A general two-process model describes the hydrogen exchange behavior of RNase A in unfolding conditions

Probing the energy barriers and stages of membrane protein unfolding using solid-state NMR spectroscopy

Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.

Equilibrium unfolding thermodynamics of beta2-microglobulin analyzed through native-state H/D exchange

The exchange rates for the amide hydrogens of beta(2)-microglobulin, the protein responsible for dialysis-related amyloidosis, were measured under native conditions at different temperatures ranging from 301 to 315 K. The pattern of protection factors within different regions of the protein correlates well with the hydrogen-bonding pattern of the deposited structures. Analysis of the exchange rates indicates the presence of mixed EX1- and EX2-limit mechanisms. The measured parameters are consistent with a two-process model in which two competing pathways, i.e., global unfolding in the core region and partial openings of the native state, determine the observed exchange rates. These findings are analyzed with respect to the amyloidogenic properties of the protein.

NMR analysis of native-state protein conformational flexibility by hydrogen exchange

The rate of hydrogen exchange for the most protected amides of a protein is widely used to provide an estimate of global conformational stability by analyzing the exchange kinetics in the unfolded state in terms of model peptide exchange rates. The exchange behavior of the other amides of the protein which do not exchange via a global unfolding mechanism can provide insight into the smaller-scale conformational transitions that facilitate access to solvent as required for the exchange reaction. However, since the residual tertiary structure in the exchange-competent conformation can modulate the chemistry of the exchange reaction, equilibrium values estimated from normalization with model peptide rates are open to question. To overcome this limitation, the most robust approaches utilize differential analyses as a function of experimental variables such as denaturant concentration, temperature, pH, and mutational variation. Practical aspects of these various differential analysis techniques are considered with illustrations drawn from the literature.

Scope and utility of hydrogen exchange as a tool for mapping landscapes

The ability to determine conformational parameters of protein-folding landscapes is critical for understanding the link between conformation, function, and disease. Monitoring hydrogen exchange (HX) of labile protons at equilibrium enables direct extraction of thermodynamic or kinetic landscape parameters in two limiting extremes. Here, we establish a quantitative framework for relating HX behavior to landscape. We use this framework to demonstrate that the range of predicted global HX behavior for the majority of a set of characterized two-state proteins under near-native conditions does not readily span between both extremes. For most, stability may be quantitatively determined under physiological conditions, with semiquantitative boundaries on kinetics additionally determined using modest experimental perturbations to shift HX behavior. The framework and relationships derived in the simple context of two-state global folding highlight the importance of understanding HX across the entire continuum of behavior, in order to apply HX to map landscapes.

Destabilizing mutations alter the hydrogen exchange mechanism in ribonuclease A

The effect of strongly destabilizing mutations, I106A and V108G of Ribonuclease A (RNase A), on its structure and stability has been determined by NMR. The solution structures of these variants are essentially equivalent to RNase A. The exchange rates of the most protected amide protons in RNase A (35 degrees C), the I106A variant (35 degrees C), and the V108G variant (10 degrees C) yield stability values of 9.9, 6.0, and 6.8 kcal/mol, respectively, when analyzed assuming an EX2 exchange mechanism. Thus, the destabilization induced by these mutations is propagated throughout the protein. Simulation of RNase A hydrogen exchange indicates that the most protected protons in RNase A and the V108G variant exchange via the EX2 regime, whereas those of I106A exchange through a mixed EX1 + EX2 process. It is striking that a single point mutation can alter the overall exchange mechanism. Thus, destabilizing mutations joins high temperatures, high pH and the presence of denaturating agents as a factor that induces EX1 exchange in proteins. The calculations also indicate a shift from the EX2 to the EX1 mechanism for less protected groups within the same protein. This should be borne in mind when interpreting exchange data as a measure of local stability in less protected regions.

