Folding units govern the cytochrome c alkaline transition

Compressing the free energy range of substructure stabilities in iso-1-cytochrome c

Evolutionary conservation of substructure architecture between yeast iso-1-cytochrome c and the well-characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine-HCl. Mass spectral analysis of limited proteolysis cleavage products for iso-1-cytochrome c show that its least stable substructure is the same as horse cytochrome c. The limited proteolysis data yield a free energy of 3.8 +/- 0.4 kcal mol(-1) to unfold the least stable substructure compared with 5.05 +/- 0.30 kcal mol(-1) for global unfolding of iso-1-cytochrome c. Thus, substructure stabilities of iso-1-cytochrome c span only approximately 1.2 kcal mol(-1) compared with approximately 8 kcal mol(-1) for horse cytochrome c. Consistent with the less cooperative folding thus expected for the horse protein, the guanidine-HCl m-values are approximately 3 kcal mol(-1)M(-1) versus approximately 4.5 kcal mol(-1)M(-1) for horse versus yeast cytochrome c. The tight free energy spacing of the yeast cytochrome c substructures suggests that its folding has more branch points than for horse cytochrome c. Studies on a variant of iso-1-cytochrome c with an H26N mutation indicate that the least and most stable substructures unfold sequentially and the two least stable substructures unfold independently as for horse cytochrome c. Thus, important aspects of the substructure architecture of horse cytochrome c, albeit compressed energetically, are preserved evolutionally in yeast iso-1-cytochrome c.

Evolutionary alkaline transition in human cytochrome c

Conformational transitions in cytochrome c (cyt c) are being realized to be responsible for its multi-functions. Among a number of conformational transitions in cyt c, the alkaline transition has attracted much attention. The cDNA of human cyt c is cloned by RT-PCR and a high-effective expression system for human cyt c has been developed in this study. The equilibrium and kinetics of the alkaline transition of human cyt c have been systematically investigated for the first time, and compared with those of yeast and horse cyt c from an evolutionary perspective. The pK(a) value for the alkaline transition of human cyt c is apparently higher than that of yeast and horse. Kinetic studies suggest that it is increasingly difficult for the alkaline transition of cyt c from yeast, horse and human. Molecular modeling of human cyt c shows that the omega loop where the lysine residue is located apparently further away from heme in human cyt c than in yeast iso-1 and horse heart cyt c. These results regarding alkaline conformational transition provide valuable information for understanding the molecular basis for the biological multi-functions of cyt c.

The determinants of stability and folding in evolutionarily diverged cytochromes c

Cytochrome c has served as a paradigm for the study of protein stability, folding, and molecular evolution, but it remains unclear how these aspects of the protein are related. For example, while the bovine and equine cytochromes c are known to have different stabilities, and possibly different folding mechanisms, it is not known how these differences arise from just three amino acid substitutions introduced during divergence. Using site-selectively incorporated carbon-deuterium bonds, we show that like the equine protein, bovine cytochrome c is induced to unfold by guanidine hydrochloride via a stepwise mechanism, but it does not populate an intermediate as is observed with the equine protein. The increased stability also results in more similar free energies of unfolding observed at different sites within the protein, giving the appearance of a more concerted mechanism. Furthermore, we show that the differences in stability and folding appear to result from a single amino acid substitution that stabilizes a helix by allowing for increased solvation of its N-terminus.

Chemical frustration in the protein folding landscape: grand canonical ensemble simulations of cytochrome c

A grand canonical formalism is developed to combine discrete simulations for chemically distinct species in equilibrium. Each simulation is based on a perturbed funneled landscape. The formalism is illustrated using the alkaline-induced transitions of cytochrome c as observed by FTIR spectroscopy and with various other experimental approaches. The grand canonical simulation method accounts for the acid/base chemistry of deprotonation, the inorganic chemistry of heme ligation and misligation, and the minimally frustrated folding energy landscape, thus elucidating the physics of protein folding involved with an acid/base titration of a protein. The formalism combines simulations for each of the relevant chemical species, varying by protonation and ligation states. In contrast to models based on perfectly funneled energy landscapes that contain only contacts found in the native structure, this study introduces "chemical frustration" from deprotonation and misligation that gives rise to many intermediates at alkaline pH. While the nature of these intermediates cannot be easily inferred from available experimental data, this study provides specific structural details of these intermediates, thus extending our understanding of how cytochrome c changes with an increase in pH. The results demonstrate the importance of chemical frustration for understanding biomolecular energy landscapes.

Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes

The alkaline-induced structural transitions of ferricytochrome c have been studied intensively as a model for how changes in metal ligation contribute to protein function and folding. Previous studies have demonstrated that multiple non-native species accumulate with increasing pH. Here, we used a combination of experiments and simulations to provide a high-resolution view of the changes associated with increasing alkaline conditions. Alkaline-induced transitions were characterized under equilibrium conditions by following changes in the IR absorptions of carbon-deuterium chromophores incorporated at Leu68, Lys72, Lys73, Lys79, and Met80. The data suggest that at least four intermediates are formed as the pH is increased prior to complete unfolding of the protein. The first alkaline transition observed appears to be driven by a single deprotonation and occurs with a midpoint of pH 8.8, but surprisingly, the intermediate formed does not appear to be one of the well-characterized lysine misligates. At higher pH, second and third deprotonations, with a combined apparent midpoint pH of 10.2, induce transitions to Lys73- or Lys79-misligated species. Interestingly, the lysine misligates appear to undergo iron reduction by the coordinated amine. A transition from the lysine misligates to another intermediate, likely a hydroxide-misligated species, is associated with a fourth deprotonation and a midpoint of pH 10.7. Finally, the protein loses tertiary structure with a fifth deprotonation that occurs with a midpoint of pH 12.7. Native topology-based models with enforced misligation are employed to help understand the structures of the observed intermediates.

