Protein unfolding mechanisms and their effects on folding experiments

Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants

Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 ( ~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.

Shear stress as a driver of degradation for protein-based therapeutics: More accomplice than culprit

Protein degradation is a major concern for protein-based therapeutics. It may alter the biological activity of the product and raise the potential for undesirable effects on the patients. Among the numerous drivers of protein degradation, shear stress has been the focus around which much work has revolved since the 1970s. In the pharmaceutical realm, the product is often processed through several unit operations, which include mixing, pumping, filtration, filling, and atomization. Nonetheless, the drug might be exposed to significant shear stresses, which might cooperatively contribute to product degradation, together with interfacial stress. This review presents fundamentals of shear stress about protein structure, followed by an overview of the drivers of product degradation. The impact of shear stress on protein stability in different unit operations is then presented, and recommendations for limiting the adverse effects on the biopharmaceutical formulations are outlined. Finally, several devices used to explore the effects of shear stress are discussed.

Unfolding under Pressure: An NMR Perspective

This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.

Folding-unfolding asymmetry and a RetroFold computational algorithm

We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process as the driving force is opposed by damping. Protein folding takes two orders of magnitude longer than unfolding. We suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modelling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns, while unfolding (denaturation) takes only about 5.0 ns and, therefore, fewer computational resources are needed for its simulation. This RetroFold approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.

Analysis of the Shear Stresses in a Filling Line of Parenteral Products: The Role of Tubing

Parenteral products appear to be sensitive to process conditions in bioprocessing steps, such as interfacial stress and shear stress. The combination of these elements is widely believed and proven to influence product stability, but the defined roles of these players in the product damage process have not yet been identified. The present work addresses a current industrial problem, by focusing on the analysis of shear stress on protein-based therapeutics flowing in tubing by means of Computational Fluid Dynamics simulations. The purpose of this article is not to pinpoint the mechanism triggering the damage of the product, but it represents the first step towards wider experimental investigations and introduces a new strategy to quantify the average shear stress. The field of scale-down approaches, used to scale the commercial process down to the laboratory level, is also explored. Since quality control is critical in the pharmaceutical realm, it is essential that the scale-down approach preserves the same stress exposure as the commercial scale, which in the present work is considered to be that resulting from shear effects. Therefore, a new approach for scaling down the commercial process is proposed, which has been compared with traditional approaches and shown to provide greater representativeness between the two scales.

Structural basis for the mutation-induced dysfunction of the human IL-15/IL-15α receptor complex

In silico strategies offer a reliable, fast, and inexpensive, way compared to the clumsy in vitro approaches to boost understanding of the effect of amino acid substitution on the structure and consequently the associated function of proteins. In the present work, we report an atomistic-based, reliable in silico structural and energetic framework of the interactions between the receptor-binding domain of the Interleukin-15 (IL-15) protein and its receptor Interleukin-15α (IL-15α), consequently, providing qualitative and quantitative details of the key molecular determinants in ligand/receptor recognition. Molecular dynamics simulations were used to investigate the dynamic behavior of the specific binding between IL-15 and IL-15α followed by estimation of the free energies via molecular mechanics/generalized Born surface area (MM/GBSA). In particular, residues Y26, E46, E53, and E89 of the IL-15 protein receptor-binding domain are identified as main hot spots, shaping and governing the stability of the assembly. These results can be used for the development of neutralizing antibodies and the effective structure-based design of protein-protein interaction inhibitors against the so-called orphan disease, vitiligo.

Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems

The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.

Using in vitro bioassays to guide the development of safer bio-based polymers for use in food packaging

