Rapid Adaptive Evolution of the Tumor Suppressor Gene Pten in an Insect Lineage

The Pten gene was initially identified in humans as a tumor suppressor. It has since been shown to play important roles in the control of cell size, cell motility, apoptosis, and organ size, and it has also been implicated in aging. Pten is highly conserved among organisms as diverse as nematodes, insects, and vertebrates. In contrast, a phylogenetic analysis by maximum likelihood of a 133-amino acid region showed an average nonsynonymous-to-synonymous rate ratio of 10.4 for Pten in the lineage leading to parasitoid wasps of the Nasonia genus, indicating very strong positive selection. A previous study identified Pten as a potential QTL candidate gene for differences in male wing size in Nasonia. Most of the amino acid replacements that occurred in the Nasonia lineage cluster in a small region of the protein surface, suggesting that they might be involved in an interaction between Pten and another protein. The phenotypic changes due to Pten are not yet known, although it is not associated with known differences in male wing size. Introgression of Pten from one species to another does affect longevity, but a causal relationship is not established.

Characterization of a high-affinity complex between the bacterial outer membrane protein FhuA and the phage T5 protein pb5

Binding of bacteriophage T5 to Escherichia coli cells is mediated by specific interactions between the receptor-binding protein pb5 (67.8 kDa) and the outer membrane iron-transporter FhuA. A histidine-tagged form of pb5 was overproduced and purified. Isolated pb5 is monomeric and organized mostly as beta-sheets (51%). pb5 functionality was attested in vivo by its ability to impair infection of E. coli cells by phage T5 and Phi80, and to prevent growth of bacteria on iron-ferrichrome as unique iron source. pb5 was functional in vitro, since addition of an equimolar concentration of pb5 to purified FhuA prevented DNA release from phage T5. However, pb5 alone was not sufficient for the conversion of FhuA into an open channel. Direct interaction of pb5 with FhuA was demonstrated by isolating a pb5/FhuA complex using size-exclusion chromatography. The stoichiometry, 1 mol of pb5/1 mol of FhuA, was deduced from its molecular mass, established by analytical ultracentrifugation after determination of the amount of bound detergent. SDS-PAGE and differential scanning calorimetry experiments highlighted the great stability of the complex: (i) it was not dissociated by 2% SDS even when the temperature was raised to 70 degrees C; (ii) thermal denaturation of the complex occurred at 85 degrees C, while pb5 and FhuA were denatured at 45 degrees C and 74 degrees C, respectively. The stability of the complex renders it suitable for high-resolution structural studies, allowing future analysis of conformational changes into both FhuA and pb5 upon adsorption of the virus to its host.

Key interactions in the immunoglobulin-like structure of apo-neocarzinostatin: evidence from nuclear magnetic resonance relaxation data and molecular dynamics simulations

The three-dimensional structure of apo-neocarzinostatin (apo-NCS, MW: ca.11000, antitumoral chromophore carrier protein) is based on a seven-stranded antiparallel beta-sandwich, very similar to the immunoglobulin folding domain. We investigated the backbone dynamics of apo-NCS by (13)C-NMR relaxation measurements and molecular dynamics simulation. Model-free parameters determined from the experimental data are compared with a 1.5-nsec molecular simulation of apo-NCS in aqueous solution. This comparison provides an accurate description of both local and collective movements within the protein. This analysis enabled us to correlate dynamic processes with key interactions of this beta-protein. Local motions that could be relevant for the intermolecular association with the ligand are also described.

Role of loops in the folding and stability of yeast phosphoglycerate kinase

Yeast phosphoglycerate kinase (yPGK) is a monomeric two domain protein used as folding model representative of large proteins. We inserted short unstructured sequences (four Gly or four Thr) into the connections between secondary structure elements and studied the consequences of these insertions on the folding process and stability of yPGK. All the mutated proteins can refold efficiently. The effect per residue on stability is larger for the first inserted residue. Insertion in two long betaalpha loops (at residue positions 71 and 129) is more destabilizing than an insertion in a short alphabeta loop (at residue position 89) located on the opposite side of the N-terminal domain. The effect on stability is mainly due to a large increase of the unfolding rate rather than a decrease of the folding rate. This suggests that these connections between secondary structure elements do not play an active role in directing the folding process. Insertion into the short alphabeta loop (position 89) has limited effects on stability and results in the detection of a kinetic phase not previously seen with the wild-type protein, suggesting that insertions in this particular loop do qualitatively affect the folding process without a large effect on folding efficiency. For the two long betaalpha loops (positions 71 and 129) located in the inner surface of the N-terminal domain, the effects on stability are possibly associated with decoupling of the two domains as observed by differential scanning calorimetry during thermal unfolding.

Heat-induced unfolding of neocarzinostatin, a small all-β protein investigated by small-angle X-ray scattering 1 1Edited by M. F. Moody

Neocarzinostatin is an all-beta protein, 113 amino acid residues long, with an immunoglobulin-like fold. Its thermal unfolding has been studied by small-angle X-ray scattering. Preliminary differential scanning calorimetry and fluorescence measurements suggest that the transition is not a simple, two-state transition. The apparent radius of gyration is determined using three different approaches, the validity of which is critically assessed using our experimental data as well as a simple, two-state model. Similarly, each step of data analysis is evaluated and the underlying assumptions plainly stated. The existence of at least one intermediate state is formally demonstrated by a singular value decomposition of the set of scattering patterns. We assume that the pattern of the solution before the onset of the transition is that of the native protein, and that of the solution at the highest temperature is that of the completely unfolded protein. Given these, actually not very restrictive, boundary constraints, a least-squares procedure yields a scattering pattern of the intermediate state. However, this solution is not unique: a whole class of possible solutions is derived by adding to the previous linear combination of the native and completely unfolded states. Varying the initial conditions of the least-squares calculation leads to very similar solutions. Whatever member of the class is considered, the conformation of this intermediate state appears to be weakly structured, probably less than the transition state should be according to some proposals. Finally, we tried and used the classical model of three thermodynamically well-defined states to account for our data. The failure of the simple thermodynamic model suggests that there is more than the single intermediate structure required by singular value decomposition analysis. Formally, there could be several discrete intermediate species at equilibrium, or an ensemble of conformations differently populated according to the temperature. In the latter case, a third state would be a weighted average of all non native and not completely unfolded states of the protein but, since the weights change with temperature, no meaningful curve is likely to be derived by a global analysis using the simple model of three thermodynamically well-defined states.

