Isolation and characterization of the host protein groE involved in bacteriophage lambda assembly

A molecular device for the redox quality control of GroEL/ES substrates

Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these chaperonins promote folding remain unsolved. Here, we report that the bacterial Hsp60 chaperonin GroEL forms a stable, functionally relevant complex with the chaperedoxin CnoX, a protein combining a chaperone and a redox function. Binding of GroES (Hsp10 cofactor) to GroEL induces CnoX release. Cryoelectron microscopy provided crucial structural information on the GroEL-CnoX complex, showing that CnoX binds GroEL outside the substrate-binding site via a highly conserved C-terminal α-helix. Furthermore, we identified complexes in which CnoX, bound to GroEL, forms mixed disulfides with GroEL substrates, indicating that CnoX likely functions as a redox quality-control plugin for GroEL. Proteins sharing structural features with CnoX exist in eukaryotes, suggesting that Hsp60 molecular plugins have been conserved through evolution.

Heat shock proteins: Biological functions, pathological roles, and therapeutic opportunities

The heat shock proteins (HSPs) are ubiquitous and conserved protein families in both prokaryotic and eukaryotic organisms, and they maintain cellular proteostasis and protect cells from stresses. HSP protein families are classified based on their molecular weights, mainly including large HSPs, HSP90, HSP70, HSP60, HSP40, and small HSPs. They function as molecular chaperons in cells and work as an integrated network, participating in the folding of newly synthesized polypeptides, refolding metastable proteins, protein complex assembly, dissociating protein aggregate dissociation, and the degradation of misfolded proteins. In addition to their chaperone functions, they also play important roles in cell signaling transduction, cell cycle, and apoptosis regulation. Therefore, malfunction of HSPs is related with many diseases, including cancers, neurodegeneration, and other diseases. In this review, we describe the current understandings about the molecular mechanisms of the major HSP families including HSP90/HSP70/HSP60/HSP110 and small HSPs, how the HSPs keep the protein proteostasis and response to stresses, and we also discuss their roles in diseases and the recent exploration of HSP related therapy and diagnosis to modulate diseases. These research advances offer new prospects of HSPs as potential targets for therapeutic intervention.

Diversity in heat shock protein families: functional implications in virus infection with a comprehensive insight of their role in the HIV-1 life cycle

Heat shock proteins (HSPs) are a group of cellular proteins that are induced during stress conditions such as heat stress, cold shock, UV irradiation and even pathogenic insult. They are classified into families based on molecular size like HSP27, 40, 70 and 90 etc, and many of them act as cellular chaperones that regulate protein folding and determine the fate of mis-folded or unfolded proteins. Studies have also shown multiple other functions of these proteins such as in cell signalling, transcription and immune response. Deregulation of these proteins leads to devastating consequences, such as cancer, Alzheimer's disease and other life threatening diseases suggesting their potential importance in life processes. HSPs exist in multiple isoforms, and their biochemical and functional characterization still remains a subject of active investigation. In case of viral infections, several HSP isoforms have been documented to play important roles with few showing pro-viral activity whereas others seem to have an anti-viral role. Earlier studies have demonstrated that HSP40 plays a pro-viral role whereas HSP70 inhibits HIV-1 replication; however, clear isoform-specific functional roles remain to be established. A detailed functional characterization of all the HSP isoforms will uncover their role in cellular homeostasis and also may highlight some of them as potential targets for therapeutic strategies against various viral infections. In this review, we have tried to comprehend the details about cellular HSPs and their isoforms, their role in cellular physiology and their isoform-specific functions in case of virus infection with a specific focus on HIV-1 biology.

Chaperonin-assisted protein folding: a chronologue

This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.

A History of Molecular Chaperone Structures in the Protein Data Bank

Thirty years ago a class of proteins was found to prevent the aggregation of Rubisco. These proteins’ ability to prevent unwanted associations led to their being called chaperones. These chaperone proteins also increased in expression as a response to heat shock, hence their label as heat shock proteins (Hsps). However, neither label encompasses the breadth of these proteins’ functional capabilities. The term “unfoldases” has been proposed, as this basic function is shared by most members of this protein family. Onto this is added specializations that allow the different family members to perform various cellular functions. This current article focuses on the resolved structural bases for these functions. It reviews the currently available molecular structures in the Protein Data Bank for several classes of Hsps (Hsp60, Hsp70, Hsp90, and Hsp104). When possible, it discusses the complete structures for these proteins, and the types of molecular machines to which they have been assigned. The structures of domains and the associated functions are discussed in order to illustrate the rationale for the proposed unfoldase function.

GroEL and the GroEL-GroES Complex

Chaperonin is categorized as a molecular chaperone and mediates the formation of the native conformation of proteins by first preventing folding during synthesis or membrane translocation and subsequently by mediating the step-wise ATP-dependent release that result in proper folding. In the GroEL-GroES complex, a single heptameric GroEL ring binds one GroES ring in the presence of ATP/ADP, in this vein, the double ring GroEL tetradecamer is present in two distinct types of GroEL-GroES complexes: asymmetric 1:1 "bullet"-shaped GroEL:GroES and symmetric 1:2 "football" (American football)-shaped GroEL:GroES₂. There have been debates as to which complex is critical to the productive protein folding mediated by the GroEL-GroES complex, and how GroES coordinates with GroEL in the chaperonin reaction cycle in association with regulation by adenine nucleotides and through the interplay of substrate proteins. A lot of knowledge on chaperonins has been accumulating as if expanding as ripples spread around the GroEL-GroES from Escherichia coli. In this article, an overview is presented on GroEL and the GroEL-GroES complex, with emphasis on their morphological variations, and some potential applications to the fabrication of nanocomposites using GroEL as a nano-block. In parallel, a guideline is presented that supports the recognition that the E. coli and its GroEL-GroES complex do not always receive in standard literature because the biochemical features of chaperonins derived from others special, such as mammals, are not always the same as those confirmed using GroEL-GroES derived from E. coli.

