An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR.

The interaction of a protein antigen, horse cytochrome c (cyt c), with a monoclonal antibody has been studied by hydrogen-deuterium (H-D) exchange labeling and two-dimensional nuclear magnetic resonance (2D NMR) methods. The H-exchange rate of residues in three discontiguous regions of the cyt c polypeptide backbone was slowed by factors up to 340-fold in the antibody-antigen complex compared with free cyt c. The protected residues, 36 to 38, 59, 60, 64 to 67, 100, and 101, and their hydrogen-bond acceptors, are brought together in the three-dimensional structure to form a contiguous, largely exposed protein surface with an area of about 750 square angstroms. The interaction site determined in this way is consistent with prior epitope mapping studies and includes several residues that were not previously identified. The hydrogen exchange labeling approach can be used to map binding sites on small proteins in antibody-antigen complexes and may be applicable to protein-protein and protein-ligand interactions in general.

Chaperonin function: folding by forced unfolding.

The ability of the GroEL chaperonin to unfold a protein trapped in a misfolded condition was detected and studied by hydrogen exchange. The GroEL-induced unfolding of its substrate protein is only partial, requires the complete chaperonin system, and is accomplished within the 13 seconds required for a single system turnover. The binding of nucleoside triphosphate provides the energy for a single unfolding event; multiple turnovers require adenosine triphosphate hydrolysis. The substrate protein is released on each turnover even if it has not yet refolded to the native state. These results suggest that GroEL helps partly folded but blocked proteins to fold by causing them first to partially unfold. The structure of GroEL seems well suited to generate the nonspecific mechanical stretching force required for forceful protein unfolding.

On the prevalence of room-temperature protein phosphorescence.

A large number of proteins were tested for the property of intrinsic phosphorescence in deoxygenated aqueous solution at room temperature. The majority of proteins exhibit phosphorescence under normal solution conditions. Phosphorescence lifetimes from 0.5 millisecond to 2 seconds were observed in three-fourths of the proteins tested. The lifetime appears to correlate with relative isolation of the tryptophan indole side chain from solvent. With few exceptions, proteins in general can be expected to display a phosphorescence lifetime greater than 30 microseconds. This widespread characteristic of proteins has been largely overlooked because long-lived phosphorescence is highly sensitive to quenching by low levels of dissolved oxygen in solution. Protein phosphorescence offers a new time domain and a far wider dynamic range than has been used before for photoluminescence experimentation.

Protein folding intermediates: native-state hydrogen exchange.

The hydrogen exchange behavior of native cytochrome c in low concentrations of denaturant reveals a sequence of metastable, partially unfolded forms that occupy free energy levels reaching up to the fully unfolded state. The step from one form to another is accomplished by the unfolding of one or more cooperative units of structure. The cooperative units are entire omega loops or mutually stabilizing pairs of whole helices and loops. The partially unfolded forms detected by hydrogen exchange appear to represent the major intermediates in the reversible, dynamic unfolding reactions that occur even at native conditions and thus may define the major pathway for cytochrome c folding.

Hydrogen exchange measurement of the free energy of structural and allosteric change in hemoglobin.

The inability to localize and measure the free energy of protein structure and structure change severely limits protein structure-function investigations. The local unfolding model for protein hydrogen exchange quantitatively related the free energy of local structural stability with the hydrogen exchange rate of concerted sets of structurally related protons. In tests with a number of modified hemoglobin forms, the loss in structural free energy obtained locally from hydrogen exchange results matches the loss in allosteric free energy measured globally by oxygen-binding and subunit dissociation experiments.

How much is a stabilizing bond worth?

It is commonly supposed that the contribution of a bond to protein or nucleic acid stability is equal to the in situ stability of the bond itself. This is not true for the noncovalent bonds that stabilize molecular folding. In general, a bonding interaction contributes a free energy increment to protein or nucleic acid stability that is larger, an enthalpy increment that is smaller, and entropy and heat capacity increments that are more positive than the corresponding bond parameter.

Mechanisms and uses of hydrogen exchange.

