Structure and heterogeneity of the one- and two-disulfide folding intermediates of tick anticoagulant peptide

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.

Diverse pathways of oxidative folding of disulfide proteins: underlying causes and folding models

The pathway of oxidative folding of disulfide proteins exhibits a high degree of diversity, which is manifested mainly by distinct structural heterogeneity and diverse rearrangement pathways of folding intermediates. During the past two decades, the scope of this diversity has widened through studies of more than 30 disulfide-rich proteins by various laboratories. A more comprehensive landscape of the mechanism of protein oxidative folding has emerged. This review will cover three themes. (1) Elaboration of the scope of diversity of disulfide folding pathways, including the two opposite extreme models, represented by bovine pancreatic trypsin inhibitor (BPTI) and hirudin. (2) Demonstration of experimental evidence accounting for the underlying mechanism of the folding diversity. (3) Discussion of the convergence between the extreme models of oxidative folding and models of conventional conformational folding (framework model, hydrophobic collapse model).

Distinct folding pathways of two homologous disulfide proteins: bovine pancreatic trypsin inhibitor and tick anticoagulant peptide

The folding pathways of disulfide proteins vary substantially (Arolas et al., Trends Biochem Sci 31: 292-301, 2006). The diversity is mainly manifested by (a) the extent of heterogeneity of folding intermediates, (b) the extent of presence of native-like intermediates, and (c) the variation of folding kinetics. Even among structurally similar proteins, the difference can be enormous. This is demonstrated in this concise review with two structurally homologous kunitz-type protease inhibitors, bovine pancreatic trypsin inhibitor and tick anticoagulant peptide, as well as a group of cystine knot proteins. The diversity of their folding mechanisms is illustrated with two different folding techniques: (a) the conventional method of disulfide oxidation (oxidative folding), and (b) the novel method of disulfide scrambling (Chang, J Biol Chem 277: 120-126, 2002). This review also highlights the convergence of folding models concluded form the conventional conformational folding and those obtained by oxidative folding.

Pathway of oxidative folding of a 3-disulfide alpha-lactalbumin may resemble either BPTI model or hirudin model

Pathways of oxidative folding of disulfide proteins display a high degree of diversity and vary among two extreme models. The BPTI model is defined by limited species of folding intermediates adopting mainly native disulfide bonds. The hirudin model is characterized by highly heterogeneous folding intermediates containing mostly non-native disulfide bonds. alphaLA-IIIA is a 3-disulfide variant of alpha-lactalbumin (alphaLA) with a 3-D conformation essentially identical to that of intact alphaLA. alphaLA-IIIA contains 3 native disulfide bonds of alphaLA, two of them are located at the calcium binding beta-subdomain (Cys61-Cys77 and Cys73-Cys91) and the third bridge is located within the alpha-helical domain of the molecule (Cys28-Cys111). We investigate here the pathway of oxidative folding of fully reduced alphaLA-IIIA with and without stabilization of its beta-subdomain by calcium binding. In the absence of calcium, the folding pathway of alphaLA-IIIA was shown to resemble that of hirudin model. Upon stabilization of beta-sheet domain by calcium binding, the folding pathway of alphaLA-IIIA exhibits a striking similarity to that of BPTI model. Three predominant folding intermediates of alphaLA-IIIA containing exclusively native disulfide bonds were isolated and structurally characterized. Our results further demonstrate that stabilization of subdomains in a protein may dictate its folding pathway and represent a major cause for the existing diversity in the folding pathways of the disulfide-containing proteins.

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.

