Involvement of prolines-114 and -117 in the slow refolding phase of ribonuclease A as determined by isomer-specific proteolysis

The measurement of volume change by capillary dilatometry

Capillary dilatometry enables direct measurement of changes in volume, an extensive thermodynamic property. The results provide insight into the changes in hydration that occur upon protein folding, ligand binding, and the interactions of proteins with nucleic acids and other cellular components. Often the entropy change arising from release of hydrating solvent provides the main driving force of a binding reaction. For technical reasons, though, capillary dilatometry has not been as widely used in protein biochemistry and biophysics as other methods such as calorimetry. Described here are simple apparatus and simple methods, which bring the technique within the capacity of any laboratory. Even very simple results are shown to have implications for macromolecular‐based phenomena. Protein examples are described.

Identification of the protonation site of gaseous triglycine: the cis-peptide bond conformation as the global minimum

Extensive ab initio investigations have been performed to characterize stable conformers of protonated triglycine (GGGH) in the gas phase.

Parallel channels and rate-limiting steps in complex protein folding reactions: prolyl isomerization and the alpha subunit of Trp synthase, a TIM barrel protein

A kinetic folding mechanism for the alpha subunit of tryptophan synthase (alphaTS) from Escherichia coli, involving four parallel channels with multiple native, intermediate and unfolded forms, has recently been proposed. The hypothesis that cis/trans isomerization of several Xaa-Pro peptide bonds is the source of the multiple folding channels was tested by measuring the sensitivity of the three rate-limiting phases (tau(1), tau(2), tau(3)) to catalysis by cyclophilin, a peptidyl-prolyl isomerase. Although the absence of catalysis for the tau(1) (fast) phase leaves its assignment ambiguous, our previous mutational analysis demonstrated its connection to the unique cis peptide bond preceding proline 28. The acceleration of the tau(2) (medium) and tau(3) (slow) refolding phases by cyclophilin demonstrated that cis/trans prolyl isomerization is also the source of these phases. A collection of proline mutants, which covered all of the remaining 18 trans proline residues of alphaTS, was constructed to obtain specific assignments for these phases. Almost all of the mutant proteins retained the complex equilibrium and kinetic folding properties of wild-type alphaTS; only the P217A, P217G and P261A mutations caused significant changes in the equilibrium free energy surface. Both the P78A and P96A mutations selectively eliminated the tau(1) folding phase, while the P217M and P261A mutations eliminated the tau(2) and tau(3) folding phases, respectively. The redundant assignment of the tau(1) phase to Pro28, Pro78 and Pro96 may reflect their mutual interactions in non-random structure in the unfolded state. The non-native cis isomers for Pro217 and Pro261 may destabilize an autonomous C-terminal folding unit, thereby giving rise to kinetically distinct unfolded forms. The nature of the preceding amino acid, the solvent exposure, or the participation in specific elements of secondary structure in the native state, in general, are not determinative of the proline residues whose isomerization reactions can limit folding.

A cis-prolyl peptide bond isomerization dominates the folding of the alpha subunit of Trp synthase, a TIM barrel protein

The cis/trans isomerization of prolyl peptide bonds has been suggested to dominate the folding of the alpha subunit of tryptophan synthase from Escherichia coli (alphaTS). To test the role of the unique cis isomer between Asp27 and Pro28, the folding properties of P28A, P28G and G(3)P28G, a three-glycine insertion mutant between Asp27 and Gly28, were investigated using urea as a denaturant. Circular dichroism analysis demonstrated that none of the mutations perturb the secondary structure significantly, although the aromatic side-chain packing is altered for P28A and P28G. All three mutant proteins inherited the three-state thermodynamic behavior observed in wild-type alphaTS, ensuring that the fundamental features of the energy surface are intact. Kinetic studies showed that neither alanine nor glycine substitutions at Pro28 results in the elimination of any slow-refolding phases. By contrast, the G(3)P28G mutant eliminates the fastest of the slow-refolding phases and one of the two unfolding phases. Double-jump experiments on G(3)P28G confirm the assignment of the missing refolding phase to the isomerization of the Asp27-Pro28 peptide bond. These results imply that the local stability conveyed by the tight, overlapping turns containing the cis peptide bond is sufficient to favor the cis isomer for several non-prolyl residues. The free energy required to drive the isomerization reaction is provided by the formation of the stable intermediate, demonstrating that the acquisition of structure and stability is required to induce subsequent rate-limiting steps in the folding of alphaTS.