Petroleum-based polymers traditionally used for plastic packaging production have been shown to leach dangerous chemicals such as bisphenol-A (BPA). Bio-based polymers are potentially safer alternatives, and many can be sustainably sourced from waste streams in the food industry. This study assesses bio-based polymers undergoing food packaging development for migration of endocrine disrupting leachates at the level of estrogen, androgen and progestagen nuclear receptor transcriptional activity. Reporter gene assays were coupled with migration testing, performed using standardised test conditions for storage and temperature. Test samples include nine bio-based polymers and four inorganic waste additives mixed with a traditional petroleum-based polymer, polypropylene. Thermoplastic starch material, polybutylene succinate, polycaprolactone, polybutylene adipate terephthalate (PBAT), two polylactic acid (PLA)/PBAT blends, polyhydroxybutyrate (PHB) and eggshell/polypropylene (10:90) presented no significant reduction in metabolic activity or hormonal activity under any test condition. Polypropylene (PP) presented no hormonal activity. Metabolic activity was reduced in the estrogen responsive cell line after 10 days migration testing of eggshell/polypropylene (0.1:99.9) in MeOH at 40°C, and PP in MeOH and dH₂0. Estrogenic agonist activity was observed after 10 days in poultry litter ash/polypropylene (10:90) in MeOH at 20°C and 40°C, poultry feather based polymer in MeOH and dH₂O at 40°C, and eggshell/polypropylene (40:60) and PLA in dH₂O at 40°C. Activity was within a range of 0.26–0.50 ng 17β-estradiol equivalents per ml, equating to an estrogenic potency of 3–∼2800 times less than the estrogenic leachate BPA. Poultry litter ash/polypropylene (10:90) in MeOH for 10 days presented estrogenic activity at 20°C and 40°C within the above range and anti-androgenic activity at 40°C. Progestagenic activity was not observed for any of the compounds under any test condition. Interestingly, lower concentrations of eggshell or PP may eliminate eggshell estrogenicity and PP toxicity. Alternatively eggshell may bind and eliminate the toxic elements of PP. Similarly, PLA estrogenic activity was removed in both PLA/PBAT blends. This study demonstrates the benefits of bioassay guidance in the development of safer and sustainable packaging alternatives to petroleum-based plastics. Manipulating the types of additives and their formulations alongside toxicological testing may further improve safety aspects.

Regulation by Different Types of Chaperones of Amyloid Transformation of Proteins Involved in the Development of Neurodegenerative Diseases

The review highlights various aspects of the influence of chaperones on amyloid proteins associated with the development of neurodegenerative diseases and includes studies conducted in our laboratory. Different sections of the article are devoted to the role of chaperones in the pathological transformation of alpha-synuclein and the prion protein. Information about the interaction of the chaperonins GroE and TRiC as well as polymer-based artificial chaperones with amyloidogenic proteins is summarized. Particular attention is paid to the effect of blocking chaperones by misfolded and amyloidogenic proteins. It was noted that the accumulation of functionally inactive chaperones blocked by misfolded proteins might cause the formation of amyloid aggregates and prevent the disassembly of fibrillar structures. Moreover, the blocking of chaperones by various forms of amyloid proteins might lead to pathological changes in the vital activity of cells due to the impaired folding of newly synthesized proteins and their subsequent processing. The final section of the article discusses both the little data on the role of gut microbiota in the propagation of synucleinopathies and prion diseases and the possible involvement of the bacterial chaperone GroE in these processes.

New Insights for Biosensing: Lessons from Microbial Defense Systems

Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.

Dynamical Manifestations of Supercooling in Amyloid Hydration

The effect of extreme temperature on amyloidogenic species remains sparsely explored. In a recent study (J. Phys. Chem. Lett., 2019, 10, (10)), we employed exhaustive molecular dynamics simulations to explore the cold thermal response of a putative small amyloid oligomer and to elicit the role of solvent modulation. Herein, we investigate the dynamical response of the hydration waters of the oligomer within the supercooled states. Using NMR-based formalism, we delineate the entropic response in terms of the side-chain conformational entropy that corroborates the weakening of the hydrophobic core with lowering of temperature. The translational dynamics of the protein and hydration waters reveal the coupling of protein dynamical fluctuations with solvent dynamics under supercooled conditions. Probing the translational motion as a space-time correlation indicates glassy dynamics exhibited by hydration waters in the supercooled regime. Caging of the water molecules with lowering of temperature and the resultant hopping dynamics are reflected in the longer β-relaxation timescales of translational motion. Furthermore, we utilized mode-coupling theory (MCT) and derived the ideal glass transition temperature from translational and rotational dynamics, around ∼196 and 209 K, respectively. Interestingly, rotational motion in the supercooled regime deviates from the MCT law, exhibits Arrhenius motion, and marks a fragile-to-strong crossover at 227 K. The low-frequency vibrational modes also coincide with the dynamical transition. This exposition lends dynamical insights into the hydration coupling of an amyloid aggregate under cryogenic conditions.

