Hydrogen-exchange kinetics of reduced alpha-lactalbumin bound to the chaperonin GroEL

The H/D-exchange kinetics of the Escherichia coli co-chaperonin GroES studied by 2D NMR and DMSO-quenched exchange methods

We studied hydrogen/deuterium-exchange reactions of peptide amide protons of GroES using two different techniques: (1) two-dimensional (1)H-(15)N transverse-optimized NMR spectroscopy and (2) the dimethylsulfoxide-quenched hydrogen-exchange method combined with conventional (1)H-(15)N heteronuclear single quantum coherence spectroscopy. By using these techniques together with direct heteronuclear single quantum coherence experiments, we quantitatively evaluated the exchange rates for 33 out of the 94 peptide amide protons of GroES and their protection factors, and for the remaining 61 residues, we obtained the lower limits of the exchange rates. The protection factors of the most highly protected amide protons were on the order of 10(6)-10(7), and the values were comparable in magnitude to those observed in typical small globular proteins, but the number of the highly protected amide protons with a protection factor larger than 10(6) was only 10, significantly smaller than the numbers reported for the small globular proteins, indicating that significant portions of free heptameric GroES are flexible and natively unfolded. The highly protected amino acid residues with a protection factor larger than 10(5) were mainly located in three β-strands that form the hydrophobic core of GroES, while the residues in a mobile loop (residues 17-34) were not highly protected. The protection factors of the most highly protected amide protons were orders of magnitude larger than the value expected from the equilibrium unfolding parameters previously reported, strongly suggesting that the equilibrium unfolding of GroES is more complicated than a simple two-state or three-state mechanism and may involve more than a single intermediate.

Amyloidogenesis of natively unfolded proteins

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis.

Factors governing the substrate recognition by GroEL chaperone: a sequence correlation approach

The chaperonin GroEL binds to a large number of polypeptides, prevents their self-association, and mediates appropriate folding in a GroES and adenosine triphosphate-dependent manner. But how the GroEL molecule actually recognizes the polypeptide and what are the exact GroEL recognition sites in the substrates are still poorly understood. We have examined more than 50 in vivo substrates as well as well-characterized in vitro substrates, for their binding characteristics with GroEL. While addressing the issue, we have been driven by the basic concept that GroES, being the cochaperonin of GroEL, is the best-suited substrate for GroEL, as well as by the fact that polypeptide substrate and GroES occupy the same binding sites on the GroEL apical domain. GroES interacts with GroEL through selective hydrophobic residues present on its mobile loop region, and we have considered the group of residues on the GroES mobile loop as the key element in choosing a substrate for GroEL. Considering the hydrophobic region on the GroES mobile loop as the standard, we have attempted to identify the homologous region on the peptide sequences in the proteins of our interest. Polypeptides have been judged as potential GroEL substrates on the basis of the presence of the GroES mobile loop-like hydrophobic segments in their amino acid sequences. We have observed 1 or more GroES mobile loop-like hydrophobic patches in the peptide sequence of some of the proteins of our interest, and the hydropathy index of most of these patches also seems to be approximately close to that of the standard. It has been proposed that the presence of hydrophobic patches having substantial degree of hydropathy index as compared with the standard segment is a necessary condition for a peptide sequence to be recognized by GroEL molecules. We also observed that the overall hydrophobicity is also close to 30% in these substrates, although this is not the sufficient criterion for a polypeptide to be assigned as a substrate for GroEL. We found that the binding of aconitase, alpha-lactalbumin, and murine dihydrofolate reductase to GroEL falls in line with our present model and have also predicted the exact regions of their binding to GroEL. On the basis of our GroEL substrate prediction, we have presented a model for the binding of apo form of some proteins to GroEL and the eventual formation of the holo form. Our observation also reveals that in most of the cases, the GroES mobile loop-like hydrophobic patch is present in the unstructured region of the protein molecule, specifically in the loop or beta-sheeted region. The outcome of our study would be an essential feature in identifying a potential substrate for GroEL on the basis of the presence of 1 or more GroES mobile loop-like hydrophobic segments in the amino acid sequence of those polypeptides and their location in three-dimensional space.