Multiple roles of prolyl residues in structure and folding

To explore the ways that proline residues may influence the conformational options of a polypeptide backbone, we have characterized Pro-->Ala mutants of cellular retinoic acid-binding protein I (CRABP I). While all three Xaa-Pro bonds are in the trans conformation in the native protein and the equilibrium stability of each mutant is similar to that of the parent protein, each has distinct effects on folding and unfolding kinetics. The mutation of Pro105 does not alter the kinetics of folding of CRABP I, which indicates that the flexible loop containing this residue is passive in the folding process. By contrast, replacement of Pro85 by Ala abolishes the observable slow phase of folding, revealing that correct configuration of the 84-85 peptide bond is prerequisite to productive folding. Substitution of Pro39 by Ala yields a protein that folds and unfolds more slowly. Removal of the conformational constraint imposed by the proline ring likely raises the transition state barrier by increasing the entropic cost of narrowing the conformational ensemble. Additionally, the Pro-->Ala mutation removes a helix-termination signal that is important for efficient folding to the native state.

Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations

An analysis of a non-redundant set of protein structures from the Brookhaven Protein Data Bank has been carried out to find out the residue preference, local conformation, hydrogen bonding and other stabilizing interactions involving cis peptide bonds. This has led to a reclassification of turns mediated by cis peptides, and their average geometrical parameters have been evaluated. The interdependence of the side and main-chain torsion angles of proline rings provided an explanation why such rings in cis peptides are found to have the DOWN puckering. A comparison of cis peptides containing proline and non-proline residues show differences in conformation, location in the secondary structure and in relation to the centre of the molecule, and relative accessibilities of residues. Relevance of the results in mutation studies and the cis-trans isomerization during protein folding is discussed.

Evidence for a dynamic role for proline376 in the purine-cytosine permease of Saccharomyces cerevisiae

The purine-cytosine permease (PCP), a carrier located in the plasma membrane of Saccharomyces cerevisiae, mediates the active transport of purine (adenine, guanine and hypoxanthine) and cytosine into the cell. Previous studies [Ferreira, T, Brèthes, D., Pinson, B., Napias, C. & Chevallier, J. et al. (1997) J. Biol. Chem. 272, 9697-9702] suggest that the hydrophilic segment 371-377 (-I-A-N-N-I-P-N-) of the polypeptide chain may play a key role in the correct three-dimensional structure of the active carrier. This paper describes the effects of mutations in this particular segment: a four-residue deletion, Delta374-377, and two substitutions, P376G and P376R. The Delta374-377 PCP was expressed in tiny amounts and was totally inactive. When compared with the wild-type, the P376G PCP showed slightly decreased amounts and was able to transport the bases with significantly increased affinity and decreased turnover. The P376R PCP was normally expressed and targeted to the plasma membrane; however, despite a normal number of base-binding sites [1000-1200 pmol.(mg protein)-1], this mutated carrier was completely unable to transport any of its ligands. In addition, the Kd(app) for hypoxanthine binding was completely independent of the pH (within the range 3.5-6.0), showing that the conformational change induced by ligand binding was no longer present. Our results show that the 374-377 segment is essential for the expression and activity of this carrier. They also show that the P376 residue is part of an unusual secondary structure, probably a beta-turn motif, which must play a crucial dynamic role in the translocation process.

A model for transmembrane helix with a cis-proline in the middle

The presence of a higher percentage of Proline in the transmembrane helices of transport proteins indicates that they are involved in the function of these integral membrane proteins (IMPs). In many cases, the possible involvement of cis-trans isomerization in function/folding of IMPs has been suggested. The introduction of cis-Pro in an ideal alpha-helix results in a helix-turn-helix motif. A molecular dynamics (MD) simulation is carried out on the sequence ACE-(ALA)10-cis-Pro-(ALA)10-NME with ideal alpha-helical structure to investigate if and how a straight helix can accommodate a cis-Pro. The analysis of the conformations accessed during MD simulation showed that the residues near cis-Pro can adopt alternate conformations other than the right-handed helical conformation such that an almost straight helix is obtained. This may have implications in the involvement of cis-trans isomerization in folding and/or function of IMPs.

Folding pathway of guanidine-denatured disulfide-intact wild-type and mutant bovine pancreatic ribonuclease A

The refolding kinetics of guanidine-denatured disulfide-intact bovine pancreatic ribonuclease A (RNase A) and its proline-42-to-alanine mutant (Pro42Ala) have been studied by monitoring tyrosine burial and 2'-cytidine monophosphate (2'CMP) inhibitor binding. The folding rate for wild-type RNase A is faster in the presence of the inhibitor 2'CMP than in its absence, indicating that the transition-state structure in the rate-determining step is stabilized by 2'CMP. The folding rate monitored by 2'CMP binding to the major slow-folding species of Pro42Ala RNase A is faster than the folding rate monitored by tyrosine burial; however, the folding rate monitored by inhibitor binding to the minor slow-folding species is decreased significantly over the folding rate monitored by tyrosine burial, indicating that the major and minor slow-folding species of Pro42Ala fold to the native state with different transition-state conformations in the rate-determining step.