Hsp60 in Skeletal Muscle Fiber Biogenesis and Homeostasis: From Physical Exercise to Skeletal Muscle Pathology

Hsp60 is a molecular chaperone classically described as a mitochondrial protein with multiple roles in health and disease, participating to the maintenance of protein homeostasis. It is well known that skeletal muscle is a complex tissue, rich in proteins, that is, subjected to continuous rearrangements, and this homeostasis is affected by many different types of stimuli and stresses. The regular exercise induces specific histological and biochemical adaptations in skeletal muscle fibers, such as hypertrophy and an increase of mitochondria activity and oxidative capacity. The current literature is lacking in information regarding Hsp60 involvement in skeletal muscle fiber biogenesis and regeneration during exercise, and in disease conditions. Here, we briefly discuss the functions of Hsp60 in skeletal muscle fibers during exercise, inflammation, and ageing. Moreover, the potential usage of Hsp60 as a marker for disease and the evaluation of novel treatment options is also discussed. However, some questions remain open, and further studies are needed to better understand Hsp60 involvement in skeletal muscle homeostasis during exercise and in pathological condition.

Atomic-Level Description of Protein Folding inside the GroEL Cavity

Chaperonins (ubiquitous facilitators of protein folding) sequester misfolded proteins within an internal cavity, thus preventing protein aggregation during the process of refolding. GroEL, a tetradecameric bacterial chaperonin, is one of the most studied chaperonins, but the role of the internal cavity in the refolding process is still unclear. It has been suggested that rather than simply isolating proteins while they refold, the GroEL cavity actively promotes protein folding. A detailed characterization of the folding dynamics and thermodynamics of protein substrates encapsulated within the cavity, however, has been difficult to obtain by experimental means, due to the system's complexity and the many steps in the folding cycle. Here, we examine the influence of the GroEL cavity on protein folding based on the results of unbiased, atomistic molecular dynamics simulations. We first verified that the computational setup, which uses a recently developed state-of-the-art force field that more accurately reproduces the aggregation propensity of unfolded states, could recapitulate the essential structural dynamics of GroEL. In these simulations, the GroEL tetradecamer was highly dynamic, transitioning among states corresponding to most of the structures that have been observed experimentally. We then simulated a small, unfolded protein both in the GroEL cavity and in bulk solution and compared the protein's folding process within these two environments. Inside the GroEL cavity, the unfolded protein interacted strongly with the disordered residues in GroEL's C-terminal tails. These interactions stabilized the protein's unfolded states relative to its compact states and increased the roughness of its folding free-energy surface, resulting in slower folding compared to the rate in solution. For larger proteins, which are more typical GroEL substrates, we speculate that these interactions may allow substrates to more quickly escape kinetic traps associated with compact, misfolded states, thereby actively promoting folding.

Roger Hendrix: Gentle Provocateur

Roger W. Hendrix was at the forefront of bacteriophage biology for nearly 50 years and was central to our understanding of both viral capsid assembly and phage genomic diversity and evolution. Roger's warm and gentle demeanor belied a razor-sharp mind and warmed him to numerous highly productive collaborations that amplified his scientific impact. Roger was always completely open with scientific ideas while at the same time quietly agitating with a stream of new ways of thinking about problems and nudging our communities to search for innovative solutions: a gentle but highly effective provocateur.

Chaperonin of Group I: Oligomeric Spectrum and Biochemical and Biological Implications

Chaperonins play various physiological roles and can also be pathogenic. Elucidation of their structure, e.g., oligomeric status and post-translational modifications (PTM), is necessary to understand their functions and mechanisms of action in health and disease. Group I chaperonins form tetradecamers with two stacked heptameric rings. The tetradecamer is considered the typical functional complex for folding of client polypeptides. However, other forms such as the monomer and oligomers with smaller number of subunits than the classical tetradecamer, also occur in cells. The properties and functions of the monomer and oligomers, and their roles in chaperonin-associated diseases are still incompletely understood. Chaperonin I in eukaryotes occurs in various locations, not just the mitochondrion, which is its canonical place of residence and function. Eukaryotic Chaperonin I, namely Hsp60 (designated HSP60 or HSPD1 in humans) has, indeed, been found in the cytosol; the plasma-cell membrane; on the outer surface of cells; in the intercellular space; in biological liquids such as lymph, blood, and cerebrospinal fluid; and in secretions, for instance saliva and urine. Hsp60 has also been found in cell-derived vesicles such as exosomes. The functions of Hsp60 in all these non-canonical locales are still poorly characterized and one of the questions not yet answered is in what form, i.e., monomer or oligomer, is the chaperonin present in these non-canonical locations. In view of the steady increase in interest on chaperonopathies over the last several years, we have studied human HSP60 to determine its role in various diseases, its locations in cells and tissues and migrations in the body, and its post-translational modifications that might have an impact on its location and function. We also carried out experiments to characterize the oligomeric status of extramitochondrial of HSP60 in solution. Here, we provide an overview of our results, focusing on the oligomeric equilibrium and stability of the various forms of HSP60 in comparison with GroEL. We also discuss post-translational modifications associated with anti-cancer drugs to indicate the potential of Hsp60 in Medicine, as a biomarker and etiopathogenic factor.

Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes

Molecular chaperones control the cellular folding, assembly, unfolding, disassembly, translocation, activation, inactivation, disaggregation, and degradation of proteins. In 1989, groundbreaking experiments demonstrated that a purified chaperone can bind and prevent the aggregation of artificially unfolded polypeptides and use ATP to dissociate and convert them into native proteins. A decade later, other chaperones were shown to use ATP hydrolysis to unfold and solubilize stable protein aggregates, leading to their native refolding. Presently, the main conserved chaperone families Hsp70, Hsp104, Hsp90, Hsp60, and small heat-shock proteins (sHsps) apparently act as unfolding nanomachines capable of converting functional alternatively folded or toxic misfolded polypeptides into harmless protease-degradable or biologically active native proteins. Being unfoldases, the chaperones can proofread three-dimensional protein structures and thus control protein quality in the cell. Understanding the mechanisms of the cellular unfoldases is central to the design of new therapies against aging, degenerative protein conformational diseases, and specific cancers.

GroEL of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31 exhibits GroES and ATP-independent refolding activity

The nitrogen-fixing cyanobacterium, Anabaena L-31 has two Hsp60 proteins, 59 kDa GroEL coded by the second gene of groESL operon and 61 kDa Cpn60 coded by cpn60 gene. Anabaena GroEL formed stable higher oligomer (>12-mer) in the presence of K(+) and prevented thermal aggregation of malate dehydrogenase (MDH). Using three protein substrates (MDH, All1541 and green fluorescent protein), it was found that the refolding activity of Anabaena GroEL was lower than that of Escherichia coli GroEL, but independent of both GroES and ATP. This correlated with in vivo data. GroEL exhibited ATPase activity which was enhanced in the presence of GroES and absence of a denatured protein, contrary to that observed for bacterial GroEL. However, a significant role for ATP could not be ascertained during in vitro folding assays. The monomeric Cpn60 exhibited much lower refolding activity than GroEL, unaffected by GroES and ATP. In vitro studies revealed inhibition of the refolding activity of Anabaena GroEL by Cpn60, which could be due to their different oligomeric status. The role of GroES and ATP may have been added during the course of evolution from the ancient cyanobacteria to modern day bacteria enhancing the refolding ability and ensuring wider scope of substrates for GroEL.

The Chemical Biology of Molecular Chaperones--Implications for Modulation of Proteostasis

Protein homeostasis (proteostasis) is inextricably tied to cellular health and organismal lifespan. Aging, exposure to physiological and environmental stress, and expression of mutant and metastable proteins can cause an imbalance in the protein-folding landscape, which results in the formation of non-native protein aggregates that challenge the capacity of the proteostasis network (PN), increasing the risk for diseases associated with misfolding, aggregation, and aberrant regulation of cell stress responses. Molecular chaperones have central roles in each of the arms of the PN (protein synthesis, folding, disaggregation, and degradation), leading to the proposal that modulation of chaperone function could have therapeutic benefits for the large and growing family of diseases of protein conformation including neurodegeneration, metabolic diseases, and cancer. In this review, we will discuss the current strategies used to tune the PN through targeting molecular chaperones and assess the potential of the chemical biology of proteostasis.

Bacteriophage lambda: Early pioneer and still relevant

Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.

Reaction Cycle of Chaperonin GroEL via Symmetric "Football" Intermediate

Chaperonin GroEL is an essential chaperone that assists in protein folding in the cell. Since one GroEL ring binds one GroES heptamer, the GroEL double ring permits the formation of two types of GroEL:GroES complexes: asymmetric 1:1 "bullet"-shaped and symmetric 1:2 "football"-shaped GroEL:GroES2 complexes. There have been continuing debates about the mechanism and which complex is critical to the chaperonin-assisted folding. In this review, I summarize the recent progress on the football complex.

Chaperone discovery

Molecular chaperones assist de novo protein folding and facilitate the refolding of stress-denatured proteins. The molecular chaperone concept was coined nearly 35 years ago, and since then, tremendous strides have been made in understanding how these factors support protein folding. Here, we focus on how various chaperone proteins were first identified to play roles in protein folding. Examples are used to illustrate traditional routes of chaperone discovery and point out their advantages and limitations. Recent advances, including the development of folding biosensors and promising methods for the stabilization of proteins in vivo, provide new routes for chaperone discovery.

Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations

The Escherichia coli chaperonin GroEL is a complex of identical subunit proteins (57 kDa each) arranged in a back-to-back stacking of two heptameric rings. Its hallmarks include nested positive intra-ring and negative inter-ring cooperativity in adenosine trisphosphate (ATP) binding and the ability to mediate the folding of newly transcribed and/or denatured substrate proteins. We performed unbiased molecular dynamics simulations of the GroEL subunit protein in explicit water both with and without the nucleotide KMgATP to understand better the details of the structural transitions that enable these behaviors. Placing KMgATP in the equatorial domain binding pocket of a t state subunit, which corresponds to a low ATP-affinity state, produced a short-lived (6 ns) state that spontaneously transitioned to the high ATP-affinity r state. The important feature of this transition is a large-scale rotation of the intermediate domain's helix M to close the ATP binding pocket. Pivoting of helix M is accompanied by counterclockwise rotation and slight deformation of the apical domain, important for lowering the affinity for substrate protein. Aligning simulation conformations into model heptamer rings demonstrates that the t-->r transition in one subunit is not sterically hindered by t state neighbors, but requires breakage of Arg(197)-Glu(386) intersubunit salt bridges, which are important for inter-ring positive cooperativity. Lowest-frequency quasi-harmonic modes of vibration computed pre- and post-transition clearly show that natural vibrations facilitate the transition. Finally, we propose a novel mechanism for inter-ring cooperativity in ATP binding inspired by the observation of spontaneous insertion of the side chain of Ala(480) into the empty nucleotide pocket.

