Correspondence between anomalous m- and DeltaCp-values in protein folding

Quantitating denaturation by formic acid: imperfect repeats are essential to the stability of the functional amyloid protein FapC

Bacterial functional amyloids are evolutionarily optimized to aggregate, so much so that the extreme robustness of functional amyloid makes it very difficult to examine their structure-function relationships in a detailed manner. Previous work has shown that functional amyloids are resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. However, systematic investigation requires a quantitative analysis of FA's ability to denature proteins. Amyloid formed by Pseudomonas sp. protein FapC provides an excellent model to investigate FA denaturation. It contains three imperfect repeats, and stepwise removal of these repeats slows fibrillation and increases fragmentation during aggregation. However, the link to stability is unclear. We first calibrated FA denaturation using three small, globular, and acid-resistant proteins. This revealed a linear relationship between the concentration of FA and the free energy of unfolding with a slope of mFA+pH (the combined contribution of FA and FA-induced lowering of pH), as well as a robust correlation between protein size and mFA+pH We then measured the solubilization of fibrils formed from different FapC variants with varying numbers of repeats as a function of the concentration of FA. This revealed a decline in the number of residues driving amyloid formation upon deleting at least two repeats. The midpoint of denaturation declined with the removal of repeats. Complete removal of all repeats led to fibrils that were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one repeat is required for the stability of functional amyloid.

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Protein folding has been extensively studied, but many questions remain regarding the mechanism. Characterizing early unstable intermediates and the high-free-energy transition state (TS) will help answer some of these. Here, we use effects of denaturants (urea, guanidinium chloride) and temperature on folding and unfolding rate constants and the overall equilibrium constant as probes of surface area changes in protein folding. We interpret denaturant kinetic m-values and activation heat capacity changes for 13 proteins to determine amounts of hydrocarbon and amide surface buried in folding to and from TS, and for complete folding. Predicted accessible surface area changes for complete folding agree in most cases with structurally determined values. We find that TS is advanced (50-90% of overall surface burial) and that the surface buried is disproportionately amide, demonstrating extensive formation of secondary structure in early intermediates. Models of possible pre-TS intermediates with all elements of the native secondary structure, created for several of these proteins, bury less amide and hydrocarbon surface than predicted for TS. Therefore, we propose that TS generally has both the native secondary structure and sufficient organization of other regions of the backbone to nucleate subsequent (post-TS) formation of tertiary interactions. The approach developed here provides proof of concept for the use of denaturants and other solutes as probes of amount and composition of the surface buried in coupled folding and other large conformational changes in TS and intermediates in protein processes.

Stabilization of a protein conferred by an increase in folded state entropy

Entropic stabilization of native protein structures typically relies on strategies that serve to decrease the entropy of the unfolded state. Here we report, using a combination of experimental and computational approaches, on enhanced thermodynamic stability conferred by an increase in the configurational entropy of the folded state. The enhanced stability is observed upon modifications of a loop region in the enzyme acylphosphatase and is achieved despite significant enthalpy losses. The modifications that lead to increased stability, as well as those that result in destabilization, however, strongly compromise enzymatic activity, rationalizing the preservation of the native loop structure even though it does not provide the protein with maximal stability or kinetic foldability.

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins

We compared folding properties of designed protein Top7 and natural protein S6 by using coarse-grained chain models with a mainly native-centric construct that accounted also for nonnative hydrophobic interactions and desolvation barriers. Top7 and S6 have similar secondary structure elements and are approximately equal in length and hydrophobic composition. Yet their experimental folding kinetics were drastically different. Consistent with experiment, our simulated folding chevron arm for Top7 exhibited a severe rollover, whereas that for S6 was essentially linear, and Top7 model kinetic relaxation was multiphasic under strongly folding conditions. The peculiar behavior of Top7 was associated with several classes of kinetic traps in our model. Significantly, the amino acid residues participating in nonnative interactions in trapped conformations in our Top7 model overlapped with those deduced experimentally. These affirmations suggest that the simple ingredients of native topology plus sequence-dependent nonnative interactions are sufficient to account for some key features of protein folding kinetics. Notably, when nonnative interactions were absent in the model, Top7 chevron rollover was not correctly predicted. In contrast, nonnative interactions had little effect on the quasi linearity of the model folding chevron arm for S6. This intriguing distinction indicates that folding cooperativity is governed by a subtle interplay between the sequence-dependent driving forces for native topology and the locations of favorable nonnative interactions entailed by the same sequence. Constructed with a capability to mimic this interplay, our simple modeling approach should be useful in general for assessing a designed sequence's potential to fold cooperatively.