Characterization of the denatured states distribution of neocarzinostatin by small-angle neutron scattering and differential scanning calorimetry

The denatured states of a small globular protein, apo-neocarzinostatin (NCS), have been characterized using several techniques. Structural properties were investigated by optical spectroscopy techniques and small-angle neutron scattering (SANS), as a function of guanidinium chloride (GdmCl) concentration. SANS experiments show that in heavy water, the protein keeps its native size at GdmCl concentrations below 2.5 M. A sharp transition occurs at about 3.6 M GdmCl, and NCS behaves like an excluded volume chain above 5 M. The same behavior is observed in deuterated buffer by fluorescence and circular dichroism measurements. For the H(2)O buffer, the transition occurs with lower concentration of denaturant, the shift being about 0.6 M. 8-Anilino-1-naphthalenesulfonate (ANS) was used as a hydrophobic fluorescent probe for studying the early stages of protein unfolding. Protein denaturation modifies the fluorescence intensity of ANS, a maximum of intensity being detected close to 2 M GdmCl in hydrogenated buffer, which shows the existence of at least one intermediate state populated at the beginning of the unfolding pathway. Differential scanning calorimetry (DSC) was used to obtain thermodynamic values for NCS denaturation. The melting curves recorded between 20 and 90 degrees C in the presence of various GdmCl concentrations (0-3 M) cannot be explained by a simple two-state model. Altogether, the data presented in this paper suggest that before unfolding the protein explores a distribution of states which is centered around compact states at denaturant concentrations below 2 M in H(2)O, and then shifts to less structured states by increasing denaturant concentrations.

Stability studies of FhuA, a two-domain outer membrane protein from Escherichia coli

FhuA (MM 78.9 kDa) is an Escherichia coli outer membrane protein that transports iron coupled to ferrichrome and is the receptor for a number of bacteriophages and protein antibiotics. Its three-dimensional structure consists of a 22-stranded beta-barrel lodged in the membrane, extracellular hydrophilic loops, and a globular domain (the "cork") located within the beta-barrel and occluding it. This unexpected structure raises questions about the connectivity of the different domains and their respective roles in the different functions of the protein. To address these questions, we have compared the properties of the wild-type receptor to those of a mutated FhuA (FhuA Delta) missing a large part of the cork. Differential scanning calorimetry experiments on wild-type FhuA indicated that the cork and the beta-barrel behave as autonomous domains that unfold at 65 and 75 degrees C, respectively. Ferrichrome had a strong stabilizing effect on the loops and cork since it shifted the first transition to 71.4 degrees C. Removal of the cork destabilized the protein since a unique transition at 61.6 degrees C was observed even in the presence of ferrichrome. FhuA Delta showed an increased sensitivity to proteolysis and to denaturant agents and an impairment in phage T5 and ferrichrome binding.

Gamma radiation effects on alpha-lactalbumin: structural modifications

Alpha-lactalbumin was irradiated in the lyophilized state in air at ambient temperature. The irradiated protein was examined by size exclusion chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis, circular dichroism, and microcalorimetry. Irradiation induced the loss of aromatic amino acids and of helicity so that fragmentation and aggregation products were obtained. The thermodynamic properties of the protein were also modified. The irradiated protein had lower stability, however, the temperature at which denaturation occurred process remained constant.

Gamma radiation effects on α-lactalbumin: structural modifications

α-Lactalbumin was irradiated in the lyophilized state in air at ambient temperature. The irradiated protein was examined by size exclusion chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis, circular dichroism, and microcalorimetry. Irradiation induced the loss of aromatic amino acids and of helicity so that fragmentation and aggregation products were obtained. The thermodynamic properties of the protein were also modified. The irradiated protein had lower stability, however, the temperature at which denaturation occurred process remained constant.Key words: ionizing radiation, radiation-induced conformational changes, protein structural modifications, protein thermodynamic properties.

Functionally accepted insertions of proteins within protein domains

Experiments were designed to explore the tolerance of protein structure and folding to very large insertions of folded protein within a structural domain. Dihydrofolate reductase and beta-lactamase have been inserted in four different positions of phosphoglycerate kinase. The resultant chimeric proteins are all overexpressed, and the host as well as the inserted partners are functional. Although not explicitly designed, functional coupling between the two fused partners was observed in some of the chimeras. These results show that the tolerance of protein structures to very large structured insertions is more general than previously expected and supports the idea that the natural sequence continuity of a structural domain is not required for the folding process. These results directly suggest a new experimental approach to screen, for example, for folded protein in randomized polypeptide sequences.

Reinvestigation of the proteolytic activity of neocarzinostatin

Neocarzinostatin (NCS) is the most studied member of a family of chromoproteins secreted by a range of actinomycetes species. It has been proposed that in addition to their antitumoral activity related to the bound chromophores, this group of related proteins could be a secreted proteases superfamily. With the aim of dissecting the molecular basis of the proteolytic activity of NCS, an expression system allowing efficient expression of apo-NCS in Escherichia coli was constructed. The recombinant protein was properly folded and functional. Its histone-specific proteolytic activity was similar to the activity described for the natural protein. Further analyses unambiguously demonstrated that the proteolytic activity could be physically separated from NCS. This activity is therefore due not to NCS itself but to minor contaminating proteases, the nature of which differed in the recombinant and natural NCS preparations. The histone degradation test commonly used to monitor proteolytic activity is extremely sensitive and may easily generate false-positive results. These results strongly suggest that the possible proteolytic activity of the proteins of this family should be critically reconsidered.

Role of hydrophobic interactions in yeast phosphoglycerate kinase stability

Cold denaturation of yeast phosphoglycerate kinase (yPGK) was investigated by a combination of far UV circular dichroism (CD), steady-state and time-resolved fluorescence, and small angle X-ray scattering. It was shown that cold denaturation of yPGK cannot be accounted for by a simple two-state process and that an intermediate state can be stabilized under mild denaturing conditions. Comparison between far UV CD and fluorescence shows that in this state the protein displays a fluorescence signal corresponding mainly to exposed tryptophans, whereas its CD signal is only partially modified. Comparison with spectroscopic data obtained from a mutant missing the last 12 amino-acids (yPGK delta404) suggests that lowering the temperature mainly results in a destabilization of hydrophobic interactions between the two domains. Small angle X-ray scattering measurements give further information about this stabilized intermediate. At 4 degrees C and in the presence of 0.45 M Gdn-HCl, the main species corresponds to a protein as compact as native yPGK, whereas a significant proportion of ellipticity has been lost. Although various techniques have shown the existence of residual structures in denatured proteins, this is one example of a compact denatured state devoid of its main content in alpha helices.