An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate

Electron cryomicroscopy reveals an unprecedented conformation of the single-ring mutant of GroEL (SR398) bound to GroES in the presence of Mg-ATP. This conformation exhibits a considerable expansion of the folding cavity, with approximately 80% more volume than the X-ray structure of the equivalent cis cavity in the GroEL-GroES-(ADP)(7) complex. This expanded conformation can encapsulate an 86 kDa heterodimeric (alphabeta) assembly intermediate of mitochondrial branched-chain alpha-ketoacid dehydrogenase, the largest substrate ever observed to be cis encapsulated. The SR398-GroES-Mg-ATP complex is found to exist as a mixture of standard and expanded conformations, regardless of the absence or presence of the substrate. However, the presence of even a small substrate causes a pronounced bias toward the expanded conformation. Encapsulation of the large assembly intermediate is supported by a series of electron cryomicroscopy studies as well as the protection of both alpha and beta subunits of the substrate from tryptic digestion.

Molecular cloning and characterization of Cpn60 in the free-living nematode Plectus acuminatus

Heat shock proteins (Hsps) have provoked interest not only because of their involvement in human diseases but also for their potential as biomarkers of environmental pollution. Whereas the former interest is covered by numerous reports, the latter is an exciting new field of research. We report the isolation of the full-length cpn60 messenger ribonucleic acid (mRNA) and partial genomic deoxyribonucleic acid from the free-living, environmental sentinel nematode Plectus acuminatus, a species used in classical ecotoxicity tests. Although the primary sequence displays high identity scores to other nematodes and human Cpn60 (75% and 70%, respectively), the intron-exon structure differs markedly. Furthermore, although mRNA levels remained constant after exposure to ZnCl2 (0-330 microM) under laboratory conditions, protein levels increased significantly in a dose-dependent manner. In conclusion, this first account of molecular genetic similarities and differences of Cpn60 in a neglected nematode taxon provides a valuable insight into its potential uses in gene-based ecotoxicological risk assessment exercises.

Structure of holo-chaperonin studied with electron microscopy Oligomeric cpn10 on top of two layers of cpn60 rings with two stripes each

A structural model of holo-chaperonin, known as a protein-folding control protein comprising 60 kDa (cpn60) and 10 kDa polypeptides (cpn10), is proposed based on the electron microscopic images of holo-chaperonin from Thermus thermophilus and cpn60 from Paracoccus denitrificans. Isolated Paracoccus cpn60 shows very similar images to those of Escherichia coli tetradecameric cpn60, a seven-membered ring in the top view and a rectangular shape with four stripes in the side view. However, a small number of half-thick rectangles with two stripes are also seen which indicates that a single cpn60-heptamer ring has two stripes parallel to the plane of the ring. Thermus holo-chaperonin shows a bullet-like shape in the side view, and antibody against cpn10 binds only to the round side of the bullet. We conclude that a single cpn60-heptamer ring with two stripes stacks into two layers, and a cpn10 oligomer binds to one side of the layers.

Crystallization of the cpn6O/cpn10 complex (‘holo-chaperonin’) fromThermus thermophilus

A stable complex of the chaperonins, cpn60 and cpn10 (Escherichia coli GroEL and GroES homologues), from the extremely thermophilic bacterium Thermus thermophilus has been isolated and crystallized. The crystals have dimensions up to 30 x 200 x 200 microns. Ultra-thin sections of the crystals estimated by electron microscopy showed a rectangular lattice with unit cell parameters of a = 17 nm, b = 27 nm, gamma = 90 degrees.

Microbial molecular chaperones

Protein folding in the cell, long thought to be a spontaneous process, in fact often requires the assistance of molecular chaperones. This is thought to be largely because of the danger of incorrect folding and aggregation of proteins, which is a particular problem in the crowded environment of the cell. Molecular chaperones are involved in numerous processes in bacterial cells, including assisting the folding of newly synthesized proteins, both during and after translation; assisting in protein secretion, preventing aggregation of proteins on heat shock, and repairing proteins that have been damaged or misfolded by stresses such as a heat shock. Within the cell, a balance has to be found between refolding of proteins and their proteolytic degradation, and molecular chaperones play a key role in this. In this review, the evidence for the existence and role of the major cytoplasmic molecular chaperones will be discussed, mainly from the physiological point of view but also in relationship to their known structure, function and mechanism of action. The two major chaperone systems in bacterial cells (as typified by Escherichia coli) are the GroE and DnaK chaperones, and the contrasting roles and mechanisms of these chaperones will be presented. The GroE chaperone machine acts by providing a protected environment in which protein folding of individual protein molecules can proceed, whereas the DnaK chaperones act by binding and protecting exposed regions on unfolded or partially folded protein chains. DnaK chaperones interact with trigger factor in protein translation and with ClpB in reactivating proteins which have become aggregated after heat shock. The nature of the other cytoplasmic chaperones in the cell will also be reviewed, including those for which a clear function has not yet been determined, and those where an in vivo chaperone function has still to be proven, such as the small heat shock proteins IbpA and IbpB. The regulation of expression of the genes of the heat shock response will also be discussed, particularly in the light of the signals that are needed to induce the response. The major signals for induction of the heat shock response are elevated temperature and the presence of unfolded protein within the cell, but these are sensed and transduced differently by different bacteria. The best characterized example is the sigma 32 subunit of RNA polymerase from E. coli, which is both more efficiently translated and also transiently stabilized following heat shock. The DnaK chaperones modulate this effect. However, a more widely conserved system appears to be typified by the HrcA repressor in Bacillus subtilis, the activity of which is modulated by the GroE chaperone machine. Other examples of regulation of molecular chaperones will also be discussed. Finally, the likely future research directions for molecular chaperone biology in the post-genomic era will be briefly evaluated.

