Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A

The Non-native Disulfide-Bond-Containing Landscape Orthogonal to the Oxidative Protein-Folding Trajectory: A Necessary Evil?

Oxidative protein folding describes the process by which disulfide-bond-containing proteins mature from their ribosomal, fully reduced and unfolded, origins. Over the past 40 years, a number of exemplar proteins including bovine pancreatic ribonuclease A (RNaseA), bovine pancreatic trypsin inhibitor (BPTI), and hen egg-white lysozyme (HEWL), among others, have provided rich insight into the nature of the intermolecular interactions that drive the formation of the native, biologically active fold. In this Review Article, we revisit the oxidative folding process of RNase A with a focus on reconciling the role of non-native disulfide-bond-containing species that populate the oxidative folding landscape. Toward gaining such an understanding, we project the regeneration pathway onto a Cartesian coordinate system. This helps not only to recognize the magnitude of the seemingly "fruitless", non-native disulfide-bond-containing species that lie orthogonal to the "native-protein-forming" reaction progress but also to reconcile a role for their existence in the regenerative trajectory. Finally, we superimpose the folding funnel onto the regeneration trajectory to draw parallels between oxidative folders and conformational folders (proteins that lack disulfide bonds). The overall objective is to provide the reader with a semi-quantitative description of oxidative protein folding and the barriers to successful regeneration while underscoring a role of seemingly fruitless intermediates.

Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field

Many proteins contain disulfide bonds that are usually essential for maintaining function and a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds in the context of protein structure prediction, but none can simulate the entire process of oxidative folding, including dynamic formation and breaking of disulfide bonds. In this work, a potential function developed to model disulfide bonds is coupled with the united-residue (UNRES) force field, and used in both canonical and replica exchange molecular dynamics simulations to produce complete oxidative folding pathways. The potential function is obtained by introducing a transition barrier that separates the bonded and nonbonded states of the half-cystine residues. Tests on several helical proteins show that improved predictions are obtained when dynamic disulfide-bond formation and breaking are considered. The effect of the disulfide bonds on the folding kinetics is also investigated, particularly their role in stabilizing folding intermediates, resulting in slower folding.

Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway

In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding). However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a K_d of ca. 10⁻⁵ M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding – differential affinity, rapid ligand exchange and conformational flexibility.

Investigating the effects of double mutation C30A/C75A on onconase structure: Studies at atomic resolution

The structure of onconase C30A/C75A double mutant has been determined at 1.12Å resolution. The structure has high structural homology to other onconase structures. The changes being results of mutation are relatively small, distributed asymmetrically around the two mutated positions, and they are observed not only in the mutation region but expanded to entire molecule. Different conformation of Lys31 side chain that influences the hydrogen bonding network around catalytic triad is probably responsible for lower catalytic efficiency of double mutant. The decrease in thermal stability observed for the onconase variant might be explained by a less dense packing as manifested by the increase of the molecular volume and the solvent accessible surface area.

Kinetic and thermodynamic analysis of the conformational folding process of SS-reduced bovine pancreatic ribonuclease A using a selenoxide reagent with high oxidizing ability

Redox-coupled folding pathways of bovine pancreatic ribonuclease A (RNase A) with four intramolecular disulfide (SS) bonds comprise three phases: (I) SS formation to generate partially oxidized intermediate ensembles with no rigid folded structure; (II) SS rearrangement from the three SS intermediate ensemble (3S) to the des intermediates having three native SS linkages; (III) final oxidation of the last native SS linkage to generate native RNase A. We previously demonstrated that DHS^ox, a water-soluble selenoxide reagent for rapid and quantitative SS formation, allows clear separation of the three folding phases. In this study, the main conformational folding phase (phase II) has been extensively analyzed at pH 8.0 under a wide range of temperatures (5–45 °C), and thermodynamic and kinetic parameters for the four des intermediates were determined. The free-energy differences (ΔG) as a function of temperature suggested that the each SS linkage has different thermodynamic and kinetic roles in stability of the native structure. On the other hand, comparison of the rate constants and the activation energies for 3S → des with those reported for the conformational folding of SS-intact RNase A suggested that unfolded des species (desU) having three native SS linkages but not yet being folded are involved in very small amounts (<1%) in the 3S intermediate ensemble and the desU species would gain the native-like structures via X-Pro isomerization like SS-intact RNase A. It was revealed that DHS^ox is useful for kinetic and thermodynamic analysis of the conformational folding process on the oxidative folding pathways of SS-reduced proteins.

Identification of formation of initial native structure in onconase from an unfolded state

In the oxidative folding of onconase, the stabilization of intermediates early in the folding process gives rise to efficient formation of its biologically active form. To identify the residues responsible for the initial formation of structured intermediates, the transition from an ensemble of unstructured three-disulfide species, 3S(U), to a single structured three-disulfide intermediate species, des-[30-75] or 3S(F), at pH 8.0 and 25 °C was examined. This transition was first monitored by far-UV circular dichroism spectroscopy at pH 8.0 and 25 °C, showing that it occurs with the formation of secondary structure, presumably because of native interactions. The time dependence of formation of nativelike structure was then followed by nuclear magnetic resonance spectroscopy after we had arrested the transition at different times by lowering the pH to 3 and then acquiring (1)H-(15)N heteronuclear single-quantum coherence spectra at pH 3 and 16 °C to identify amide hydrogens that become part of nativelike structure. H/D exchange was utilized to reduce the intensity of resonances from backbone amide hydrogens not involved in structure, without allowing exchange of backbone amide hydrogens involved in initial structure. Six hydrogen-bonding residues, namely, Tyr38, Lys49, Ser82, Cys90, Glu91, and Ala94, were identified as being involved in the earliest detectable nativelike structure before complete formation of des-[30-75] and are further stabilized later in the formation of this intermediate through S-S/SH interchange. By observing the stabilization of the structures of these residues by their neighboring residues, we have identified the initial, nativelike structural elements formed in this transition, providing details of the initial events in the oxidative folding of onconase.