Slow-folding kinetics of ribonuclease-A by volume change and circular dichroism: evidence for two independent reactions

The slow refolding of guanidine-HCl-denatured ribonuclease-A was studied by volume change and by kinetic CD at 222 and 276 nm. Dilatometric measurements revealed that on refolding there is a fast volume change of +232 mL/mol of protein. This is followed by a very slow nonexponential change that takes about 25 min to reach equilibrium. By adding varying amounts of (NH4)2SO4, the slow volume change curve was resolved into 2 concurrent reactions. The faster of the 2 slow events entails a negative volume change of -64 mL/mol of protein and appears to arise from proline isomerization. The slower process, attended by a positive change of +53 mL/mol of protein, has properties consistent with the "XY" reaction of Lin and Brands (1983, Biochemistry 22:563-573). This reaction is so named because the conformational nature of neither its initial (Y) nor its final state (X) is known; the transition is characterized solely by its absorbance and fluorescence kinetics. These are the first direct physical measures attributable to the "XY" process. The early formation of a compact structure in the event responsible for the rapid +232-mL/mol volume change, however, is consistent with the sequential model of folding (Cook KH, Schmid FX, Baldwin RL, 1979, Proc Natl Acad Sci USA 76:6157-6161; Kim PS, Baldwin RL, 1980, Biochemistry 19:6124-6129). The usefulness of volume change measurements as a method of detecting structural rearrangements was confirmed by finding agreement between time constants obtained from parallel volume change and kinetic CD experiments. The measured volume changes arise from both changes in hydration and changes in the packing of atoms in the interior of the protein.

Cis proline mutants of ribonuclease A. I. Thermal stability

A chemically synthesized gene for ribonuclease A has been expressed in Escherichia coli using a T7 expression system (Studier, F.W., Rosenberg, A.H., Dunn, J.J., & Dubendorff, J.W., 1990, Methods Enzymol. 185, 60-89). The expressed protein, which contains an additional N-terminal methionine residue, has physical and catalytic properties close to those of bovine ribonuclease A. The expressed protein accumulates in inclusion bodies and has scrambled disulfide bonds; the native disulfide bonds are regenerated during purification. Site-directed mutations have been made at each of the two cis proline residues, 93 and 114, and a double mutant has been made. In contrast to results reported for replacement of trans proline residues, replacement of either cis proline is strongly destabilizing. Thermal unfolding experiments on four single mutants give delta Tm approximately equal to 10 degrees C and delta delta G0 (apparent) = 2-3 kcal/mol. The reason is that either the substituted amino acid goes in cis, and cis<==>trans isomerization after unfolding pulls the unfolding equilibrium toward the unfolded state, or else there is a conformational change, which by itself is destabilizing relative to the wild-type conformation, that allows the substituted amino acid to form a trans peptide bond.

Cis proline mutants of ribonuclease A. II. Elimination of the slow-folding forms by mutation

Ribonuclease A is known to form an equilibrium mixture of fast-folding (UF) and slow-folding (US) species. Rapid unfolding to UF is then followed by a reaction in the unfolded state, which produces a mixture of UF, USII, USI, and possibly also minor populations of other US species. The two cis proline residues, P93 and P114, are logical candidates for producing the major US species after unfolding, by slow cis <==> trans isomerization. Much work has been done in the past on testing this proposal, but the results have been controversial. Site-directed mutagenesis is used here. Four single mutants, P93A, P93S, P114A, and P114G, and also the double mutant P93A, P114G have been made and tested for the formation of US species after unfolding. The single mutants P114G and P114A still show slow isomerization reactions after unfolding that produce US species; thus, Pro 114 is not required for the formation of at least one of the major US species of ribonuclease A. Both the refolding kinetics and the isomerization kinetics after unfolding of the Pro 93 single mutants are unexpectedly complex, possibly because the substituted amino acid forms a cis peptide bond, which should undergo cis --> trans isomerization after unfolding. The kinetics of peptide bond isomerization are not understood at present and the Pro 93 single mutants cannot be used yet to investigate the role of Pro 93 in forming the US species of ribonuclease A. The double mutant P93A, P114G shows single exponential kinetics measured by CD, and it shows no evidence of isomerization after unfolding.(ABSTRACT TRUNCATED AT 250 WORDS)