The Chaperones of the archaeon Thermoplasma acidophilum

Chaperonesare an essential component of a cell's ability to respond to environmental challenges. Chaperones have been studied primarily in bacteria, but in recent years it has become apparent that some classes of chaperones either are very divergent in bacteria relative to archaea and eukaryotes or are missing entirely. In contrast, a high degree of similarity was found between the chaperonins of archaea and those of the eukaryotic cytosol, which has led to the establishment of archaeal model systems. The archaeon most extensively used for such studies is Thermoplasma acidophilum, which thrives at 59 degrees C and pH 2. Here we review information on its chaperone complement in light of the recently determined genome sequence.

DNA packaging and developmental intermediates of a broad host range Vibrio vulnificus bacteriophage 71A-6

The structural intermediates in the capsid assembly and DNA packaging pathway of Vibrio vulnificus bacteriophage 71A-6, a rod-shaped double-stranded DNA podovirus, were isolated by ultracentrifugation and studied by electron microscopy, SDS-PAGE and pulsed-field gel electrophoretic analysis. Bacteriophage 71A-6 synthesized rod-shaped capsids (mean length=200+/-8 nm; mean width=47+/-3 nm n=50) during its development. Several host proteins that probably help in the assembly and maturation of the capsids were attached to these capsids as spherical structures. A capsid-DNA or DNA packaging complex that consisted of the mature capsids, DNA and a 42.5-kDa protein was also isolated. The size of the capsids increased in length and decreased in width (mean length=220+/-8 nm; mean width=45+/-3 nm n=50) either during or after the DNA packaging. The capsid fractions contained about 12 phage structural proteins and eight host proteins. At least three proteins were tentatively identified: a 38.5-kDa major capsid protein, a 35.2-kDa tail protein and 42.5-kDa packaging initiator or terminator protein. The size of the bacteriophage 71A-6 genome was determined to be 143.0-kb by pulsed-field gel electrophoresis. The total mass of all the mature phage proteins corresponded to only 14.0% of the coding capacity of phage genome.

Genetic analysis of bacteriophage-encoded cochaperonins

Early genetic studies identified the Escherichia coli groES and groEL genes because mutations in them blocked the growth of bacteriophages lambda and T4. Subsequent genetic and biochemical analyses have shown that GroES and GroEL constitute a chaperonin machine, absolutely essential for E. coli growth, because it is needed for the correct folding of many of its proteins. In spite of very little sequence identity to GroES, the bacteriophage T4-encoded Gp31 protein and the bacteriophage RB49-encoded CocO protein are bona fide GroEL cochaperonins, even capable of substituting for GroES in E. coli growth. A major functional distinction is that only Gp31 and CocO can assist GroEL in the correct folding of Gp23, the major bacteriophage capsid protein. Conserved structural features between CocO and Gp31, which are absent from GroES, highlight their potential importance in specific cochaperonin function.

The importance of a mobile loop in regulating chaperonin/ co-chaperonin interaction: humans versus Escherichia coli

Chaperonins are universally conserved proteins that nonspecifically facilitate the folding of a wide spectrum of proteins. While bacterial GroEL is functionally promiscuous with various co-chaperonin partners, its human homologue, Hsp60 functions specifically with its co-chaperonin partner, Hsp10, and not with other co-chaperonins, such as the bacterial GroES or bacteriophage T4-encoded Gp31. Co-chaperonin interaction with chaperonin is mediated by the co-chaperonin mobile loop that folds into a beta-hairpin conformation upon binding to the chaperonin. A delicate balance of flexibility and conformational preferences of the mobile loop determines co-chaperonin affinity for chaperonin. Here, we show that the ability of Hsp10, but not GroES, to interact specifically with Hsp60 lies within the mobile loop sequence. Using mutational analysis, we show that three substitutions in the GroES mobile loop are necessary and sufficient to acquire Hsp10-like specificity. Two of these substitutions are predicted to preorganize the beta-hairpin turn and one to increase the hydrophobicity of the GroEL-binding site. Together, they result in a GroES that binds chaperonins with higher affinity. It seems likely that the single ring mitochondrial Hsp60 exhibits intrinsically lower affinity for the co-chaperonin that can be compensated for by a higher affinity mobile loop.