Cooperative α-helix unfolding in a protein-DNA complex from hydrogen-deuterium exchange

We present experimental evidence for a cooperative unfolding transition of an alpha-helix in the lac repressor headpiece bound to a symmetric variant of the lac operator, as inferred from hydrogen-deuterium (H-D) exchange experiments monitored by NMR spectroscopy. In the EX1 limit, observed exchange rates become pH-independent and exclusively sensitive to local structure fluctuations that expose the amide proton HN to exchange. Close to this regime, we measured decay rates of individual backbone HN signals in D2O, and of their mutual HN-HN NOE by time-resolved two-dimensional (2D) NMR experiments. The data revealed correlated exchange at the center of the lac headpiece recognition helix, Val20-Val23, and suggested that the correlation breaks down at Val24, at the C terminus of the helix. A lower degree of correlation was observed for the exchange of Val9 and Ala10 at the center of helix 1, while no correlation was observed for Val38 and Glu39 at the center of helix 3. We conclude that HN exchange in the recognition helix and, to some extent, in helix 1 is a cooperative event involving the unfolding of these helices, whereas the HN exchange in helix 3 is dominated by random local structure fluctuations.

Hydrogen exchange mass spectrometry for the analysis of protein dynamics

Hydrogen exchange coupled to mass spectrometry (MS) has become a valuable analytical tool for the study of protein dynamics. By combining information about protein dynamics with more classical functional data, a more thorough understanding of protein function can be obtained. In many cases, protein dynamics are directly related to specific protein functions such as conformational changes during enzyme activation or protein movements during binding. The method is made possible because labile backbone hydrogens in a protein will exchange with deuterium atoms when the protein is placed in a D2O solution. The subsequent increase in protein mass over time is measured with high-resolution MS. The location of the deuterium incorporation is determined by monitoring deuterium incorporation in peptic fragments that are produced after the labeling reaction. In this review, we will summarize the general principles of the method, discuss the latest variations on the experimental protocol that probe different types of protein movements, and review other recent work and improvements in the field.

Probing the unfolding region of ribonuclease A by site-directed mutagenesis

Ribonuclease A contains two exposed loop regions, around Ala20 and Asn34. Only the loop around Ala20 is sufficiently flexible even under native conditions to allow cleavage by nonspecific proteases. In contrast, the loop around Asn34 (together with the adjacent beta-sheet around Thr45) is the first region of the ribonuclease A molecule that becomes susceptible to thermolysin and trypsin under unfolding conditions. This second region therefore has been suggested to be involved in early steps of unfolding and was designated as the unfolding region of the ribonuclease A molecule. Consequently, modifications in this region should have a great impact on the unfolding and, thus, on the thermodynamic stability. Also, if the Ala20 loop contributes to the stability of the ribonuclease A molecule, rigidification of this flexible region should stabilize the entire protein molecule. We substituted several residues in both regions without any dramatic effects on the native conformation and catalytic activity. As a result of their remarkably differing stability, the variants fell into two groups carrying the mutations: (a) A20P, S21P, A20P/S21P, S21L, or N34D; (b) L35S, L35A, F46Y, K31A/R33S, L35S/F46Y, L35A/F46Y, or K31A/R33S/F46Y. The first group showed a thermodynamic and kinetic stability similar to wild-type ribonuclease A, whereas both stabilities of the variants in the second group were greatly decreased, suggesting that the decrease in DeltaG can be mainly attributed to an increased unfolding rate. Although rigidification of the Ala20 loop by introduction of proline did not result in stabilization, disturbance of the network of hydrogen bonds and hydrophobic interactions that interlock the proposed unfolding region dramatically destabilized the ribonuclease A molecule.

Cytochrome c folding pathway: kinetic native-state hydrogen exchange

Native-state hydrogen exchange experiments under EX1 conditions can distinguish partially unfolded intermediates by their formation rates and identify the amide hydrogens exposed and protected in each. Results obtained define a cytochrome c intermediate seen only poorly before and place it early on the major unfolding pathway. Four distinct unfolding steps are found to be kinetically ordered in the same pathway sequence inferred before.

Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method

We recently reported on a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based technique, termed SUPREX, that removes several important limitations associated with measuring the thermodynamic stability of proteins. In contrast to conventional spectroscopy-based techniques for characterizing the equilibrium unfolding behavior of proteins, SUPREX is amenable to the thermodynamic analysis of both purified and unpurified proteins using mg to ng quantities of material. Here we report on the application of SUPREX to the analysis of multimeric protein systems. Included in this work are the SUPREX results we obtained in studies on six model multimeric proteins including the GCN4p1 dimer, the coil-V(a)L(d) trimer, the 4-oxalocrotonate tautomerase (4-OT) hexamer, the Trp repressor (TrpR) dimer, the Arc repressor (ArcR) dimer, and an ArcR mutant (the (DOA20)ArcR) dimer which contained two destabilizing mutations including an Asp to Ala mutation at position 20 and an amide to ester bond mutation between amino acid (aa) residues 19 and 20. As part of the work described here, we present a new method for the analysis of SUPREX data that is generally applicable to both monomeric and multimeric protein systems. Our results on the model proteins in this study indicate that this new method can be used to determine folding free energies for proteins with the accuracy and precision of conventional spectroscopy-based methods.

On the nature of conformational openings: native and unfolded-state hydrogen and thiol-disulfide exchange studies of ferric aquomyoglobin

Native-state amide hydrogen exchange (HX) of proteins in the presence of denaturant has provided valuable details on the structures of equilibrium folding intermediates. Here, we extend HX theory to model thiol group exchange (SX) in single cysteine-containing variants of sperm whale ferric aquomyoglobin. SX is complementary to HX in that it monitors conformational opening events that expose side-chains, rather than the main chain, to solvent. A simple two-process model, consisting of EX2-limited local structural fluctuations and EX1-limited global unfolding, adequately accounts for all HX data. SX is described by the same model except at very low denaturant concentrations and when the bulky labeling reagent 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB) is used. Under these conditions SX can occur by a novel denaturant-dependent process. This anomalous behavior is not observed when the smaller labeling reagent methyl methanethiosulfonate is employed, suggesting that it reflects a denaturant-induced increase in the amplitudes of local structural fluctuations. It also is not seen in heme-free apomyoglobin, which may indicate that local openings are sufficiently large in the absence of denaturant to allow DTNB unhindered access. Differences in SX kinetics obtained using the two labeling reagents provide estimates of the sizes of local opening reactions at different sites in the protein. At all sequence positions examined except for position 73, the same opening event appears to facilitate exchange of both backbone amide and side-chain thiol groups. The C73 thiol group is exposed by a low-energy fluctuation that does not expose its amide group to exchange.

A quantitative, high-throughput screen for protein stability

In proteomic research, it is often necessary to screen a large number of polypeptides for the presence of stable structure. Described here is a technique (referred to as SUPREX, stability of unpurified proteins from rates of H/D exchange) for measuring the stability of proteins in a rapid, high-throughput fashion. The method uses hydrogen exchange to estimate the stability of microgram quantities of unpurified protein extracts by using matrix-assisted laser desorption/ionization MS. The stabilities of maltose binding protein and monomeric lambda repressor variants determined by SUPREX agree well with stability data obtained from conventional CD denaturation of purified protein. The method also can detect the change in stability caused by the binding of maltose to maltose binding protein. The results demonstrate the precision of the method over a wide range of stabilities.

Microsecond to minute dynamics revealed by EX1-type hydrogen exchange at nearly every backbone hydrogen bond in a native protein

A previous comprehensive analysis of the pH dependence of native-state amide hydrogen (NH) exchange in turkey ovomucoid third domain (OMTKY3) yielded apparent opening and closing rate constants (k(op) and k(cl)) at 14 NH groups involved in global conformational changes. This analysis has been extended to 18 additional slowly exchanging NH groups. Quench-flow experiments were performed to monitor NH exchange in native OMTKY3 from neutral to very alkaline pH ( approximately 12) conditions. Above pH 10 the mechanism of exchange switched from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e. EX2 exchange), to one where exchange was limited by the rate of opening (i.e. EX1 exchange). Kinetics of solvent exposure are now known for nearly all backbone NH groups in native OMTKY3, yielding rate constants that span five orders of magnitude, 0.004 to 200 s(-1).