Conformational prerequisites for alpha-lactalbumin fibrillation

Bovine alpha-lactalbumin, a small acidic Ca(2+)-binding milk protein, formed amyloid fibrils at low pH, where it adopted the classical molten globule-like conformation. Fibrillation was accompanied by a dramatic increase in the beta-structure content and a characteristic increase in the thioflavin T fluorescence intensity. S-(Carboxymethyl)-alpha-lactalbumin, a disordered form of the protein with three out of four disulfide bridges reduced, was even more susceptible to fibrillation. Other partially folded conformations induced in the intact protein at neutral pH, either by the removal of Ca(2+) or by the binding of Zn(2+) to the Ca(2+)-protein complex, did not fibrillate, although Zn(2+)-loaded alpha-lactalbumin precipitated out of solution as amorphous aggregates. Our data suggest that the transformation of a protein into an essentially unfolded (thus, highly flexible) conformation is required for successful fibril formation, whereas more rigid (but still flexible) species may form amorphous aggregates.

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.

Secondary structure forming propensity coupled with amphiphilicity is an optimal motif in a peptide or protein for association with chaperonin 60 (GroEL)

The interactions of GroEL with six dansyl peptides were investigated by means of our previously established fluorescence binding assay [Hutchinson, J. P., Oldham, T. C., El-Thaher, T. S. H., and Miller, A. D. (1997) J. Chem. Soc., Perkin Trans. 2, 279-288]. Three peptides (AMPH series) were constructed with a hierarchy of alpha-helix-forming propensities and amphiphilic characteristics. The remaining three peptides (NON-AMPH series) were prepared with a reordered amino acid sequence designed to form peptides of differing non-amphiphilic alpha-helix-forming propensity. Of these six peptides, two (AMPH(+) and NON-AMPH(+)) were N-capped with an S-form alpha-helix-inducing template (Ro 47-1615, Hoffmann-La Roche), two (AMPH(-) and NON-AMPH(-)) were N-capped with an R-form non-inducing template (Ro 47-1614, Hoffmann-La Roche), and two (AMPH(R) and NON-AMPH(R)) were without N-cap modification. This paper describes how the known strength of interaction of an unfolded protein substrate with the molecular chaperone GroEL (K(d) micromolar to nanomolar) may be emulated with a single peptide (AMPH(+)) (apparent K(d) 5 nM) which has a high propensity to form an amphiphilic alpha-helical structure in solution. Secondary structure forming propensity is not, in and of itself, an important contributor to the strength of interaction with GroEL. However, secondary structure forming propensity coupled with amphiphilicity may be sufficient to account for most, if not all, of the interaction strength between GroEL and an unfolded peptide or protein substrate.

Identification of the binding surface on beta-lactamase for GroEL by limited proteolysis and MALDI-mass spectrometry

Escherichia coli beta-lactamase, alone or as a complex with GroEL at 48 degreesC, was partially digested with trypsin, endoproteinase Glu-C, or thermolysin. Peptides were analyzed by matrix-assisted laser desorption and ionization mass spectrometry and aligned with the known sequence. From the protease cleavage sites which become protected upon binding and those which become newly accessible, a model of the complex is proposed in which the carboxy-terminal helix has melted, two loops form the binding interface and the large beta-sheet become partially uncovered by the slight dislocation of other structural elements. This explains how hydrophobic surface on the substrate protein can become accessible while scarcely disrupting the hydrogen bond network of the native structure. An analysis of the GroEL-bound peptides bound after digestion of the beta-lactamase showed no obvious sequence motifs, indicating that binding is provided by hydrophobic patches in the three-dimensional structure.

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.

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.

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.