Oxidative folding and structural analyses of a Kunitz-related inhibitor and its disulfide intermediates: functional implications

Tick-derived protease inhibitor (TdPI) is a tight-binding Kunitz-related inhibitor of human tryptase β with a unique structure and disulfide-bond pattern. Here we analyzed its oxidative folding and reductive unfolding by chromatographic and disulfide analyses of acid-trapped intermediates. TdPI folds through a stepwise generation of heterogeneous populations of one-disulfide, two-disulfide, and three-disulfide intermediates, with a major accumulation of the nonnative three-disulfide species IIIa. The rate-limiting step of the process is disulfide reshuffling within the three-disulfide population towards a productive intermediate that oxidizes directly into the native four-disulfide protein. TdPI unfolds through a major accumulation of the native three-disulfide species IIIb and the subsequent formation of two-disulfide and one-disulfide intermediates. NMR characterization of the acid-trapped and further isolated IIIa intermediate revealed a highly disordered conformation that is maintained by the presence of the disulfide bonds. Conversely, the NMR structure of IIIb showed a native-like conformation, with three native disulfide bonds and increased flexibility only around the two free cysteines, thus providing a molecular basis for its role as a productive intermediate. Comparison of TdPI with a shortened variant lacking the flexible prehead and posthead segments revealed that these regions do not contribute to the protein conformational stability or the inhibition of trypsin but are important for both the initial steps of the folding reaction and the inhibition of tryptase β. Taken together, the results provide insights into the mechanism of oxidative folding of Kunitz inhibitors and pave the way for the design of TdPI variants with improved properties for biomedical applications.

Respice, adspice, and prospice

The title, "Look to the past, Look to the present, and Look to the future," the motto of City College of New York, expresses how my family life and education led me to an academic career in physical chemistry and ultimately to a study of proteins. The economic depression of the 1930s left a lasting impression on my outlook and career aspirations. With fortunate experiences at several stages in my life, I was able to participate in the great adventure of the last half of the twentieth century: the revolution in biology that advanced the field of protein chemistry to so great an extent. The future is bright and limitless, with greater understanding of biology yet to come.

Conformational exchange is critical for the productivity of an oxidative folding intermediate with buried free cysteines

Much has been learned about the folding of proteins from comparative studies of the folding of proteins that are related in sequence and structure. Observation of the effects of mutations helps account for sequence-specific properties and large variations in folding rates observed in homologous proteins, which are not explained by structure-derived descriptions. The folding kinetics of variants of a β-stranded protein, toxin α from Naja nigricollis, depends on the length of their loop lk1. These proteins, named Tox60, Tox61, and Tox62, contain four disulfide bonds. We show that their oxidative refolding pathways are similar. Differences in these pathways are restricted to the last step of the reaction, that is, the closure of the last disulfide. At this step, two species of three-disulfide intermediates are observed: intermediate C lacking the B3 disulfide and intermediate D lacking the B2 disulfide. Surprisingly, D is the most productive intermediate for Tox61 despite the low accessibility of its free cysteines. However, in the case of Tox62, its conversion efficiency drops by 2 orders of magnitude and C becomes the most productive intermediate. NMR was used in order to study the structural dynamics of each of these intermediates. Both three-disulfide intermediates of Tox61 exist in two forms, exchanging on the 1- to 100-ms scale. One of these forms is structurally very close to the native Tox61, whereas the other is always significantly more flexible on a picosecond-to-nanosecond timescale. On the other hand, in the case of Tox62, the three-disulfide intermediates only show a native-like structure. The higher conformational heterogeneity of Tox61 intermediate D allows an increased accessibility of its free cysteines to oxidative agents, which explains its faster native disulfide formation. Thus, residue deletion in loop lk1 probably abrogates stabilizing intramolecular interactions, creates conformational heterogeneity, and increases the folding rate of Tox60 and Tox61 compared to Tox62.

Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues

The oxidative folding pathways of two four-disulfide proteins of the ribonuclease family, ONC and RNase A, which have similar three-dimensional folds but only 30% sequence homology, are compared. In this study, a mechanism for the oxidative folding pathway of ONC is proposed. In particular, the kinetic roles and thermodynamic characteristics of key intermediates along the oxidative folding pathway, specifically, the structured intermediates, I(1), I(2), and I(3), previously identified as des-[19-68,30-75], des-[30-75], and des-[19-68], respectively, are discussed. In addition, the effects of temperature on the oxidative folding pathway have been examined. Differences in the folding mechanism between ONC and RNase A are attributed to the differences in their amino acid sequences and related inter-residue interactions, including differences in hydrophobic interactions. Compared to RNase A, ONC utilizes more efficient interactions along the oxidative folding pathway to adopt its native fold more rapidly.

Effects of tyrosine mutations on the conformational and oxidative folding of ribonuclease a: a comparative study

Ribonuclease A (RNase A) undergoes more rapid conformational folding with its disulfide bonds intact than during oxidative folding from its reduced form. In this study, the effects of the mutants Y92G, Y92A, and Y92L on both the conformational and oxidative folding pathways were examined to determine the role of native interactions in different types of conformational searches for the biologically active structure of a protein. These mutations did not affect the overall conformational folding pathway of RNase A. However, in the mutants Y92G and Y92A, a key structured disulfide-bonded species, des-[65-72], involved in the oxidative folding pathway of RNase A, was destabilized. These results demonstrate the importance of native interactions in the folding process, namely, protection of a native (40-95) disulfide bond by a nearby tyrosyl-prolyl stacking interaction, when disulfide bonds are allowed to undergo SH/S-S reshuffling.

