beta-Lactamase binds to GroEL in a conformation highly protected against hydrogen/deuterium exchange

Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry

Fragmentation of intact proteins in the gas phase is influenced by amino acid composition, the mass and charge of precursor ions, higher order structure, and the dissociation technique used. The likelihood of fragmentation occurring between a pair of residues is referred to as the fragmentation propensity and is calculated by dividing the total number of assigned fragmentation events by the total number of possible fragmentation events for each residue pair. Here, we describe general fragmentation propensities when performing top-down mass spectrometry (TDMS) using denaturing or native electrospray ionization. A total of 5311 matched fragmentation sites were collected for 131 proteoforms that were analyzed over 165 experiments using native top-down mass spectrometry (nTDMS). These data were used to determine the fragmentation propensities for 399 residue pairs. In comparison to denatured top-down mass spectrometry (dTDMS), the fragmentation pathways occurring either N-terminal to proline or C-terminal to aspartic acid were even more enhanced in nTDMS compared with other residues. More generally, 257/399 (64%) of the fragmentation propensities were significantly altered (P ≤ 0.05) when using nTDMS compared with dTDMS, and of these, 123 were altered by 2-fold or greater. The most notable enhancements of fragmentation propensities for TDMS in native versus denatured mode occurred (1) C-terminal to aspartic acid, (2) between phenylalanine and tryptophan (F|W), and (3) between tryptophan and alanine (W|A). The fragmentation propensities presented here will be of high value in the development of tailored scoring systems used in nTDMS of both intact proteins and protein complexes. Graphical Abstract ᅟ.

Chaperones GroEL/GroES accelerate the refolding of a multidomain protein through modulating on-pathway intermediates

Despite a vast amount information on the interplay of GroEL, GroES, and ATP in chaperone-assisted folding, the molecular details on the conformational dynamics of folding polypeptide during its GroEL/GroES-assisted folding cycle is quite limited. Practically no such studies have been reported to date on large proteins, which often have difficulty folding in vitro. The effect of the GroEL/GroES chaperonin system on the folding pathway of an 82-kDa slow folding protein, malate synthase G (MSG), was investigated. GroEL bound to the burst phase intermediate of MSG and accelerated the slowest kinetic phase associated with the formation of native topology in the spontaneous folding pathway. GroEL slowly induced conformational changes on the bound burst phase intermediate, which was then transformed into a more folding-compatible form. Subsequent addition of ATP or GroES/ATP to the GroEL-MSG complex led to the formation of the native state via a compact intermediate with the rate several times faster than that of spontaneous refolding. The presence of GroES doubled the ATP-dependent reactivation rate of bound MSG by preventing multiple cycles of its GroEL binding and release. Because GroES bound to the trans side of GroEL-MSG complex, it may be anticipated that confinement of the substrate underneath the co-chaperone is not required for accelerating the rate in the assisted folding pathway. The potential role of GroEL/GroES in assisted folding is most likely to modulate the conformation of MSG intermediates that can fold faster and thereby eliminate the possibility of partial aggregation caused by the slow folding intermediates during its spontaneous refolding pathway.

Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding

The chaperonin ring assembly GroEL provides kinetic assistance to protein folding in the cell by binding non-native protein in the hydrophobic central cavity of an open ring and subsequently, upon binding ATP and the co-chaperonin GroES to the same ring, releasing polypeptide into a now hydrophilic encapsulated cavity where productive folding occurs in isolation. The fate of polypeptide during binding, encapsulation, and folding in the chamber has been the subject of recent experimental studies and is reviewed and considered here. We conclude that GroEL, in general, behaves passively with respect to its substrate proteins during these steps. While binding appears to be able to rescue non-native polypeptides from kinetic traps, such rescue is most likely exerted at the level of maximizing hydrophobic contact, effecting alteration of the topology of weakly structured states. Encapsulation does not appear to involve 'forced unfolding', and if anything, polypeptide topology is compacted during this step. Finally, chamber-mediated folding appears to resemble folding in solution, except that major kinetic complications of multimolecular association are prevented.