Simultaneous induction of mitochondrial heat shock protein mRNAs in rat forebrain ischemia

Several investigations have postulated evidence of the involvement of apoptosis in delayed neuronal death following brief periods of global cerebral ischemia. Apoptosis may be closely linked to mitochondrial dysfunction. Heat shock protein (HSP) 60 and HSP10 are mitochondrial matrix proteins induced by stress and form the chaperonin complex that is implicated in protein folding and assembly within the mitochondria. This study investigated the induction of these mitochondrial stress protein genes in the hippocampal CA1 region and less vulnerable regions following transient forebrain ischemia. In situ hybridization analysis revealed that the induction pattern of HSP60 mRNA was identical to that of HSP10 mRNA throughout the entire ischemic course. No changes occurred in the expression of both mRNAs after 2 min ischemia. Strong induction of both mRNAs occurred in the CA1 region after 10 min ischemia and persisted until 1 d after reperfusion. In contrast, induction of both mRNAs in the less vulnerable regions was terminated by 1 d after reperfusion. These results demonstrate that mitochondrial stress conditions persist concomitantly with cytosolic stress conditions in regions vulnerable to transient forebrain ischemia.

A kinetic analysis of the nucleotide-induced allosteric transitions of GroEL

Single-point mutants of GroEL were constructed with tryptophan replacing a tyrosine residue in order to examine nucleotide-induced structural transitions spectrofluorometrically. The tyrosine residues at positions 203, 360, 476 and 485 were mutated. Of these, the probe at residue 485 gave the clearest fluorescence signals upon nucleotide binding. The probe at 360 reported similar signals. In response to the binding of ATP, the indole fluorescence reports four distinct structural transitions occurring on well-separated timescales, all of which precede hydrolysis of the nucleotide. All four of these rearrangements were analysed, two in detail. The fastest is an order of magnitude more rapid than previously identified rearrangements and is proposed to be a T-to-R transition. The next kinetic phase is a rearrangement to the open state identified by electron cryo-microscopy and this we designate an R to R* transition. Both of these rearrangements can occur when only a single ring of GroEL is loaded with ATP, and the results are consistent with the occupied ring behaving in a concerted, cooperative manner. At higher ATP concentrations both rings can be loaded with the nucleotide and the R to R* transition is accelerated. The resultant GroEL:ATP14 species can then undergo two final rearrangements, RR*-->[RR](+)-->[RR](#). These final slow steps are completely blocked when ADP occupies the second ring, i.e. it does not occur in the GroEL:ATP7:ADP7 or the GroEL:ATP7 species. All equilibrium and kinetic data conform to a minimal model in which the GroEL ring can exist in five distinct states which then give rise to seven types of oligomeric conformer: TT, TR, TR*, RR, RR*, [RR](+) and [RR](#), with concerted transitions between each. The other eight possible conformers are presumably disallowed by constraints imposed by inter-ring contacts. This kinetic behaviour is consistent with the GroEL ring passing through distinct functional states in a binding-encapsulation-folding process, with the T-form having high substrate affinity (binding), the R-form being able to bind GroES but retaining substrate affinity (encapsulation), and the R*-form retaining high GroES affinity but allowing the substrate to dissociate into the enclosed cavity (folding). ADP induces only one detectable rearrangement (designated T to T*) which has no properties in common with those elicited by ATP. However, asymmetric ADP binding prevents ATP occupying both rings and, hence, restricts the system to the T*T, T*R and T*R* complexes.

Compensatory changes in GroEL/Gp31 affinity as a mechanism for allele-specific genetic interaction

Previous work has shown that the GroEL-GroES interaction is primarily mediated by the GroES mobile loop. In bacteriophage T4 infection, GroES is substituted by the gene 31-encoded cochaperonin, Gp31. Using a genetic selection scheme, we have identified a new set of mutations in gene 31 that affect interaction with GroEL; all mutations result in changes in the mobile loop of Gp31. Biochemical analyses reveal that the mobile loop mutations alter the affinity between Gp31 and GroEL, most likely by modulating the stability of the GroEL-bound hairpin conformation of the mobile loop. Surprisingly, mutations in groEL that display allele-specific interactions with mutations in gene 31 alter residues in the GroEL intermediate domain, distantly located from the mobile loop binding site. The observed patterns of genetic and biochemical interaction between GroES or Gp31 and GroEL point to a mechanism of genetic allele specificity based on compensatory changes in affinity of the protein-protein interaction. Mutations studied in this work indirectly alter affinity by modulating a folding transition in the Gp31 mobile loop or by modulating a hinged conformational change in GroEL.

Structure and function in GroEL-mediated protein folding

Recent structural and biochemical investigations have come together to allow a better understanding of the mechanism of chaperonin (GroEL, Hsp60)-mediated protein folding, the final step in the accurate expression of genetic information. Major, asymmetric conformational changes in the GroEL double toroid accompany binding of ATP and the cochaperonin GroES. When a nonnative polypeptide, bound to one of the GroEL rings, is encapsulated by GroES to form a cis ternary complex, these changes drive the polypeptide into the sequestered cavity and initiate its folding. ATP hydrolysis in the cis ring primes release of the products, and ATP binding in the trans ring then disrupts the cis complex. This process allows the polypeptide to achieve its final native state, if folding was completed, or to recycle to another chaperonin molecule, if the folding process did not result in a form committed to the native state.