The Mad2 partial unfolding model: regulating mitosis through Mad2 conformational switching

The metamorphic Mad2 protein acts as a molecular switch in the checkpoint mechanism that monitors proper chromosome attachment to spindle microtubules during cell division. The remarkably slow spontaneous rate of Mad2 switching between its checkpoint inactive and active forms is catalyzed onto a physiologically relevant time scale by a self–self interaction between its two forms, culminating in a large pool of active Mad2. Recent structural, biochemical, and cell biological advances suggest that the catalyzed conversion of Mad2 requires a major structural rearrangement that transits through a partially unfolded intermediate.

The foldon substructure of staphylococcal nuclease

To search for submolecular foldon units, the spontaneous reversible unfolding and refolding of staphylococcal nuclease under native conditions was studied by a kinetic native-state hydrogen exchange (HX) method. As for other proteins, it appears that staphylococcal nuclease is designed as an assembly of well-integrated foldon units that may define steps in its folding pathway and may regulate some other functional properties. The HX results identify 34 amide hydrogens that exchange with solvent hydrogens under native conditions by way of large transient unfolding reactions. The HX data for each hydrogen measure the equilibrium stability (Delta G(HX)) and the kinetic unfolding and refolding rates (k(op) and k(cl)) of the unfolding reaction that exposes it to exchange. These parameters separate the 34 identified residues into three distinct HX groupings. Two correspond to clearly defined structural units in the native protein, termed the blue and red foldons. The remaining HX grouping contains residues, not well separated by their HX parameters alone, that represent two other distinct structural units in the native protein, termed the green and yellow foldons. Among these four sets, a last unfolding foldon (blue) unfolds with a rate constant of 6 x 10(-6) s(-1) and free energy equal to the protein's global stability (10.0 kcal/mol). It represents part of the beta-barrel, including mutually H-bonding residues in the beta 4 and beta 5 strands, a part of the beta 3 strand that H-bonds to beta 5, and residues at the N-terminus of the alpha2 helix that is capped by beta 5. A second foldon (green), which unfolds and refolds more rapidly and at slightly lower free energy, includes residues that define the rest of the native alpha2 helix and its C-terminal cap. A third foldon (yellow) defines the mutually H-bonded beta1-beta2-beta 3 meander, completing the native beta-barrel, plus an adjacent part of the alpha1 helix. A final foldon (red) includes residues on remaining segments that are distant in sequence but nearly adjacent in the native protein. Although the structure of the partially unfolded forms closely mimics the native organization, four residues indicate the presence of some nonnative misfolding interactions. Because the unfolding parameters of many other residues are not determined, it seems likely that the concerted foldon units are more extensive than is shown by the 34 residues actually observed.

Protein folding and misfolding: mechanism and principles

Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.

pH-Induced changes in adsorbed cytochrome c. voltammetric and surface-enhanced resonance Raman characterization performed simultaneously at chemically modified silver electrodes

The influence of pH on the redox properties of cytochrome c (cyt c) adsorbed on roughened silver electrodes chemically modified with a self-assembled monolayer (SAM) of 11-mercapto-1-undecanoic acid (MUA) was studied with voltammetric techniques in combination with surface-enhanced resonance Raman scattering (SERRS). The experiments were performed simultaneously on the same electrode sample in a homemade spectroelectrochemical cell suitable for such applications. At pH 7.0 cyt c was found in its native state; at higher pH values (ranging from 8.0 to 9.0) the redox properties of the adsorbed protein varied considerably, featuring a redox behavior which does not resemble the one reported for the alkaline transition. Our results instead indicate the presence of an electrochemically inactive 6cLS species immobilized on MUA at pH 9.0. The pH-induced conformational changes observed for cyt c immobilized on the SAM of MUA were found to be repeatable and chemically reversible, meaning that the recovery of the electrochemical signal due to the native protein occurred instantaneously (on the second time scale) when the electrode was switched back to pH 7.0. The pH-induced changes observed were attributed to a conformational change involving a heme reorientation with respect to the electrode surface.

Alkaline conformational transition and gated electron transfer with a Lys 79 --> his variant of iso-1-cytochrome c

To probe the mechanism of the alkaline conformational transition and its effect on the dynamics of gated electron transfer (ET) reactions, a Lys 79 --> His (K79H) variant of iso-1-cytochrome c has been prepared. Guanidine hydrochloride denaturation monitored by circular dichroism and absorbance at 695 nm indicates that this variant unfolds from a partially unfolded state. The conformation of the wild type (WT) and K79H proteins was monitored at 695 nm from pH 2 to 11. These data indicate that acid unfolding is multi-state for both K79H and WT proteins and that the His 79-heme alkaline conformer is more stable than a previously reported His 73-heme alkaline conformer. Fast and slow phases are observed in the kinetics of the alkaline transition of the K79H variant. The pH dependence of the fast phase kinetic data shows that ionizable groups with pKa values near 6.8 and 9 modulate the formation of the His 79-heme alkaline conformer. The slow phase kinetic data are consistent with a single ionizable group with a pKa near 9.5 promoting the Lys 73-heme alkaline transition. In the broader context of data on the alkaline transition, ionization of the ligand replacing Met 80 appears to play a primary role in promoting the formation of the alkaline conformer, with other ionizable groups acting as secondary modulators. Intermolecular ET with hexaammineruthenium(II) chloride shows conformational gating due to both His 79-heme and Lys 73-heme alkaline conformers. Both the position and the nature of the alkaline state ligand modulate the dynamics of ET gating.