Role of the C-terminal extremities of the smooth muscle myosin heavy chains: implication for assembly properties

The two light meromyosin isoforms from rabbit smooth muscle were prepared as recombinant proteins in Escherichia coli. These species which differed only by their C-terminal extremity showed the same circular dichroism spectra and endotherms in measurements of differential scanning calorimetry. Their solubility properties were different at pH 7.0 in the absence of monovalent salts. Their paracrystals formed at low pH differed by their aspect and number. These data suggest a role for the C-terminal extremity of myosin heavy chains in the assembly of myosin molecules in filaments and consequently in the contractility of smooth muscles.

Kinetic evidence for the formation of a Michaelis-Menten-like complex between horseradish peroxidase compound II and di-(N-acetyl-L-tyrosine)

The formation of a reversible adsorption complex between a dimer of N-acetyl-L-tyrosine [di-(N-acetyl-L-tyrosine), (NAT)2] and horseradish peroxidase (HRP) compound II (CII) was demonstrated using a kinetic approach. A specific KIIm value (0.58 mM) was deduced for this step from stopped-flow measurements. The dimerization of the dipeptide Gly-Tyr was analysed at the steady state and compared with (NAT)2 dimerization [(NAT)2-->(NAT)4]. A saturation of the enzyme was observed for both substrates within their range of solubility. In each case the rate of dimerization reflected the rate-limiting step of compound II reduction to the native HRP (E) (kappcat/Kappm approximately kII-->E). The kappcat values for (Gly-Tyr)2 and (NAT)4 formation were 254 s-1 and 3.6 s-1 respectively. The KappM value of Gly-Tyr was 24 mM. It was observed that the value (0.7 mM) for (NAT)2 was close both to its specific KIIm value for the second step of reduction (CII-->E) and to its thermodynamic dissociation constant (Kd=0.7 mM) with the resting form of the enzyme. As (NAT)2 was a tighter ligand but a poorer substrate than Gly-Tyr, a steady-state kinetic study was performed in the presence of both substrates. A kinetic model which includes an enzyme-substrate adsorption prior to each of the two steps of reduction was derived. This one agreed reasonably well with the experimental data.

Steady state and time-resolved fluorescence study of residual structures in an unfolded form of yeast phosphoglycerate kinase

A previous study performed using steady state fluorescence has revealed the existence of residual structures surrounding the two tryptophan residues in an unfolded form of yeast phosphoglycerate kinase [Garcia, P., et al. (1995) Biochemistry 34, 397-404]. In this paper, we present a more detailed characterization of these residual structures, through the study of two single tryptophan-containing mutants of yPGK, W333F and W308Y. Denaturation experiments have first been performed at low temperatures to assess the nature of the interactions stabilizing these residual structures. On the other hand, the compactness and dynamics of the protein matrix were probed using tryptophan fluorescence quenching by acrylamide at various denaturant concentrations. Taking into consideration the changes in sample viscosity induced by addition of guanidinium chloride made feasible the use of this technique during the denaturation process. These different approaches have shown that the residual structures around tryptophan 308 are mainly stabilized by hydrophobic interactions and are more compact and less fluctuant than the ones surrounding tryptophan 333. Native and denatured yPGK have also been studied by time-resolved fluorescence spectroscopy. In the native protein, tryptophan buried in the core, W333, is mainly associated with a lifetime close to 0.1 ns, whereas tryptophan that is partially accessible to the solvent, W308, has a lifetime close to 0. 5 ns. The time-resolved tryptophan fluorescence emission of wild-type yPGK can be accounted for quantitatively by the summed emissions of its two single tryptophan mutants. The significance of minor long lifetime components is discussed for the two tryptophan residues. This new assignment of fluorescent decay times has allowed for the detection of a folding intermediate in which the environment of tryptophan 333 is modified for denaturant concentrations lower than those for tryptophan 308.

Repulsive interparticle interactions in a denatured protein solution revealed by small angle neutron scattering

In order to investigate the effect of concentration in biological processes such as protein folding, small angle neutron scattering measurements were used to determine the second virial coefficient of solutions of both native and strongly denatured phosphoglycerate kinase and the radius of gyration of the protein at zero concentration. The value of the second virial coefficient is a good probe of the non-ideality of a solution. The present results show that the unfolding of the protein leads to a drastic change in the repulsive intermolecular interactions. We conclude that these interactions are due mainly to the behaviour of the denatured polypeptide chain as an excluded volume polymer.

Horseradish peroxidase oxidation of tyrosine-containing peptides and their subsequent polymerization: a kinetic study

Tyrosine-containing model peptides were oxidized by horseradish peroxidase (HRP). This led to a peptide polymerization via condensation of the aromatic rings. Dimers, trimers, and tetramers (depending on the peptide length and on the position of the tyrosine in the sequence) were identified by electron spray mass spectroscopy. The second-order rate constants of the second step of the HRP reduction (CII --> E) was decreased by the presence of a positively charged amino group in the vicinity of the aromatic ring as determined by stopped flow measurements [k3 = 19 398 M-1 s-1 and k3 = 1016 M-1 s-1 for N-acetyltyrosine (NAT) and l-Tyr oxidations, respectively]. High-performance liquid chromatography was used to follow the kinetics of polymerization of some model peptides after their enzymatic oxidation. The first polymerization products exhibited a strong inhibitory effect toward further oxidation by HRP. This effect was not observed when using manganese-dependent peroxidase (MnP) which does not bind directly to the tyrosine residue but rather acts as a "distant catalyst". Saturation of the HRP was achieved with Pro-Gln-Gln-Pro-Tyr (kcat = 58 s-1, = 2.1 mM), NAT (kcat = 94 s-1, = 5.6 mM), and Gly-Tyr (kcat = 175 s-1, = 10.8 mM). Analysis of steady state kinetics of the reaction showed that the dimers formed initially behaved like competitive inhibitors. The value of the dissociation constant between HRP and dimers was 20 microM. A simplified model which accounts for these observations, including the formation of a Michaelis-Menten-like complex involving the donor and enzyme, is proposed and discussed.

Picosecond dynamical changes on denaturation of yeast phosphoglycerate kinase revealed by quasielastic neutron scattering

Quasielastic neutron scattering experiments performed on yeast phosphoglycerate kinase in the native form and denatured in 1.5 M guanidinium chloride reveal a change in the fast (picosecond time scale) diffusive internal dynamics of the protein. The momentum and energy transfer dependences of the scattering for both states are fitted by an analytical model in which, on the experimentally accessible picosecond time scale and angstrom length scale, the dynamics of a fraction of the nonexchangeable hydrogens in the protein is described as a superposition of vibrations with uniform diffusion in a sphere, the rest of the hydrogens undergoing only vibrational motion. The fraction diffusing changes, from approximately 60% in the native protein to approximately 82% in the denatured protein. The radius of the sphere also changes slightly, from approximately 1.8 A in the native protein to approximately 2.2 A in the denatured protein. Possible implications of these results for the general protein folding problem are discussed.

Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory

Small-angle neutron scattering profiles are presented from phosphoglycerate kinase, in the native form and strongly denatured in 4 M guanidinium chloride (GdnHCl) solution. The data are interpreted using a model in which the excess scattering density associated with the protein is represented as a finite freely jointed chain of spheres. The similarity of the model-derived scattering function to experiment increases asymptotically with the number of spheres. The improvement of the fit obtained with more than approximately 200 spheres (i.e., two residues per sphere) is insignificant. The effects of finite size of the scattering units and of scattering length variation along the polypeptide chain are examined. Improved agreement with experiment is obtained when these effects are taken into account. A method for rapid calculation of the scattering profile of a full, all-atom configuration is examined. It is found that a representation of the chain containing two scattering units per residue, placed at the backbone and side-chain scattering length centroids, reproduces the full, all-atom profile to within 2%.

Phosphorylation of nucleoside diphosphate kinase at the active site studied by steady-state and time-resolved fluorescence

Nucleoside diphosphate (NDP) kinase is the enzyme responsible in the cell for the phosphorylation of nucleoside or deoxynucleoside diphosphates into the corresponding triphosphates at the expense of ATP. Transfer of the gamma-phosphate is very fast (turnover number above 1000 s-1) and involves the phosphorylation of a histidine residue at the active site of the enzyme. We have used intrinsic protein fluorescence of the single tryptophan of Dictyostelium discoideum NDP kinase as a sensitive probe for monitoring the interaction of the enzyme with its substrates. We demonstrate that the 20% quenching of steady-state fluorescence observed upon addition of ATP is due to formation of the phosphorylated intermediate. Time-resolved fluorescence indicates that the Trp-137 side chain is rigidly bound to the protein core with a unique lifetime of 4.5 ns for the free enzyme at 20 degrees C and that it remains tightly immobilized during the time course of the reaction. Phosphorylation of this catalytic residue (His-122) in the presence of ATP induces a similar decrease in mean lifetime, due to the splitting of the signal and the appearance of a shorter decay. This splitting is discussed in terms of a slow conformational equilibrium. We demonstrate that, in the wild-type enzyme, the conserved His-55 quenches the fluorescence of Trp-137 as the H55A mutant protein fluorescence displays an increase in quantum yield. Even though H55A mutant enzyme is active, the absence of the imidazole ring prevents the detection of the phosphorylated state of His-122 by Trp-137. We conclude that His-55 serves as a relay between His-122 and Trp-137.

Purification and structural and functional characterization of FhuA, a transporter of the Escherichia coli outer membrane

The Escherichia coli outer membrane ferrichrome transporter FhuA was purified chromatographically in a neutral detergent (octyl glucoside or dodecyl maltoside). The amount of dodecyl maltoside bound to the protein (1.2 +/- 0.15 g/g of FhuA) and the Stokes radius of the FhuA-dodecyl maltoside complex (Rs = 4.2 nm) were determined using size exclusion chromatography. Sedimentation equilibrium and velocity experiments indicated that the FhuA preparation was monodisperse and that the protein was monomeric. The value found for the frictional coefficient of the protein-detergent complex (1.18) suggested a globular shape for the complex. Sedimentation experiments gave values for the molecular mass of the FhuA-dodecyl maltoside complex (180 kDa) and for the Stokes radius in complete agreement with those calculated from size exclusion chromatography. The circular dichroism spectrum indicated a 51% beta-sheet content. Functionality of the purified protein was assessed from fluorescence measurements using the DNA probe YO-PRO-1. Interaction of nM concentrations of FhuA with bacteriophage T5 resulted in the release of 90 +/- 8% of the phage DNA. The limiting step in DNA ejection was binding of the phage to its receptor. Release of DNA took place in a few seconds. Ferrichrome (0.8 microM) competed with the phage for binding to FhuA and prevented DNA ejection.

Folding and functional complementation of engineered fragments from yeast phosphoglycerate kinase

A set of protein fragments was produced by site-directed mutagenesis followed by chemical cleavage of phosphoglycerate kinase according to a previously described method [Pecorari et al. (1993) Protein Eng. 6, 313-325]. The cleavage positions were chosen in order to correspond to limits between structural subdomains. These isolated fragments were studied by circular dichroism, folding transitions, and cross-linking analyses. It appears that fragments corresponding to globular subdomains in the protein can recover the expected helix content. However, the cooperativity classically observed in the folding transitions of natural proteins is only observed for fragments larger than a domain. Previous studies have shown that the isolated C-terminal domain is an autonomous folding unit which displays a single cooperatine transition [Missiakas et al. (1990) Biochemistry 29, 8683-8689]. The results presented here show that the presence in a fragment of a sequence overpassing that of the C-terminal domain modifies its folding process. Reassociation experiments suggest that the efficiency of the complementation process is not related to the folding autonomy of the isolated fragments.

Occurrence of transient multimeric species during the refolding of a monomeric protein

A set of protein fragments from yeast phosphoglycerate kinase were produced by chemical cleavage at a unique cysteinyl residue previously introduced by site-directed mutagenesis. Cross-linking experiments showed that the fragments corresponding to incomplete N-terminal domain form stable oligomeric species. Transient oligomeric species were also observed by both cross-linking and light scattering experiments during the folding process of the whole protein. These transient oligomeric species are formed during the fast folding phase and dissociate during the slow folding phase to produce the monomeric active protein. The multimeric species are not required for the protein to fold correctly. Unexpectedly, the distribution of oligomeric species is not dependent on protein concentration during the folding process. A kinetic competition mechanism is proposed as a possible solution to this paradox. These results provide direct evidence that the polypeptide chain can explore nonnative interactions during the folding process.

Structural and functional properties of mutant Arg203Pro from yeast phosphoglycerate kinase, as a model of phosphoglycerate kinase-Uppsala

A pathological variant of human phosphoglycerate kinase, phosphoglycerate kinase-Uppsala, associated with chronic nonspherocytic hemolytic anemia has been found to differ from the normal enzyme by substitution of an arginine at position 206 (corresponding to position 203 in yeast) by a proline. In order to understand the structural and functional consequences of this mutation, the corresponding mutant in yeast phosphoglycerate kinase was constructed. The three-dimensional structure of this mutant was resolved at 2.9 A. Although the overall structure is not modified, small local changes were observed. The kinetic parameters of the mutant were not found to be greatly affected, the catalytic constant being lowered by only 10-20%. The most significant difference when compared with the wild-type enzyme is a decrease in stability by about 3 kcal/mol. The physiological implications of this instability are discussed.