Disulfide-linked protein folding pathways

Determining the mechanism by which proteins attain their native structure is an important but difficult problem in basic biology. The study of protein folding is difficult because it involves the identification and characterization of folding intermediates that are only very transiently present. Disulfide bond formation is thermodynamically linked to protein folding. The availability of thiol trapping reagents and the relatively slow kinetics of disulfide bond formation have facilitated the isolation, purification, and characterization of disulfide-linked folding intermediates. As a result, the folding pathways of several disulfide-rich proteins are among the best known of any protein. This review discusses disulfide bond formation and its relationship to protein folding in vitro and in vivo.

Impact of an easily reducible disulfide bond on the oxidative folding rate of multi-disulfide-containing proteins

The burial of native disulfide bonds, formed within stable structure in the regeneration of multi-disulfide-containing proteins from their fully reduced states, is a key step in the folding process, as the burial greatly accelerates the oxidative folding rate of the protein by sequestering the native disulfide bonds from thiol-disulfide exchange reactions. Nevertheless, several proteins retain solvent-exposed disulfide bonds in their native structures. Here, we have examined the impact of an easily reducible native disulfide bond on the oxidative folding rate of a protein. Our studies reveal that the susceptibility of the (40-95) disulfide bond of Y92G bovine pancreatic ribonuclease A (RNase A) to reduction results in a reduced rate of oxidative regeneration, compared with wild-type RNase A. In the native state of RNase A, Tyr 92 lies atop its (40-95) disulfide bond, effectively shielding this bond from the reducing agent, thereby promoting protein oxidative regeneration. Our work sheds light on the unique contribution of a local structural element in promoting the oxidative folding of a multi-disulfide-containing protein.

The structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein

We have determined the three-dimensional structure of a two-disulfide intermediate (Cys(8)-Cys(20), Cys(14)-Cys(26)) on the oxidative folding pathway of the cyclotide MCoTI-II. Cyclotides have a range of bioactivities and, because of their exceptional stability, have been proposed as potential molecular scaffolds for drug design applications. The three-dimensional structure of the stable two-disulfide intermediate shows for the most part identical secondary and tertiary structure to the native state. The only exception is a flexible loop, which is collapsed onto the protein core in the native state, whereas in the intermediate it is more loosely associated with the remainder of the protein. The results suggest that the native fold of the peptide does not represent the free energy minimum in the absence of the Cys(1)-Cys(18) disulfide bridge and that although there is not a large energy barrier, the peptide must transiently adopt an energetically unfavorable state before the final disulfide can form.

Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues

The oxidative folding of frog onconase (ONC), a member of the ribonuclease A family, was examined and shows markedly different behavior compared to its structural homologue bovine pancreatic ribonuclease A (RNase A) under similar conditions. Application of a reduction pulse (using a small amount of reduced dithiothreitol) during the oxidative regeneration of ONC indicated the survival of the native protein along with three other (structured) species, I(1), I(2) and I(3), with the rest of the unstructured species being converted to fully reduced protein. Mass spectrometry indicates that I(1) has two disulfide bonds, whereas I(2) and I(3) have three disulfide bonds each. A disulfide mapping method, based on cyanylation, was used to identify I(2) and I(3) as des-[30-75] and des-[19-68], respectively. On enzymatic digestion using trypsin, I(1) was identified as des-[19-68, 30-75]. Differences in the intermediates that are generated during the oxidative folding of the two structural homologues, RNase A and ONC, demonstrate that regenerative pathways are not necessarily influenced by tertiary structure. This indicates that the lack of a disulfide bond in ONC, analogous to the (65-72) disulfide bond in RNase A which plays an important role in its oxidative regeneration, does not adversely affect the oxidative folding of ONC.

Oxidative folding and N-terminal cyclization of onconase

Cyclization of the N-terminal glutamine residue to pyroglutamic acid in onconase, an anti-cancer chemotherapeutic agent, increases the activity and stability of the protein. Here, we examine the correlated effects of the folding/unfolding process and the formation of this N-terminal pyroglutamic acid. The results in this study indicate that cyclization of the N-terminal glutamine has no significant effect on the rate of either reductive unfolding or oxidative folding of the protein. Both the cyclized and uncyclized proteins seem to follow the same oxidative folding pathways; however, cyclization altered the relative flux of the protein in these two pathways by increasing the rate of formation of a kinetically trapped intermediate. Glutaminyl cyclase (QC) catalyzed the cyclization of the unfolded, reduced protein but had no effect on the disulfide-intact, uncyclized, folded protein. The structured intermediates of uncyclized onconase were also resistant to QC catalysis, consistent with their having a native-like fold. These observations suggest that, in vivo, cyclization takes place during the initial stages of oxidative folding, specifically, before the formation of structured intermediates. The competition between oxidative folding and QC-mediated cyclization suggests that QC-catalyzed cyclization of the N-terminal glutamine in onconase occurs in the endoplasmic reticulum, probably co-translationally.

Correlation of folding kinetics with the number and isomerization states of prolines in three homologous proteins of the RNase family

Several studies attribute the slower phases in protein folding to prolyl isomerizations, and several others do not. A correlation exists between the number of prolines in a protein and the complexity of the mechanism with which it folds. In this study, we have demonstrated a direct correlation between the number of cis-prolyl bonds in a native protein and the complexity with which it folds via slower phases by studying the folding of three structurally homologous proteins of the ribonuclease family, namely RNase A, onconase and angiogenin, which differ in the number and isomerization states of their proline residues.