Secondary structure formation precedes tertiary structure in the refolding of ribonuclease A

The kinetics of refolding of ribonuclease A were monitored by circular dichroism (CD), tyrosine fluorescence and absorbance in the -40 to -10 degrees C range using a methanol cryosolvent. The native-like far-ultraviolet CD signal returned in the dead-time of the mixing, whereas the native absorbance and fluorescence signals returned in a multiphasic process at rates several orders of magnitude more slowly. Thus the secondary structure was formed much more rapidly than the tertiary structure. In addition, the absorbance signal showed evidence of an early intermediate in which one, or more, tyrosine residues was in a transiently more polar environment. A total of four kinetic phases were observed by absorbance in refolding, the slowest two of which had energies of activation consistent with proline isomerization. A refolding scheme involving initial hydrophobic collapse, concurrent with secondary structure formation, followed by much slower rearrangement to the native tertiary structure is proposed.

Identification of a new site of conformational heterogeneity in unfolded ribonuclease A

The results presented here indicate that there are two slowly exchanging conformational isomers in unfolded bovine pancreatic ribonuclease A (RNase A) in the vicinity of Lys-41. The conformational heterogeneity is not observed in the fully folded protein. Therefore, one of the isomers may correspond to one of the slow-folding forms of the protein observed when refolding is initiated. These results were obtained from a chemically modified form of the protein, CL(7-41) RNase A, that has a dinitrophenyl cross-link between the epsilon-amino groups of Lys-7 and Lys-41. Extensive physical studies have shown that the cross-link does not significantly perturb the structure or the folding pathways of the protein. Therefore, the results obtained from this modified form of the protein are relevant to intact RNase A. The one-dimensional (1D) NMR spectrum of heat-unfolded CL(7-41) RNase A reveals that the singlet resonance for the C3H ring proton of the dinitrophenyl cross-link has been split into two unequal peaks in a 3:1 ratio, indicating that there are two distinct environments for the dinitrophenyl group. Variations in temperature, and the addition of urea, do not affect the relative peak intensities. The two peaks collapse into one after the protein is refolded. The observed splitting must originate from a slow reversible isomerization (greater than 100 msec) in a neighboring bond. The two most likely candidates are either the cis/trans isomerization of the Lys-41-Pro-42 peptide bond or hindered rotation about the disulfide bond between Cys-40 and Cys-95.

Occurrence and role of cis peptide bonds in protein structures

It has been widely assumed that the occurrence of cis peptide bonds in proteins is quite rare due to unfavorable contacts between adjacent amino acid residues in this isomeric form. To investigate this assumption, the Brookhaven Protein Data Bank was examined for the occurrences of cis peptide bonds. Out of 31,005 amide bonds, only 17, or 0.05%, are cis, while 99 of the 1534 imide bonds (X-Pro), or 6.5%, are cis. These figures are considerably less than the distribution predicted on the basis of the potential energy difference between the cis and trans isomeric forms and experimental data on small peptides. It is not known whether the lower than expected occurrence of cis peptide bonds arises from constraints imposed by the protein environment, or from assumptions made in the solution of the X-ray crystal structures. However, when the occurrence of cis bonds in the data base is examined relative to the resolution of the structures, the number of cis bonds increases with increasing resolution. The distributions seen for these peptide omega bonds in the data base are not the same shape as the distributions predicted from simple potential energy barriers. They are sharper in the main, but they are also broader at the base with significant numbers of nonplanar peptide bonds. Cis peptide bonds are found primarily in bends and turns and, in the case of cis imide bonds (X-PRO), this correlation is so high that it suggests a specific role for cis imide groups in such structures.