Liquid pasteurization of an immunoglobulin preparation without stabilizer: effects on its biological and biochemical properties

Intravenous immunoglobulins (IVIg) purified by cold ethanol fractionation have a very good safety record with regard to the transmission of many viruses. However, a few cases of non-A-non-B hepatitis have been described after intravenous injection of some immunoglobulin preparations. To ensure even higher safety for our IVIg, an additional virus inactivation step, based on pasteurization, was developed. The heating of aqueous IVIg was performed without stabilizer, and at a very low salt concentration (< 1 mM) at acidic pH. No generation of polymer was detected after pasteurization and a significant decrease in the proportion of dimers was observed. Analysis of the secondary structure by circular dichroism showed a very slight change in the secondary structure. The biological properties of the Fc region as well as the Fab region were not affected by the pasteurization. Our method has several advantages: (1) improvement of viral safety; (2) there is no need to add stabilizer which may stabilize viral particles, and (3) the absence of any hypotensive effect and low anticomplementary activity indicates a good clinical tolerance of IgG preparation.

Is the continuity of the domains required for the correct folding of a two-domain protein?

The role of domains in protein folding has been widely studied and discussed. Nevertheless, it is not clear whether the continuity of the domains in a protein is an essential requirement in determining the folding pathway. Previous studies have shown that the isolated structural domains of the two-domain monomeric enzyme, yeast phosphoglycerate kinase (yPGK), are able to fold independently into a quasinative structure, but they neither reassociate nor generate a functional enzyme [Minard, P., Hall, L., Betton, J. M., Missiakas, D., & Yon, J. M. (1989) Protein Eng. 3, 55-60; Fairbrother, W. J., Bowen, D., Hall, L., Williams, R. J. P. (1989) Eur. J. Biochem. 184, 617-625; Missiakas, D., Betton, J. M., Minard, P., & Yon, J. M. (1990) Biochemistry 29, 8683-8689]. In the present work, two circularly permuted variants of the yPGK gene were constructed. The natural adjacent chain termini were directly connected and the new extremities were created within the N-domain (at residues 71 and 72) or the C-domain (at residues 291 and 292), respectively. These two proteins were overexpressed and purified. They exhibit 14% and 23% of the wild-type enzyme activity, respectively. The two mutants fold in a compact conformation with slight changes in the secondary and tertiary structure probably related to the presence of a heterogeneous population of molecules. The unfolding studies reveal a large decrease in stability. From the present data it appears that, although the circular permutations induce some perturbations in the structure and stability of the protein, the continuity of the domains is not required for the protein to reach a native-like and functional structure.

Cold denaturation of yeast phosphoglycerate kinase: which domain is more stable?

Under destabilising conditions both heat and cold denaturation of yeast phosphoglycerate kinase (PGK) can be observed. According to previous interpretation of experimental data and theoretical calculations, the C-terminal domain should be more stable than the N-terminal domain at all temperatures. We report on thermal unfolding experiments with PGK and its isolated domains, which give rise to a revision of this view. While the C-terminal domain is indeed the more stable one on heating, it reveals lower stability in the cold. These findings are of importance, because PGK has been frequently used as a model for protein folding and mutual domain interactions.

Role of the C-terminal helix in the folding and stability of yeast phosphoglycerate kinase

In order to determine the role of the C-terminal helix in the folding and stability of yeast phosphoglycerate kinase, a mutant deleted of the 12 C-terminal residues (PGK delta 404-415) was constructed. This mutant folds in a conformation very similar to that of the wild-type protein, but exhibits a very low activity (0.1% of that of the wild-type enzyme). The main structural effect of the deletion of the C-terminal helix is an increase in flexibility of the whole protein and a decrease in stability by about 5 kcal/mol. The structural properties of the truncated protein are very similar, at least qualitatively, to those in the isolated domains. The accessibility of the thiol group of Cys 97 is identical to that in the isolated N-domain. The large solvent effect on the tryptophan fluorescence in the native protein at very low concentration of denaturant reveals an increase of flexibility of the C-domain, similar to that observed on the isolated C-domain. NMR measurements show that the pH dependence of His C2H and C4H chemical shifts in the truncated protein perfectly matches those of the isolated domains. The addition of the missing peptide provokes a 40-fold increase in enzyme activity at saturation. A dissociation constant of 80 microM was determined. This peptide, which displays a random structure in solution, folds in a helical structure in the region 405-410 as assessed by TRNOESY. All these results show that the C-terminal part of yeast phosphoglycerate kinase is not necessary for most of the initial folding steps but acts to lock the C-domain on the N-domain, thus ensuring the expression of full enzyme activity. Without this sequence, the protein has the sum of the properties of the two isolated domains.

Transferred nuclear Overhauser effect study of the C-terminal helix of yeast phosphoglycerate kinase: NMR solution structure of the C-terminal bound peptide

Two-dimensional 1H nuclear magnetic resonance spectroscopy is used to determine the structure of the C-terminal complementary peptide (404-415) bound to a mutant phosphoglycerate kinase (1-403). Conformational changes in the peptide induced by the formation of the peptide-protein complex are followed by transferred nuclear Overhauser effect spectroscopy. Measurement of transferred NOEs and molecular modeling reveal an alpha-helix fold in the 405-409 region. This fold is in good agreement with the corresponding helix XIV of the crystallographic structure of wild-type PGK (Watson et al., 1982). The role of the alpha-helix from the C-terminal peptide in the recovery of catalytic activity in the mutant PGK is discussed.

Evidence for residual structures in an unfolded form of yeast phosphoglycerate kinase

The unfolding-refolding transition of phosphoglycerate kinase followed by steady-state fluorescence has clearly shown the existence of a hyperfluorescent form [Missiakas et al. (1990) Biochemistry 29, 8683-8689]. In order to determine the contribution of each of the two tryptophans to the fluorescence properties of the enzyme in the equilibrium transition and to characterize the hyperfluorescent form, two single tryptophan mutants in which tryptophans 308 and 333 were replaced by a tyrosine and a phenylalanine, respectively, were constructed. Neither the catalytic nor the physicochemical properties of the enzyme are significantly altered by these mutations. The unfolding-refolding transitions were studied using circular dichroism and tryptophan fluorescence emission. Both tryptophans contribute to the hyperfluorescence observed in the first transition. For guanidine hydrochloride concentrations higher than 0.9 M, it clearly appears that the second transition results from a further unfolding. It is accompanied by a decrease in fluorescence intensity and a 5 mm red shift of the maximum emission wavelength. When the unfolding is induced by urea, the end of the transition corresponds to the hyperfluorescent state. Further addition of guanidine hydrochloride induces complete unfolding. These results suggest the presence of residual microstructures around tryptophan 308 and tryptophan 333 in the hyperfluorescent state. The characterization of these clusters and their contribution as starting structures in the folding process are now under investigation.