Branching in the sequential folding pathway of cytochrome c

Previous results indicate that the folding pathways of cytochrome c and other proteins progressively build the target native protein in a predetermined stepwise manner by the sequential formation and association of native-like foldon units. The present work used native state hydrogen exchange methods to investigate a structural anomaly in cytochrome c results that suggested the concerted folding of two segments that have little structural relationship in the native protein. The results show that the two segments, an 18-residue omega loop and a 10-residue helix, are able to unfold and refold independently, which allows a branch point in the folding pathway. The pathway that emerges assembles native-like foldon units in a linear sequential manner when prior native-like structure can template a single subsequent foldon, and optional pathway branching is seen when prior structure is able to support the folding of two different foldons.

Thermodynamics of the alkaline transition in phytocyanins

The thermodynamics of the alkaline transition which influences the spectral and redox properties of the type 1 copper center in phytocyanins has been determined spectroscopically. The proteins investigated include Rhus vernicifera stellacyanin, cucumber basic protein and its Met89Gln variant, and umecyanin, the stellacyanin from horseradish roots, along with its Gln95Met variant. The changes in reaction enthalpy and entropy within the protein series show partial compensatory behavior. Thus, the reaction free energy change (hence the pK (a) value) is rather variable. This indicates that species-dependent differences in reaction thermodynamics, although containing an important contribution from changes in the hydrogen-bonding network of water molecules in the hydration sphere of the protein (which feature enthalpy-entropy compensation), are to a large extent protein-based. The data for axial ligand variants are consistent with the hypothesis of a copper-binding His as the deprotonating residue responsible for this transition.

A millisecond infrared stopped-flow apparatus

In this paper, we have described a stopped-flow apparatus that is capable of measuring infrared kinetics in the amide I' region of a protein's vibrational spectrum. The dead time of this setup, determined by the reducing reaction of 2,6-Dichlorophenolindophenol by L-ascorbic acid, is between 6 to 15 ms, depending on the flow rate. Therefore, this stopped-flow IR method provides a means of measuring infrared kinetics in a time window that is not easily accessible to other mixing-based IR techniques. Using this apparatus, we have studied the alkaline transition of cytrochrome c and have found that this conformational event proceeds in a biphasic manner. The characteristic time constants of these two phases were determined to be 68 +/- 20 ms and 624 +/- 37 ms, respectively.

The Alkali Molten Globule State of Horse Ferricytochrome c: Observation of Cold Denaturation

Here, we present the basic structural properties and the thermodynamic description of a previously unknown alkali molten globule state of horse "ferricytochrome c". Both sodium and guanidinium cations stabilize the alkali-denatured state at pH 13, presumably by a charge screening mechanism. The Na(+)-stabilized conformation (B state) clearly meets with the molecular organizational definition of the generic molten globule state. The B state exhibits highly cooperative thermal unfolding transitions monitored by both near and far-UV CD. Analyses of these transitions show substantial heat capacity change, suggesting that the hydrophobic effect contributes considerably to its energetic stability. At low salt concentration where molten globules are less stable, the B state undergoes reversible cold denaturation.

Local stability of Rhodobacter capsulatus cytochrome c2 probed by solution phase hydrogen/deuterium exchange and mass spectrometry

The hydrogen/deuterium exchange kinetics of Rhodobacter capsulatus cytochrome c2 have been determined using mass spectrometry. As expected, the relative domain stability was generally similar to that of the cytochrome c2 structural homolog, horse heart cytochrome c, but we were able to find evidence to support the presence of a second, small beta-sheet not found in the horse cytochrome, which stabilizes a structural region dominated by Omega loops. Importantly, we find that the so-called hinge region, comprised of 15 amino acids, which include the methionine sixth heme ligand (M96), is destabilized on oxidation, and this destabilization is propagated to a portion of the second Omega loop, most likely through perturbation of two hydrogen bonds that couple these two domains in the three dimensional structure. The mutation of a lysine at position 93 to proline amplifies the destabilization observed on oxidation of the wild-type cytochrome c2 and results in further destabilization observed in regions 52-60, 75-82, and 83-97. This suggests that hydrogen bond interactions involving two bound waters, the T94 hydroxyl, the front heme propionate and the Y75 hydroxyl, are significantly compromised upon mutation. In summary, these observations are consistent with the approximately 20-fold increase in the movement of the hinge away from the heme face in the oxidized cytochrome c2 as determined by ligand binding kinetics. Thus, H/D exchange kinetics can be used to identify relatively subtle structural features and at least in some cases facilitate the understanding of the structural basis of the dynamic properties of proteins.

