The rate of isomerisation of peptidyl-proline bonds as a probe for interactions in the physiological denatured state of chymotrypsin inhibitor 2

Structure and evolution of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27

Cwc27 is a spliceosomal cyclophilin-type peptidyl-prolyl cis-trans isomerase (PPIase). Here, the crystal structure of a relatively protease-resistant N-terminal fragment of human Cwc27 containing the PPIase domain was determined at 2.0 Å resolution. The fragment exhibits a C-terminal appendix and resides in a reduced state compared with the previous oxidized structure of a similar fragment. By combining multiple sequence alignments spanning the eukaryotic tree of life and secondary-structure prediction, Cwc27 proteins across the entire eukaryotic kingdom were identified. This analysis revealed the specific loss of a crucial active-site residue in higher eukaryotic Cwc27 proteins, suggesting that the protein evolved from a prolyl isomerase to a pure proline binder. Noting a fungus-specific insertion in the PPIase domain, the 1.3 Å resolution crystal structure of the PPIase domain of Cwc27 from Chaetomium thermophilum was also determined. Although structurally highly similar in the core domain, the C. thermophilum protein displayed a higher thermal stability than its human counterpart, presumably owing to the combined effect of several amino-acid exchanges that reduce the number of long side chains with strained conformations and create new intramolecular interactions, in particular increased hydrogen-bond networks.

Folding machineries displayed on a cation-exchanger for the concerted refolding of cysteine- or proline-rich proteins

BACKGROUND

Escherichia coli has been most widely used for the production of valuable recombinant proteins. However, over-production of heterologous proteins in E. coli frequently leads to their misfolding and aggregation yielding inclusion bodies. Previous attempts to refold the inclusion bodies into bioactive forms usually result in poor recovery and account for the major cost in industrial production of desired proteins from recombinant E. coli. Here, we describe the successful use of the immobilized folding machineries for in vitro refolding with the examples of high yield refolding of a ribonuclease A (RNase A) and cyclohexanone monooxygenase (CHMO).

RESULTS

We have generated refolding-facilitating media immobilized with three folding machineries, mini-chaperone (a monomeric apical domain consisting of residues 191-345 of GroEL) and two foldases (DsbA and human peptidyl-prolyl cis-trans isomerase) by mimicking oxidative refolding chromatography. For efficient and simple purification and immobilization simultaneously, folding machineries were fused with the positively-charged consecutive 10-arginine tag at their C-terminal. The immobilized folding machineries were fully functional when assayed in a batch mode. When the refolding-facilitating matrices were applied to the refolding of denatured and reduced RNase A and CHMO, both of which contain many cysteine and proline residues, RNase A and CHMO were recovered in 73% and 53% yield of soluble protein with full enzyme activity, respectively.

CONCLUSION

The refolding-facilitating media presented here could be a cost-efficient platform and should be applicable to refold a wide range of E. coli inclusion bodies in high yield with biological function.

Cis/trans heterogeneity of Gln30-Pro31 peptide bond determines whether a 79-residue fragment of staphylococcal nuclease self-associates

The self-association reaction of a 79-residue fragment of staphylococcal nuclease (SNase79) was studied by far-UV CD, size-exclusion chromatography, and heteronuclear multidimensional NMR spectroscopy. A large population of SNase79 is in self-associated state while a small population of SNase79 is essentially in a monomeric state. The sequence region Thr13-Val39 is responsible for association interface of SNase79. The trans-conformation of X-prolyl bond Gln30-Pro31 may make residues Tyr27-Gln30, serve as a folding nucleation site, and lead the segment Thr13-Val39 of SNase79 to adopt a native-like beta-sheet conformation, which results in the self-association of SNase79. The non-native conformation of the segment Thr13-Val39 of SNase79 associated with the cis-conformation of X-prolyl bond Gln30-Pro31 may preclude SNase79 from the soluble aggregates.

Proline replacements and the simplification of the complex, parallel channel folding mechanism for the alpha subunit of Trp synthase, a TIM barrel protein

The kinetic folding mechanism for the alpha subunit of tryptophan synthase (alphaTS) from Escherichia coli involves four parallel channels whose inter-conversions are controlled by three cis/trans prolyl isomerization reactions (tau(1), tau(2) and tau(3)). A previous mutational analysis of all 19 proline positions, including the unique cis Asp27-Pro28 peptide bond, revealed that the G(3)P28G, P78A or P96A mutations selectively eliminated the fast, tau(1) (ten seconds), folding phase, while the P217M and P261A mutations eliminated the medium, tau(2) (40 seconds) and the slow, tau(3) ( approximately 300 seconds) folding phases, respectively. To further elucidate the role of these proline residues and to simplify the folding mechanism, a series of double and triple mutants were constructed at these critical positions, and comprehensive kinetic and thermodynamic experiments were performed. Although it was not possible to construct a stable system that was free of proline isomerization constraints, a double mutant variant, G(3)P28G/P217M, in which the refolding of more than 90% of the unfolded protein is not limited by proline isomerization reactions was identified. Further, long-range interactions between several of these residues appear to be a crucial part of the cooperative network of structure that stabilizes the TIM barrel motif for alphaTS.