GroEL-mediated protein folding: making the impossible, possible

Protein folding is a spontaneous process that is essential for life, yet the concentrated and complex interior of a cell is an inherently hostile environment for the efficient folding of many proteins. Some proteins-constrained by sequence, topology, size, and function-simply cannot fold by themselves and are instead prone to misfolding and aggregation. This problem is so deeply entrenched that a specialized family of proteins, known as molecular chaperones, evolved to assist in protein folding. Here we examine one essential class of molecular chaperones, the large, oligomeric, and energy utilizing chaperonins or Hsp60s. The bacterial chaperonin GroEL, along with its co-chaperonin GroES, is probably the best-studied example of this family of protein-folding machine. In this review, we examine some of the general properties of proteins that do not fold well in the absence of GroEL and then consider how folding of these proteins is enhanced by GroEL and GroES. Recent experimental and theoretical studies suggest that chaperonins like GroEL and GroES employ a combination of protein isolation, unfolding, and conformational restriction to drive protein folding under conditions where it is otherwise not possible.

Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution

Nucleotide regulates the affinity of the bacterial chaperonin GroEL for protein substrates. GroEL binds protein substrates with high affinity in the absence of ATP and with low affinity in its presence. We report the crystal structure of (GroEL-KMgATP)(14) refined to 2.0 A resolution in which the ATP triphosphate moiety is directly coordinated by both K(+) and Mg(2+). Upon the binding of KMgATP, we observe previously unnoticed domain rotations and a 102 degrees rotation of the apical domain surface helix I. Two major consequences are a large lateral displacement of, and a dramatic reduction of hydrophobicity in, the apical domain surface. These results provide a basis for the nucleotide-dependent regulation of protein substrate binding and suggest a mechanism for GroEL-assisted protein folding by forced unfolding.

Identification of the interface of a large protein-protein complex using H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry

An infrared multiphoton dissociation (IRMPD) spectrum, obtained by Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS), was used to dissociate and to identify fragment ions from recombinant human interleukin-6 (IL-6; 21 KDa). The entire sequence was assigned by a single IRMPD experiment, and the observed fragment ions reflected the IL-6 secondary structure. This method was combined with H/D off-exchange to identify IL-6 and anti-human IL-6 mouse monoclonal antibody MH166 (150-kDa) binding sites in the IL-6 molecule. To facilitate the data analysis, the protein complex formation and the hydrogen exchange were performed with an immobilized antibody. Quenching of the hydrogen exchange reaction and collection of the deuterated IL-6 were performed by elution under acidic conditions to measure the mass spectrum directly. IL-6 was dissociated by using IRMPD, and the interface of IL-6 bound to anti-IL-6 antibody MH166 was determined to analyze the deuterium incorporation level of each fragment ion. Thus, two discontinuous regions, Leu 126-Lys 131 and Asp 160-Met 184, were identified as the antibody binding sites. These regions are adjacent to each other on the tertiary structures determined by NMR and X-ray analyses.

GroEL binds artificial proteins with random sequences

Chaperonin GroEL from Escherichia coli binds to the non-native states of many unrelated proteins, and GroEL-recognizable structural features have been argued. As model substrate proteins of GroEL, we used seven artificial proteins (138 approximately 141 residues), each of which has a unique but randomly chosen amino acid sequence and no propensity to fold into a certain structure. Two of them were water-soluble, and the rest were soluble in 3 m urea. The soluble ones interacted with GroEL in a manner similar to that of a natural substrate; they stimulated the ATPase cycle of GroEL and GroEL/GroES and inhibited GroEL-assisted folding of other protein. All seven artificial proteins were able to bind to GroEL. The results suggest that the secondary structure as well as the specific sequence motif of the substrate proteins are not necessary to be recognized by GroEL.

Interaction with GroEL destabilises non-amphiphilic secondary structure in a peptide

The Escherichia coli molecular chaperone GroEL can functionally interact with non-native forms of many proteins. An inherent property of non-native proteins is the exposure of hydrophobic residues and the presence of secondary structure elements. Whether GroEL unfolds or stabilises these structural elements in protein substrates as a result of binding has been the subject of extended debate in the literature. Based on our studies of model peptides of pre-formed helical structure, we conclude that the final state of a GroEL-bound substrate is dependent on the conformational flexibility of the substrate protein and the distribution of hydrophobic residues, with optimal association when these are able to present a cluster of hydrophobic residues in the binding interface.

Chaperone-percolator model: a possible molecular mechanism of Anfinsen-cage-type chaperones

Although we have a rather elaborate "working-cycle" for the 60 kDa molecular chaperones, which possess a cavity, and are called Anfinsen-cage-type chaperones to emphasize that they provide a closed, protected environment to help the folding of their substrates, our understanding of the molecular mechanism of how these chaperones help protein folding is still incomplete. The present study adds two novel elements to the mechanism of how Anfinsen-cage-type chaperones (members of the 60 kDa chaperone family) aid protein folding. It is proposed that (1) these chaperones do not generally unfold their targets, but by a multidirectional expansion preferentially loosen the tight, inner structure of the collapsed target protein; and (2) during the expansion water molecules enter the hydrophobic core of the target, this percolation being a key step in chaperone action. This study compares this chaperone-percolator model with existing explanations and suggests further experiments to test it. BioEssays 1999;21:959-965.