The hyperthermophilic nature of the metallo-oxidase from Aquifex aeolicus

The stability of the Aquifex aeolicus multicopper oxidase (McoA) was studied by spectroscopy, calorimetry and chromatography to understand its thermophilic nature. The enzyme is hyperthermostable as deconvolution of the differential scanning calorimetry trace shows that thermal unfolding is characterized by temperature values at the mid-point of 105, 110 and 114 degrees C. Chemical denaturation revealed however a very low stability at room temperature (2.8 kcal/mol) because copper bleaching/depletion occur before the unfolding of the tertiary structure and McoA is highly prone to aggregate. Indeed, unfolding kinetics measured with the stopped-flow technique quantified the stabilizing effect of copper on McoA (1.5 kcal/mol) and revealed quite an uncommon observation further confirmed by light scattering and gel filtration chromatography: McoA aggregates in the presence of guanidinium hydrochloride, i.e., under unfolding conditions. The aggregation process results from the accumulation of a quasi-native state of McoA that binds to ANS and is the main determinant of the stability curve of McoA. Kinetic partitioning between aggregation and unfolding leads to a very low heat capacity change and determines a flat dependence of stability on temperature.

Thermodynamics and mechanism of cutinase stabilization by trehalose

Trehalose has been widely used to stabilize cellular structures such as membranes and proteins. The effect of trehalose on the stability of the enzyme cutinase was studied. Thermal unfolding of cutinase reveals that trehalose delays thermal unfolding, thus increasing the temperature at the midpoint of unfolding by 7.2 degrees . Despite this stabilizing effect, trehalose also favors pathways that lead to irreversible denaturation. Stopped-flow kinetics of cutinase folding and unfolding was measured and temperature was introduced as experimental variable to assess the mechanism and thermodynamics of protein stabilization by trehalose. The main stabilizing effect of trehalose was to delay the rate constant of the unfolding of an intermediate. A full thermodynamic analysis of this step has revealed that trehalose induces the phenomenon of entropy-enthalpy compensation, but the enthalpic contribution increases more significantly leading to a net stabilizing effect that slows down unfolding of the intermediate. Regarding the molecular mechanism of stabilization, trehalose increases the compactness of the unfolded state. The conformational space accessible to the unfolded state decreases in the presence of trehalose when the unfolded state acquires residual native interactions that channel the folding of the protein. This residual structure results into less hydrophobic groups being newly exposed upon unfolding, as less water molecules are immobilized upon unfolding.

Thermodynamics of unfolding of an integral membrane protein in mixed micelles

Quantitative studies of membrane protein folding and unfolding can be difficult because of difficulties with efficient refolding as well as a pronounced propensity to aggregate. However, mixed micelles, consisting of the anionic detergent sodium dodecyl sulfate and the nonionic detergent dodecyl maltoside facilitate reversible and quantitative unfolding and refolding. The 4-transmembrane helix protein DsbB from the inner membrane of Escherichia coli unfolds in mixed micelles according to a three-state mechanism involving an unfolding intermediate I. The temperature dependence of the kinetics of this reaction between 15 degrees and 45 degrees C supports that unfolding from I to the denatured state D is accompanied by a significant decrease in heat capacity. For water-soluble proteins, the heat capacity increases upon unfolding, and this is generally interpreted as the increased binding of water to the protein as it unfolds, exposing more surface area. The decrease in DsbB's heat capacity upon unfolding is confirmed by independent thermal scans. The decrease in heat capacity is not an artifact of the use of mixed micelles, since the water soluble protein S6 shows conventional heat-capacity changes in detergent. We speculate that it reflects the binding of SDS to parts of DsbB that are solvent-exposed in the native DM-bound state. This implies that the periplasmic loops of DsbB are relatively unstructured. This anomalous thermodynamic behavior has not been observed for beta-barrel membrane proteins, probably because they do not bind SDS so extensively. Thus the thermodynamic behavior of membrane proteins appears to be intimately connected to their detergent-binding properties.