How random is a highly denatured protein?

There has been renewed interest in determining the physicochemical properties of denatured states of proteins. In many denatured states there is evidence for the existence of nonrandom configurational distributions. Here we examine the small-angle neutron scattering profile of yeast phosphoglycerate kinase in the native state and in highly denaturing conditions. We show that the denatured protein scattering profile can be interpreted using a model developed for synthetic polymers in which the chain behaves as a random coil in a good solvent, i.e. with excluded volume interactions. The implications of this result for our appreciation of the protein folding process are discussed.

Configurational distribution of denatured phosphoglycerate kinase

Physiochemical characterization of the denatured states of proteins is important for a complete understanding of the factors stabilizing their folded conformations. Using a combination of small angle neutron scattering (SANS), statistical mechanical modelling and molecular mechanics calculations, we examine the configurational distribution of phosphoglycerate kinase denatured in 4 M guanidine hydrochloride solution. The denaturing of the protein produces a clear change in the form of the SANS profile and a large increase of the radius of gyration. In the statistical mechanical model, the region of contrast neutron scattering density associated with the protein is pictured as a chain of freely jointed spheres. The model is fitted to the SANS data for the denatured protein. It is found that a model with a small number of spheres cannot account for the higher resolution scattering, indicating an absence of detectable structuration; a good fit is found with 100 spheres of 8.5 A radius. Single configurations of the fitted chain of spheres are used as low-resolution bounds for model-building and molecular mechanics calculations to obtain plausible atomic-detail models of the denatured chain.

Structure and functional complementation of engineered fragments from yeast phosphoglycerate kinase

Previous studies have shown that, although the isolated structural domains of yeast phosphoglycerate kinase recover a quasi-native structure in vitro as well as in vivo, they do not reassociate nor generate a functional enzyme. The aim of this work was first to study the folding of complementary fragments different from structural domains and second to determine the requirements for their reassociation and functional complementation. The method used for producing rigorously defined fragments consists of the introduction of a unique cysteinyl residue in the protein followed by a specific cleavage by 5'5'-dithiobis(2-nitrobenzoate)/potassium cyanide at this residue. Two pairs of complementary fragments were thus obtained, 1-96/97-415 and 1-248/249-415. The structure and stabilities of the different fragments were studied. The short fragments, i.e. 1-96 and 249-415 were found to contain some secondary structure, but to have a low stability. Each large fragment has a high structural content and a stability close to that of the corresponding domain. In contrast to that observed with the isolated domains, a weak but significant complementation was observed for the two pairs of fragments; the pair of fragments 1-248/249-415 recovered 8% of the activity of the native enzyme upon complementation. An independent refolding of the complementary fragments before reassociation decreased the yield of complementation for the pair of fragments 1-96/97-415, but did not affect the complementation for the other pair (1-248/249-415). From the present data and previous work on the isolated domains, it appears that the correct folding of the isolated fragments is not a prerequisite for their complementation.

Characterization of an intermediate in the folding pathway of phosphoglycerate kinase: chemical reactivity of genetically introduced cysteinyl residues during the folding process

The unfolding-refolding kinetics of yeast phosphoglycerate kinase were studied using the chemical reactivity of genetically introduced cysteinyl residues as conformational probes and far-ultraviolet circular dichroism. A unique internal cysteinyl residue was introduced in several mutants at selected positions in the N- and C-domains. The cysteinyl residues were at positions 97 (the unique cysteinyl residue of the wild-type enzyme), 183 in the N-domain, 285 and 324 in the C-domain. A similar strategy has been used to study the unfolding-refolding transition under equilibrium conditions [Ballery et al. (1990) Protein Eng. 3, 199-204]. Except for the mutant C97A,A183C, whose cysteinyl residue is located at the domain interface, three labeling phases were observed during the refolding process, indicating the presence of three species, the unfolded, intermediate, and folded proteins. The comparison of the data obtained following the accessibility of the thiol group to 5,5'-dithiobis(2-nitrobenzoate) and ellipticity at 218 nm indicated that all mutants have the same folding pathway and allowed us to characterize the intermediate. In this species, each domain appeared to have a high content of secondary structure but a flexible tertiary structure; this intermediate, which had the characteristics of a molten globule, remained in fluctuating equilibrium with a widely unfolded form. The same folding intermediate was detected for mutant C97A,A183C; however, the cysteinyl residue being totally accessible to the reagent, it is likely that in this intermediate the interdomain interactions are not established. Domain pairing and formation of the native tertiary structure occur simultaneously in the slow phase of refolding. The validity and limitations of the methodology are discussed.

First determination of the secondary structure of purified factor VIII light chain

The first analysis of the secondary structure of human factor VIII light chain was performed by c.d. spectroscopy. The purification process described in this paper allowed us to obtain the large amounts of purified factor VIII light chains required for c.d. experiments. Since this 80 kDa protein is non-covalently associated with a heavy chain to form the active molecule, isolated factor VIII light chains were obtained after immunoadsorption and dissociation of the immobilized active complexes by EDTA. Furthermore, factor VIII light chains were discriminated from the residual active complexes and the free heavy chains by a final ion-exchange-chromatography step. This f.p.l.c. analysis showed that factor VIII light chains were less electronegative than the active complexes. The results of conformational analysis by c.d. show that the protein possesses a high degree of regular secondary structure (58%) with approx. 22% of alpha-helix and 36% of beta-strand structures. The protein was completely unfolded by 3 M-guanidine hydrochloride. The results obtained from the analysis of c.d. spectra were compared with those predicted from three different statistical methods based on amino-acid sequence. The secondary structure information obtained from these methods was in good agreement with the c.d. results. These results were comparable with the secondary structure prediction of ceruloplasmin, a protein known to show sequence identity to factor VIII.