Conformational stability and dynamics of cytochrome c affect its alkaline isomerization

The alkaline isomerization of horse heart ferricytochrome c (cyt c) has been studied by electronic absorption spectroscopy in the presence of the Hofmeister series of anions: chloride, bromide, rhodanide and perchlorate. The anions significantly affect the apparent pK (a) value of the transition in a concentration-dependent manner according to their position in the Hofmeister series. The Soret region of the absorption spectra is not affected by the presence of the salts and shows no significant structural perturbation of the heme crevice. In the presence of perchlorate and rhodanide anions, the cyanide exchange rate between the bulk solvent and the binding site is increased. These results imply higher flexibility of the protein structure in the presence of chaotropic salts. The thermal and isothermal denaturations monitored by differential scanning calorimetry and circular dichroism, respectively, showed a decrease in the conformational stability of cyt c in the presence of the chaotropic salts. A positive correlation between the stability, DeltaG, of cyt c and the apparent pK (a) values that characterize the alkaline transition indicates the presence of a thermodynamic linkage between these conformational transitions. In addition, the rate constant of the cyanide binding and the partial molar entropies of anions negatively correlate with the pK (a) values. This indicates the important role of anion-induced solvent reorganization on the structural flexibility of cyt c in the alkaline transitions.

The native-state ensemble of proteins provides clues for folding, misfolding and function

The predominant equilibrium in proteins is not between native and unfolded states, it is between the native and multiple partially unfolded forms. Some of these partially unfolded forms can be energetically close to the native state and, therefore, have the potential to become appreciably populated. This could have an important role in protein function or misfolding diseases. The recent identification and characterization of the partially unfolded forms of apoflavodoxin furthers our understanding of their formation.

Tuning the Rate and pH Accessibility of a Conformational Electron Transfer Gate

Methods to fine-tune the rate of a fast conformational electron transfer (ET) gate involving a His-heme alkaline conformer of iso-1-cytochrome c (iso-1-Cytc) and to adjust the pH accessibility of a slow ET gate involving a Lys-heme alkaline conformer are described. Fine-tuning the fast ET gate employs a strategy of making surface mutations in a substructure unfolded in the alkaline conformer. To make the slow ET gate accessible at neutral pH, the strategy involves mutations at buried sequence positions which are expected to more strongly perturb the stability of native versus alkaline iso-1-Cytc. To fine-tune the rate of the fast His 73-heme ET gate, we mutate the surface-exposed Lys 79 to Ala (A79H73 variant). This mutation also simplifies ET gating by removing Lys 79, which can serve as a ligand in the alkaline conformer of iso-1-Cytc. To adjust the pH accessibility of the slow Lys 73-heme ET gate, we convert the buried side chain Asn 52 to Gly and also mutate Lys 79 to Ala to simplify ET gating (A79G52 variant). ET kinetics is studied as a function of pH using hexaammineruthenium(II) chloride (a6Ru2+) to reduce the variants. Both variants show fast direct ET reactions dependent on [a6Ru2+] and slower gated ET reactions that are independent of [a6Ru2+]. The observed gated ET rates correlate well with rates for the alkaline-to-native state conformational change measured independently. Together with the previously reported H73 variant (Baddam, S.; Bowler, B. E. J. Am. Chem. Soc. 2005, 127, 9702-9703), the A79H73 variant allows His 73-heme-mediated ET gating to be fine-tuned from 75 to 200 ms. The slower Lys 73-heme (15-20 s time scale) ET gate for the A79G52 variant is now accessible over the pH range 6-8.

Mutation of asparagine 52 to glycine promotes the alkaline form of iso-1-cytochrome c and causes loss of cooperativity in acid unfolding

The kinetics and thermodynamics of the alkaline and acid conformational transitions of a Lys 79 --> Ala/Asn 52 --> Gly (A79G52) variant of iso-1-cytochrome c are studied. The Lys 79 --> Ala mutation is designed to limit heme ligation in the alkaline conformer to Lys 73. The Asn 52 --> Gly mutation is intended to shift the population of the alkaline conformer to physiological pH based on the hierarchical nature of the cooperative substructures of this protein. The midpoint pH for formation of the alkaline conformer is approximately 7.45. The kinetics for the alkaline conformational transition of the A79G52 variant are consistent with the ionization constant, pK(H), for the trigger group controlling formation of the alkaline conformer being approximately 9.5. This pK(H) is low for alkaline conformers involving lysine-heme ligation but is consistent with the pK(a) of the highest of three ionizable groups which modulate formation of the histidine-heme alkaline conformer of a His 73 variant of iso-1-cytochrome c [Martinez, R. E., and Bowler, B. E. (2004) J. Am. Chem. Soc. 126, 6751-6758]. The acid transition of the A79G52 variant is split into two phases. Both the Lys 79 --> Ala and Asn 52 --> Gly mutations are expected to affect the buried hydrogen bond network of cytochrome c, suggesting that this network is an important modulator of the acid unfolding of cytochrome c.