Energetic evidence for formation of a pH-dependent hydrophobic cluster in the denatured state of Thermus thermophilus ribonuclease H

NMR studies on the denatured states of proteins indicate that residual structure often resides predominantly in hydrophobic clusters. Such hydrophobic cluster formation implies burial of apolar surface and, consequently, is expected to cause a decrease in heat capacity. We report here that, in the case of ribonuclease H from the thermophile Thermus thermophilus, a sharp decrease in denatured-state heat capacity occurs at about pH 3.8; this result points to the formation of hydrophobic clusters triggered by the protonation of several (about four) carboxylic acid groups, and indicates that the burial of apolar surface is favored by the less hydrophilic character of the uncharged forms of Asp and Glu side-chains. The process is not accompanied by large changes in optically active structure, but appears to be highly cooperative, as indicated by the sharpness of the pH-induced transition in the heat capacity. This acid-induced hydrophobic burial in denatured T.thermophilus ribonuclease H is clearly reflected in the pH dependence of the denaturation temperature (i.e. an abrupt change of slope at about pH 3.8 is seen in the plot of denaturation temperature versus pH), supporting a role for such denatured-state hydrophobic clusters in protein stability. The finding of cooperative protonation of several groups coupled to surface burial in denatured T.thermophilus ribonuclease H emphasizes the potential complexity of denatured-state electrostatics and advises caution when attempting to predict denatured-state properties on the basis of simple electrostatic models. Finally, our results suggest a higher propensity for hydrophobic cluster formation in the denatured state of T.thermophilus ribonuclease H as compared with that of its mesophilic counterpart from Escherichia coli.

High concentrations of viscogens decrease the protein folding rate constant by prematurely collapsing the coil

In several studies, viscogenic osmolytes have been suggested to decrease the folding rate constant of polypeptides by slowing their motion through the solvent. Here, we show that osmolytes may slow protein folding by prematurely collapsing the coil. At low or moderate concentrations of osmolytes (<30%), folding of the two-state protein CI2 becomes faster with increasing osmolyte concentrations, suggesting that the kinetics are governed by protein stability. However, at higher concentrations of osmolyte, the coil collapses in the dead-time of the refolding experiment, causing a dramatic drop in the folding rate. The collapsed state is non-native and appears to be different for different osmolytes.

Chaperone-like activity of peptidyl-prolyl cis-trans isomerase during creatine kinase refolding

Porcine kidney 18 kD peptidyl-prolyl cis-trans isomerase (PPIase) belongs to the cyclophilin family that is inhibited by the immunosuppressive drug cyclosporin A. The chaperone activity of PPIase was studied using inactive, active, and alkylated PPIase during rabbit muscle creatine kinase (CK) refolding. The results showed that low concentration inactive or active PPIase was able to improve the refolding yields, while high concentration PPIase decreased the CK reactivation yields. Aggregation was inhibited by inactive or active PPIase, and completely suppressed at 32 or 80 times the CK concentration (2.7 microM). However, alkylated PPIase was not able to prevent CK aggregation. In addition, the ability of inactive PPIase to affect CK reactivation and prevent CK aggregation was weaker than that of active PPIase. These results indicate that PPIase interacted with the early folding intermediates of CK, thus preventing their aggregation in a concentration-dependent manner. PPIase exhibited chaperone-like activity during CK refolding. The results also suggest that the isomerase activity of PPIase was independent of the chaperone activity, and that the proper molar ratio was important for the chaperone activity of PPIase. The cysteine residues of PPIase may be a peptide binding site, and may be an essential group for the chaperone function.

A simple way to measure protein refolding rates in water

Refolding of proteins is traditionally carried out either by diluting the denaturant-unfolded protein into buffer (GdmCl-jump) or by mixing the acid-denatured protein with strong buffer (pH-jump). The first method does not allow direct measurement of folding rates in water since the GdmCl cannot be infinitely diluted, and the second method suffers from the limitation that many proteins cannot be pH-denatured. Further, some proteins do not refold reversibly from low pH where they get trapped as aggregation prone intermediates. Here, we present an alternative approach for direct measurement of refolding rates in water, which does not rely on extrapolation. The protein is denatured in SDS, and is then mixed with alpha-cyclodextrin, which rapidly strips SDS molecules from the protein, leaving the naked unfolded protein to refold.