Hydration of the folding transition state ensemble of a protein

A complete description of the mechanisms of protein folding requires knowledge of the structural and physical character of the folding transition state ensembles (TSEs). A key question concerning the role of hydration of the hydrophobic core in determining folding mechanisms remains. To address this, we probed the state of hydration of the TSE of staphylococcal nuclease (SNase) by examining the fluorescence-detected pressure-jump relaxation behavior of six SNase variants in which a residue in the hydrophobic core, Val-66, was replaced with polar or ionizable residues (Lys, Arg, His, Asp, Glu, and Asn). Because of a large positive activation volume for folding, the major effect of pressure on the wild-type protein is to decrease the folding rate. By the time wild-type SNase reaches the folding transition state, most water has already been expelled from its hydrophobic core. In contrast, the major effect of pressure on the variant proteins is an increase in the unfolding rate due to a large negative activation volume for unfolding. This results from a significant increase in the level of hydration of the TSE when an internal ionizable group is present. These data confirm that the role of water in the folding reaction can differ from protein to protein and that even a single substitution in a critical position can modulate significantly the properties of the TSE.

The changing face of glucagon fibrillation: structural polymorphism and conformational imprinting

We have established a time-resolved fluorescence assay to study fibrillation of the 29 residue peptide hormone glucagon under a variety of different conditions in a high-throughput format. Fibrils formed at pH 2.5 differ in fibrillation kinetics, morphology, thioflavin T staining and FTIR/CD spectra depending on salts, glucagon concentration and fibrillation temperature. Apparent fibrillar stability correlates with spectral and kinetic properties; generally, fibrils formed under conditions favourable for rapid fibrillation (ambient temperatures, high glucagon concentration or high salt concentration) appear less thermostable than those formed under more challenging conditions (high temperatures, low glucagon or low salt concentrations). Properties of preformed fibrils used for seeding are inherited in a prion-like manner. Thus, we conclude that the structure of fibrils formed by glucagon is not the result of the global energy minimization, but rather kinetically controlled by solvent conditions and seed-imprinting. Fibrillar polymorphism, which is being reported for an increasing number of proteins, probably reflects that fibrils have not been under evolutionary constraints to retain a single active conformation. Our results highlight the complexity of the fibrillation mechanism of glucagon, since even subtle changes in fibrillation conditions can alter the type of fibrils formed, or result in formation of mixtures of several types of fibrils.

Solvation and desolvation effects in protein folding: native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions

As different parts of a protein chain approach one another during folding, they are expected to encounter desolvation barriers before optimal packing is achieved. This impediment originates from the water molecule's finite size, which entails a net energetic cost for water exclusion when the formation of compensating close intraprotein contacts is not yet complete. Based on recent advances, we extend our exploration of these microscopic elementary desolvation barriers' roles in the emergence of generic properties of protein folding. Using continuum Gō-like C(alpha) chain models of chymotrypsin inhibitor 2 (CI2) and barnase as examples, we underscore that elementary desolvation barriers between a protein's constituent groups can significantly reduce native conformational fluctuations relative to model predictions that neglected these barriers. An increasing height of elementary desolvation barriers leads to thermodynamically more cooperative folding/unfolding transitions (i.e., higher overall empirical folding barriers) and higher degrees of kinetic cooperativity as manifested by more linear rate-stability relationships under constant temperature. Applying a spatially non-uniform thermodynamic parametrization we recently introduced for the pairwise C(alpha) potentials of mean force, the present barnase model further illustrates that desolvation is a probable physical underpinning for the experimentally observed high intrinsic enthalpic folding barrier under isostability conditions.

Antagonism, non-native interactions and non-two-state folding in S6 revealed by double-mutant cycle analysis

When folding to the native state N in the presence of salt, the apparent two-state folder S6 transiently forms a transient off-pathway state C with substantial secondary and tertiary structure. Fifteen double mutant cycles were analysed to compare side-chain interaction energies DeltaDeltaG(int) in C, N and TS (the transition state between N and the denatured state). The kinetic signatures of these destabilizing mutants suggest folding scenarios involving unfolding intermediates and even alternative unfolding pathways. However, restricting the kinetic data to linear parts of the chevron plot allows reliable extrapolation to zero molar denaturant of rate constants of folding, unfolding and misfolding. Side-chain interactions appear to contribute to the stability of C, but in a substantially non-native environment, as shown by changes in the sign of DeltaDeltaG(int) between C and N. Remarkably, there appear to be significant (0.7-2 kcal/mol) antagonistic interactions between the two residues Leu30 and Leu75 in N and TS, which may be linked to subtle structural changes seen in the crystal structures of the mutants. A small number of overlapping residues are involved in these kinds of antagonistic interactions in N, TS and C, suggesting that repulsive interactions are coded into the protein topology whether the protein folds or misfolds. Destabilizing double mutants indicate that apparent two-state folders can be induced to behave in more complex ways provided that the native state is suitably destabilized.