Protein Unfolding: Denaturant vs. Force

While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods.

An "Onion-like" Model of Protein Unfolding: Collective versus Site Specific Approaches

Approximating protein unfolding by an all-or-none cooperative event is a convenient assumption that can provide precious global information on protein stability. It is however quickly emerging that the scenario is far more complex and that global denaturation curves often hide a rich heterogeneity of states that are largely probe dependent. In this review, we revisit the importance of gaining site-specific information on the unfolding process. We focus on nuclear magnetic resonance, as this is the main technique able to provide site-specific information. We review historical and most modern approaches that have allowed an appreciable advancement of the field of protein folding. We also demonstrate how unfolding is a reporter dependent event, suggesting the outmost importance of selecting the reporter carefully.

Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2

Intrinsic disorder plays an important functional role in proteins. Disordered regions are linked to posttranslational modifications, conformational switching, extra/intracellular trafficking, and allosteric control, among other phenomena. Disorder provides proteins with enhanced plasticity, resulting in a dynamic protein conformational/functional landscape, with well-structured and disordered regions displaying reciprocal, interdependent features. Although lacking well-defined conformation, disordered regions may affect the intrinsic stability and functional properties of ordered regions. MeCP2, methyl-CpG binding protein 2, is a multifunctional transcriptional regulator associated with neuronal development and maturation. MeCP2 multidomain structure makes it a prototype for multidomain, multifunctional, intrinsically disordered proteins (IDP). The methyl-binding domain (MBD) is one of the key domains in MeCP2, responsible for DNA recognition. It has been reported previously that the two disordered domains flanking MBD, the N-terminal domain (NTD) and the intervening domain (ID), increase the intrinsic stability of MBD against thermal denaturation. In order to prove unequivocally this stabilization effect, ruling out any artifactual result from monitoring the unfolding MBD with a local fluorescence probe (the single tryptophan in MBD) or from driving the protein unfolding by temperature, we have studied the MBD stability by differential scanning calorimetry (reporting on the global unfolding process) and chemical denaturation (altering intramolecular interactions by a different mechanism compared to thermal denaturation).

Effects of Ionic Liquids on Metalloproteins

In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.

Probing the interactions of novel europium coordination complexes with serum albumin

Molecular interactions between novel europium coordination complexes (EC) possessing superior cytotoxic activity and bovine serum albumin (BSA), the most prominent representative of plasma proteins, were assessed using fluorescence spectroscopy and molecular docking techniques. Cumulative results from fluorescent probe binding, fluorescence quenching and Förster resonance energy transfer studies revealed that the europium complexes V4 and V8 do not perturb the BSA structure, while V3, V5, and V7 induce partial unfolding of the polypeptide chain. Molecular docking studies coupled with analysis of the three-dimensional structure of the BSA-EC complexes showed that V4 and V8 reside in the vicinity of the protein IIA subdomain (Sudlow's site I), while V3, V5 and V5 were localized predominantly in the BSA IIIA subdomain (Sudlow's site II). Due to the intactness of the protein structure upon association with V4 and V8, these compounds may be recommended for further evaluation as potential antineoplastic agents.

Understanding the structure and conformation of bovine hemoglobin in presence of the drug hydroxyurea: multi-spectroscopic studies supported by docking and molecular dynamics simulation

Binding interaction between the small antitumor drug Hydroxyurea (HU) and Bovine Hemoglobin (BHb) has been explored in details from multi-spectroscopic and computational studies. The formation of ground state complex between BHb and HU has been suggested from the electronic UV-Vis and steady-state fluorescence spectroscopic studies. The quenching in fluorescence of BHb in presence of HU at varied concentrations has been analyzed from the SV plots. Static type of quenching has been suggested from time-resolved fluorescence spectroscopic studies. Binding parameters associated with the BHb-HU complex have also been estimated from the temperature dependent fluorescence spectroscopic studies. Alterations in the micro-environment of the Tyr and Trp residues of BHb in presence of HU have been observed from the synchronous fluorescence measurement. The result obtained from CD spectroscopic measurements signify partial unfolding in the secondary structure of BHb due to binding with HU molecule. The experimental observations are supported by theoretical studies. Molecular docking and molecular dynamics simulations have been performed to investigate the structural stability and compactness of BHb in the binding interaction between BHb and HU. The interaction of BHb with HU is expected to provide fundamental insights towards understanding the therapeutic effectiveness of HU upon interaction with BHb used in chemo-, radio therpeutic procedures and also in the treatment of SCD.