Comparison of muscle phosphofructokinase from euthermic and hibernating Jaculus orientalis. Purification and determination of the quaternary structure

1. The structural properties of skeletal muscle phosphofructokinase from euthermic and hibernating jerboa were compared. 2. The enzyme was purified by a rapid procedure; suspended in ammonium sulfate in the presence of ATP, it was found to be stable for three weeks. 3. A specific activity of 76 U/mg and at most 65 U/mg was obtained for the enzyme from the euthermic and hibernating jerboa, respectively. 4. The molecular weight was estimated to be 320 kDa for the oligomer and 80 kDa for the subunit. 5. A unique alanine residue was found at the C-terminal end, suggesting that the enzyme is a tetramer made of four identical subunits. 6. The tetrameric structure of phosphofructokinase was confirmed by using crosslinking with disuccinimidyl esters. 7. The kinetics of formation of the different crosslinked species were found to be in agreement with a model of the tetramer corresponding to a dihedral symmetry with isologuous contacts between protomers. 8. The same molecular characteristics and immunochemical properties were found for the enzyme extracted from the euthermic and hibernating animals.

Conformational changes in yeast phosphoglycerate kinase upon ligand binding: fluorescence of a linked probe and chemical reactivity of genetically introduced cysteinyl residues

The effects of ligands on the conformation of yeast phosphoglycerate kinase were explored by introducing cysteinyl residues at different positions in the molecule by site-directed mutagenesis. Thus several mutants were constructed, each containing a unique cysteinyl residue. Neither the conformation nor the enzyme activity was affected by the substitutions. The reactivity of the thiol groups and the fluorescence of N-acetyl-N'-(5-sulfo-1-naphthyl)ethylene-diamine covalently linked to these thiols were used to monitor the conformational changes induced upon ligand binding. It was found that the observed changes mainly involve the part of the protein located in the cleft, particularly the environment of residues 35 and 183. No alteration was observed on the external side of the protein. Only 3-Phosphoglycerate induced these conformational changes. However, when the fluorescent probe was attached to residue 377, the binding of the two substrates was required to induce a modification in the fluorescence of the probe. These results indicate that the substrates separately or together induce discrete molecular motions in phosphoglycerate kinase.

Flexibility and folding of phosphoglycerate kinase

Flexibility and folding of phosphoglycerate kinase, a two-domain monomeric enzyme, have been studied using a wide variety of methods including theoretical approaches. Mutants of yeast phosphoglycerate kinase have been prepared in order to introduce cysteinyl residues as local probes throughout the molecule without perturbating significantly the structural or the functional properties of the enzyme. The apparent reactivity of a unique cysteine in each mutant has been used to study the flexibility of PGK. The regions of larger mobility have been found around residue 183 on segment beta F in the N-domain and residue 376 on helix XII in the C-domain. These regions are also parts of the molecule which unfold first. Ligand binding induces conformational motions in the molecule, especially in the regions located in the cleft. Moreover, the results obtained by introducing a fluorescent probe covalently linked to a cysteine are in agreement with the helix scissor motion of helices 7 and 14 assumed by Blake to direct the hinge bending motion of the domains during the catalytic cycle. The folding process of both horse muscle and yeast phosphoglycerate kinases involves intermediates. These intermediates are more stable in the horse muscle than in the yeast enzyme. In both enzymes, domains behave as structural modules capable of folding and stabilizing independently, but in the horse muscle enzyme the C-domain is more stable and refolds prior to the N-domain, contrary to that which has been observed in the yeast enzyme. A direct demonstration of the independence of domains in yeast phosphoglycerate kinase has been provided following the obtention of separated domains by site-directed mutagenesis. These domains have a native-like structure and refold spontaneously after denaturation by guanidine hydrochloride.

The effects of ligands on the conformation of phosphoglycerate kinase: fluorescence anisotropy decay and theoretical interpretation

Horse muscle phosphoglycerate kinase (PGK) is a monomer folded into two widely distant domains. In the glycolytic pathway, this enzyme catalyzes the first reaction that produces ATP. It was suggested, by analogy with yeast hexokinase, that a hinge-bending motion may be induced by the binding of specific substrates to the protein. To analyze such a motion, or any structural changes induced by ligand binding, fluorescence anisotropy decay of tryptophan residues in free and liganded PGK was studied. At 293 K, for the free protein and the binary complex with 3-phosphoglycerate, a single correlation time of 26 ns was observed, corresponding to the rotation of the overall protein, whereas upon addition of MgADP, this correlation time decreased to 10 ns. Such a decrease cannot be merely due to a change of the protein's shape and volume. To explain this, it was suggested that the fluorescence anisotropy decay of the PGK-MgADP complex corresponded to the rotation of the only buried tryptophan (Trp 335). The rotational paths of this tryptophan, in the presence and absence of the nucleotide, were established by potential energy minimization calculations. The results indicated that MgADP induces a displacement of helix alpha-13 that decreases the rotational energy barrier of Trp 335 from 16 kcal/mol in the free protein to 8 kcal/mol in the complex.

Introduction of internal cysteines as conformational probes in yeast phosphoglycerate kinase

Several mutants of yeast phosphoglycerate kinase, each containing only one internal cysteine residue, were constructed from a single mutant devoid of cysteine. These cysteines were introduced as local conformational probes in selected buried positions. The enzyme activity, conformational characteristics and stability indicated that the mutations introduced only small perturbations in the molecule. The folding-unfolding process mediated by guanidine hydrochloride under equilibrium conditions was studied by following the variations in ellipticity and the reactivity of the cysteine residue towards 5,5'-dithiobis(nitrobenzoate). The process was found to be reversible except for mutant C97A, V49C, suggesting that this region located in helix I might be crucial in determining an intermediate on the folding pathway. The transitions obtained by the two signals did not coincide, indicating that the local structures, in several parts inside the molecule, are more sensitive to the denaturant than the overall conformation.

Regulation of the skeletal muscle metabolism during hibernation of Jaculus orientalis

1. The glycolytic flow in the skeletal muscle was considerably depressed during hibernation of Jaculus orientalis. 2. Although the ATP content was not modified, the ATP/AMP ratio was twice as large than under homeothermic conditions. 3. Furthermore, the hexose phosphates were markedly depressed. 4. The total activities of the key enzymes, hexokinase, phosphofructokinase and pyruvate kinase, which are regulated through the adenylates, decreased. 5. Under in vivo conditions, taking into account the small amount of fructose-6-phosphate and the ATP/AMP ratio, it is likely that phosphofructokinase was totally inhibited, explaining the undetectable amount of fructose 1.6 bisphosphate.

