozyme, longer T(1) (and T(1rho)) values were seen for lactose than for lysozyme. Although longer T(1) values were related to an increase in protein stability, the effect of crystallization and sugar type appeared to be major contributing factors. Trehalose and lactose decreased relaxation rates in the lysozyme-sugar systems while hydration increased relaxation rates that were correlated with changes in aggregation and activity of the protein.

Cooperative folding of the isolated alpha-helical domain of hen egg-white lysozyme

Proteins in the alpha-lactalbumin and c-type lysozyme family have been studied extensively as model systems in protein folding. Early formation of the alpha-helical domain is observed in both alpha-lactalbumin and c-type lysozyme; however, the details of the kinetic folding pathways are significantly different. The major folding intermediate of hen egg-white lysozyme has a cooperatively formed tertiary structure, whereas the intermediate of alpha-lactalbumin exhibits the characteristics of a molten globule. In this study, we have designed and constructed an isolated alpha-helical domain of hen egg-white lysozyme, called Lyso-alpha, as a model of the lysozyme folding intermediate that is stable at equilibrium. Disulfide-exchange studies show that under native conditions, the cysteine residues in Lyso-alpha prefer to form the same set of disulfide bonds as in the alpha-helical domain of full-length lysozyme. Under denaturing conditions, formation of the nearest-neighbor disulfide bonds is strongly preferred. In contrast to the isolated alpha-helical domain of alpha-lactalbumin, Lyso-alpha with two native disulfide bonds exhibits a well-defined tertiary structure, as indicated by cooperative thermal unfolding and a well-dispersed NMR spectrum. Thus, the determinants for formation of the cooperative side-chain interactions are located mainly in the alpha-helical domain. Our studies suggest that the difference in kinetic folding pathways between alpha-lactalbumin and lysozyme can be explained by the difference in packing density between secondary structural elements and support the hypothesis that the structured regions in a protein folding intermediate may correspond to regions that can fold independently.

Quantitative analysis of the stabilization by substrate of Staphylococcus aureus PC1 beta-lactamase

BACKGROUND

The stabilization of enzymes in the presence of substrates has been recognized for a long time. Quantitative information regarding this phenomenon is, however, rather scarce since the enzyme destroys the potential stabilizing agent during the course of the experiments. In this work, enzyme unfolding was followed by monitoring the progressive decrease of the rate of substrate utilization by the Staphylococcus aureus PC1 beta-lactamase, at temperatures above the melting point of the enzyme.

RESULTS

Enzyme inactivation was directly followed by spectrophotometric measurements. In the presence of substrate concentrations above the K(m) values, significant stabilization was observed with all tested compounds. A combination of unfolding kinetic measurements and enzymatic studies, both under steady-state and non-steady-state regimes, allowed most of the parameters characteristic of the two concurrent phenomena (i.e. substrate hydrolysis and enzyme denaturation) to be evaluated. In addition, molecular modelling studies show a good correlation between the extent of stabilization, and the magnitude of the energies of interaction with the enzyme.

CONCLUSIONS

Our analysis indicates that the enzyme is substantially stabilized towards heat-induced denaturation, independently of the relative proportions of non-covalent Henri-Michaelis complex (ES) and acyl-enzyme adduct (ES*). Thus, for those substrates with which the two catalytic intermediates are expected to be significantly populated, both species (ES and ES*) appear to be similarly stabilized. This analysis contributes a new quantitative approach to the problem.

Structural events during the refolding of an all beta-sheet protein

The refolding kinetics of the 140-residue, all beta-sheet, human fibroblast growth factor (hFGF-1) is studied using a variety of biophysical techniques such as stopped-flow fluorescence, stopped-flow circular dichroism, and quenched-flow hydrogen exchange in conjunction with multidimensional NMR spectroscopy. Urea-induced unfolding of hFGF-1 under equilibrium conditions reveals that the protein folds via a two-state (native <--> unfolded) mechanism without the accumulation of stable intermediates. However, measurement of the unfolding and refolding rates in various concentrations of urea shows that the refolding of hFGF-1 proceeds through accumulation of kinetic intermediates. Results of the quenched-flow hydrogen exchange experiments reveal that the hydrogen bonds linking the N- and C-terminal ends are the first to form during the refolding of hFGF-1. The basic beta-trefoil framework is provided by the simultaneous formation of beta-strands I, IV, IX, and X. The other beta-strands comprising the beta-barrel structure of hFGF-1 are formed relatively slowly with time constants ranging from 4 to 13 s.

Understanding protein folding via free-energy surfaces from theory and experiment

The ability of protein molecules to fold into their highly structured functional states is one of the most remarkable evolutionary achievements of biology. In recent years, our understanding of the way in which this complex self-assembly process takes place has increased dramatically. Much of the reason for this advance has been the development of energy surfaces (landscapes), which allow the folding reaction to be described and visualized in a meaningful manner. Analysis of these surfaces, derived from the constructive interplay between theory and experiment, has led to the development of a unified mechanism for folding and a recognition of the underlying factors that control the rates and products of the folding process.