Role of two proline-containing turns in the folding of porcine ribonuclease

Unfolded ribonuclease (RNase) from porcine pancreas consists of a mixture of fast and slow-refolding species. The equilibrium distribution of these species differs strongly from other homologous RNases, because an additional proline residue is present at position 115 of the porcine protein. The major slow-folding species of porcine RNase contains incorrect proline isomers at Pro93 and at Pro114-Pro115. Both positions are presumably part of beta-turn structures in the native protein, as deduced from the structure of the homologous bovine RNase A. The folding kinetics of these molecules depend strongly on the conditions used. Under unfavorable conditions (near the unfolding transition), refolding is virtually blocked by the presence of the incorrect proline peptide bonds and partially folded intermediates with incorrect isomers could not be detected. As a consequence, folding is very slow under such conditions and the re-isomerization of Pro114-Pro115 is the first and rate-limiting step of folding. Under strongly native conditions (such as in the presence of ammonium sulfate), refolding is much faster. A largely folded intermediate accumulates with the turns around Pro93 and Pro114-Pro115 still in the non-native conformation. These results suggest that incorrect proline isomers strongly influence protein folding and that, under favorable conditions, the polypeptide chain can fold with two beta-turns locked into a non-native conformation. We conclude, therefore, that early formation of correct turn structure is not necessarily required for protein folding. However, the presence of incorrect turns, locked-in by non-native proline isomers, strongly decreases the rate of refolding. Alternative pathways of folding exist. The choice of pathway depends on the number and distribution of incorrect proline isomers and on the folding conditions.

The effect of methanol and temperature on the kinetics of refolding of ribonuclease A

Unfolded ribonuclease A consists of 20% fast refolding (Uf) and 80% slow refolding material (Us). The latter consists of at least two different forms which refold at different rates. We have used absorbance and fluorescence spectrophotometry to compare the kinetics of refolding in aqueous and aqueous-methanol solutions. At 1 degree C and pH 3.0, the addition of increasing concentrations of methanol (to 50%, v/v) had negligible effect on the rates and amplitudes of the slow refolding Us states. The effect of temperature on the two slow phases of refolding was determined in 35 and 50% methanol. From Arrhenius plots the energies of activation were found to be in the vicinity of 20 kcal/mol for both processes. The results suggest that both slow phases correspond to proline isomerization, and that the presence of methanol does not significantly perturb the overall refolding process. It is possible that the faster of the slow refolding phases corresponds to the isomerization of a proline residue which is trans in the folded native state but which undergoes extensive isomerization to the cis conformation in the unfolded state.

Toward a better understanding of protein folding pathways

Experimental observations of how unfolded proteins refold to their native three-dimensional structures contrast with many popular theories of protein folding mechanisms. The available experimental evidence (ignoring slow cis-trans peptide bond isomerization) is largely consistent with the following general scheme: under folding conditions, unfolded protein molecules rapidly equilibrate between different conformations prior to complete refolding. This rapid prefolding equilibrium favors certain compact conformations that have somewhat lower free energies than the other unfolded conformations. Some of the favored conformations are important for productive folding. The rate-limiting step occurs late in the pathway and involves a high-energy, distorted form of the native conformation; there appears to be a single transition state through which essentially all molecules refold. Consequently, proteins are not assembled via a large number of independent pathways, nor is folding initiated by a nucleation event in the unfolded protein followed by rapid growth of the folded structure. The known folding pathways involving disulfide bond formation follow the same general principles. An exceptional folding mechanism for reduced ribonuclease A proposed by Scheraga et al. (Scheraga, H.A., Konishi, Y., Rothwarf, D.M. & Mui, P.W. (1987) Proc. Natl. Acad. Sci. USA 84, 5740-5744) is shown to result from experimental shortcomings, an incorrect kinetic analysis, and a failure to consider the kinetics of unfolding.

Trapping the fast-refolding state of ribonuclease A at subzero temperatures

Unfolded ribonuclease A consists of a mixture of fast- and slow-refolding species. It is generally accepted that the slow-refolding states arise from isomerization of proline residues. We show that unfolding at subzero temperatures may be used to trap the fast-refolding species Uf, since the rate of proline isomerization slows down at a much faster rate than protein unfolding. The unfolding was carried out in 5 M guanidine hydrochloride; at -15 degrees C the protein unfolding process is complete within 30 s and under these conditions there is less than 1.5% proline isomerization. By using ribonuclease in which Tyr-115 was nitrated it was possible to rule out significant isomerization of Pro-114 in the observed slow-unfolding step.

Proline isomerism in staphylococcal nuclease characterized by NMR and site-directed mutagenesis

Nuclear magnetic resonance (NMR) studies have shown that two distinct folded conformations of staphylococcal nuclease coexist in solution and that these two states can interconvert directly without passing through an unfolded state. These experiments have also revealed that the two forms have very different folding kinetics, although the possibility that one component is an obligatory intermediate for the folding of the other form could be discounted. Here we report NMR data which show that alternative unfolded states are also distinguishable. These observations led us to hypothesize that cis/trans isomerism at a single peptide bond between a proline and its preceding residue might be the origin of the conformational multiplicity. Proline 117 was identified as a likely candidate for the site concerned and a mutant protein, in which Pro 117 was replaced by Gly, was constructed in order to test this. Alternative conformations are not observed in the spectrum of this mutant, lending powerful support to this hypothesis.