Disassembly of intact multiprotein complexes in the gas phase

The observation of multiprotein complexes by mass spectrometry formerly relied upon chemical cross-linking to maintain interactions. Recent technological developments have enabled the observation of intact macromolecular complexes without modification. These assemblies, with masses far in excess of those measured previously, can be examined through controlled dissociation in the mass spectrometer, revealing information about their subunit interactions and topology.

The oligomeric structure of GroEL/GroES is required for biologically significant chaperonin function in protein folding

Two models are being considered for the mechanism of chaperonin-assisted protein folding in E. coli: (i) GroEL/GroES act primarily by enclosing substrate polypeptide in a folding cage in which aggregation is prevented during folding. (ii) GroEL mediates the repetitive unfolding of misfolded polypeptides, returning them onto a productive folding track. Both models are not mutually exclusive, but studies with the polypeptide-binding domain of GroEL have suggested that unfolding is the primary mechanism, enclosure being unnecessary. Here we investigate the capacity of the isolated apical polypeptide-binding domain to functionally replace the complete GroEL/GroES system. We show that the apical domain binds aggregation-sensitive polypeptides but cannot significantly assist their refolding in vitro and fails to replace the groEL gene or to complement defects of groEL mutants in vivo. A single-ring version of GroEL cannot substitute for GroEL. These results strongly support the view that sequestration of aggregation-prone intermediates in a folding cage is an important element of the chaperonin mechanism.

Conformation of aspartate aminotransferase isozymes folding under different conditions probed by limited proteolysis

The partially homologous mitochondrial (mAAT) and cytosolic (cAAT) aspartate aminotransferase have nearly identical three-dimensional structures but differ in their folding rates in cell-free extracts and in their affinity for binding to molecular chaperones. In its native state, each isozyme is protease-resistant. Using limited proteolysis as an index of their conformational states, we have characterized these proteins (a) during the early stages of spontaneous refolding; (b) as species trapped in stable complexes with the chaperonin GroEL; or (c) as newly translated polypeptides in cell-free extracts. Treatment of the refolding proteins with trypsin generates reproducible patterns of large proteolytic fragments that are consistent with the formation of defined folding domains soon after initiating refolding. Binding to GroEL affords considerable protection to both isozymes against proteolysis. The tryptic fragments are similar in size for both isozymes, suggesting a common distribution of compact and flexible regions in their folding intermediates. cAAT synthesized in cell-free extracts becomes protease-resistant almost instantaneously, whereas trypsin digestion of the mAAT translation product produces a pattern of fragments qualitatively akin to that observed with the protein refolding in buffer. Analysis of the large tryptic peptides obtained with the GroEL-bound proteins reveals that the cleavage sites are located in analogous regions of the N-terminal portion of each isozyme. These results suggest that (a) binding to GroEL does not cause unfolding of AAT, at least to an extent detectable by proteolysis; (b) the compact folding domains identified in AAT bound to GroEL (or in mAAT fresh translation product) are already present at the early stages of refolding of the proteins in buffer alone; and (c) the two isozymes seem to bind in a similar fashion to GroEL, with the more compact C-terminal portion completely protected and the more flexible N-terminal first 100 residues still partially accessible to proteolysis.

Refolding kinetics of staphylococcal nuclease and its mutants in the presence of the chaperonin GroEL

We have analyzed the effect of the chaperonin GroEL on the refolding kinetics of staphylococcal nuclease and its three mutants by stopped-flow fluorescence measurements. It was found that a transient folding intermediate of staphylococcal nuclease was tightly bound to GroEL and refolded in the GroEL-bound state without releasing the non-native protein in solution, and the refolding rate in the GroEL-bound state was 0.01 s-1. The GroEL-affected refolding of the nuclease appears to be in decided contrast to that of apo-alpha-lactalbumin reported in our previous study, wherein alpha-lactalbumin was shown to be more weakly bound by GroEL and to refold in the free state in solution. In spite of the apparent difference between the proteins, the GroEL-affected refolding reactions of both the proteins can be represented by a common unified reaction scheme. On the basis of this scheme, the binding constant between the nuclease intermediate and GroEL was estimated to be larger than 10(9) M-1. The stoichiometry of binding of the nuclease and its mutants to GroEL was found to be two (nuclease/GroEL 14-mer). The increase in ionic strength resulted in a weakening of the interaction between the nuclease and GroEL, which was attributed to a weakening of the electrostatic attraction between the two proteins as a result of electrostatic screening by ions. Although ATP was found to accelerate the GroEL-affected refolding of the nuclease, the refolding rate was still far from the rate of the free refolding. The free refolding behavior of the nuclease and its mutants was restored in the presence of the cochaperonin GroES and ATP.