Thermodynamics and kinetics of formation of the alkaline state of a Lys 79-->Ala/Lys 73-->His variant of iso-1-cytochrome c

The alkaline transition kinetics of a Lys 73-->His (H73) variant of iso-1-cytochrome c are triggered by three ionizable groups [Martinez, R. E., and Bowler, B. E. (2004) J. Am. Chem. Soc. 126, 6751-6758]. To eliminate ambiguities caused by overlapping phases due to formation of the Lys 79 alkaline conformer and proline isomerization associated with the His 73 alkaline conformer, we mutated Lys 79 to Ala in the H73 variant (A79H73). The stability and guanidineHCl m-values of the A79H73 and H73 variants at pH 7.5 are the same. The Ala 79 mutation causes formation of the alkaline conformer to depend on [NaCl]. The salt dependence saturates at 500 mM NaCl, and the thermodynamics of alkaline state formation for the A79H73 and H73 variants become identical. The salt dependence is consistent with loss of an electrostatic contact between Lys 79 and heme propionate D in the A79H73 variant. The kinetics of alkaline state formation for the A79H73 variant support the three trigger group model developed for the H73 variant, with the primary trigger, pK(HL), being ionization of His 73. The low pH ionization, pK(H1), is perturbed by the Ala 79 mutation indicating that this ionization is modulated by the buried hydrogen bond network involving heme propionate D. The A79H73 variant has a high spin heme above pH 9 suggesting that the high pH ionization, pK(H2), involves a high spin heme conformer. The proline isomerization phase is modulated by both pK(HL) and pK(H2) indicating that it is sensitive to protein conformation.

Insights into the role of the histidines in the structure and stability of cytochrome c

In this paper we investigate the role played by each histidine in the amino acid sequence of yeast iso-1-cytochrome c (with the exception of H18, the residue axially coordinated to the heme iron) in determining the protein structure and stability. To this end, we have generated and characterized the double mutants H26Y/H33Y, H26Y/H39K and H33Y/H39K obtained from the C102T variant of the protein, which retain only one histidine side chain in the amino acid sequence. In particular, the H39K mutation inserts a lysine at position 39 as in the sequence of equine cytochrome c. The H26Y/H33Y/H39K triple mutant, which lacks all three histidines, was also produced and its spectroscopic properties are compared with those of the double mutants. The data highlight the critical role played by H26 in determining protein stability. Recombinant horse cytochrome c and the corresponding H26Y mutant were also generated and characterized. Since equine cytochrome c exhibits higher stability than the yeast protein, this provides a valuable opportunity to understand the role played by the invariant H26 residue in determining structure and stability.

Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study

Molecular dynamics (MD) simulations on a bacterial cytochrome c were performed to investigate the lifetime and fluctuations of backbone hydrogen bonds and to correlate these data with protection factors for hydrogen exchange measured by NMR spectroscopy (Bartalesi et al. in Biochemistry, 42:10923-10930, 2003). The MD simulations provide a consistent pattern in that long lifetimes of hydrogen bonds go along with small amplitude fluctuations. In agreement with experiments, differences in stability were found with a rather flexible N-terminal segment as compared with a more rigid C-terminal part. Protection factors of backbone hydrogen exchange correlate strongly with the number of contacts but also with hydrogen-bond occupancy, hydrogen-bond survival times, as well as the inverse of fluctuations of backbone atoms and hydrogen-bond lengths derived from MD simulation data. We observed a conformational transition in the C-terminal loop, and significant motion in the N-terminal loop, which can be interpreted as being the structural units involved in the onset of the protein unfolding process in agreement with experimental evidence on mitochondrial cytochrome c.

Functional role of a protein foldon-An Ω-loop foldon controls the alkaline transition in ferricytochrome c

Hydrogen exchange results for cytochrome c and several other proteins show that they are composed of a number of foldon units which continually unfold and refold and account for some functional properties. Previous work showed that one Omega-loop foldon controls the rate of the structural switching and ligand exchange behavior of cytochrome c known as the alkaline transition. The present work tests the role of foldons in the alkaline transition equilibrium. We measured the effects of denaturant and 14 destabilizing mutations. The results show that the ligand exchange equilibrium is controlled by the stability of the same foldon unit implicated before. In addition, the results obtained confirm the epsilon-amino group of Lys79 and Lys73 as the alkaline replacement ligands and bear on the search for a triggering group.

A size dependent folding contour for cytochrome C

The paper describes an experimental construct of the folding route of the heme protein cytochrome-C. The construct highlights a slowing down near the nose of the folding funnel caused by the multiplicity of the energy traps near the native conformation created as a result of complex heme-peptide interaction. Interestingly the hydrodynamic size, the size heterogeneity and peroxidase activity serve as a triple measure of the distance of this near equilibrium departure from native conformation. Accordingly, the folding process is marked with a gradual and reversible reduction of mean hydrodynamic size, size heterogeneity and peroxidase activity (higher in unfolded state). The Dynamic Light Scattering based straightforward illustration of hydrodynamic size variation may serve as a model to slow folding observed in case of heme proteins, the heme itself serving as a natural facilitator for the native peptide conformation.

The effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from Paracoccus versutus assessed by X-ray crystallography and unfolding

The structure of cytochrome c-550 from the nonphotosynthetic bacteria Paraccocus versutus has been solved by X-ray crystallography to 1.90 A resolution, and reveals a high structural homology to other bacterial cytochromes c(2). The effect of replacing the axial heme-iron methionine ligand with a lysine residue on protein structure and unfolding has been assessed using the M100K variant. From X-ray structures at 1.95 and 1.55 A resolution it became clear that the amino group of the lysine side chain coordinates to the heme-iron. Structural differences compared to the wild-type protein are confined to the lysine ligand loop connecting helices four and five. In the heme cavity an additional water molecule is found which participates in an H-bonding interaction with the lysine ligand. Under cryo-conditions extra electron density in the lysine ligand loop is revealed, leading to residues K97 to T101 being modeled with a double main-chain conformation. Upon unfolding, dissociation of the lysine ligand from the heme-iron is shown to be pH dependent, with NMR data consistent with the occurrence of a ligand exchange mechanism similar to that seen for the wild-type protein.