Folding of small disulfide-rich proteins: clarifying the puzzle

The process by which small proteins fold to their native conformations has been intensively studied over the past few decades. The particular chemistry of disulfide-bond formation has facilitated the characterization of the oxidative folding of numerous small, disulfide-rich proteins with results that illustrate a high level of diversity in folding mechanisms, differing in the heterogeneity and native disulfide-bond content of their intermediates. Information from folding studies of these proteins, together with the recent structural determinations of predominant intermediates, has provided new molecular insights into oxidative folding and clarifies the major rules that govern it.

A localized specific interaction alters the unfolding pathways of structural homologues

Reductive unfolding studies of proteins are designed to provide information about intramolecular interactions that govern the formation (and stabilization) of the native state and about folding/unfolding pathways. By mutating Tyr92 to G, A, or L in the model protein, bovine pancreatic ribonuclease A, and through analysis of temperature factors and molecular dynamics simulations of the crystal structures of these mutants, it is demonstrated that the markedly different reductive unfolding rates and pathways of ribonuclease A and its structural homologue onconase can be attributed to a single, localized, ring-stacking interaction between Tyr92 and Pro93 in the bovine variant. The fortuitous location of this specific stabilizing interaction in a disulfide-bond-containing loop region of ribonuclease A results in the localized modulation of protein dynamics that, in turn, enhances the susceptibility of the disulfide bond to reduction leading to an alteration in the reductive unfolding behavior of the homologues. These results have important implications for folding studies involving topological determinants to obtain folding/unfolding rates and pathways, for protein structure-function prediction through fold recognition, and for predicting proteolytic cleavage sites.

Study of a Major Intermediate in the Oxidative Folding of Leech Carboxypeptidase Inhibitor: Contribution of the Fourth Disulfide Bond

The oxidative folding pathway of leech carboxypeptidase inhibitor (LCI; four disulfide bonds) proceeds through the formation of two major intermediates (III-A and III-B) that contain three native disulfide bonds and act as strong kinetic traps in the folding process. The III-B intermediate lacks the Cys19-Cys43 disulfide bond that links the beta-sheet core with the alpha-helix in wild-type LCI. Here, an analog of this intermediate was constructed by replacing Cys19 and Cys43 with alanine residues. Its oxidative folding follows a rapid sequential flow through one, two, and three disulfide species to reach the native form; the low accumulation of two disulfide intermediates and three disulfide (scrambled) isomers accounts for a highly efficient reaction. The three-dimensional structure of this analog, alone and in complex with carboxypeptidase A (CPA), was determined by X-ray crystallography at 2.2A resolution. Its overall structure is very similar to that of wild-type LCI, although the residues in the region adjacent to the mutation sites show an increased flexibility, which is strongly reduced upon binding to CPA. The structure of the complex also demonstrates that the analog and the wild-type LCI bind to the enzyme in the same manner, as expected by their inhibitory capabilities, which were similar for all enzymes tested. Equilibrium unfolding experiments showed that this mutant is destabilized by approximately 1.5 kcal mol(-1) (40%) relative to the wild-type protein. Together, the data indicate that the fourth disulfide bond provides LCI with both high stability and structural specificity.

NMR Structural Characterization and Computational Predictions of the Major Intermediate in Oxidative Folding of Leech Carboxypeptidase Inhibitor

The III-A intermediate constitutes the major rate-determining step in the oxidative folding of leech carboxypeptidase inhibitor (LCI). In this work, III-A has been directly purified from the folding reaction and structurally characterized by NMR spectroscopy. This species, containing three native disulfides, displays a highly native-like structure; however, it lacks some secondary structure elements, making it more flexible than native LCI. III-A represents a structurally determined example of a disulfide-insecure intermediate; direct oxidation of this species to the fully native protein seems to be restricted by the burial of its two free cysteine residues inside a native-like structure. We also show that theoretical approaches based on topological constraints predict with good accuracy the presence of this folding intermediate. Overall, the derived results suggest that, as it occurs with non-disulfide bonded proteins, native-like interactions between segments of secondary structure rather than the crosslinking of disulfide bonds direct the folding of LCI.

The Importance of Dynamic Effects on the Enzyme Activity

Onconase (ONC), a member of the RNase A superfamily extracted from oocytes of Rana pipiens, is an effective cancer killer. It is currently used in treatment of various forms of cancer. ONC antitumor properties depend on its ribonucleolytic activity that is low in comparison with other members of the superfamily. The most damaging side effect from Onconase treatment is renal toxicity, which seems to be caused by the unusual stability of the enzyme. Therefore, mutants with reduced thermal stability and/or increased catalytic activity may have significant implications for human cancer chemotherapy. In this context, we have determined the crystal structures of two Onconase mutants (M23L-ONC and C87S,des103-104-ONC) and performed molecular dynamic simulations of ONC and C87S,des103-104-ONC with the aim of explaining on structural grounds the modifications of the activity and thermal stability of the mutants. The results also provide the molecular bases to explain the lower catalytic activity of Onconase compared with RNase A and the unusually high thermal stability of the amphibian enzyme.