Recent work has largely completed our understanding of the hydrogen-exchange chemistry of unstructured proteins and nucleic acids. Some of the high-energy structural fluctuations that determine the hydrogen-exchange behavior of native macromolecules have been explained; others remain elusive. A growing number of applications are exploiting hydrogen-exchange behavior to study difficult molecular systems and elicit otherwise inaccessible information on protein structure, dynamics and energetics.

Stable submolecular folding units in a non-compact form of cytochrome c.

Studies of structure, dynamics, and stability of cytochrome c (cyt c) at low pH in a non-compact pre-molten globule state indicate that the protein contains submolecular folding units that are independently stable. In high salt, acid cyt c (pD 2.2; where D is deuterium) is nearly as compact as the native form. Nuclear magnetic resonance (n.m.r.) line broadening typical of the molten globule form is seen, indicating loosened packing and increased mobility not only for side-chains but also for the main chain. As NaCl concentration is decreased below 0.05 M, cyt c expands due to the deshielding of electrostatic repulsions, attaining a linear extent perhaps double that of the native protein (viscosity, fluorescence). In the extended form, tertiary structural hydrogen bonds are largely broken (hydrogen exchange rate), some normally buried parts of the protein are exposed to water (fluorescence), and many of the native side-chain contacts must be lost. Nevertheless, almost all of the helical content is retained (circular dichroism). The helices involve the same amino acid residues that are helical in the native state (hydrogen exchange labeling monitored by 2-dimensional n.m.r.). The equilibrium constant for helix formation at 20 degrees C (0.02 M-NaCl, pD 2.2) is about 10 (hydrogen exchange rate), even though the individual helical segments when isolated have little or no structure. Additional experiments were done to check assumptions and calibrate parameters that underlie the hydrogen exchange analysis of protein folding. These results indicate that the native-like helical segments in the expanded non-globular form of cyt c exist as part of somewhat larger submolecular folding units that possess significant equilibrium stability. Results from equilibrium and kinetic studies of protein folding support the generality of this conclusion. This view is contrary to the two-state paradigm for equilibrium folding and inconsistent with the idea that side-chain packing constraints determine folding motifs. The result suggests an extension of the thermodynamic hypothesis for protein structure to kinetic folding processes, so that the amino acid code for equilibrium and kinetic folding may be the same, and also seems pertinent to the biological evolution of contemporary protein structures.

Salt, phosphate and the Bohr effect at the hemoglobin beta chain C terminus studied by hydrogen exchange.

Hydrogen exchange experiments using functional labeling and fragment separation methods were performed to study interactions at the C terminus of the hemoglobin beta subunit that contribute to the phosphate effect and the Bohr effect. The results show that the H-exchange behavior of several peptide NH at the beta chain C terminus is determined by a transient, concerted unfolding reaction involving five or more residues, from the C-terminal His146 beta through at least Ala142 beta, and that H-exchange rate can be used to measure the stabilization free energy of interactions, both individually and collectively, at this locus. In deoxy hemoglobin at pH 7.4 and 0 degrees C, the removal of 2,3-diphosphoglycerate (DPG) or pyrophosphate (loss of a salt to His143 beta) speeds the exchange of the beta chain C-terminal peptide NH protons by 2.5-fold (at high salt), indicating a destabilization of the C-terminal segment by 0.5 kcal of free energy. Loss of the His146 beta 1 to Asp94 beta 1 salt link speeds all these protons by 6.3-fold, indicating a bond stabilization free energy of 1.0 kcal. When both these salt links are removed together, the effect is found to be strictly additive; all the protons exchange faster by 16-fold indicating a loss of 1.5 kcal in stabilization free energy. Added salt is slightly destabilizing when DPG is present but provides some increased stability, in the 0.2 kcal range, when DPG is absent. The total allosteric stabilization energy at each beta chain C terminus in deoxy hemoglobin under these conditions is measured to be 3.8 kcal (pH 7.4, 0 degrees C, with DPG). In oxy hemoglobin at pH 7.4 and 0 degrees C, stability at the beta chain C terminus is essentially independent of salt concentration, and the NES modification, which in deoxy hemoglobin blocks the His146 beta to Asp94 beta salt link, has no destabilizing effect, either at high or low salt. These results appear to show that the His146 beta salt link, which participates importantly in the alkaline Bohr effect, does not reform to Asp94 beta or to any other salt link acceptor in a stable way in oxy hemoglobin at low or high salt conditions.