ATP specifically drives refolding of non-native conformations of cytochrome c

An increasing body of evidence ascribes to misfolded forms of cytochrome c (cyt c) a role in pathophysiological events such as apoptosis and disease. Here, we examine the conformational changes induced by lipid binding to horse heart cyt c at pH 7 and study the ability of ATP (and other nucleotides) to refold several forms of unfolded cyt c such as oleic acid-bound cyt c, nicked cyt c, and acid denatured cyt c. The CD and fluorescence spectra demonstrate that cyt c unfolded by oleic acid has an intact secondary structure, and a disrupted tertiary structure and heme environment. Furthermore, evidence from the Soret CD, electronic absorption, and resonance Raman spectra indicates the presence of an equilibrium of at least two low-spin species having distinct heme-iron(III) coordination. As a whole, the data indicate that binding of cyt c to oleic acid leads to a partially unfolded conformation of the protein, resembling that typical of the molten globule state. Interestingly, the native conformation is almost fully recovered in the presence of ATP or dATP, while other nucleotides, such as GTP, are ineffective. Molecular modeling of ATP binding to cyt c and mutagenesis experiments show the interactions of phosphate groups with Lys88 and Arg91, with adenosine ring interaction with Glu62 explaining the unfavorable binding of GTP. The finding that ATP and dATP are unique among the nucleotides in being able to turn non-native states of cyt c back to native conformation is discussed in the light of cyt c involvement in cell apoptosis.

The stability of the cytochrome c scaffold as revealed by NMR spectroscopy

NMR spectroscopy was used to study the effect of guanidinium chloride on the unfolding of horse heart and yeast iso-1 cytochrome c under mild alkaline conditions. The structural changes on the horse heart protein were detected through NOESY (Nuclear Overhauser Effect SpectroscopY) experiments whereas (15)N-(1)H heteronuclear NMR was used to monitor the behavior of the yeast protein. The latter represents the first characterization through (15)N-(1)H heteronuclear NMR spectroscopy of the guanidinium chloride induced unfolding of mitochondrial cytochrome c. The presence of denaturants decreases the temperature at which the native Met80 axial ligand is displaced from the iron center under the present mild alkaline conditions. The process can be described in terms of protein fragments behaving as unfolding units of different stability. The comparison between the two proteins indicates that the loop+helix connecting the proximal and distal sites, as well as the long Met80-containing loop immediately after a short helix, are structural characteristics of mitochondrial cytochrome c that appear to be responsible for the Met80-iron(III) bond fragility.

Protein folding: the stepwise assembly of foldon units

Equilibrium and kinetic hydrogen exchange experiments show that cytochrome c is composed of five foldon units that continually unfold and refold even under native conditions. Folding proceeds by the stepwise assembly of the foldon units rather than one amino acid at a time. The folding pathway is determined by a sequential stabilization process; previously formed foldons guide and stabilize subsequent foldons to progressively build the native protein. Four other proteins have been found to show similar behavior. These results support stepwise protein folding pathways through discrete intermediates.

Investigating the Cause of the Alkaline Transition of Phytocyanins

The phytocyanins are a family of plant cupredoxins that have been subdivided into the stellacyanins, plantacyanins, and uclacyanins. All of these proteins possess the typical type 1 His(2)Cys equatorial ligand set at their mononuclear copper sites, but the stellacyanins have an axial Gln ligand in place of the weakly coordinated Met of the plantacyanins, uclacyanins, and most other cupredoxins. The stellacyanins exhibit altered visible, EPR, and paramagnetic (1)H NMR spectra at elevated pH values and also modified reduction potentials. This alkaline transition occurs with a pK(a) of approximately 10 [Dennison, C., Lawler, A. T. (2001) Biochemistry 40, 3158-3166]. In this study we demonstrate that the alkaline transition has a similar influence on the visible, EPR, and paramagnetic NMR spectra of cucumber basic protein (CBP), which is a plantacyanin. The mutation of the axial Gln95 ligand into a Met in umecyanin (UMC), the stellacyanin from horseradish roots, and the axial Met89 into a Gln in CBP have very limited, yet similar, influence on the pK(a) for the alkaline transition as judged from alterations in visible spectra. The complete removal of the axial ligand in the Met89Val variant of CBP results in a slightly larger decrease in the pK(a) for this effect, but similar spectral alterations are still observed at elevated pH. Thus, the axial Gln ligand is not the cause of the alkaline transition in Cu(II) stellacyanins, and alterations in the active site structures of the phytocyanins have a limited effect on this feature. The conserved Lys residue found adjacent to the axial ligand in the sequences of all phytocyanins, and implicated as the trigger for the alkaline transition, has been mutated to an Arg in UMC. The influence of increasing pH on the spectroscopic properties of Lys96Arg UMC is almost identical to those of the wild type protein, and thus, this residue is not responsible for the alkaline transition. However, a positively charged residue in this position seems to be important for the correct folding of UMC. Other possible triggers for the effects seen in the phytocyanins at elevated pH are discussed along with the relevance of the alkaline transition.