Dissimilarity in the Reductive Unfolding Pathways of Two Ribonuclease Homologues

Using DTT(red) as the reducing agent, the kinetics of the reductive unfolding of onconase, a frog ribonuclease, has been examined. An intermediate containing three disulfides, Ir, that is formed rapidly in the reductive pathway, is more resistant to further reduction than the parent molecule, indicating that the remaining disulfides in onconase are less accessible to DTT(red). Disulfide-bond mapping of Ir indicated that it is a single species lacking the (30-75) disulfide bond. The reductive unfolding pattern of onconase is consistent with an analysis of the exposed surface area of the cysteine sulfur atoms in the (30-75) disulfide bond, which reveals that these atoms are about four- and sevenfold, respectively, more exposed than those in the next two maximally exposed disulfides. By contrast, in the reductive unfolding of the homologue, RNase A, there are two intermediates, arising from the reduction of the (40-95) and (65-72) disulfide bonds, which takes place in parallel, and on a much longer time-scale, compared to the initial reduction of onconase; this behavior is consistent with the almost equally exposed surface areas of the cysteine sulfur atoms that form the (40-95) and (65-72) disulfide bonds in RNase A and the fourfold more exposed cysteine sulfur atoms of the (30-75) disulfide bond in onconase. Analysis and in silico mutation of the residues around the (40-95) disulfide bond in RNase A, which is analogous to the (30-75) disulfide bond of onconase, reveal that the side-chain of tyrosine 92 of RNase A, a highly conserved residue among mammalian pancreatic ribonucleases, lies atop the (40-95) disulfide bond, resulting in a shielding of the corresponding sulfur atoms from the solvent; such burial of the (30-75) sulfur atoms is absent from onconase, due to the replacement of Tyr92 by Arg73, which is situated away from the (30-75) disulfide bond and into the solvent, resulting in the large exposed surface-area of the cysteine sulfur atoms forming this bond. Removal of Tyr92 from RNase A resulted in the relatively rapid reduction of the mutant to form a single intermediate (des [40-95] Y92A), i.e. it resulted in an onconase-like reductive unfolding behavior. The reduction of the P93A mutant of RNase A proceeds through a single intermediate, the des [40-95] P93A species, as in onconase. Although mutation of Pro93 to Ala does not increase the exposed surface area of the (40-95) cysteine sulfur atoms, structural analysis of the mutant reveals that there is greater flexibility in the (40-95) disulfide bond compared to the (65-72) disulfide bond that may make the (40-95) disulfide bond much easier to expose, consistent with the reductive unfolding pathway and kinetics of P93A. Mutation of Tyr92 to Phe92 in RNase A has no effect on its reductive unfolding pathway, suggesting that the hydrogen bond between the hydroxyl group of Tyr92 and the carbonyl group of Lys37 has no impact on the local unfolding free energy required to expose the (40-95) disulfide bond. Thus, these data shed light on the differences between the reductive unfolding pathways of the two homologous proteins and provide a structural basis for the origin of this difference.

Oxidative Folding of Amaranthus α-Amylase Inhibitor

Oxidative folding is the fusion of native disulfide bond formation with conformational folding. This complex process is guided by two types of interactions: first, covalent interactions between cysteine residues, which transform into native disulfide bridges, and second, non-covalent interactions giving rise to secondary and tertiary protein structure. The aim of this work is to understand both types of interactions in the oxidative folding of Amaranthus alpha-amylase inhibitor (AAI) by providing information both at the level of individual disulfide species and at the level of amino acid residue conformation. The cystine-knot disulfides of AAI protein are stabilized in an interdependent manner, and the oxidative folding is characterized by a high heterogeneity of one-, two-, and three-disulfide intermediates. The formation of the most abundant species, the main folding intermediate, is favored over other species even in the absence of non-covalent sequential preferences. Time-resolved NMR and photochemically induced dynamic nuclear polarization spectroscopies were used to follow the oxidative folding at the level of amino acid residue conformation. Because this is the first time that a complete oxidative folding process has been monitored with these two techniques, their results were compared with those obtained at the level of an individual disulfide species. The techniques proved to be valuable for the study of conformational developments and aromatic accessibility changes along oxidative folding pathways. A detailed picture of the oxidative folding of AAI provides a model study that combines different biochemical and biophysical techniques for a fuller understanding of a complex process.

Assessing the magnitude of folding forces along the oxidative folding pathway of multi-disulfide-containing proteins

Oxidative folding involves the acquisition of the native set of disulfide bonds and native structure of a protein from its reduced, unfolded form. Two major factors that influence the distribution of disulfide bonds (over their entropically favored probability of formation) during the regeneration, eventually favoring and sustaining the native set of disulfide bonds, are enthalpic interactions that lead to conformational ordering among intermediates and conformational folding, resulting in native (or nativelike) structure which protects the native disulfide bonds from reduction and intramolecular thiol-disulfide exchange reactions. Here, we report a novel technique to provide a quantitative description of the enthalpic and conformational folding forces present at any stage of the oxidative folding process of multi-disulfide-containing proteins which is made feasible by assessing their ability to form "structures" that are able to protect disulfide bonds from reduction.

Identifying and modulating disulfide formation in the biopharmaceutical production of a recombinant protein vaccine candidate

Structural conversion of the serotype A recombinant botulinum neurotoxin heavy chain fragment (rBoNTA(Hc)) produced intracellularly in Pichia pastoris yeast was observed and characterized during purification development efforts. A pH screening study captured the transformation stages of the original recovered species into its derived counterpart and a number of analytical tools such as peptide mapping by LC/MS confirmed the formation of a disulfide bond, especially in samples of neutral to basic pH. A cation exchange chromatographic method proved useful in following the incidence of the reaction in various rBoNTA(Hc) samples. The disulfide formation kinetics were characterized using a one-quarter quadratic factorial design, following the investigation and development of controlled oxidation conditions using cysteine and cystamine as the redox pair. Temperature, pH and concentration of the redox pair had a significant effect on the yield and rate of the disulfide formation. This controlled reaction was eventually introduced as a functional unit operation in the purification process. The summation of preliminary scale-up and potency data showed scalability and robustness in the production of an active disulfide-bonded form of a recombinant botulism vaccine candidate. The presence of the disulfide bond did not effect the vaccine potency and it enhanced the molecule's thermal stability.