Catalysis of protein folding by prolyl isomerase

Rates of protein folding reactions vary considerably. Some denatured proteins regain the native conformation within milliseconds or seconds, whereas others refold very slowly in the time range of minutes or hours. Varying folding rates are observed not only for different proteins, but can also be detected for single polypeptide species. This originates from the co-existence of fast- and slow-folding forms of the unfolded protein, which regain the native state with different rates. The proline hypothesis provides a plausible explanation for this heterogeneity. It assumes that the slow-folding molecules possess non-native isomers of peptide bonds between proline and another residue, and that crucial steps in the refolding of the slow-folding molecules are limited in rate by the slow reisomerization of such incorrect proline peptide bonds. Recently the enzyme peptidyl-prolyl cis-trans isomerase (PPIase) was discovered and purified from pig kidney. It catalyses efficiently the cis in equilibrium trans isomerization of proline imidic peptide bonds in oligopeptides. Here we show that it also catalyses slow steps in the refolding of a number of proteins of which fast- and slow-folding species have been observed and where it was suggested that proline isomerization was involved in slow refolding. The efficiency of catalysis depends on the accessibility for the isomerase of the particular proline peptide bonds in the refolding protein chain.

Toward an understanding of the folding of ribonuclease A

A mechanism was proposed several years ago for the regeneration of native ribonuclease A (EC 3.1.27.5) from the fully reduced form by a mixture of oxidized and reduced glutathiones. Several folding pathways, depending on the solution conditions, were deduced. It is shown here that recent criticisms of those results are due to a misinterpretation of the analysis of our data. A more detailed description of our method of analysis of our previous kinetic and energetic data is presented in order to clarify possible misconceptions.

Folding/unfolding kinetics of mutant forms of iso-1-cytochrome c with replacement of proline-71

Proline-71, an evolutionally conserved residue that separates two short alpha-helical regions, is replaced by valine, threonine, or isoleucine in at least partially functional forms of iso-1-cytochrome c from Saccharomyces cerevisiae [Ernst, J. F., Hampsey, D. M., Stewart, J. W., Rackovsky, S., Goldstein, D., & Sherman, F. (1985) J. Biol. Chem. 260, 13225-13236]. To assign the effects of perturbations at position 71 to steps in the process of protein folding, the kinetic properties of the folding/unfolding reactions of normal protein and the three mutant forms are compared. At pH 6.0, 20 degrees C, fluorescence-detected folding/unfolding kinetics are monitored below, within, and above the equilibrium transition zone by using stopped-flow mixing to perform guanidine hydrochloride concentration jumps. Three kinetic phases are detected for each of the four proteins. The fastest of these phases (tau 3) differs in rate for the wild type and mutant proteins. The remaining kinetic phases (tau 1 and tau 2) have similar rates for all four proteins over the entire range of folding/unfolding conditions. The guanidine hydrochloride dependence of the relative amplitudes of the kinetic phases is complex and is sensitive to the nature of the substituent at position 71: each of the four proteins shows differences in the fraction of folding/unfolding associated with the two fastest rate processes. The results suggest that it is the location of the mutation in the primary structure rather than the nature of the substituent that determines which kinetic step (or steps) is changed in rate.(ABSTRACT TRUNCATED AT 250 WORDS)

Elution-band relaxation method. A method to analyze isomerization kinetics by HPLC and application to protein denaturation-renaturation

We present a novel method, the 'elution-band relaxation method', to analyze quantitatively reversible isomerization kinetics by elution chromatography, taking advantage of the high resolution and speed of high-performance liquid chromatography (HPLC). The kinetic information is obtained by measuring the first temporal moments of chromatograms of molecules undergoing isomerization and analyzing their dependence on the column length or flow rate. The major advantage of this method is that it is applicable to reactions as fast as the time of elution in HPLC, a speed which has not been attained previously in analysis of isomerization reactions based on the chromatographic property of molecules. We describe the method and report an experimental application to the denaturation-renaturation kinetics of bovine pancreatic ribonuclease A as an example.