Insight into the conformation of protein folding intermediate(s) trapped by GroEL

Many aspects of the mechanism by which the GroEL/ES chaperonins mediate protein folding are still unclear, including the amount of structure present in the substrate bound to GroEL. To address this issue we have analyzed the susceptibility to limited proteolysis and to alkylation of cysteine residues of mitochondrial aspartate aminotransferase (mAAT) bound to GroEL. Several regions of the N-terminal portion of GroEL-bound mAAT are highly susceptible to proteolysis, whereas a large core of about 200 residues containing the C-terminal half of the polypeptide chain is protected in the complex. This protection does not extend to the mAAT sulfhydryl groups which in the GroEL-mAAT complex have similar reactivity as in fully unfolded mAAT. These results suggest that the mAAT species bound to GroEL represent folding intermediates with a conformation that is substantially more disorganized than that of the native state. The N-terminal half of the molecule is more flexible and lies exposed at the mouth of the central cavity of GroEL. The more compact C-terminal section of mAAT, which contains residues located at the subunit interface in the native dimer, appears to be hidden in the central cavity of GroEL. Thus, the bulk of the interactions in the GroEL.mAAT complex seems to involve residues from the more compact C-terminal section of the substrate.

Hydrogen exchange studies of protein structure

Hydrogen exchange techniques, with their residue-level specificity, exquisite sensitivity, and adaptability to many solution conditions, are becoming essential to the study of protein stability, folding and dynamics. Recent studies have elucidated the structures of intermediates formed transiently during protein folding and rare partially folded ensembles present at equilibrium. Analysis of hydrogen exchange mechanisms has revealed protein stability and kinetics at the level of individual residues.

Hydrogen exchange and protein folding

Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins. The significant increase in the number of small, model proteins that have been studied has allowed a better understanding of the structural fluctuations that lead to hydrogen exchange. Recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.

Structural aspects of GroEL function

The chaperonin GroEL and its cofactor GroES facilitate protein folding in an ATP-regulated manner. The recently solved crystal structure of the GroEL.GroES.(ADP)7 complex shows that the lining of the cavity in the polypeptide acceptor state is hydrophobic, whereas in the protein-release state it becomes hydrophilic. Other highlights of the past year include the visualization of the allosteric states of GroEL with respect to ATP using cryo-electron microscopy, and an X-ray crystallographic analysis of the interaction between the apical domain of GroEL and a peptide.

Two conformational states of beta-lactamase bound to GroEL: a biophysical characterization

Escherichia coli RTEM beta-lactamase, in which both cysteine residues which form the single disulfide bond have been mutated to alanine residues, can form stable reversible complexes with GroEL under two different sets of conditions. Starting with the GdmCl-denatured enzyme, it is bound to GroEL in a state where no protons are protected against exchange with 2H2O, as determined by electrospray ionization mass spectrometry (ESI-MS). In contrast, when native protein is destabilized at high temperature and added to GroEL, a conformation is bound with 18 protected protons after two hours of exchange. While the high-temperature complex can form both with the wild-type enzyme (with intact disulfide bond) and the Cys-Ala double mutant, only the latter protein can form a complex starting from GdmCl denatured states. Thus, two different sets of conformations of the same protein can be bound, depending both on the conditions used to form the complex and on the intrinsic stability of the intermediate recognized by GroEL, and we have characterized the properties of both complexes.

Structural and mechanistic consequences of polypeptide binding by GroEL

The remarkable ability of the chaperonin GroEL to recognise a diverse range of non-native states of proteins constitutes one of the most fascinating molecular recognition events in protein chemistry. Recent structural studies have revealed a possible model for substrate binding by GroEL and a high-resolution image of the GroEL-GroES folding machinery has provided important new insights into our understanding of the mechanism of action of this chaperonin. Studies with a variety of model substrates reveal that the binding of substrate proteins to GroEL is not just a passive event, but can result in significant changes in the structure and stability of the bound polypeptide. The potential impact of this on the mechanism of chaperonin-assisted folding is not fully understood, but provides exciting scope for further experiment.