Experimental study of the protein folding landscape: unfolding reactions in cytochrome c

Hydrogen exchange results for cytochrome c have been interpreted in terms of transient hydrogen bond-breaking reactions that include large unfolding reactions and small fluctuational distortions. The differential sensitivity of these opening reactions to denaturant, temperature, and protein stability makes it possible to distinguish the different opening reactions and to characterize their structural and thermodynamic parameters. The partially unfolded forms (PUFs) observed are few and discrete, evidently because they are produced by the reversible unfolding of the protein's several intrinsically cooperative secondary structural elements. The PUFs are robust, evidently because the structural elements do not change over a wide range of conditions. The discrete nature of the PUFs and their small number is as expected for classical folding intermediates but not for theoretically derived folding models apparently because the simplified non-protein models usually analyzed in theoretical studies encompass only a single cooperative unit rather than multiple separable units.

Hydrogen exchange kinetics of proteins in denaturants: a generalized two-process model

The recent progress in measurements on the amide hydrogen exchange (HX) in proteins under varying denaturing conditions, both at equilibrium and in transient relaxation, necessitates the development of a unifying theory which quantitatively relates the HX rates to the conformational energetics of the proteins. We present here a comprehensive kinetic model for the site-specific HX of proteins under varying solvent denaturing conditions based on the two-state protein folding model. The generalized two-process model considers both conformational fluctuations and residual protections, respectively, within the folded and unfolded states of a protein, as well as a global kinetic folding-unfolding transition between the two states. The global transition can be either rapid or slow, depending on the solvent condition for the protein. This novel model is applicable to the traditional equilibrium HX measurements in both EX2 and EX1 regimes, and also the recently introduced transient pulse-labeling HX experiments. A set of simple analytical equations is provided for quantitative interpretation of experimental data. The model emphasizes the use of full time-course of bi-exponential HX kinetics, rather than fitting time-course data to single rate constants, to obtain quantitative information about fluctuating conformers within the folded and unfolded states of proteins. This HX kinetic model naturally unfolds into a simple two-state and two-stage kinetic interpretation for protein folding. It suggests that the various observed intermediates of a protein can be interpreted as dominant isomers of either the folded or the unfolded state under different solvent conditions. This simple, minimalist's view of protein folding is consistent with various recent experimental observations on folding kinetics by HX.

Changes in side chain packing during apomyoglobin folding characterized by pulsed thiol-disulfide exchange

It is clear that close-packed side chain interactions play a dominant role in stabilizing native proteins, but the extent to which they stabilize kinetic intermediates and shape the energetic landscape of folding is not known. A method for characterizing structural changes at the level of individual side chains is presented and applied to study the refolding of apomyoglobin mutants containing engineered cysteine residues at key helical packing interfaces. The formation of buried side chain structure at the probe sites is followed by the extent of thiol-disulfide exchange during a pulse of thiol labeling reagent (either methyl methanethiosulfonate or 5,5'-dithiobis (2-nitrobenzoic acid)) applied at various stages of folding. The results suggest that the eight helices pack in at least three distinct stages, involving formation of two intermediates with time constants of <2 ms and 50 ms. In some parts of the refolding protein, stable side chain structure can be attained very rapidly, possibly in advance of backbone hydrogen bond formation as detected by previous pulsed amide hydrogen exchange experiments.