Energetic components of the allosteric machinery in hemoglobin measured by hydrogen exchange.

A hydrogen exchange (HX) functional labeling method was used to study allosterically active segments in human hemoglobin (Hb) at the alpha-chain N terminus and the beta-chain C terminus. Allosterically important interactions that contact these segments were removed one or more at a time by mutation (Hbs Cowtown, Bunbury, Barcelona, Kariya), proteolysis (desArg141alpha, desHis146beta), chemical modification (N-ethylsuccinimidyl-Cys93beta), and the withdrawal of extrinsic effectors (phosphate groups, chloride). The effects of each modification on HX rate at the local and the remote position were measured in the deoxy Hb T-state and translated into change in structural free energy at each position.The removal of individual salt links destabilizes local structure by 0.4 to 0.75 kcal/mol (pH 7.4, 0 degreesC, 0.35 M ionic strength) and often produces cross-subunit effects while hemoglobin remains in the T-state. In doubly modified hemoglobins, different changes that break the same links produce identical destabilization, changes that are structurally independent show energetic additivity, and changes that intersect show energetic overlap. For the overall T-state to R-state transition and for some but not all modifications within the T-state, the summed loss in stabilization free energy measured at the two chain termini matches the total loss in allosteric free energy measured by global methods. These observations illustrate the importance of evaluating the detailed energetics and the modes of energy transfer that define the allosteric machinery.

Signal transmission between subunits in the hemoglobin T-state.

To study allosteric mechanism in hemoglobin, a hydrogen-exchange method was used to measure ligand-dependent changes in structural free energy at defined allosterically sensitive positions. When the two alpha-subunits are CN-met liganded, effects can be measured locally, within the alpha-subunit, and also remotely, within the beta-subunit, even though the quaternary structure remains in the T conformation. When the two beta-subunits are liganded, effects occur at the same positions. The effects seen are the same, independently of whether ligands occupy the alpha-chain hemes or the beta-chain hemes. Control experiments rule out modes of energy transfer other than programmed cross-subunit interaction within the T-state. Cross-subunit transfer may depend on pulling the heme trigger (moving the heme iron into the heme plane) rather than on liganding alone.

Allosteric energy at the hemoglobin beta chain C terminus studied by hydrogen exchange.

When hemoglobin switches from the deoxy (T) to the liganded (R) form, several of its peptide group NH experience a great increase in their rate of exchange with water. Selective labeling and fragment isolation experiments identify some of the sensitive protons as three to four near-neighbor H-bonded peptide NH placed between Ala140 beta and the C-terminal His146 beta residue. These NH have differing solvent accessibilities, yet all exchange at about the same rate, and they maintain a common rate in the face of modifications that change their exchange rate over a 1000-fold range. This suggests that their exchange is mediated by a concerted transient unfolding reaction. The removal of allosterically important salt links at the distant alpha subunit N termini (des-Arg141 alpha hemoglobin) has little if any effect on the indicator NH at the beta C terminus. This demonstrates the restricted reach of the separate allosteric interactions in the T form as well as the localized nature of the H-exchange probe. Breakage of a salt link at the beta chain C terminus (His146 beta to Asp94 beta) by chemical modification (NES-Cys93 beta hemoglobin) speeds exchange of the indicator peptide NH in T-state hemoglobin by six-fold, which corresponds to an allosteric destabilization at the C-terminal segment of 1 kcal (pH 7.4, 0 degrees C), according to local unfolding theory. This is in quantitative agreement with energy values obtainable from other measurements. These NH exchange with an average halftime of five hours in deoxy hemoglobin and 15 seconds in oxy hemoglobin. According to the unfolding model for protein H-exchange, the 1200-fold increase in rate indicates a loss of 3.8 kcal in structural stabilization free energy at or near the C terminus of each beta chain in the T to R transition (pH 7.4, 0 degrees C, with 2,3-diphosphoglycerate). This result together with other available data places about 70% of hemoglobin's total allosterically significant structural energy change at the beta chain C termini.

Identification of an allosterically sensitive unfolding unit in hemoglobin.

