Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study

A Review: Molecular Chaperone-mediated Folding, Unfolding and Disaggregation of Expressed Recombinant Proteins

The advancements in biotechnology over time have led to an increase in the demand of pure, soluble and functionally active proteins. Recombinant protein production has thus been employed to obtain high expression of purified proteins in bulk. E. coli is considered as the most desirable host for recombinant protein production due to its inexpensive and fast cultivation, simple nutritional requirements and known genetics. Despite all these benefits, recombinant protein production often comes with drawbacks, such as, the most common being the formation of inclusion bodies due to improper protein folding. Consequently, this can lead to the loss of the structure-function relationship of a protein. Apart from various strategies, one major strategy to resolve this issue is the use of molecular chaperones that act as folding modulators for proteins. Molecular chaperones assist newly synthesized, aggregated or misfolded proteins to fold into their native conformations. Chaperones have been widely used to improve the expression of various proteins which are otherwise difficult to produce in E. coli. Here, we discuss the structure, function, and role of major E. coli molecular chaperones in recombinant technology such as trigger factor, GroEL, DnaK and ClpB.

Why do eukaryotic proteins contain more intrinsically disordered regions?

Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins. Methods predicting intrinsic disorder are based on the amino acid sequence of a protein. Therefore, there must exist an underlying difference in the sequences between eukaryotic and prokaryotic proteins causing the (predicted) difference in intrinsic disorder. By comparing proteins, from complete eukaryotic and prokaryotic proteomes, we show that the difference in intrinsic disorder emerges from the linker regions connecting Pfam domains. Eukaryotic proteins have more extended linker regions, and in addition, the eukaryotic linkers are significantly more disordered, 38% vs. 12-16% disordered residues. Next, we examined the underlying reason for the increase in disorder in eukaryotic linkers, and we found that the changes in abundance of only three amino acids cause the increase. Eukaryotic proteins contain 8.6% serine; while prokaryotic proteins have 6.5%, eukaryotic proteins also contain 5.4% proline and 5.3% isoleucine compared with 4.0% proline and ≈ 7.5% isoleucine in the prokaryotes. All these three differences contribute to the increased disorder in eukaryotic proteins. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. The differences are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. The observation that differences in the abundance of three amino acids cause the difference in disorder between eukaryotic and prokaryotic proteins raises the question: Are amino acid frequencies different in eukaryotic linkers because the linkers are more disordered or do the differences cause the increased disorder?

Intrinsic disorder is essential for various functions in eukaryotic cells and is a signature of eukaryotic proteins. Here, we try to understand the origin of the difference in disorder between eukaryotic and prokaryotic proteins. We show that eukaryotic proteins contain more extended linker regions and that these linker regions are significantly more disordered. Further, we show, for the first time, that the difference in disorder originates from a systematic difference in amino acid frequencies between eukaryotic and prokaryotic proteins. Three amino acids contribute to the difference in disorder; serine and proline are more abundant in eukaryotic linkers, while isoleucine is less frequent. These shifts in frequencies are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. Anyhow the widespread of the shifts in abundance indicates that the differences are ancient and caused be some yet not fully understood selective difference acting on eukaryotic and prokaryotic proteins.

Allosteric Mechanisms in Chaperonin Machines

Chaperonins are nanomachines that facilitate protein folding by undergoing energy (ATP)-dependent movements that are coordinated in time and space owing to complex allosteric regulation. They consist of two back-to-back stacked oligomeric rings with a cavity at each end where protein substrate folding can take place. Here, we focus on the GroEL/GroES chaperonin system from Escherichia coli and, to a lesser extent, on the more poorly characterized eukaryotic chaperonin CCT/TRiC. We describe their various functional (allosteric) states and how they are affected by substrates and allosteric effectors that include ATP, ADP, nonfolded protein substrates, potassium ions, and GroES (in the case of GroEL). We also discuss the pathways of intra- and inter-ring allosteric communication by which they interconvert and the coupling between allosteric transitions and protein folding reactions.