Folding mechanism of porcine ribonuclease

The kinetics of unfolding and refolding of porcine ribonuclease were investigated. The unfolded state of this protein was found to consist of a fast-refolding species (UF) and two slow-refolding species (UIS and UIIS). After the rapid collapse of the structure during the N (native)----UF unfolding reaction, UIS and UIIS are produced from UF by two independent slow isomerizations of the unfolded polypeptide chain, leading ultimately to a mixture of about 10% UF, 20% UIIS and 70% UIS molecules at equilibrium. This is at variance with all other ribonucleases investigated to date, which show a distribution of 20% UF, 60 to 70% UIIS and only 10 to 20% UIS. The two isomerizations of the unfolded porcine protein differ strongly in rate. The first process with tau = 250 seconds (10 degrees C) leads to an increase in the fluorescence of Tyr92 and was identified as cis in equilibrium trans isomerization of Pro93. At equilibrium, most unfolded molecules contain an incorrect trans Pro93. The second isomerization is much slower (tau = 1300 s at 10 degrees C) and leads to a predominance of the incorrect isomer as well. Like isomerization of Pro93, it is governed by an activation enthalpy of 22 kcal/mol (92 kJ/mol) and it was tentatively assigned to the Pro114-Pro115 sequence of porcine ribonuclease. Because of the wide separation in rate between the two reactions, molecules with an incorrect isomer only at Pro93 accumulate transiently after unfolding. These are the UIIS molecules. Most of them are finally converted to UIS by the 1300 second process. All molecules that have undergone this isomerization refold very slowly, i.e. the UIS molecules. The major fraction contains two incorrect isomers. A 1300 second isomerization after unfolding and a predominant very slow refolding reaction were observed only for the porcine protein. We suggest that these changes in the folding mechanism may be correlated with the presence of the Pro114-Pro115 sequence, which occurs only in porcine ribonuclease. The refolding pathway of porcine UIIS involves the rapid formation of a native-like intermediate with an incorrect trans Pro93 as was found previously for the bovine ribonuclease, where the UIIS species predominates in the unfolded state.

Use of a trypsin-pulse method to study the refolding pathway of ribonuclease

Trypsin pulses, applied after varying times of refolding, have been employed to probe the accessibility of the polypeptide chain of ribonuclease A during the process of refolding. The increase in resistance against proteolytic cleavage was measured by activity assays and by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The sites of cleavage which become inaccessible in the course of refolding are located in the 31 - 39 chain segment of the ribonuclease chain. Protection of this region against attack by trypsin is attained on the major slow refolding pathway in parallel with the formation of a native-like folded, active intermediate, when refolding is carried out under conditions which strongly stabilize the folded state. Under conditions of marginal stability intermediates are not observed during refolding and the formation of trypsin-resistant molecules occurs with the same kinetics as the generation of native ribonuclease. In the native protein the 31 - 39 region of the ribonuclease chain largely forms a loop structure, which is located at the surface of the molecule. Our results indicate that this part of the sequence is still accessible at early stages of refolding, when a hydrogen-bonded network is formed. It is structured and hence does not become inaccessible until the formation of the overall folded native or native-like structure. This suggests that the 31 - 39 region of the ribonuclease chain is not important for early steps which direct the pathway of refolding.

Folding kinetics of mammalian ribonucleases

The folding kinetics of seven different pancreatic ribonucleases are compared both under native conditions and within the unfolding transition. In general, the folding kinetics of these proteins are similar despite numerous amino acid substitutions. Ribonucleases with 4-6 proline residues show 80% slow-folding species. For three ribonucleases with 7 prolines this number increases to 90%. Porcine ribonuclease with a unique Pro 114-Pro 115 sequence folds significantly slower than other ribonucleases which do not show this sequence.

Effects of the phenylalanine-22----leucine, glutamic acid-49----methionine, glycine-234----aspartic acid, and glycine-234----lysine mutations on the folding and stability of the alpha subunit of tryptophan synthase from Escherichia coli

The effects of four single amino acid replacements on the stability and folding of the alpha subunit of tryptophan synthase from Escherichia coli have been investigated by ultraviolet differences spectroscopy. In previous studies [Miles, E. W., Yutani, K., & Ogasahara, K. (1982) Biochemistry 21, 2586], it had been shown that the urea-induced unfolding at pH 7.8, 25 degrees C, proceeds by the initial unfolding of the less stable carboxyl domain (residues 189-268) followed by the unfolding of the more stable amino domain (residues 1-188). The effects of the Phe-22----Leu, Glu-49----Met, Gly-234----Asp, and Gly-234----Lys mutants on the equilibrium unfolding process can all be understood in terms of the domain unfolding model. With the exception of the Glu-49----Met replacement, the effects on stability are small. In contrast, the effects of three of the four mutations on the kinetics of interconversion of the native form and one of the stable partially folded intermediates are dramatic. The results for the Phe-22----Leu and Gly-234----Asp mutations indicate that these residues play a key role in the rate-limiting step. The Glu-49----Met mutation increases the stability of the native form with respect to that of the intermediate but does not affect the rate-limiting step. The Gly-234----Lys mutation does not affect either the stability or the kinetics of folding for the transition between native and intermediate forms. The changes in stability calculated from the unfolding and refolding rate constants agree quantitatively with those obtained from the equilibrium data. When considered with the results from a previous study on the Gly-211----Glu replacement [Matthews, C. R., Crisanti, M. M., Manz, J. T., & Gepner G. L. (1983) Biochemistry 22, 1445], it can be concluded that the rate-limiting step in the conversion of the intermediate to the native conformation involves either domain association or some other type of molecule-wide phenomenon.