Communication of Stabilizing Energy between Substructures of a Protein

Thermodynamic communication between protein substructures has been investigated by determining the stabilizing effect of mutations at position 52 in the least stable, N-yellow, substructure of cytochrome c on the second least stable, Red, and most stable, Blue, substructures of the protein. A Lys 73 --> His (H73) variant of iso-1-cytochrome c, containing these mutations was used to measure the stability of the Red substructure of cytochrome c through the pH and guanidine hydrochloride (gdnHCl) dependence of the His 73-mediated alkaline conformational transition. The stability of the Blue substructure was measured by global unfolding with gdnHCl and increased by 1 to 3.5 kcal/mol versus the H73 variant. The data demonstrate that the increase in stability of the Red substructure is similar to the increase in global stability, consistent with upward propagation of stabilizing energy from less (N-yellow) to more stable (Red and Blue) protein substructures. The result also supports sequential rather than independent unfolding of the N-yellow and Red substructures of cytochrome c. The data indicate that a leucine at position 52 alters the nature of partial unfolding of the Red substructure, a surprising effect for a single-site mutation. For all variants, the thermodynamics of formation of the Lys 79 alkaline state, which does not unfold the entire Red substructure, shows less stabilization of the portion of the protein unfolded relative to the stabilization of the Blue substructure, indicating that propagation of energy between substructures is somewhat disrupted when unfolding does not correspond to a natural substructure.

Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity

To investigate the character and role of misfolded intermediates in protein folding, a recombinant cytochrome c without the normally blocking histidine to heme misligation was studied. Folding remains heterogeneous as in the wild-type protein. Half of the population folds relatively rapidly to the native state in a two-state manner. The other half collapses (fluorescence quenching) and forms a full complement of helix (CD) with the same rate and denaturant dependence as the fast folding fraction but then is blocked and reaches the native structure (695nm absorbance) much more slowly. The factors that transiently block folding are not intrinsic to the folding process but depend on ambient conditions, including protein aggregation (f(concentration)), N terminus to heme misligation (f(pH)), and proline mis-isomerization (f(U state equilibration time)). The misfolded intermediate populated by the slowly folding fraction was characterized by hydrogen exchange pulse labeling. It is very advanced with all of the native-like elements fairly stably formed but not the final Met80-S to heme iron ligation, similar to a previously studied molten globule form induced by low pH. To complete final native state acquisition, some small back unfolding is required (error repair) but the misfolded intermediate does not revisit the U state before proceeding to N. These properties show that the intermediate is a normal on-pathway form that contains, in addition, adventitious misfolding errors that transiently block its forward progress. Related observations for other proteins (partially misfolded intermediates, pathway heterogeneity) might be similarly explained in terms of the optional insertion of error-dependent barriers into a classical folding pathway.

Proton-mediated dynamics of the alkaline conformational transition of yeast iso-1-cytochrome c

The kinetics of the alkaline conformational transition of a Lys 73-->His variant of iso-1-cytochrome c have been investigated using pH jump stopped-flow methods to probe the nature of the ionizable "trigger" group for this conformational change. This mutation moves the pK(a) of the ligand replacing Met 80 from about 10.5 to approximately 6.6 and has unmasked two other ionizable groups, besides the ligand replacing Met 80, that modulate the kinetics of this process. The results are discussed in terms of the impact of ionization equilibria on protein folding mechanisms.

The 40s ?-loop plays a critical role in the stability and the alkaline conformational transition of cytochrome c

The structural and redox properties of a non-covalent complex reconstituted upon mixing two non-contiguous fragments of horse cytochrome c, the residues 1-38 heme-containing N-fragment with the residues 57-104 C-fragment, have been investigated. With respect to native cyt c, the complex lacks a segment of 18 residues, corresponding, in the native protein, to an omega (Omega)-loop region. The fragment complex shows compact structure, native-like alpha-helix content but a less rigid atomic packing and reduced stability with respect to the native protein. Structural heterogeneity is observed at pH 7.0, involving formation of an axially misligated low-spin species and consequent partial displacement of Met80 from the sixth coordination position of the heme-iron. Spectroscopic data suggest that a lysine (located in the Met80-containing loop, namely Lys72, Lys73, or Lys79) replaces the methionine residue. The residues 1-38/57-104 fragment complex shows an unusual biphasic alkaline titration characterized by a low (p K(a1)=6.72) and a high p K(a)-associated state transition (p K(a2)=8.56); this behavior differs from that of native cyt c, which shows a monophasic alkaline transition (p K(a)=8.9). The data indicate that the 40s Omega-loop plays an important role in the stability of cyt c and in ensuring a correct alkaline conformational transition of the protein.

Protein stiffening and entropic stabilization in the subdenaturing limit of guanidine hydrochloride

Subdenaturing concentrations of guanidine hydrochloride (GdnHCl) stabilize proteins. For ferrocytochrome c the stabilization is detected at subglobal level with no measured change in global stability. These deductions are made by comparing observed rates of thermally driven ferrocytochrome cHCO reactions with global unfolding rates of ferrocytochrome c measured by stopped flow and NMR hydrogen exchange in the presence of a wide range of GdnHCl concentrations at pH 7, 22 degrees C.