Divergent folding pathways of two homologous proteins, BPTI and tick anticoagulant peptide: Compartmentalization of folding intermediates and identification of kinetic traps

Bovine pancreatic trypsin inhibitor (BPTI) and tick anticoagulant peptide (TAP) are two structurally homologous proteins, which have been shown to exhibit distinct mechanisms of oxidative folding. We demonstrate here differences of their folding properties using the technique of disulfide scrambling. Two extensively unfolded homologous isomers (beads-form) of BPTI (Cys5-Cys14, Cys30-Cys38, Cys51-Cys55) and TAP (Cys5-Cys15, Cys33-Cys39, Cys55-Cys59) were allowed to refold in parallel via disulfide shuffling of 13 potential isomers to form the native structure. Folding intermediates were trapped by acid quenching and analyzed by HPLC. The results reveal the following diversities: (a) there are two predominant folding intermediates of BPTI and seven well-populated folding intermediates of TAP. One of the two predominant BPTI intermediates (Cys5-Cys14, Cys30-Cys51, Cys38-Cys55) contains a native disulfide Cys30-Cys51 and constitutes about 34% of the total BPTI folding intermediates. In contrast, the TAP counterpart (Cys5-Cys15, Cys33-Cys55, Cys39-Cys59) represents only 5% of the total TAP intermediates; (b) three isomers of TAP sharing a stable non-native disulfide bond Cys15-Cys33 are shown to act as kinetic traps of TAP folding. Their counterparts are conspicuously absent in the BPTI folding; and (c) most significantly, folding intermediates of BPTI are found to be energetically compartmentalized, whereas most folding intermediates of TAP are inter-convertible and exist in dynamic equilibrium. Our studies further demonstrate optimal concentrations of denaturant required for destabilization of kinetic traps and acceleration of TAP folding.

Role of kinetic intermediates in the folding of leech carboxypeptidase inhibitor

The oxidative folding and reductive unfolding pathways of leech carboxypeptidase inhibitor (LCI; four disulfides) have been characterized in this work by structural and kinetic analysis of the acid-trapped folding intermediates. The oxidative folding of reduced and denatured LCI proceeds rapidly through a sequential flow of 1-, 2-, 3-, and 4-disulfide (scrambled) species to reach the native form. Folding intermediates of LCI comprise two predominant 3-disulfide species (designated as III-A and III-B) and a heterogeneous population of scrambled isomers that consecutively accumulate along the folding reaction. Our study reveals that forms III-A and III-B exclusively contain native disulfide bonds and correspond to stable and partially structured species that interconvert, reaching an equilibrium prior to the formation of the scrambled isomers. Given that these intermediates act as kinetic traps during the oxidative folding, their accumulation is prevented when they are destabilized, thus leading to a significant acceleration of the folding kinetics. III-A and III-B forms appear to have both native disulfides bonds and free thiols similarly protected from the solvent; major structural rearrangements through the formation of scrambled isomers are required to render native LCI. The reductive unfolding pathway of LCI undergoes an apparent all-or-none mechanism, although low amounts of intermediates III-A and III-B can be detected, suggesting differences in protection against reduction among the disulfide bonds. The characterization of III-A and III-B forms shows that the former intermediate structurally and functionally resembles native LCI, whereas the III-B form bears more resemblance to scrambled isomers.

The folding pathway of alpha-lactalbumin elucidated by the technique of disulfide scrambling. Isolation of on-pathway and off-pathway intermediates