Retarded protein folding of the human Z-type α₁-antitrypsin variant is suppressed by Cpr2p

The human Z-type α1-antitrypsin variant has a strong tendency to accumulate folding intermediates due to extremely slow protein folding within the endoplasmic reticulum (ER) of hepatocytes. Human α1-antitrypsin has 17 peptidyl-prolyl bonds per molecule; thus, the effect of peptidyl-prolyl isomerases on Z-type α1-antitrypsin protein folding was analyzed in this study. The protein level of Cpr2p, a yeast ER peptidyl-prolyl isomerase, increased more than two-fold in Z-type α1-antitrypsin-expressing yeast cells compared to that in wild-type α1-antitrypsin-expressing cells. When CPR2 was deleted from the yeast genome, the cytotoxicity of Z-type α1-antitrypsin increased significantly. The interaction between Z-type α1-antitrypsin and Cpr2p was confirmed by co-immunoprecipitation. In vitro folding assays showed that Cpr2p facilitated Z-type α1-antitrypsin folding into the native state. Furthermore, Cpr2p overexpression significantly increased the extracellular secretion of Z-type α1-antitrypsin. Our results indicate that ER peptidyl-prolyl isomerases may rescue Z-type α1-antitrypsin molecules from retarded folding and eventually relieve clinical symptoms caused by this pathological α1-antitrypsin.

On the characterization and software implementation of general protein lattice models

models of proteins have been widely used as a practical means to computationally investigate general properties of the system. In lattice models any sterically feasible conformation is represented as a self-avoiding walk on a lattice, and residue types are limited in number. So far, only two- or three-dimensional lattices have been used. The inspection of the neighborhood of alpha carbons in the core of real proteins reveals that also lattices with higher coordination numbers, possibly in higher dimensional spaces, can be adopted. In this paper, a new general parametric lattice model for simplified protein conformations is proposed and investigated. It is shown how the supporting software can be consistently designed to let algorithms that operate on protein structures be implemented in a lattice-agnostic way. The necessary theoretical foundations are developed and organically presented, pinpointing the role of the concept of main directions in lattice-agnostic model handling. Subsequently, the model features across dimensions and lattice types are explored in tests performed on benchmark protein sequences, using a Python implementation. Simulations give insights on the use of square and triangular lattices in a range of dimensions. The trend of potential minimum for sequences of different lengths, varying the lattice dimension, is uncovered. Moreover, an extensive quantitative characterization of the usage of the so-called "move types" is reported for the first time. The proposed general framework for the development of lattice models is simple yet complete, and an object-oriented architecture can be proficiently employed for the supporting software, by designing ad-hoc classes. The proposed framework represents a new general viewpoint that potentially subsumes a number of solutions previously studied. The adoption of the described model pushes to look at protein structure issues from a more general and essential perspective, making computational investigations over simplified models more straightforward as well.

Weak intra-ring allosteric communications of the archaeal chaperonin thermosome revealed by normal mode analysis

Chaperonins are molecular machines that use ATP-driven cycles to assist misfolded substrate proteins to reach the native state. During the functional cycle, these machines adopt distinct nucleotide-dependent conformational states, which reflect large-scale allosteric changes in individual subunits. Distinct allosteric kinetics has been described for the two chaperonin classes. Bacterial (group I) chaperonins, such as GroEL, undergo concerted subunit motions within each ring, whereas archaeal and eukaryotic chaperonins (group II) undergo sequential subunit motions. We study these distinct mechanisms through a comparative normal mode analysis of monomer and double-ring structures of the archaeal chaperonin thermosome and GroEL. We find that thermosome monomers of each type exhibit common low-frequency behavior of normal modes. The observed distinct higher-frequency modes are attributed to functional specialization of these subunit types. The thermosome double-ring structure has larger contribution from higher-frequency modes, as it is found in the GroEL case. We find that long-range intersubunit correlation of amino-acid pairs is weaker in the thermosome ring than in GroEL. Overall, our results indicate that distinct allosteric behavior of the two chaperonin classes originates from different wiring of individual subunits as well as of the intersubunit communications.