How Cytochrome c Folds, and Why: Submolecular Foldon Units and their Stepwise Sequential Stabilization

Native state hydrogen exchange experiments have shown that the cytochrome c (Cyt c) protein consists of five cooperative folding-unfolding units, called foldons. These are named, in the order of increasing unfolding free energy, the nested-Yellow, Red, Yellow, Green, and Blue foldons. Previous results suggest that these units unfold in a stepwise sequential way so that each higher energy partially unfolded form includes all of the previously unfolded lower free energy units. If this is so, then selectively destabilizing any given foldon should equally destabilize each subsequent unfolding step above it in the unfolding ladder but leave the lower ones before it unaffected. To perform this test, we introduced the mutation Glu62Gly, which deletes a salt link in the Yellow unit and destabilizes the protein by 0.8 kcal/mol. Native state hydrogen exchange and other experiments show that the stability of the Yellow unit and the states above it in the free energy ladder are destabilized by about the same amount while the lower lying states are unaffected. These results help to confirm the sequential stepwise nature of the Cyt c unfolding pathway and therefore a similar refolding pathway. The steps in the pathway are dictated by the concerted folding-unfolding property of the individual unit foldons; the order of steps is determined by the sequential stabilization of progressively added foldons in the native context. Much related information for Cyt c strongly conforms with this mechanism. Its generality is supported by available information for other proteins.

pH-dependent conformational changes of ferricytochrome c induced by electrode surface microstructure

pH-dependent processes of bovine heart ferricytochrome c have been investigated by electronic absorption and circular dichroism (CD) spectra at functionalized single-wall carbon nanotubes (SWNTs) modified glass carbon electrode (SWNTs/GCE) using a long optical path thin layer cell. These methods enabled the pH-dependent conformational changes arising from the heme structure change to be monitored. The spectra obtained at functionalized SWNTs/GCE reflect electrode surface microstructure-dependent changes for pH-induced protein conformation, pK(a) of alkaline transition and structural microenvironment of the ferricytochrome c heme. pH-dependent conformational distribution curves of ferricytochrome c obtained by analysis of in situ CD spectra using singular value decomposition least square (SVDLS) method show that the functionalized SWNTs can retain native conformational stability of ferricytochrome c during alkaline transition.

Cytochrome c and SDS: a molten globule protein with altered axial ligation

Saccharomices cerevisiae (yeast iso-1) cytochrome c has been investigated in the presence of 100 mM SDS in order to simulate the interaction of cytochrome c with membrane. Under these circumstances, a high spin species with detached methionine axial ligand is observed through NMR, in analogy to findings on the horse heart protein. However, at variance with the latter system, for the yeast protein also a low spin species is detected, which appears to be present with a concentration of about 40% with respect to that of the high spin species. The R(1), R(2), [1H]-15N NOE of backbone amides which are not affected by paramagnetism are homogeneous and allow a simultaneous analysis of the data for the two species. The result is that the rotational correlation time is larger than in water and larger than expected on the basis of viscosity of the SDS-containing solution. This finding suggests interactions of cytochrome c with SDS. Furthermore, it appears that there is subnanosecond backbone mobility, which also accounts for the decreased intensity of NOE cross-peaks and may be associated with equilibria between helical and random coil structure. The dynamic behavior appears to be a common feature of the high spin and low spin species and is consistent with the presence of a molten globule state. The molten globule nature of the protein could account for the presence of the different axial coordination of the heme iron. Such findings are meaningful with respect to the physiology of cytochrome c as electron transfer protein and as promoter of apoptosis.

Intimate View of a Kinetic Protein Folding Intermediate: Residue-resolved Structure, Interactions, Stability, Folding and Unfolding Rates, Homogeneity

A cytochrome c kinetic folding intermediate was studied by hydrogen exchange (HX) pulse labeling. Advances in the technique and analysis made it possible to define the structured and unstructured regions, equilibrium stability, and kinetic opening and closing rates, all at an amino acid-resolved level. The entire N-terminal and C-terminal helices are formed and docked together at their normal native positions. They fray in both directions from the interaction region, due to a progression in both unfolding and refolding rates, leading to the surprising suggestion that helix propagation may proceed very slowly in the condensed milieu. Several native-like beta turns are formed. Some residues in the segment that will form the native 60s helix are protected but others are not, suggesting energy minimization to some locally non-native conformation in the transient intermediate. All other regions are unprotected, presumably dynamically disordered. The intermediate resembles a partially constructed native state. It is early, on-pathway, and all of the refolding molecules pass through it. These and related results consistently point to distinct, homogeneous, native-like intermediates in a stepwise sequential pathway, guided by the same factors that determine the native structure. Previous pulse labeling efforts have always assumed EX2 exchange during the labeling pulse, often leading to the suggestion of heterogeneous intermediates in alternative parallel pathways. The present work reveals a dominant role for EX1 exchange in the high pH labeling pulse, which will mimic heterogeneous behavior when EX2 exchange is assumed. The general problem of homogeneous versus heterogeneous intermediates and pathways is discussed.

Cooperative omega loops in cytochrome c: role in folding and function

Hydrogen exchange experiments under slow exchange conditions show that an omega loop in cytochrome c (residues 40-57) acts as a cooperative unfolding/refolding unit under native conditions. This unit behavior accounts for an initial step on the unfolding pathway, a final step in refolding, and a number of other structural, functional and evolutionary properties.