Determinants of protein hydrogen exchange studied in equine cytochrome c

The exchange of a large number of amide hydrogens in oxidized equine cytochrome c was measured by NMR and compared with structural parameters. Hydrogens known to exchange through local structural fluctuations and through larger unfolding reactions were separately considered. All hydrogens protected from exchange by factors greater than 10(3) are in defined H-bonds, and almost all H-bonded hydrogens including those at the protein surface were measured to exchange slowly. H-exchange rates do not correlate with H-bond strength (length) or crystallographic B factors. It appears that the transient structural fluctuation necessary to bring an exchangeable hydrogen into H-bonding contact with the H-exchange catalyst (OH(-)-ion) involves a fairly large separation of the H-bond donor and acceptor, several angstroms at least, and therefore depends on the relative resistance to distortion of immediately neighboring structure. Accordingly, H-exchange by way of local fluctuational pathways tends to be very slow for hydrogens that are neighbored by tightly anchored structure and for hydrogens that are well buried. The slowing of buried hydrogens may also reflect the need for additional motions that allow solvent access once the protecting H-bond is separated, although it is noteworthy that burial in a protein like cytochrome c does not exceed 4 angstroms. When local fluctuational pathways are very slow, exchange can become dominated by a different category of larger, cooperative, segmental unfolding reactions reaching up to global unfolding.

Folding intermediates of wild-type and mutants of barnase. II. Correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate

There is an unanswered question from previous studies of 1H/2H-exchange of amide protons of barnase. Under certain conditions, there is a relatively abrupt change from EX2 towards EX1 kinetics as the temperature is slightly increased. The change in kinetics for different mutants is not directly related to their changes in stability. We have measured the stability of the folding intermediate of barnase (I) in 2H2O under a variety of conditions and calculated its population at different temperatures. The change in kinetics correlates with the change in the population of the folding intermediate. At higher temperatures and pH, the free energy of I becomes higher than that of the denatured state, D, and the kinetics becomes EX1. The data fit a simple kinetic scheme. Such changes in kinetics may be used to detect the presence of intermediates in the folding reaction at equilibrium in native conditions, but cannot distinguish whether they are on or off-pathway.

Characterization of the free energy spectrum of peptostreptococcal protein L

BACKGROUND

Native state hydrogen/deuterium exchange studies on cytochrome c and RNase H revealed the presence of excited states with partially formed native structure. We set out to determine whether such excited states are populated for a very small and simple protein, the IgG-binding domain of peptostreptococcal protein L.

RESULTS

Hydrogen/deuterium exchange data on protein L in 0-1.2 M guanidine fit well to a simple model in which the only contributions to exchange are denaturant-independent local fluctuations and global unfolding. A substantial discrepancy emerged between unfolding free energy estimates from hydrogen/deuterium exchange and linear extrapolation of earlier guanidine denaturation experiments. A better determined estimate of the free energy of unfolding obtained by global analysis of a series of thermal denaturation experiments in the presence of 0-3 M guanidine was in good agreement with the estimate from hydrogen/deuterium exchange.

CONCLUSIONS

For protein L under native conditions, there do not appear to be partially folded states with free energies intermediate between that of the folded and unfolded states. The linear extrapolation method significantly underestimates the free energy of folding of protein L due to deviations from linearity in the dependence of the free energy on the denaturant concentration.

Hydrogen exchange and protein folding

Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins. The significant increase in the number of small, model proteins that have been studied has allowed a better understanding of the structural fluctuations that lead to hydrogen exchange. Recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.

Conformational stability of ribonuclease T1 determined by hydrogen-deuterium exchange