The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results

The biological activity of proteins depends on their three-dimensional structure, known as the native state. The main force driving the correct folding mechanism is the hydrophobic effect and when this folding kinetics is altered, aggregation phenomena intervene causing the occurrence of illnesses such as Alzheimer and Parkinson’s diseases. The other important effect is performed by water molecules and by their ability to form a complex network of hydrogen bonds whose dynamics influence the mobility of protein amino acids. In this work, we review the recent results obtained by means of spectroscopic techniques, such as Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopies, on hydrated lysozyme. In particular, we explore the Energy Landscape from the thermal region of configurational stability up to that of the irreversible denaturation. The importance of the coupling between the solute and the solvent will be highlighted as well as the different behaviors of hydrophilic and hydrophobic moieties of protein amino acid residues.

Modulating charge patterning and ionic strength as a strategy to induce conformational changes in intrinsically disordered proteins

We present an analytical theory to describe conformational changes as a function of salt for polymers with a given sequence of charges. We apply this model to describe Intrinsically Disordered Proteins (IDPs) by explicitly accounting for charged residues and their exact placement in the primary sequence while approximating the effect of non-electrostatic interactions at a mean-field level by effective short-range (two body and three-body) interaction parameters. The effect of ions is introduced by treating electrostatic interactions within Debye-Huckle approximation. Using typical values of the short-range mean-field parameters derived from all-atom Monte Carlo simulations (at zero salt), we predict the conformational changes as a function of salt concentration. We notice that conformational transitions in response to changes in ionic strength strongly depend on sequence specific charge patterning. For example, globule to coil transition can be observed upon increasing salt concentration, in stark contrast to uniformly charged polyelectrolyte theories based on net charge only. In addition, it is possible to observe non-monotonic behavior with salt as well. Drastic differences in salt-induced conformational transitions is also evident between two doubly phosphorylated sequences-derived from the same wild type sequence-that only differ in the site of phosphorylation. Similar effects are also predicted between two sequences derived from the same parent sequence differing by a single site mutation where a negative charge is replaced by a positive charge. These effects are purely a result of charge decoration and can only be understood in terms of metrics based on specific placement of charges, and cannot be explained by models based on charge composition alone. Identifying sequences and hot spots within sequences-for post translational modification or charge mutation-using our high-throughput theory will yield fundamental insights into design and biological regulation mediated by phosphorylation and/or local changes in salt concentration.

Modeling protein folding in vivo

A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo.

REVIEWERS

This article was reviewed by Eugene Koonin and Frank Eisenhaber.

A staphylococcal anti-sigma factor possesses a single-domain, carries different denaturant-sensitive regions and unfolds via two intermediates

RsbW, an anti-sigma factor possessing kinase activity, is expressed by many Gram-positive bacteria including Staphylococcus aureus. To obtain clues about the domain structure and the folding-unfolding mechanism of RsbW, we have elaborately studied rRsbW, a recombinant S. aureus RsbW. Sequence analysis of the protein fragments, generated by the limited proteolysis of rRsbW, has proposed it to be a single-domain protein. The unfolding of rRsbW in the presence of GdnCl or urea was completely reversible in nature and occurred through the formation of at least two intermediates. The structure, shape, and the surface hydrophobicity of no intermediate completely matches with those of other intermediates or the native rRsbW. Interestingly, one of the intermediates, formed in the presence of less GdnCl concentrations, has a molten globule-like structure. Conversely, all of the intermediates, like native rRsbW, exist as dimers in aqueous solution. The putative molten globule and the urea-generated intermediates also have retained some kinase activity. Additionally, the putative ATP binding site/catalytic site of rRsbW shows higher denaturant sensitivity than the tentative dimerization region of this enzyme.