Folding of large multidomain proteins by partial encapsulation in the chaperonin TRiC/CCT

The eukaryotic chaperonin, TRiC/CCT (TRiC, TCP-1 ring complex; CCT, chaperonin containing TCP-1), uses a built-in lid to mediate protein folding in an enclosed central cavity. Recent structural data suggest an effective size limit for the TRiC folding chamber of ∼70 kDa, but numerous chaperonin substrates are substantially larger. Using artificial fusion constructs with actin, an obligate chaperonin substrate, we show that TRiC can mediate folding of large proteins by segmental or domain-wise encapsulation. Single or multiple protein domains up to ∼70 kDa are stably enclosed by stabilizing the ATP-hydrolysis transition state of TRiC. Additional domains, connected by flexible linkers that pass through the central opening of the folding chamber, are excluded and remain accessible to externally added protease. Experiments with the physiological TRiC substrate hSnu114, a 109-kDa multidomain protein, suggest that TRiC has the ability to recognize domain boundaries in partially folded intermediates. In the case of hSnu114, this allows the selective encapsulation of the C-terminal ∼45-kDa domain and segments thereof, presumably reflecting a stepwise folding mechanism. The capacity of the eukaryotic chaperonin to overcome the size limitation of the folding chamber may have facilitated the explosive expansion of the multidomain proteome in eukaryotes.

Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed.

Proteins are essential molecules for performing a majority of functions in all biological systems. These functions often depend on the three-dimensional structures of proteins. Here, we investigate a fundamental question in molecular evolution: how can proteins acquire new advantageous structures via mutations while not sacrificing their existing structures that are still needed? Some authors have suggested that the same protein may adopt two or more alternative structures, switch between them and thus perform different functions with each of the alternative structures. Intuitively, such a protein could provide an evolutionary compromise between conflicting demands for existing and new protein structures. Yet no theoretical study has systematically tackled the biophysical basis of such compromises during evolutionary processes. Here we devise a model of evolution that specifically recognizes protein molecules that can exist in several different stable structures. Our model demonstrates that proteins can indeed utilize multiple structures to satisfy conflicting evolutionary requirements. In light of these results, we identify data from known protein structures that are consistent with our predictions and suggest novel directions for future investigation.

A new approach for investigating protein flexibility based on Constraint Logic Programming. The first application in the case of the estrogen receptor

We describe the potential of a novel method, based on Constraint Logic Programming (CLP), developed for an exhaustive sampling of protein conformational space. The CLP framework proposed here has been tested and applied to the estrogen receptor, whose activity and function is strictly related to its intrinsic, and well known, dynamics. We have investigated in particular the flexibility of H12, focusing on the pathways followed by the helix when moving from one stable crystallographic conformation to the others. Millions of geometrically feasible conformations were generated, selected and the traces connecting the different forms were determined by using a shortest path algorithm. The preliminary analyses showed a marked agreement between the crystallographic agonist-like, antagonist-like and hypothetical apo forms, and the corresponding conformations identified by the CLP framework. These promising results, together with the short computational time required to perform the analyses, make this constraint-based approach a valuable tool for the study of protein folding prediction. The CLP framework enables one to consider various structural and energetic scenarious, without changing the core algorithm. To show the feasibility of the method, we intentionally choose a pure geometric setting, neglecting the energetic evaluation of the poses, in order to be independent from a specific force field and to provide the possibility of comparing different behaviours associated with various energy models.

Chaperonins: two rings for folding

Chaperonins are ubiquitous chaperones found in Eubacteria, eukaryotic organelles (group I), Archaea and the eukaryotic cytosol (group II). They all share a common structure and a basic functional mechanism. Although a large amount of information has been gathered for the simpler group I, much less is known about group II chaperonins. Recent crystallographic and electron microscopy structures have provided new insights into the mechanism of these chaperonins and revealed important differences between group I and II chaperonins, mainly in the molecular rearrangements that take place during the functional cycle. These differences are evident for the most complex chaperonin, the eukaryotic cytosolic CCT, which highlights the uniqueness of this important molecular machine.

Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase

Clp ATPases are ring-shaped AAA+ motors in the degradation pathway that perform critical actions of unfolding and translocating substrate proteins (SPs) through narrow pores to deliver them to peptidase components. These actions are effected by conserved diaphragm-forming loops found in the central channel of the Clp ATPase hexamer. Conformational changes, that take place in the course of repetitive ATP-driven cycles, result in mechanical forces applied by the central channel loops onto the SP. We use coarse-grained simulations to elucidate allostery-driven mechanisms of unfolding and translocation of a tagged four-helix bundle protein by the ClpY ATPase. Unfolding is initiated at the tagged C-terminal region via an obligatory intermediate. The resulting nonnative conformation is competent for translocation, which proceeds on a different time scale than unfolding and involves sharp stepped transitions. Completion of the translocation process requires assistance from the ClpQ peptidase. These mechanisms contrast nonallosteric mechanical unfolding of the SP. In atomic force microscopy experiments, multiple unfolding pathways are available and large mechanical forces are required to unravel the SP relative to those exerted by the central channel loops of ClpY. SP threading through a nonallosteric ClpY nanopore involves simultaneous unfolding and translocation effected by strong pulling forces.

Facilitating chromophore formation of engineered Ca(2+) binding green fluorescent proteins

Green fluorescent protein (GFP) containing a self-coded chromophore has been applied in protein trafficking and folding, gene expression, and as sensors in living cells. While the "cycle3" mutation denoted as C3 mutation (F99S/M153T/V163A) offers the ability to increase GFP fluorescence at 37 degrees C, it is not clear whether such mutations will also be able to assist the folding and formation of the chromophore upon the addition of metal ion binding sites. Here, we investigate in both bacterial and mammalian systems, the effect of C2 (M153T/V163A) and C3 (F99S/M153T/V163A) mutations on the folding of enhanced GFP (EGFP, includes F64L/S65T) and its variants engineered with two types of Ca(2+) binding sites: (1) a designed discontinuous Ca(2+) binding site and (2) a grafted continuous Ca(2+) binding motif. We show that, for the constructed EGFP variants, the C2 mutation is sufficient to facilitate the production of fluorescence in both bacterial and mammalian cells. Further addition of the mutation F99S decreases the folding efficiency of these variants although a similar effect is not detectable for EGFP, likely due to the already greatly enhanced mutation F64L/S65T from the original GFP, which hastens the chromophore formation. The extinction coefficient and quantum yield of purified proteins of each construct were also examined to compare the effects of both C2 and C3 mutations on protein spectroscopic properties. Our quantitative analyses of the effect of C2 and C3 mutations on the folding and formation of GFP chromophore that undergoes different folding trajectories in bacterial versus mammalian cells provide insights into the development of fluorescent protein-based analytical sensors.

Identification of differentially expressed genes in haemocytes of the crayfish (Procambarus clarkii) infected with white spot syndrome virus by suppression subtractive hybridization and cDNA microarrays

By using suppression subtractive hybridization (SSH) and cDNA microarrays, we studied the differentially expressed genes in haemocytes of the crayfish (Procambarus clarkii) infected with white spot syndrome virus (WSSV). Thirty three differentially expressed genes were detected in which 31 were up-regulated and 2 were down-regulated. The up-regulated genes include serine protease inhibitors, chaperonin, synaptasome-associated protein of 25 kD(SNAP25), tubulin, zinc-finger protein, intracellular fatty acid binding protein, extracellular superoxide dismutase precursor, arginine kinase, 70 kD heat shock like protein and Bax inhibitor-1. A lot of genes including the 2 down-regulated genes are still unknown. All these immuno-related genes responding to the virus infection provide a new insight for further study in the shrimp innate immunity.

Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin

A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin folding and unfolding pathways are collated and then re-examined from this perspective, allowing us to determine the position of the CCT intervention on the actin free-energy folding landscape. The essential role for CCT in actin folding is to provide a free-energy contribution from its ATP cycle, which drives actin to fold from a stable, trapped intermediate I3, to a less stable but now productive folding intermediate I2. We develop two hypothetical mechanisms for actin folding founded upon concepts established for the bacterial type I chaperonin GroEL and extend them to the much more complex CCT system of eukaryotes. A new model is presented in which CCT facilitates free-energy transfer through direct coupling of the nucleotide hydrolysis cycle to the phases of actin substrate maturation.