The hydrogen-deuterium exchange kinetics of 37 backbone amide residues in RNase T1 have been monitored at 25, 40, 45, and 50 degrees C at pD 5.6 and at 40 and 45 degrees C at pD 6.6. The hydrogen exchange rate constants of the hydrogen-bonded residues varied over eight orders of magnitude at 25 degrees C with 13 residues showing exchange rates consistent with exchange occurring as a result of global unfolding. These residues are located in strands 2-4 of the central beta-pleated sheet. The residues located in the alpha-helix and the remaining strands of the beta-sheet exhibited exchange behaviors consistent with exchange occurring due to local structural fluctuations. For several residues at 25 degrees C, the global free energy change calculated from the hydrogen exchange data was over 2 kcal/mol greater than the free energy of unfolding determined from urea denaturation experiments. The number of residues showing this unexpected behavior was found to increase with temperature. This apparent inconsistency can be explained quantitatively if the cis-trans isomerization of the two cis prolines, Pro-39 and Pro-55, is taken into account. The cis-trans isomerization equilibrium calculated from kinetic data indicates the free energy of the unfolded state will be 2.6 kcal/mol higher at 25 degrees C when the two prolines are cis rather than trans (Mayr LM, Odefey CO, Schutkowski M, Schmid FX. 1996. Kinetic analysis of the unfolding and refolding of ribonuclease T1 by a stopped-flow double-mixing technique. Biochemistry 35: 5550-5561). The hydrogen exchange results are consistent with the most slowly exchanging hydrogens exchanging from a globally higher free energy unfolded state in which Pro-55 and Pro-39 are still predominantly in the cis conformation. When the conformational stabilities determined by hydrogen exchange are corrected for the proline isomerization equilibrium, the results are in excellent agreement with those from an analysis of urea denaturation curves.

Thermodynamic hierarchy and local energetics of folded proteins

The cooperativity of local fluctuations within the folded state of a protein is demonstrated based on applying the "multiple-probe principle" to the hydrogen exchange (HX) rates of a set of amide protons of the protein. A hierarchical thermodynamic analysis is presented for the protein energetics, which includes both global two-state folding-unfolding transition and local cooperative fluctuations within the folded state. The analysis dissects the local fluctuations from the global unfolding; both lead to the HX but from the folded and unfolded states, respectively. It provides the newly observed HX behavior of proteins in mild denaturant, namely solvent and temperature dependent HX rates from the folded state, with a quantitative interpretation in terms of a set of local energetic parameters. These local energetic parameters contain much information concerning the structures and stabilities of native proteins.

Mass spectrometric determination of isotopic exchange rates of amide hydrogens located on the surfaces of proteins

The rates at which peptide amide hydrogens in folded proteins undergo isotopic exchange are reduced by factors of 10(0)-10(-8) relative to exchange rates at the same peptide linkages in unfolded proteins. To measure the isotopic exchange rates of the most rapidly exchanging peptide amide hydrogens in proteins, a flow-quench deuterium exchange-in step has been added to the protein fragmentation/mass spectrometry method (Zhang, Z.; Smith, D. L. Protein Sci. 1993, 2, 522-531). Isotopic exchange rates in eight short segments spanning the entire backbone of cytochrome c have been determined for exchange-in times of 0.2-120 s. These results show that the isotopic exchange rates of 10 of the peptide amide hydrogens in cytochrome c are similar to those expected for unfolded cyt c, while the exchange rates for 33 other non-hydrogen-bonded amide hydrogens are much less than expected for unfolded cyt c. Since the isotopic exchange rates of the most rapidly exchanging amide hydrogens in folded proteins are a direct measure of their access to the aqueous solvent, the ability to determine these isotopic exchange rates points to the possibility of using quenched-flow amide hydrogen exchange and mass spectrometry as a tool for identifying protein surfaces involved with binding.

An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway

BACKGROUND

Methods have been developed recently for probing local fluctuations of protein structure using H/2H-exchange of amide protons at equilibrium. It has been suggested that equilibrium exchange methods can identify the order of events in folding pathways and detect folding cores. We have applied the procedure of measuring the effects of denaturant on the H/2H-exchange of amide protons of barnase, the folding pathway of which is well established.

RESULTS

The addition of relatively low concentrations of denaturant causes the mechanism of exchange of amide protons of barnase to change from EX2 to EX1 for the residues that require global unfolding for exchange to occur. This change of mechanism, which would have been missed by some of the standard tests, causes artefacts that could be easily misinterpreted. We also present the thermodynamic argument that measurements at equilibrium cannot give the order of events in folding.

CONCLUSIONS

Measurement of H/2H-exchange of amide protons at equilibrium, when applied correctly, is an excellent method for analyzing the equilibrium distribution of unfolded and partly folded states. It cannot, in theory and in practice, be used for determining protein folding pathways by itself.