Biphasic reductive unfolding of ribonuclease A is temperature dependent

The kinetics of the reversible thermal unfolding, irreversible thermal unfolding, and reductive unfolding processes of bovine pancreatic ribonuclease A (RNase A) were investigated in NaCl/Pi solutions. Image parameters including Shannon entropy, Hamming distance, mutual information and correlation coefficient were used in the analysis of the CD and 1D NMR spectra. The irreversible thermal unfolding transition of RNase A was not a cooperative process, pretransitional structure changes occur before the main thermal denaturation. Different dithiothreitol (dithiothreitolred) concentration dependencies were observed between 303 and 313 K during denaturation induced by a small amount of reductive reagent. The protein selectively follows a major unfolding kinetics pathway with the selectivity can be altered by temperature and reductive reagent concentration. Two possible explanations of the selectivity mechanism were discussed.

Oxidative folding of bovine pancreatic ribonuclease A: insight into the overall catalysis of the refolding pathway by phosphate

The effects of the strong stabilizing anion, phosphate, on the oxidative folding of bovine pancreatic ribonuclease A were examined. Phosphate was found to catalyze several steps involved in the oxidative folding process at pH 8.0 and 25 degrees C, resulting in an increase in the rate of pre-equilibration of unstructured species on the folding pathway. In the presence of 400 mM phosphate, the overall increase in the rate of regeneration of native protein was caused primarily by the increased formation and stabilization of tertiary structure in the nativelike intermediates, des-[40-95] and des-[65-72], involved in the rate-determining step. Based on the regeneration of native protein and the stability of Cys--> Ala substituted mutant analogs of the des-species, (C40A, C95A) and (C65A, C72A), it is suggested that the primary role of phosphate is to catalyze the overall regeneration of native protein through nonspecific electrostatic and hydrogen-bonding effects on the protein and solvent.

Structural determinants of oxidative folding in proteins

A method for determining the kinetic fate of structured disulfide species (i.e., whether they are preferentially oxidized or reshuffle back to an unstructured disulfide species) is introduced. The method relies on the sensitivity of unstructured disulfide species to low concentrations of reducing agents. Because a structured des species that preferentially reshuffles generally first rearranges to an unstructured species, a small concentration of reduced DTT (e.g., 260 microM) suffices to distinguish on-pathway intermediates from dead-end species. We apply this method to the oxidative folding of bovine pancreatic ribonuclease A (RNase A) and show that des[40-95] and des[65-72] are productive intermediates, whereas des[26-84] and des[58-110] are metastable dead-end species that preferentially reshuffle. The key factor in determining the kinetic fate of these des species is the relative accessibility of both their thiol groups and disulfide bonds. Productive intermediates tend to be disulfide-secure, meaning that their structural fluctuations preferentially expose their thiol groups, while keeping their disulfide bonds buried. By contrast, dead-end species tend to be disulfide-insecure, in that their structural fluctuations expose their disulfide bonds in concert with their thiol groups. This distinction leads to four generic types of oxidative folding pathways. We combine these results with those of earlier studies to suggest a general three-stage model of oxidative folding of RNase A and other single-domain proteins with multiple disulfide bonds.

Two-phase unfolding pathway of ribonuclease A during denaturation induced by dithiothreitol

The dynamics of the unfolding process of bovine pancreatic ribonuclease A (RNase A) unfolded by dithiothreitol (DTT) at a low concentration of 1:30 were investigated in alkaline phosphate-buffered saline solutions at 303K and 313K by using proton nuclear magnetic resonance ((1)H NMR) spectra. Three NMR spectral parameters including Shannon entropy, mutual information, and correlation coefficient were introduced into the analysis. The results show that the unfolding process of RNase A was slowed to the order of many hours, and the kinetics of the unfolding pathway described by the three parameters is best fit by a model of two consecutive first-order reactions. Temperature greatly influences the rate constants of the unfolding kinetics with different temperature effects observed for the fast and the slow processes. The consistencies and the differences between the three sets of parameters show that they reflect the same relative denaturation pathway but different spectra windows of the unfolding process of RNase A. The results suggest that the unfolding process of RNase A induced by low concentrations of DTT is a two-phase pathway containing fast and slow first-order reactions.

Oxidative folding of proteins

The oxidative folding of proteins is reviewed and illustrated with bovine pancreatic ribonuclease A (RNase A). The mutual effects of conformational folding and disulfide bond regeneration are emphasized, particularly the "locking in" of native disulfide bonds by stable tertiary structure in disulfide intermediates. Two types of structured metastable disulfide species are discerned, depending on the relative protection of their disulfide bonds and thiol groups. Four generic pathways for oxidative folding are identified and characterized.

Nanosecond temperature jump and time-resolved Raman study of thermal unfolding of ribonuclease A

A nanosecond temperature jump (T-jump) apparatus was constructed and combined with time-resolved Raman measurements to investigate thermal unfolding of a protein for the first time. The 1.56-microm heat pulse with 9 ns width at 10 Hz was obtained through the two-step stimulated Raman scattering in D(2) gas involving seeding and amplification. To achieve uniform temperature rise, the counter-propagation geometry was adopted for the heat pulse. The temperature rise was determined by anti-Stokes to Stokes intensity ratios of the 317 and 897 cm(-1) bands of MoO(4)(2-) ions in an aqueous solution. The T-jump as large as 9 degrees C in 10 ns was attained. The unfolding of bovine pancreatic ribonuclease A was monitored with time-resolved Raman spectra excited at 532 nm. The C-S stretching band of Met residues exhibited 10% change of that expected from the stationary state temperature-difference spectra in the initial 200 ns following T-jump and another 10% in 5 ms. The Raman intensity of SO(4)(2-) ions around 980 cm(-1) increased at 100 micros, presumably due to some conformational changes of the protein around the active site. The S-S stretches and tyrosine doublet displayed little changes within 5 ms. Thus, the conformational changes in the initial step of unfolding are not always concerted.