Multiple cycles of global unfolding of GroEL-bound cyclophilin A evidenced by NMR

GroE, the chaperonin system of Escherichia coli, prevents the aggregation of partially folded or misfolded proteins by complexing them in a form competent for subsequent folding to the native state. We examined the exchange of amide protons of cyclophilin A (CypA) interacting with GroEL, using NMR spectroscopy. We have applied labeling pulses in H2O to the deuterated GroEL-CypA-complex. When ATP and GroES were added after the labeling pulse, refolding of CypA could be accelerated to rates comparable to the amide proton exchange. This allowed the calculation of protection factors (PF) for the backbone amide protons in the GroEL-bound substrate protein. A set of highly protected protons in the native state (PF 10(5) to 10(7)) was observed to be much less protected (PF 10(2) to 10(4)) in complex with GroEL and, in contrast to the native structure, the protection factors were found to be quite uniform along the sequence suggesting that CypA with native-like structure undergoes multiple cycles of unfolding while bound to GroEL, which are faster than unfolding in free solution. Because of the small sequence dependence of the protection factors, unfolding must be global, and in this way the chaperone appears to resolve off-pathway intermediates and to support protein folding by annealing. Although in the complex with GroEL native-like states still predominate over globally unfolded states, this equilibrium is shifted 10(2) to 10(4)-fold toward the unfolded state when compared to CypA in free solution. Repeated global unfolding may be a key step in achieving a high yield of correctly folded proteins.

The chaperonin cycle cannot substitute for prolyl isomerase activity, but GroEL alone promotes productive folding of a cyclophilin-sensitive substrate to a cyclophilin-resistant form

The chaperonin GroEL and the peptidyl-prolyl cis-trans isomerase cyclophilin are major representatives of two distinct cellular systems that help proteins to adopt their native three-dimensional structure: molecular chaperones and folding catalysts. Little is known about whether and how these proteins cooperate in protein folding. In this study, we have examined the action of GroEL and cyclophilin on a substrate protein in two distinct prolyl isomerization states. Our results indicate that: (i) GroEL binds the same substrate in different prolyl isomerization states. (ii) GroEL-ES does not promote prolyl isomerizations, but even retards isomerizations. (iii) Cyclophilin cannot promote the correct isomerization of prolyl bonds of a GroEL-bound substrate, but acts sequentially after release of the substrate from GroEL. (iv) A denatured substrate with all-native prolyl bonds is delayed in folding by cyclophilin due to isomerization to non-native prolyl bonds; a substrate that has proceeded in folding beyond a stage where it can be bound by GroEL is still sensitive to cyclophilin. (v) If a denatured cyclophilin-sensitive substrate is first bound to GroEL, however, productive folding to a cyclophilin-resistant form can be promoted, even without GroES. We conclude that GroEL and cyclophilin act sequentially and exert complementary functions in protein folding.

How GroES regulates binding of nonnative protein to GroEL

At present, it is still enigmatic how the reaction cycle by which the Escherichia coli GroE chaperones mediate protein folding in the cell is coordinated with respect to the sequential order of binding and release of GroES, nucleotide, and nonnative protein. It is generally assumed that the asymmetric GroEL.GroES complex is the acceptor state for substrate protein. Nevertheless, this species is poorly understood in its binding characteristics for nucleotide and nonnative protein. We show here that this species has a high affinity binding site for nonnative protein. In addition to this, binding of nucleotide to one GroEL ring is strongly favored by GroES binding to the other ring. However, the slow rate of release of substrate protein from the unproductive trans-position kinetically favors the binding of a second GroES, thereby forming a symmetric GroEL14.(GroES7)2 complex and simultaneously ensuring that substrate protein is sequestered in a position underneath GroES. Our results demonstrate that the intrinsic binding characteristics of the trans-bullet complex determine the sequence of events during the reaction cycle.

Protein folding: how the mechanism of GroEL action is defined by kinetics

We propose a mechanism for the role of the bacterial chaperonin GroEL in folding proteins. The principal assumptions of the mechanism are (i) that many unfolded proteins bind to GroEL because GroEL preferentially binds small unstructured regions of the substrate protein, (ii) that substrate protein within the cavity of GroEL folds by the same kinetic mechanism and rate processes as in bulk solution, (iii) that stable or transient complexes with GroEL during the folding process are defined by a kinetic partitioning between formation and dissociation of the complex and the rate of folding and unfolding of the protein, and (iv) that dissociation from the complex in early stages of folding may lead to aggregation but dissociation at a late stage leads to correct folding. The experimental conditions for refolding may play a role in defining the function of GroEL in the folding pathway. We propose that the role of GroES and MgATP, either binding or hydrolysis, is to regulate the association and dissociation processes rather than affecting the rate of folding.