The technique of disulfide scrambling permits reversible conversion of the native and denatured (scrambled) proteins via shuffling and reshuffling of disulfide bonds. Under strong denaturing conditions (e.g. 6 m guanidinium chloride) and in the presence of a thiol initiator, alpha-lactalbumin (alphaLA) denatures by shuffling its four native disulfide bonds and converts to an assembly of 45 species of scrambled isomers. Among them, two predominant isomers, designated as X-alphaLA-a and X-alphaLA-d, account for about 50% of the total denatured structure of alphaLA. X-alphaLA-a and X-alphaLA-d, which adopt the disulfide patterns of (1-2,3-4,5-6,7-8) and (1-2,3-6,4-5,7-8), respectively, represent the most unfolded structures among the 104 possible scrambled isomers (Chang, J.-Y., and Li, L. (2001) J. Biol. Chem. 276, 9705-9712). In this study, X-alphaLA-a and X-alphaLA-d were purified and allowed to refold through disulfide scrambling to form the native alphaLA. Folding intermediates were trapped kinetically by acid quenching and analyzed quantitatively by reversed phase high pressure liquid chromatography. The results revealed two major on-pathway productive intermediates, two major off-pathway kinetic traps, and at least 30 additional minor transient intermediates. Of the two major on-pathway intermediates, one takes on a native-like alpha-helical domain, and the other comprises a structured beta-sheet, calcium binding domain. The two major kinetic traps are apparently stabilized by locally formed non-native-like structures. Overall, the folding mechanism of alphaLA is essentially congruent with the model of "folding funnel" furnished with a rather intricate energy landscape.

Application of the S-pyridylethylation reaction to the elucidation of the structures and functions of proteins

Cysteine (Cys) and cystine residues in proteins are unstable under conditions used for acid hydrolysis of peptide bonds. To overcome this problem, we proposed the use of the S-pyridylethylation reaction to stabilize Cys residues as pyridylethyl-cysteine (PEC) protein derivatives. This suggestion was based on our observation that two synthetic derivatives formed by pyridylethylation of the SH group of Cys with either 2-vinylpyridine (2-VP) or 4-vinylpyridine (4-VP), designated as S-beta-(2-pyridylethyl)-L-cysteine (2-PEC) and S-beta-(4-pyridylethyl)-L-cysteine (4-PEC), were stable under acid conditions used to hydrolyze proteins. This was also the case for protein-bound PEC groups. Since their discovery over 30 years ago, pyridylethylation reactions have been widely modified and automated for the analysis of many structurally different proteins at levels as low as 20 picomoles, to determine the primary structures of proteins and to define the influence of SH groups and disulfide bonds on the structures and functional, enzymatic, medical, nutritional, pharmacological, and toxic properties of proteins isolated from plant, microbial, marine, animal, and human sources. Pyridylethylation has been accepted as the best method for the modification of Cys residues in proteins for subsequent analysis and sequence determination. The reaction has also been proposed to measure D-Cys, homocysteine, glutathione, tryptophan, dehydroalanine, and furanthiol food flavors. This integrated overview of the diverse literature on these reactions emphasizes general concepts. It is intended to serve as a resource and guide for further progress based on the reported application of pyridylethylation reactions to more than 150 proteins.

Oxidative folding of murine prion mPrP(23-231)

A systematic study of the oxidative folding of murine prion protein mPrP(23-231) is reported here. Folding of mPrP(23-231) involves formation of a single disulfide bond, Cys179-Cys214. Despite this simplicity, reduced mPrP(23-231) exhibits numerous unusual folding properties. In the absence of denaturant, folding of mPrP(23-231) is extremely sluggish, regardless of pH. The optimal pH for mPrP(23-231) folding was found to be 4-5. At pH 8.0, a condition that typically favors disulfide formation, folding of mPrP(23-231) hardly occurs, and it not facilitated by inclusion of redox agent. In the presence of denaturant (4 M urea or 2 M guanidine hydrochloride) and basic pH (8.0), reduced mPrP(23-231) refolds to the native structure quantitatively. The efficiency of folding can be further promoted by the presence of oxidized glutathione. At pH 4.0 and in the presence of 4 M urea, reduced mPrP(23-231) converts to three distinctive conformational isomers, unable to form the native structure. These unusual properties lead us to the following conclusions. The reduced mPrP(23-231) adopts a highly rigid structure with the two cysteines buried or situated apart. The presence of denaturant or low pH disrupts this rigid structure and lowers the energy barrier, which permits oxidation and refolding of the reduced mPrP(23-231). Under selected conditions, reduced mPrP(23-231) is capable of taking on multiple forms of stable conformational isomer that are segregated by energy barriers.