Conformational stability is a determinant of ribonuclease A cytotoxicity

Onconasetrade mark, a homolog of bovine pancreatic ribonuclease A (RNase A) with high conformational stability, is cytotoxic and has efficacy as a cancer chemotherapeutic agent. Unlike wild-type RNase A, the G88R variant is toxic to cancer cells. Here, variants in which disulfide bonds were removed from or added to G88R RNase A were used to probe the relationship between conformational stability and cytotoxicity in a methodical manner. The conformational stability of the C40A/G88R/C95A and C65A/C72A/G88R variants is less than that of G88R RNase A. In contrast, a new disulfide bond that links the N and C termini (residues 4 and 118) increases the conformational stability of G88R RNase A and C65A/C72A/G88R RNase A. These changes have little effect on the ribonucleolytic activity of the enzyme or on its ability to evade the cytosolic ribonuclease inhibitor protein. The changes do, however, have a substantial effect on toxicity toward human erythroleukemia cells. Specifically, conformational stability correlates directly with cytotoxicity as well as with resistance to proteolysis. These data indicate that conformational stability is a key determinant of RNase A cytotoxicity and suggest that cytotoxicity relies on avoiding proteolysis. This finding suggests a means to produce new cancer chemotherapeutic agents based on mammalian ribonucleases.

Acceleration of oxidative folding of bovine pancreatic ribonuclease A by anion-induced stabilization and formation of structured native-like intermediates

Phosphate anions accelerate the oxidative folding of reduced bovine pancreatic ribonuclease A with dithiothreitol at several temperatures and ionic strengths. The addition of 400 mM phosphate at pH 8.1 increased the regeneration rate of native protein 2.5-fold at 15 degrees C, 3.5-fold at 25 degrees C, and 20-fold at 37 degrees C, compared to the rate in the absence of phosphate. In addition, the effects of other ions on the oxidative folding of RNase A were examined. Fluoride was found to accelerate the formation of native protein under the same oxidizing conditions. In contrast, cations of high charge density or ions with low charge density appear to have an opposite effect on the folding of RNase A. The catalysis of oxidative folding results largely from an anion-dependent stabilization and formation of tertiary structure in productive disulfide intermediates (des-species). Phosphate and fluoride also accelerate the initial equilibration of unstructured disulfide ensembles, presumably due to non-specific electrostatic and hydrogen bonding effects on the protein and solvent.

Disulfide bonds and protein folding

The applications of disulfide-bond chemistry to studies of protein folding, structure, and stability are reviewed and illustrated with bovine pancreatic ribonuclease A (RNase A). After surveying the general properties and advantages of disulfide-bond studies, we illustrate the mechanism of reductive unfolding with RNase A, and discuss its application to probing structural fluctuations in folded proteins. The oxidative folding of RNase A is then described, focusing on the role of structure formation in the regeneration of the native disulfide bonds. The development of structure and conformational order in the disulfide intermediates during oxidative folding is characterized. Partially folded disulfide species are not observed, indicating that disulfide-coupled folding is highly cooperative. Contrary to the predictions of "rugged funnel" models of protein folding, misfolded disulfide species are also not observed despite the potentially stabilizing effect of many nonnative disulfide bonds. The mechanism of regenerating the native disulfide bonds suggests an analogous scenario for conformational folding. Finally, engineered covalent cross-links may be used to assay for the association of protein segments in the folding transition state, as illustrated with RNase A.

Formation of native structure by intermolecular thiol-disulfide exchange reactions without oxidants in the folding of bovine pancreatic ribonuclease A

It has been shown previously that the oxidative folding of bovine pancreatic ribonuclease A proceeds through parallel pathways with two major native-like three-disulfide (3S) intermediates. We show here that, under some conditions, the native disulfide bonds can also be regenerated through disproportionation reactions; in other words, the protein can serve as its own redox reagent. The results also show that disulfide species of the unstructured 3S ensemble have a strong propensity to participate in intermolecular interactions. These interactions are favored at high protein concentration, temperature and pH, and lead to formation of the native structure during disulfide reshuffling in the rate-determining step.

Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A

Disulfide bonds between the side chains of cysteine residues are the only common crosslinks in proteins. Bovine pancreatic ribonuclease A (RNase A) is a 124-residue enzyme that contains four interweaving disulfide bonds (Cys26-Cys84, Cys40-Cys95, Cys58-Cys110, and Cys65-Cys72) and catalyzes the cleavage of RNA. The contribution of each disulfide bond to the conformational stability and catalytic activity of RNase A has been determined by using variants in which each cystine is replaced independently with a pair of alanine residues. Thermal unfolding experiments monitored by ultraviolet spectroscopy and differential scanning calorimetry reveal that wild-type RNase A and each disulfide variant unfold in a two-state process and that each disulfide bond contributes substantially to conformational stability. The two terminal disulfide bonds in the amino-acid sequence (Cys26-Cys84 and Cys58-Cys110) enhance stability more than do the two embedded ones (Cys40-Cys95 and Cys65-Cys72). Removing either one of the terminal disulfide bonds liberates a similar number of residues and has a similar effect on conformational stability, decreasing the midpoint of the thermal transition by almost 40 degrees C. The disulfide variants catalyze the cleavage of poly(cytidylic acid) with values of kcat/Km that are 2- to 40-fold less than that of wild-type RNase A. The two embedded disulfide bonds, which are least important to conformational stability, are most important to catalytic activity. These embedded disulfide bonds likely contribute to the proper alignment of residues (such as Lys41 and Lys66) that are necessary for efficient catalysis of RNA cleavage.