Proline isomerization during refolding of ribonuclease A is accelerated by the presence of folding intermediates

The trans----cis isomerization of Pro 93 was measured during refolding of bovine ribonuclease A. This isomerization is slow (tau = 500 s) under marginally stable folding conditions of 2.0 M GdmCl, pH 6, at 10 degrees C. However, it is strongly accelerated (tau = 100 s) in samples which, prior to isomerization, had been converted to a folding intermediate by a 15 s refolding pulse under strongly native conditions (0.8 M ammonium sulfate, 0 degree C). The results demonstrate that extensive folding is possible before Pro 93 isomerizes to its native cis state and that the presence of structural folding intermediates leads to a marked increase in the rate of subsequent proline isomerization.

Role of proline peptide bond isomerization in unfolding and refolding of ribonuclease

The isomerization of the proline peptide bond between tyrosine-92 and proline-93 in bovine pancreatic ribonuclease A has been investigated in the unfolded protein as well as during the slow refolding process. This bond is in the cis state in the native protein. By comparison of various homologous ribonucleases we show that isomerization of proline-93 is associated with a change in fluorescence of tyrosine-92. This provides a spectroscopic probe to monitor this process in the disordered chain after unfolding as well as its reversal in the course of slow refolding. In unfolded ribonuclease incorrect trans isomers of proline-93 are found in both slow-folding species. trans----cis reversal of isomerization of this proline peptide bond during refolding shows kinetics that are identical with the time course of formation of native protein. Isomerization of proline-93 is slower than the formation of a native-like folded intermediate that accumulates on the major slow refolding pathway. Models to explain these results are discussed.

Urea treatment allows dithiothreitol to release the binding subunit of the insulin receptor from the cell membrane: implications for the structural organization of the insulin receptor

The sequence of the human insulin receptor has only one identifiable transmembrane region which is located in the beta subunit. The structure predicts that the alpha subunit, which binds insulin, is attached to the cell only by disulfide bonds to the beta subunit. However, treatment of membranes with dithiothreitol is ineffective at releasing the alpha subunit. If the receptor structure is unfolded with urea, dithiothreitol is able to release the alpha subunit. These data provided confirmatory evidence that the alpha subunit is not a transmembrane protein.

Energy difference associated with proline isomerization in ribonuclease A

We examined energy differences caused by the cis-trans transformation of every proline residues in the native structure of RNAase A. The results show that the cis form of Pro-93 and Pro-114 gave the lowest conformational energy, i.e., conformations after conversion of one of the proline residues to the trans form had a little higher energy; the transformation of Pro-42 and Pro-117 to the cis form, on the other hand, caused a much higher energy increase.

Protection of amide protons in folding intermediates of ribonuclease A measured by pH-pulse exchange curves

pH-pulse exchange curves have been measured for samples taken during the folding of ribonuclease A. The curve gives the number of protected amide protons remaining after a 10-s pulse of exchange at pHs from 6.0 to 9.5, at 10 degrees C. Amide proton exchange is base catalyzed, and the rate of exchange increases 3000-fold between pH 6.0 and pH 9.5. The pH at which exchange occurs depends on the degree of protection against exchange provided by structure. Pulse exchange curves have been measured for samples taken at three times during folding, and these are compared to the pulse exchange curves of N, the native protein, of U, the unfolded protein in 4 M guanidinium chloride, and of IN, the native-like intermediate obtained by the prefolding method of Schmid. The results are used to determine whether folding intermediates are present that can be distinguished from N and U and to measure the average degree of protection of the protected protons in folding intermediates. The amide (peptide NH) protons of unfolded ribonuclease A were prelabeled with 3H by a previous procedure that labels only the slow-folding species. Folding was initiated at pH 4.0, 10 degrees C, where amide proton exchange is slower than the folding of the slow-folding species. Samples were taken at 0-, 10-, and 20-s folding, and their pH-pulse exchange curves were measured.(ABSTRACT TRUNCATED AT 250 WORDS)