Heat capacity analysis of oxidized Escherichia coli thioredoxin fragments (1--73, 74--108) and their noncovalent complex. Evidence for the burial of apolar surface in protein unfolded states

We have calculated the absolute heat capacities of fragments 1--73 (N fragment) and 74--108 (C fragment) from thioredoxin, their complex and the uncleaved protein, from the concentration dependence of the apparent heat capacities of the solutions determined by differential scanning calorimetry. We find that, while the absolute heat capacities of uncleaved, unfolded thioredoxin and the C fragment are in good agreement with the theoretical values expected for fully solvated chains (calculated as the sum of the contributions of the constituent amino acids), the absolute heat capacities of the N fragment and the unfolded complex are about 2 kJ x K(-1) x mol(-1) lower than the fully solvated-chain values. We attribute this discrepancy to burial of the apolar surface in the N fragment (as burial of the polar area is expected to lead to an increase in heat capacity). Illustrative calculations suggest that burial of about 1000--1600 A(2) of apolar surface takes place in the N fragment (probably accompanied by the burial of a smaller amount of polar surface). In general, this work is supportive of heat capacity measurements on protein fragments being useful as probes of surface burial in studies to characterize protein unfolded states and the high regions of protein folding landscapes.

Non-ionic detergent affects the conformation of a functionally active mutant of Bcl-X(L)

We found that a mutant, Bcl-X(L)(F131V), which was previously reported to have impaired binding capacity, can bind to Bax almost as strongly as wild-type Bcl-X(L). In the absence of detergent, the Bcl-X(L)(F131V) mutant adopts the same conformation as wild-type Bcl-X(L), as determined by circular dichroism spectroscopy and size-exclusion chromatography. However, non-ionic detergent induces a conformational change in the Bcl-X(L)(F131V) mutant and causes it to lose Bax-binding capacity. Wild-type Bcl-X(L), on the other hand, is more resistant to detergent-induced effects and retains its ability to bind Bax in the presence of detergent. Since it has been shown that the Bcl-X(L)(F131V) mutant has nearly the same anti-apoptotic activity as wild-type Bcl-X(L), it would be likely that the Bcl-X(L)(F131V) mutant can adopt the wild-type conformation, rather than the detergent-induced conformational state and can bind to Bax in vivo. Therefore, our data demonstrated that non-ionic detergent can have unpredicted effects on protein conformation, differential effects on wild-type and mutant Bcl-X(L) proteins in this case and may cause complications in the interpretation of in vitro binding studies.

NMR analysis of cleaved Escherichia coli thioredoxin (1-73/74-108) and its P76A variant: cis/trans peptide isomerization

Inspection of high resolution three-dimensional (3D) structures from the protein database reveals an increasing number of cis-Xaa-Pro and cis-Xaa-Yaa peptide bonds. However, we are still far from being able to predict whether these bonds will remain cis upon single-site substitution of Pro or Yaa and/or cleavage of a peptide bond close to it in the sequence. We have chosen oxidized Escherichia coli thioredoxin (Trx), a member of the Trx superfamily with a single alpha/beta domain and cis P76 to determine the effect of single-site substitution and/or cleavage on this isomer. Standard two-dimensional (2D) NMR analysis were performed on cleaved Trx (1-73/74-108) and its P76A variant. Analysis of the NOE connectivities indicates remarkable similarity between the secondary and supersecondary structure of the noncovalent complexes and Trx. Analysis of the 2D version of the HCCH-TOCSY and HMQC-NOESY-HMQC and 13C-filtered HMQC-NOESY spectra of cleaved Trx with uniformly 13C-labeled 175 and P76 shows surprising conservation of both cis P76 and packing of 175 against W31. A similar NMR analysis of its P76A variant provides no evidence for cis A76 and shows only subtle local changes in both the packing of 175 and the interstrand connectivities between its most protected hydrophobic strands (beta2 and beta4). Indeed, a molecular simulation model for the trans P76A variant of Trx shows only subtle local changes around the substitution site. In conclusion, cleavage of R73 is insufficient to provoke cis/trans isomerization of P76, but cleavage and single-site substitution (P76A) favors the trans isomer.

Pseudo-prolines: induction of cis/trans-conformational interconversion by decreased transition state barriers

Molecular events such as cis/trans isomerization of Xaa-Pro tertiary amide bonds in peptides and proteins are slow on the overall time scale of the formation of a final biostructure and are, therefore, rate limiting. In order to pursue a better understanding of the molecular events underlying such slow interconversions, we applied the recently introduced pseudo-proline (PsiPro) concept as a tool to study the dynamics of Xaa-Pro bonds by determining the kinetics and thermodynamics of cis/trans isomerism. We show that enhanced isomerization rates of tertiary amide bonds prior to a PsiPro unit in short model peptides is due to lowered transition state barriers. In addition, pronounced effects upon the dynamics of the reversible transition between helix I and II of oligoprolines containing one or several PsiPro units were observed.