Two new structured intermediates in the oxidative folding of RNase A

Two new three-disulfide intermediates have been found to be populated in the oxidative folding pathway of bovine pancreatic ribonuclease A at a low temperature (15 degrees C). These intermediates, des-[26-84] and des-[58-110], possess all but one of the four native disulfide bonds and have a stable tertiary structure, similar to the two previously observed intermediates, des-[65-72] and des-[40-95]. While the latter two des species each lack one surface-exposed disulfide bond, the newly discovered intermediates each lack one buried disulfide bond. The possible involvement of these species in the rate-determining steps during the oxidative folding of RNase A is discussed and a specific role for such species during oxidative folding is suggested.

Distribution of disulfide bonds in the two-disulfide intermediates in the regeneration of bovine pancreatic ribonuclease A: further insights into the folding process

The distribution of one-disulfide bonds in the two-disulfide intermediates in the oxidative refolding of bovine pancreatic ribonuclease A has been characterized. These two-disulfide intermediates were formed from the fully reduced denatured protein by oxidation with dithiothreitol, then blocked with AEMTS, purified by cation-exchange chromatography, enzymatically digested, and analyzed by reversed-phase high-performance liquid chromatography and mass spectrometry. The relative concentration of each of the 28 possible one-disulfide bonds in the two-disulfide ensemble was determined. Comparison with a statistical mechanical treatment of loop formation shows that the two-disulfide intermediates are probably compact. All 28 disulfide bonds were observed, demonstrating the absence of specific long-range interactions in these intermediates. Thermodynamic arguments suggest that the absence of such specific long-range interactions in the two-disulfide species may elevate the concentration of kinetically important three-disulfide intermediates and thereby increase the folding rate. Bond [65-72] was found to make up approximately 27% of the disulfide bonds of the two-disulfide species, significantly more than all other disulfides, because of stabilization by loop entropy factors and an energetically favorable beta-turn. This turn may be one of several chain-folding initiation sites, accelerating folding by decreasing the dimensionality of the conformational space that has to be searched.

Detection of intermolecular chemical exchange through decorrelation of two-spin order

An initial correlation between two spins is lost when they are separated by intermolecular chemical exchange. This effect, termed "decorrelation by chemical exchange," manifests itself in a decay of the corresponding two-spin modes. It can be used for monitoring intermolecular chemical exchange, as is demonstrated for l-tryptophan where the decay of 1H15N two-spin order provides information on the exchange of indole protons with solvent water.

Structure and dynamic properties of the single disulfide-deficient alpha-amylase inhibitor [C45A/C73A]tendamistat: an NMR study

Covalent linkages such as disulfide bonds are important for the stabilization of proteins. In the present NMR study we compare the structure and the dynamics of the single disulfide-deficient variant C45A/C73A of the alpha-amylase inhibitor tendamistat and the wild-type protein, which contains two disulfide bonds (C11-C27 and C45-C73). Complete proton assignment was achieved by standard homonuclear 2D techniques for the variant. Chemical shift differences, intra-strand NOE effects and protected amide proton were used to compare the connectivity of the secondary structure elements of variant and wild-type. Dynamic properties of the wild-type protein were studied by 13C(alpha) heteronuclear NOE experiments with carbon in natural abundance. 15N isotope labeling was necessary to obtain the relaxation parameters of the variant, because of sample degradation. The 15N resonance assignment was achieved by a 15N 3D-NOESY-HMQC. Removal of the C45-C73 bond by the C45A/C73A mutation has no influence upon the beta-barrel structure of tendamistat beside very local changes at the mutation site. The relaxation data revealed only subtle differences between variant and wild-type on a subnanosecond time scale. Only the N-terminus and G62 in the connecting loop between the anti-parallel beta-sheets showed an increased mobility. The results are discussed in respect to thermodynamic stability and the secretion efficiency of tendamistat.

Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3

Ribonucleases Sa, Sa2, and Sa3 are three small, extracellular enzymes produced by different strains of Streptomyces aureofaciens with amino acid sequences that are 50% identical. We have studied the unfolding of these enzymes by heat and urea to determine the conformational stability and its dependence on temperature, pH, NaCl, and the disulfide bond. All three of the Sa ribonucleases unfold reversibly by a two-state mechanism with melting temperatures, Tm, at pH 7 of 48.4 degrees C (Sa), 41.1 degrees C (Sa2), and 47.2 degrees C (Sa3). The Tm values are increased in the presence of 0.5 M NaCl by 4.0 deg. C (Sa), 0.1 deg. C (Sa2), and 7.2 deg. C (Sa3). The Tm values are decreased by 20.0 deg. C (Sa), 31.5 deg. C (Sa2), and 27.0 deg. C (Sa3) when the single disulfide bond in the molecules is reduced. We compare these results with similar studies on two other members of the microbial ribonuclease family, RNase T1 and RNase Ba (barnase), and with a member of the mammalian ribonuclease family, RNase A. At pH 7 and 25 degrees C, the conformational stabilities of the ribonucleases are (kcal/mol): 2.9 (Sa2), 5.6 (Sa3), 6.1 (Sa), 6.6 (T1), 8.7 (Ba), and 9.2 (A). Our analysis of the stabilizing forces suggests that the hydrophobic effect contributes from 90 to 110 kcal/mol and that hydrogen bonding contributes from 70 to 105 kcal/mol to the stability of these ribonucleases. Thus, we think that the hydrophobic effect and hydrogen bonding make large but comparable contributions to the conformational stability of these proteins.