GroEL-mediated folding of structurally homologous dihydrofolate reductases

Using stopped-flow fluorescence techniques, we have examined both the refolding and unfolding reactions of four structurally homologous dihydrofolate reductases (murine DHFR, wild-type E. coli DHFR, and two E. coli DHFR mutants) in the presence and absence of the molecular chaperonin GroEL. We show that GroEL binds the unfolded conformation of each DHFR with second order rate constants greater than 3 x 10(7) M(-1)s(-1) at 22 degrees C. Once bound to GroEL, the proteins refold with rate constants similar to those for folding in the absence of GroEL. The overall rate of formation of native enzyme is decreased by the stability of the complex between GroEL and the last folding intermediate. For wild-type E. coli DHFR, complex formation is transient while for the others, a stable complex is formed. The stable complexes are the same regardless of whether they are formed from the unfolded or folded DHFR. When complex formation is initiated from the native conformation, GroEL binds to a pre-existing non-native conformation, presumably a late folding intermediate, rather than to the native state, thus shifting the conformational equilibrium toward the non-native species by mass action. The model presented here for the interaction of these four proteins with GroEL quantitatively describes the difference between the formation of a transient complex and a stable complex as defined by the rate constants for release and rebinding to GroEL relative to the rate constant for the last folding step. Due to this kinetic partitioning, three different mechanisms can be proposed for the formation of stable complexes between GroEL and either murine DHFR or the two E. coli DHFR mutants. These data show that productive folding of GroEL-bound proteins can occur in the absence of nucleotides or the co-chaperonin GroES and suggest that transient complex formation may be the functional role of GroEL under normal conditions.

GroEL-mediated protein folding

I. Architecture of GroEL and GroES and the reaction pathway A. Architecture of the chaperonins B. Reaction pathway of GroEL-GroES-mediated folding II. Polypeptide binding A. A parallel network of chaperones binding polypeptides in vivo B. Polypeptide binding in vitro 1. Role of hydrophobicity in recognition 2. Homologous proteins with differing recognition-differences in primary structure versus effects on folding pathway 3. Conformations recognized by GroEL a. Refolding studies b. Binding of metastable intermediates c. Conformations while stably bound at GroEL 4. Binding constants and rates of association 5. Conformational changes in the substrate protein associated with binding by GroEL a. Observations b. Kinetic versus thermodynamic action of GroEL in mediating unfolding c. Crossing the energy landscape in the presence of GroEL III. ATP binding and hydrolysis-driving the reaction cycle IV. GroEL-GroES-polypeptide ternary complexes-the folding-active cis complex A. Cis and trans ternary complexes B. Symmetric complexes C. The folding-active intermediate of a chaperonin reaction-cis ternary complex D. The role of the cis space in the folding reaction E. Folding governed by a "timer" mechanism F. Release of nonnative polypeptides during the GroEL-GroES reaction G. Release of both native and nonnative forms under physiologic conditions H. A role for ATP binding, as well as hydrolysis, in the folding cycle V. Concluding remarks.

Native-like structure of a protein-folding intermediate bound to the chaperonin GroEL

The chaperonin GroEL binds nonnative proteins in its central channel through hydrophobic interactions and initiates productive folding in this space underneath bound co-chaperone, GroES, in the presence of ATP. The questions of where along the folding pathway a protein is recognized by GroEL, and how much structure is present in a bound substrate have remained subjects of discussion, with some experiments suggesting that bound forms are fully unfolded and others suggesting that bound species are partially structured. Here we have studied a substrate protein, human dihydrofolate reductase (DHFR), observing in stopped-flow fluorescence experiments that it can rapidly bind to GroEL at various stages of folding. We have also analyzed the structure of the GroEL-bound protein using hydrogen-deuterium exchange and NMR spectroscopy. The pattern and magnitude of amide proton protection indicate that the central parallel beta-sheet found in native DHFR is present in a moderately stable state in GroEL-bound DHFR. Considering that the strands are derived from distant parts of the primary structure, this suggests that a native-like global topology is also present. We conclude that significant native-like structure is present in protein-folding intermediates bound to GroEL.