Stability and folding of the tumour suppressor protein p16

The tumour suppressor p16 is a member of the INK4 family of inhibi tors of the cyclin D-dependent kinases, CDK4 and CDK6, that are involved in the key growth control pathway of the eukaryotic cell cycle. The 156 amino acid residue protein is composed of four ankyrin repeats (a helix-turn-helix motif) that stack linearly as two four-helix bundles resulting in a non-globular, elongated molecule. The thermodynamic and kinetic properties of the folding of p16 are unusual. The protein has a very low free energy of unfolding, Delta GH-2O/D-N, of 3.1 kcal mol-1 at 25 degreesC. The rate-determining transition state of folding/unfolding is very compact (89% as compact as the native state). The other unusual feature is the very rapid rate of unfolding in the absence of denaturant of 0.8 s-1 at 25 degreesC. Thus, p16 has both thermodynamic and kinetic instability. These features may be essential for the regulatory function of the INK4 proteins and of other ankyrin-repeat-containing proteins that mediate a wide range of protein-protein interactions. The mechanisms of inactivation of p16 by eight cancer-associated mutations were dissected using a systematic method designed to probe the integrity of the secondary structure and the global fold. The structure and folding of p16 appear to be highly vulnerable to single point mutations, probably as a result of the protein's low stability. This vulnerability provides one explanation for the striking frequency of p16 mutations in tumours and in immortalised cell lines.

Stability and folding of the cell cycle regulatory protein, p13(suc1)

p13(suc1) (suc1) is a member of the CDC28 kinase specific family of cell cycle regulatory proteins that bind to the cyclin-dependent kinase CDK2 and regulate its activity. suc1 has two distinct conformational and assembly states, a compact globular monomer and a beta strand-exchanged dimer. The dimerisation is an example of domain-swapping, and is mediated by a molecular hinge mechanism that is conserved across the entire CKS family. It has been proposed that the function of suc1 may be modulated by the dimerisation process with monomer-dimer switching occurring in response to a change in the cell environment. We have investigated the stability and folding of suc1 as a first step in determining the mechanism and functional role of the strand exchange. Suc1 unfolds reversibly at equilibrium in a two-state manner with a free energy of unfolding of 7.2 kcal mol-1. The kinetics of folding and unfolding are complex, and double-jump stopped-flow methods revealed that there are at least three parallel folding pathways arising from distinct unfolded and partly folded, intermediate states. The major population of unfolded species fold rapidly according to a three-state mechanism, D1->I1->N, with a rate constant for the formation of native species, N, from the intermediate, I1, of 65 s-1 in water. Two minor populations of unfolded molecules fold more slowly. Folding of one population is limited by proline isomerisation in a partly folded state, and some expansion of the protein is required for isomerisation to occur. The other population could be assigned to rate-limiting isomerisation of the peptidyl-proline bond of residue 90, which is located in the molecular hinge. A minor, fast phase was detected in the unfolding kinetics that corresponds to unfolding of a small population of a distinct native-like form. Heterogeneity was removed upon mutation of Pro90 to Ala. The unfolding kinetics of the strand-exchanged dimer were also investigated and showed that the dimer unfolds at the same rate as the monomer.

Side-chain effects on peptidyl-prolyl cis/trans isomerisation

Peptidyl-prolyl cis/trans isomerisation has been frequently found as a rate limiting step in the folding of proteins. In order to determine whether the nature of the amino acid preceding proline controls the probability of cis prolyl bonds in native proteins, systematic studies on the thermodynamics and kinetics of the prolyl isomerisation in the pentapeptide series Ac-Ala-Xaa-Pro-Ala-Lys-NH2 were performed. All proteinogenic amino acids were substituted in the position preceding proline. When measured by 1H-NMR and CD spectroscopy both isomers proved to be devoid of ordered structure in the whole series of the oligopeptides in aqueous solution. Thus, isomerization rates and cis/trans ratios calculated from solvent jump and 1H-NMR magnetisation transfer experiments exclusively reflect the side-chain effects of the Xaa position in the peptide series. There is a rough correlation between the cis content in the oligopeptides and the propensity of Xaa-Pro cis prolyl bonds in proteins. This correlation suggests that the prolyl bond conformation is mainly determined by local effects in proteins. The rate constants kc-->t of pentapeptides containing unionised amino acids preceding proline range from 3.2 x 10(-3) s-1 (Xaa = Ala) to 0.5 x 10(-3) s-1 (Xaa = Trp) at 4 degrees C. Proline clustering led to an isomerisation cycle indicating considerable influence on the isomerisation rates of the peptide bond conformations flanking the rotating bond. Both tyrosine and histidine specifically reduce isomerisation rates severalfold by deprotonation of their respective side-chains.