CPSP-web-tools: a server for 3D lattice protein studies

Summary: Studies on proteins are often restricted to highly simplified models to face the immense computational complexity of the associated problems. Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic (FCC)]. Here, we present CPSP-web-tools, an interactive online interface of these programs for their immediate use. They include the first method for the direct prediction of optimal energies and structures in 3D HP side-chain models. This newest extension of the CPSP approach is described here for the first time.

Availability and Implementation: Free access at http://cpsp.informatik.uni-freiburg.de

Contact:cpsp@informatik.uni-freiburg.de; cpsp@informatik.uni-freiburg.de

Classifying proteinlike sequences in arbitrary lattice protein models using LatPack

Knowledge of a protein's three-dimensional native structure is vital in determining its chemical properties and functionality. However, experimental methods to determine structure are very costly and time-consuming. Computational approaches such as folding simulations and structure prediction algorithms are quicker and cheaper but lack consistent accuracy. This currently restricts extensive computational studies to abstract protein models. It is thus essential that simplifications induced by the models do not negate scientific value. Key to this is the use of thoroughly defined proteinlike sequences. In such cases abstract models can allow for the investigation of important biological questions. Here, we present a procedure to generate and classify proteinlike sequence data sets. Our LatPack tools and the approach in general are applicable to arbitrary lattice protein models. Identification is based on thermodynamic kinetic features and incorporates the sequential assembly of proteins by addressing cotranslational folding. We demonstrate the approach in the widely used unrestricted 3D-cubic HP-model. The resulting sequence set is the first large data set for this model exhibiting the proteinlike properties required. Our data tools are freely available and can be used to investigate protein-related problems.

Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET

The chaperonin GroEL assists protein folding by undergoing ATP-induced conformational changes that are concerted within each of its two back-to-back stacked rings. Here we examined whether concerted allosteric switching gives rise to all-or-none release and folding of domains in a chimeric fluorescent protein substrate, CyPet-YPet. Using this substrate, it was possible to determine the folding yield of each domain from its intrinsic fluorescence and that of the entire chimera by measuring Förster resonance energy transfer between the two domains. Hence, it was possible to determine whether release of one domain is accompanied by release of the other domain (concerted mechanism), or whether their release is not coupled. Our results show that the chimera's release tends to be concerted when folding is assisted by a wild-type GroEL variant, but not when assisted by the F44W/D155A mutant that undergoes a sequential allosteric switch. A connection between the allosteric mechanism of this molecular machine and its biological function in assisting folding is thus established.

CPSP-tools--exact and complete algorithms for high-throughput 3D lattice protein studies

Background

The principles of protein folding and evolution pose problems of very high inherent complexity. Often these problems are tackled using simplified protein models, e.g. lattice proteins. The CPSP-tools package provides programs to solve exactly and completely the problems typical of studies using 3D lattice protein models. Among the tasks addressed are the prediction of (all) globally optimal and/or suboptimal structures as well as sequence design and neutral network exploration.

Results

In contrast to stochastic approaches, which are not capable of answering many fundamental questions, our methods are based on fast, non-heuristic techniques. The resulting tools are designed for high-throughput studies of 3D-lattice proteins utilising the Hydrophobic-Polar (HP) model. The source bundle is freely available [1].

Conclusion

The CPSP-tools package is the first set of exact and complete methods for extensive, high-throughput studies of non-restricted 3D-lattice protein models. In particular, our package deals with cubic and face centered cubic (FCC) lattices.

Chaperonins: The hunt for the Group II mechanism

Chaperonins are multi-subunit complexes that enhance the efficiency of protein-folding reactions by capturing protein substrates in their central cavities. They occur in all prokaryotic and eukaryotic cell types and, alone amongst molecular chaperones, chaperonin knockouts are always lethal. Chaperonins come in two forms; the Group I are found in bacteria, mitochondria and plastids [W.A. Fenton, A.L. Horwich, Q. Rev. Biophys. 36 (2003) 229-256, [1]] and the Group II in the eukaryotic cytoplasm and in archaea [N.J. Cowan, S.A. Lewis, Adv. Protein Chem. 59 (2001) 73-104, [2]]. Both use energy derived from ATP binding and hydrolysis to drive a series of structural rearrangements that enable them to capture, engulf and then release polypeptide chains that have either not yet acquired the native, biologically active state or have been denatured in the cell.