Hydrogen-exchange studies locate a set of seven allosterically sensitive amide NH protons side by side around two turns of the F-FG helical segment in the hemoglobin beta chain. Some of these protons are on the aqueous protein surface and some deeply inside, yet they all exchange with solvent protons at similar rates. Further, they move in unison to a new common rate when hemoglobin changes its allosteric form. These observations and analogous results for other proteins appear to be inconsistent with penetration-dependent models which relate H-exchange rate to solvent accessibility in the native state. Rather, these results point to sizeable fluctuational distortions that make small sets of protons more or less equally accessible in some transient H-exchange transition state, as visualized in the local unfolding model. The set of allosterically sensitive protons studied here exchanges 30-fold faster in liganded hemoglobin than in the deoxy form. In terms of the unfolding model, this means that the F-FG structure is relatively destabilized in oxyhemoglobin, so that the allosterically linked change in structural free energy at F-FG favors the deoxy state. The 30-fold change in H-exchange rate suggests a contribution to the allosteric free energy by this segment of 2 kcal (1 cal = 4.184 J). These experiments utilized a labeling technique, described earlier, that selectively places tritium on sites whose H-exchange rates are sensitive to the protein functional state, and used a method introduced by Rosa & Richards (1979,1981) to locate this label in the protein. The latter method, which rapidly separates protein fragments under conditions that can preserve exchangeable label, was here brought to a more quantitative level. Taken together, these techniques provide a "functional labeling" method capable of selectively labeling and identifying protein segments that participate in functional interactions.

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.

Protein complexes studied by NMR spectroscopy.

Recent advances in NMR methods now allow protein complexes to be studied in great detail in a wide range of solution conditions. Isotope-enrichment strategies, resonance-assignment approaches and structural-determination methods have evolved to the point where almost any type of complex involving proteins of reasonable size may be studied in a straightforward way. A variety of isotope editing and filtering strategies underlie these powerful methodologies. Approaches to the characterization of the dynamics of protein complexes have also matured to the point where detailed studies of the effects of complexation on dynamics can be studied over a wide range of timescales.

Two-state vs. multistate protein unfolding studied by optical melting and hydrogen exchange.

A direct conflict between the stabilization free energy parameters of cytochrome c determined by optical methods and by hydrogen exchange (HX) is quantitatively explained when the partially folded intermediates seen by HX are taken into account. The results support the previous HX measurements of intermediate populations, show how intermediates can elude the standard melting analysis, and illustrate how they confuse the analysis when they are significantly populated within the melting transition region.

Hydrogen exchange: the modern legacy of Linderstrøm-Lang.

This discussion, prepared for the Protein Society's symposium honoring the 100th anniversary of Kaj Linderstrøm-Lang, shows how hydrogen exchange approaches initially conceived and implemented by Lang and his colleagues some 50 years ago are contributing to current progress in structural biology. Examples are chosen from the active protein folding field. Hydrogen exchange methods now make it possible to define the structure of protein folding intermediates in various contexts: as tenuous molten globule forms at equilibrium under destabilizing conditions, in kinetic intermediates that exist for less than one second, and as infinitesimally populated excited state forms under native conditions. More generally, similar methods now find broad application in studies of protein structure, energetics, and interactions. This article considers the rise of these capabilities from their inception at the Carlsberg Labs to their contemporary role as a significant tool of modern structural biology.

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.

Dynamics and thermodynamics of hyperthermophilic proteins by hydrogen exchange.

The naturally occurring hydrogen exchange of protein molecules can provide nonperturbing site-resolved measurements of protein stability and flexibility and changes therein. The measurement and understanding of these issues is especially pertinent to studies of thermophilic proteins. This chapter briefly reviews the considerations necessary for measuring hydrogen exchange and translating HX measurements into these detailed protein parameters.

Thermodynamic parameters from hydrogen exchange measurements.

Just as exchangeable hydrogens that are controlled by global unfolding can be used to measure thermodynamic parameters at a global level, hydrogens that are exposed to exchange by local unfolding reactions may be used to obtain locally resolved energy parameters. Results with the hemoglobin system demonstrate the ability of HX methods to locate functionally important changes in a protein and to measure the energetic contribution of each. These results offer the promise that HX measurements may be used to delineate, in terms of definable bonds and their energies and interactions, the network of interactions that Hb and other proteins use to produce their various functions.