Study of the fast-reacting cysteines in phosphoglycerate kinase using chemical modification and site-directed mutagenesis

Horse muscle phosphoglycerate kinase, like other mammalian phosphoglycerate kinases, contains seven cysteine residues of which two react rapidly with 5,5'-dithio-bis(2-nitrobenzoate) (Nbs2) following second-order kinetics (k = 640 M-1.s-1). Selective cyanylation of the fast-reacting cysteines, followed by chemical cleavage and subsequent sodium dodecyl sulfate/polyacrylamide gel electrophoresis analysis of the resulting polypeptides, suggested that these cysteines are at positions 378 and 379. Cysteine residues were introduced into yeast phosphoglycerate kinase by site-directed mutagenesis. Mutant enzymes, each containing only one cysteine residue at position 364, 376, or 377, were constructed from a mutant devoid of cysteine (Cys97----Ala). In the last two mutants, the cysteines were at positions corresponding to Cys378 and Cys379, respectively, in the horse muscle enzyme. The chemical reactivity of the cysteine groups in these latter two yeast mutant enzymes was similar to that of the fast-reacting cysteines in the horse muscle enzyme. Furthermore, they were similarly modified upon substrate binding. All these data demonstrate unambiguously that the fast-reacting cysteines in the horse muscle enzyme are Cys378 and Cys379.

Detection of intermediates in the unfolding transition of phosphoglycerate kinase using limited proteolysis

The accessibility of peptide bonds to cleavage by Staphylococcus aureus V8 protease bound on a Sepharose matrix was used as a conformational probe in the study of the unfolding-folding transition of phosphoglycerate kinase induced by guanidine hydrochloride. It was shown that the protein is resistant to proteolysis below a denaturant concentration of 0.4 M. The transition curve, determined by susceptibility toward proteolysis, was similar to that obtained following the enzyme activity [Betton et al. (1984) Biochemistry 23, 6654-6661]. Proteolysis under conditions where the folding intermediates are more populated, i.e., 0.7 M Gdn.HCl, gave two major fragments of Mr 25K and 11K, respectively. The 25K polypeptide fragment was identified as the carboxy-terminal domain. Its conformation was similar to that of a folding intermediate trapped at a critical concentration of denaturant, and in this form, it was not able to bind nucleotide substrates [Mitraki et al. (1987) Eur. J. Biochem. 163, 29-34]. From the present data and those previously reported, we concluded that the intermediate detected on the folding pathway of phosphoglycerate kinase has a partially folded carboxy-terminal domain and an unfolded amino-terminal domain.

Conformational modification of muscle phosphofructokinase from Jaculus orientalis upon ligand binding

Phosphofructokinase from Jaculus orientalis muscle is an allosteric enzyme regulated by substrates and nucleotide effectors. The conformational modifications upon ligand binding were probed by UV difference spectra and reactivities of thiol groups towards dithiobisnitrobenzoate and N-ethylmaleimide. The binding of Fru-6-P induced significant perturbations in the environment of the aromatic residues and buried the most reactive on the three accessible cysteines per protomer. The same effect on thiol reactivity was observed upon binding of the activator AMP. Various perturbations of both difference spectra and thiol reactivity were detected in the presence of either Mg-ATP, an allosteric inhibitor, or Mg-ITP which is not an effector.

Survey of the folding pathway of a two-domain protein phosphoglycerate kinase

The role of structural domains as folding units in the folding process which generates an active enzyme, is considered through several studies on phosphoglycerate kinase, a two-domain enzyme which catalyzes the first step of ATP production in glycolysis. The folding pathway was found to be a complex multi-step process, the C-terminal domain being more stable folding first. Inactive species originating from an intermediate in the folding pathway have been identified. Isolated domains recently obtained using genetic engineering are under investigation in our laboratory; this might probably allow to understand the way by which the N-terminal domain reaches its final native conformation and interacts with the other domain.

The effect of phosphate on the unfolding-refolding of phosphoglycerate kinase induced by guanidine hydrochloride

Phosphate ions were found to stabilize the native structure of phosphoglycerate kinase without modifying the folding pathway. The transition curves obtained from different signals: enzyme activity, ellipticity at 220 nm and fluorescence intensity at 336 nm (excitation at 292 nm) are shifted to smaller guanidine hydrochloride cm values in the absence of phosphate. The kinetic characteristics are qualitatively similar, unfolding rate constants being slightly smaller in the presence of phosphate. The mechanism by which the native structure of phosphoglycerate kinase is stabilized by phosphate probably occurs upon specific phosphate binding to the nucleotide beta- or gamma-phosphate binding site of nucleotides.

Quasi-irreversibility in the unfolding-refolding transition of phosphoglycerate kinase induced by guanidine hydrochloride

The reversibility of the unfolding-refolding transition of horse muscle phosphoglycerate kinase, induced by guanidine hydrochloride (Gdn X HCl), was studied using the regain of enzyme activity as a probe of the native structure. An irreversibility in the reactivation process was detected when the protein was incubated in a critical concentration of denaturant (0.7 +/- 0.1 M Gdn X HCl). This apparent irreversibility was observed for the unfolding process (N----D) as well as for the refolding process (D----N). The formation of the trough followed biphasic kinetics at 23 degrees C, the first phase obeying a first-order reaction corresponded to an isomerization of an intermediate; the second phase, protein-concentration-dependent, was suppressed by lowering the temperature to 4 degrees C. The structural properties of the inactive species were studied; all the beta structures were recovered, but about 29% of the helical structures remained unfolded, and two SH groups were buried. Simulated kinetics were compared with the experimental results and were used to extend the minimum folding scheme previously proposed from equilibrium and kinetic studies [Betton et al. (1984) Biochemistry 23, 6654-6661; Betton et al. (1985) Biochemistry 24, 4570-4577]. The intermediates trapped under these conditions were structured but devoid of catalytic activity. Taking into account the structural properties of these species, the nature of the interactions involved in their formation and stabilization is discussed.

Kinetic studies of the unfolding-refolding of horse muscle phosphoglycerate kinase induced by guanidine hydrochloride

The kinetics of the unfolding and refolding of horse muscle phosphoglycerate kinase were studied with three different signals: fluorescence emission intensity at 336 nm (excitation at 292 nm), ellipticity at 220 nm, and enzyme activity. The results corroborate the conclusion on the existence of intermediates in the folding pathway obtained from equilibrium studies. Kinetic studies showed at least two phases of refolding, as revealed by fluorescence as well as by circular dichroism measurements. During the fast phase, an intermediate was formed with a fluorescence intensity higher than that of the native protein, but devoid of enzyme activity. The fluorescence emission spectrum of this intermediate was determined. Only the slow phase was detected for the unfolding process; it was not attributable to proline isomerization. Several models were assumed, and simulated kinetics derived from these models were compared with the experimental results. A plausible one accounting for most of the data is proposed.