The conformational stability and thermodynamics of Fur A (ferric uptake regulator) from Anabaena sp. PCC 7119

Fur (ferric uptake regulator) is a key bacterial protein that regulates iron acquisition and its storage, and modulates the expression of genes involved in the response to different environmental stresses. Although the protein is involved in several regulation mechanisms, and members of the Fur family have been identified in pathogen organisms, the stability and thermodynamic characterization of a Fur protein have not been described. In this work, the stability, thermodynamics and structure of the functional dimeric Fur A from Anabaena sp. PCC 7119 were studied by using computational methods and different biophysical techniques, namely, circular dichroism, fluorescence, Fourier-transform infrared, and nuclear magnetic resonance spectroscopies. The structure, as monitored by circular dichroism and Fourier-transform infrared, was composed of a 40% of alpha-helix. Chemical-denaturation experiments indicated that Fur A folded via a two-state mechanism, but its conformational stability was small with a value of DeltaG = 5.3 +/- 0.3 kcal mol(-1) at 298 K. Conversely, Fur A was thermally a highly stable protein. The high melting temperature (Tm = 352 +/- 5 K), despite its moderate conformational stability, can be ascribed to its low heat capacity change upon unfolding, DeltaCp, which had a value of 0.8 +/- 0.1 kcal mol(-1) K(-1). This small value is probably due to burial of polar residues in the Fur A structure. This feature can be used for the design of mutants of Fur A with impaired DNA-binding properties.

Conformational detours during folding of a collapsed state

The protein S6 is a useful model to probe the role of partially folded states in the folding process. In the absence of salt, S6 folds from the denatured state D to the native state N without detectable intermediates. High concentrations of sodium sulfate induce the accumulation of a collapsed state C, which is off the direct folding route. However, the mutation VA85 enables S6 to fold from C directly to N through the transition state TS(C). According to the denaturant dependence of this reaction, TS(C) and C are equally compact, but the data are difficult to deconvolute. Therefore, I have measured the heat capacities (DeltaC(p)) for the D-->C and C-->TS(C) transitions. The DeltaC(p)-values suggest that C needs to increase its surface area in order to fold directly to N. This underlines that it is a misfolded state that can only fold by at least partial unfolding. In contrast to the C-state formed by S6 wildtype, the VA85 C-state is just as compact as the native state, and this may be a prerequisite for direct folding. Individual "gatekeeper" residues may thus play a disproportionately large role in guiding proteins through different folding pathways.

Cold instability of aponeocarzinostatin and its stabilization by labile chromophore

The conformational stability of aponeocarzinostatin, an all-beta-sheet protein with 113 amino-acid residues, is investigated by thermal-induced equilibrium unfolding between pH 2.0 and 10.0 with and without urea. At room temperature, the protein is stable in a pH range of 4.0-10.0, whereas the stability of the protein drastically decreases below pH 4.0. The thermal unfolding of aponeocarzinostatin is reversible and follows a two-state mechanism. By two-dimensional unfolding studies, the enthalpy change, heat capacity change, and free energy change for unfolding of the protein are estimated. Circular dichroism profiles suggest that this protein undergoes both heat- and cold-induced unfolding. The ellipticity changes at far- and near-UV circular dichroism suggest that the tertiary structure is disrupted but the secondary structure remains folded at low temperatures. Interestingly, the labile enediyne chromophore, which is highly stabilized by the protein, is able to protect the protein against cold-induced unfolding, but not the heat-induced unfolding.

Determination of barrier heights and prefactors from protein folding rate data

We determine both barrier heights and prefactors for protein folding by applying constraints determined from experimental rate measurements to a Kramers theory for folding rate. The theoretical values are required to match the experimental values at two conditions of temperature and denaturant that induce the same stability. Several expressions for the prefactor in the Kramers rate equation are examined: a random energy approximation, a correlated energy approximation, and an approximation using a single Arrhenius activation energy. Barriers and prefactors are generally found to be large as a result of implementing this recipe, i.e., the folding landscape is cooperative and smooth. Interestingly, a prefactor with a single Arrhenius activation energy admits no formal solution.