Chaperonin filaments: their formation and an evaluation of methods for studying them

Chaperonins are multisubunit protein complexes that can be isolated from cells as high-molecular-weight structures that appear as double rings in the electron microscope. We recently discovered that chaperonin double rings isolated from the hyperthermophilic archaeon Sulfolobus shibatae, when incubated at physiological temperatures in the presence of ATP and Mg2+, stacked into filaments; we hypothesized that these filaments are related to filaments seen inside S. shibatae cells and that chaperonins exist as filaments in vivo (J. D. Trent et al., 1997, Proc. Natl. Acad. Sci. USA 94, 5383-5388). This paper elucidates the conditions under which we have observed S. shibatae chaperonins to form filaments and evaluates native polyacrylamide gel electrophoresis (PAGE), TEM, spectrophotometry, and centrifugation as methods for studying these filaments. We observed that in the presence of Mg2+ combined with ATP, ADP, ATPgammaS, or GTP, native PAGE indicated that chaperonin subunits assembled into double rings and that the conformation of these double rings was effected by nucleotide binding, but we saw no indication of chaperonin filament formation. Under these same conditions, however, TEM, spectroscopy, and centrifugation methods indicated that chaperonin subunits and double rings had assembled into filaments. We determined that this discrepancy in the representation of the chaperonin structure was due to the native PAGE method itself. When we exposed chaperonin filaments to the electrophoretic field used in native PAGE, the filaments dissociated into double rings. This suggests that TEM, spectrophotometry, and centrifugation are the preferred methods for studying the higher-order structures of chaperonins, which are likely to be of biological significance.

Transcription of the groESL operon in Pseudomonas aeruginosa PAO1

Northern hybridization and S1 nuclease mapping demonstrated that the groES and groEL genes in Pseudomonas aeruginosa were transcribed as a bicistronic mRNA of 2.2 kb. Two transcription start sites and a transcription termination site were mapped. Overlapping consensus sequences for sigma 32- and sigma 70-dependent promoters were found in the upstream region of groES. Levels of groESL-specific mRNA were increased about 2-fold upon heat shock. This response differs from the dramatic enhancement (more than 10-fold) of groESL transcription after heat shock observed in other bacterial species.

Purification and functional characterization of a chaperone from Methanococcus jannaschii

A chaperone from Methanococcus jannaschii has been purified to homogeneity with a single chromatographic step. The chaperone was identified and characterized using activity assays for characteristic chaperone abilities. The M. jannaschii chaperone binds unfolded proteins, protects proteins against heat-induced aggregation, and has a strongly temperature dependent ATPase activity. The chaperone has also been shown to inhibit the spontaneous refolding of a mesophilic protein at low temperatures. The purified chaperone complex has a M(r) of about 1,000,000 and consists of a single type of subunit with an approximate M(r) of 60,000. Analysis of partial sequence data reveals that this chaperone is the predicted protein product of the previously identified chaperonin gene in M. jannaschii (BULT et al., 1996). To our knowledge, this is the first functional characterization of a chaperone from a methanogen.

Structural analysis of GroE chaperonin complexes using chemical cross-linking

In this chapter, we have shown how chemical cross-linking with a bifunctional reagent, GA, can be used to investigate the structure of large oligomeric complexes such as GroEL14GroES7 and GroEL14(GroES7)2. Cross-linking, followed by denaturing electrophoresis, confirmed the number and arrangement of GroEL and GroES subunits within each individual oligomer, which was previously known from EM analysis. Furthermore, cross-linking permitted a close examination of the effect of regulatory factors, such as nucleotides and free divalent cations, on the molecular structure of GroEL14, GroEL14GroES7, and GroEL14GroES7. Finally, cross-linking analysis permitted characterization and quantitation of various chaperonin heterooligomeric complexes, GroEL14, GroEL14GroES7, and GroEL14GroES7 in solution, under conditions that also supported protein folding and ATP hydrolysis. It was shown that GA does not induce the artifactual association or the dissociation of GroES7 from the chaperonin. On the contrary, chemical cross-linking is an obligatory procedure when the subsequent analysis is carried out using methods that can displace the equilibrium.

Temperature dependence of backbone dynamics in loops of human mitochondrial heat shock protein 10

A highly flexible, yet conserved polypeptide loop of Hsp10 mediates binding to Hsp60 in the course of chaperonin-dependent protein folding. Previous transferred nuclear Overhauser effect (trNOE) studies with peptides based on the mobile loop of the Escherichiacoli and bacteriophage T4 Hsp10s suggested that the mobile loop adopts a characteristic hairpin turn upon binding to the E. coli Hsp60 GroEL. In this paper, we identify the sequence and characterize the nascent structure and dynamics of the 18-residue mobile loop in the 15N-enriched human Hsp10. We also identify four residues of another flexible loop, the roof beta hairpin. The mobile loop and/or roof beta hairpin of several subunits are absent from the X-ray crystal structure of human Hsp10. NMR data suggest that the mobile loop of Hsp10 preferentially samples a hairpin conformation despite the fact that the backbone motion resembles that of a disordered polypeptide. Analysis of backbone dynamics by measurement of 15N relaxation times, T1 and T2, and the 1H-15N nuclear Overhauser effect (1H-15N NOE) indicates that motion is greatest near the center of the loop. Inversion of the temperature dependence of the T1 near the center of the loop marks a transition to motion with a dominant time scale of less than 3 ns. Analysis of the relaxation data by spectral density mapping shows that subnanosecond motion increases uniformly along the loop at elevated temperatures, whereas nanosecond motion increases near the ends of the loop and decreases near the center of the mobile loop. The transition to dominance by fast motion in the center of the loop occurs at a distance from the well-structured part of Hsp10 that is equal to the persistence length of an unstructured polypeptide. Simulation of the spectral density function for the 15N resonance and its temperature dependence using the Lipari-Szabo formalism suggests that the dominant time scales of loop motion range from 0.6 to 18 ns. For comparison, the time scale for molecular rotation of the 70 kDa Hsp10 heptamer is estimated to be 37 ns. Complex behavior of the T2 relaxation time indicates that motion also occurs on longer time scales. All of the modes of loop motion are likely to have an impact on Hsp10/Hsp60 interaction and therefore affect Hsp10/Hsp60 function as a chaperonin.

Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage

The Gp31 protein from bacteriophage T4 functionally substitutes for the bacterial co-chaperonin GroES in assisted protein folding reactions both in vitro and in vivo. But Gp31 is required for the folding and/or assembly of the T4 major capsid protein Gp23, and this requirement cannot be satisfied by GroES. The 2.3 A crystal structure of Gp31 shows that its tertiary and quaternary structures are similar to those of GroES despite the existence of only 14% sequence identity between the two proteins. However, Gp31 shows a series of structural adaptations which will increase the size and the hydrophilicity of the "Anfinsen cage," the enclosed cavity within the GroEL/GroES complex that is the location of the chaperonin-assisted protein folding reaction.

Importance of electrostatic interactions in the rapid binding of polypeptides to GroEL

The question of how chaperones rapidly bind non-native proteins of very different sequence and function has been examined by determining the effect of ionic strength on the refolding of barnase on GroEL, and on the thermal denaturation of barnase in the presence of GroEL and SecB. Both chaperones bind the denatured state of barnase, so lowering the T(m) value. The refolding of barnase in the presence of GroEL is multiphasic, the slowest phase corresponding to the refolding of a singly bound molecule of barnase in the complex with GroEL. The fastest phase is related to the association of barnase and GroEL. At high ratios of GroEL to barnase and low ionic strength (less than 200 mM) this fast phase corresponds to the observed rate of binding. The rate of association of barnase and GroEL was found to be highly dependent on ionic strength, and at high ionic strength (greater than 600 mM) the majority of barnase molecules escaped binding and refolded free in solution. The data are consistent with an initial, transient, ionic interaction between barnase and GroEL, before hydrophobic binding occurs, allowing diffusion-controlled association and slow dissociation of unfolded polypeptide.

Role of the amino terminal domain in GroES oligomerization

Digestions of the GroES oligomer with trypsin, chymotrypsin and Glu-C protease from Staphylococcus aureus V8 (V8) have helped to locate three regions in the GroES sequence that are sensitive to limited proteolysis and have provided information of the GroES domains involved in monomer-monomer and GroEL interaction. The removal of the first 20 or 27 amino acids of the N-terminal region of each GroES monomer by trypsin or chymotrypsin respectively, abolish the oligomerization of the GroES complex and its binding to GroEL. The V8-treatment of GroES promotes the breakage of the peptide bond between Glu18 and Thr19 but not the liberation of the N-terminal fragment from the GroES oligomer, which is capable of forming with GroEL a complex active in protein folding. It is deduced from these results that the N-terminal region of the GroES monomer is involved in monomer-monomer interaction, providing experimental evidence that relates some biochemical properties of GroES with its three-dimensional structure at atomic resolution.

Six-fold rotational symmetry of ClpQ, the E. coli homolog of the 20S proteasome, and its ATP-dependent activator, ClpY

ClpQ (HslV) is a homolog of the beta-subunits of the 20S proteasome. In E. coli, it is expressed from an operon that also encodes ClpY (HslU), an ATPase homologous to the protease chaperone, ClpX. ClpQ (subunit Mr 19,000) and ClpY (subunit Mr 49,000) were purified separately as oligomeric proteins with molecular weights of approximately 220,000 and approximately 350,000, respectively, estimated by gel filtration. Mixtures of ClpY and ClpQ displayed ATP-dependent proteolytic activity against casein, and a complex of the two proteins was isolated by gel filtration in the presence of ATP. Image processing of negatively stained electron micrographs revealed strong six-fold rotational symmetry for both ClpY and ClpQ, suggesting that the subunits of both proteins are arranged in hexagonal rings. The molecular weight of ClpQ combined with its symmetry is consistent with a double hexameric ring, whereas the data on ClpY suggest only one such ring. The symmetry mismatch previously observed between hexameric ClpA and heptameric ClpP in the related ClpAP protease is apparently not reproduced in the symmetry-matched ClpYQ system.

Refolding and reassociation of glycerol dehydrogenase from Bacillus stearothermophilus in the absence and presence of GroEL

The refolding of the tetrameric, metalloenzyme glycerol dehydrogenase (GDH) from Bacillus stearothermophilus has been investigated using stopped-flow fluorescence and circular dichroism spectroscopy. The effects of metal ions on the refolding of the native enzyme and the refolding of a monomeric mutant ([A208]GDH) have also been studied. The refolding process of the wild-type enzyme is at least biphasic; 70% of the respective signal changes occur in the first 2 ms followed by a slower process with a half-life of 3 s. The presence of the metal ion does not affect the slowest biphasic refolding rate, which is virtually the same for all three versions of the enzyme. The presence of GroEL slows down the first phase of refolding. The reassociation of subunits was examined by measuring the regain in catalytic activity and the enhancement in the fluorescence emission from NADH on binding to the oligomeric form of the enzyme. The rate and extent of reassociation is dependent on enzyme concentration and the extent of reactivation is dependent on the presence of the metal ion. The reassociation process was more efficient in the presence of NADH particularly for the metal-depleted enzyme (apo-GDH). The presence of GroEL or GroEL plus ATP leads to a higher yield of reassociation and therefore catalytically active enzyme. The additional presence of Mg-ATP does not affect the extent of reassociation, but has a small positive effect on the rate of reassociation. These data suggest that GDH is bound weakly to GroEL and that GroES is not required for release of the protein.