On the emerging of thawing drip: Role of myofibrillar protein renaturation.

This study aimed to facilitate the understanding on the origin of thawing drip under different freezing rate. Eventually we observed significantly greater thaw loss produced by slow freezing (8.58%) as compared to fast freezing (6.41%) after 24 h of thawing. Back to the freezing, ice crystallization induced decline in pH and the cold denaturation of myofibrillar protein. However, independent of freezing rate, we noticed protein renaturation with pH restoring during thawing, evidenced by the decreasing surface hydrophobicity, increasing solubility and thermal stability, and gradually stabilized secondary structure. Meanwhile, the water-holding of myofibrils increased with thawing process along with the rising water mobility. Under fast freezing, the results indicated less extensive protein cold denaturation and lower water mobility during thawing. Besides, we proposed that the microenvironment of lower ionic strength in fast freezing should benefit the protein renaturation and water re-absorption, ultimately contributed to lower thaw loss.

Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation.

Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.

Reconstitution of Membrane Proteins into Platforms Suitable for Biophysical and Structural Analyses.

Integral membrane proteins have historically been challenging targets for biophysical research due to their low solubility in aqueous solution. Their importance for chemical and electrical signaling between cells, however, makes them fascinating targets for investigators interested in the regulation of cellular and physiological processes. Since membrane proteins shunt the barrier imposed by the cell membrane, they also serve as entry points for drugs, adding pharmaceutical research and development to the interests. In recent years, detailed understanding of membrane protein function has significantly increased due to high-resolution structural information obtained from single-particle cryo-EM, X-ray crystallography, and NMR. In order to further advance our mechanistic understanding on membrane proteins as well as foster drug development, it is crucial to generate more biophysical and functional data on these proteins under defined conditions. To that end, different techniques have been developed to stabilize integral membrane proteins in native-like environments that allow both structural and biophysical investigations-amphipols, lipid bicelles, and lipid nanodiscs. In this chapter, we provide detailed protocols for the reconstitution of membrane proteins according to these three techniques. We also outline some of the possible applications of each technique and discuss their advantages and possible caveats.

Reconstitution of Proteoliposomes for Phospholipid Scrambling and Nonselective Channel Assays.

Phospholipid scramblases catalyze the rapid trans-bilayer movement of lipids down their concentration gradients. This process is essential for numerous cellular signaling functions including cell fusion, blood coagulation, and apoptosis. The importance of scramblases is highlighted by the number of human diseases caused by mutations in these proteins. Because of their indispensable function, it is essential to understand and characterize the molecular function of phospholipid scramblases. Powerful tools to measure lipid transport in cells are available. However, these approaches provide limited mechanistic insights into the molecular bases of scrambling. Here we describe in detail an in vitro phospholipid scramblase assay and the accompanying analysis which allows for determination of the macroscopic rate constants associated with phospholipid scrambling. Notably, members of the TMEM16 family of scramblases also function as nonselective ion channels. To better understand the physiological relevance of this channel function as well as its relationship to the scrambling activity of the TMEM16s we also describe in detail an in vitro flux assay to measure nonselective channel activity. Together, these two assays can be used to investigate the dual activities of the TMEM16 scramblases/nonselective channels.

Stabilization and Crystallization of a Membrane Protein Involved in Lipid Transport.

Lipoteichoic acids (LTA) are ubiquitous cell wall components of Gram-positive bacteria. In Staphylococcus aureus LTA are composed of a polymer with 1,3-linked glycerol phosphate repeating units anchored to the plasma membrane. The anchor molecule is a lipid-linked disaccharide (anchor-LLD) synthesized at the cytoplasmic leaflet of the membrane. The anchor lipid becomes accessible at the outer leaflet of the membrane after the flippase LtaA catalyzes translocation. Recently we have elucidated the structure of LtaA using vapor diffusion X-ray crystallography and in situ annealing. We were able to obtain LtaA crystals after optimization of purification protocols that led to stabilization of LtaA isolated in detergent micelles. Here we report a protocol that describes the purification, stabilization, crystallization, and data collection strategies carried out to determine the structure of LtaA. We highlight key points that can be used to determine crystal structures of other membrane proteins.

Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins.

NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the ß-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.

Comparative refolding of guanidinium hydrochloride denatured bovine serum albumin assisted by cationic and anionic surfactants via artificial chaperone protocol: Biophysical insight.

In the present study, we report the cooperative refolding/renaturation behaviour of guanidinium hydrochloride (GdnHCl) denatured bovine serum albumin (BSA) in the presence of cationic surfactant cetyltrimethylammonium bromide (CTAB), anionic surfactant sodium dodecyl sulphate (SDS) and their catanionic mixture in the solution of 60 mM sodium phosphate buffer of physiological pH 7.4, using artificial chaperone-assisted two-step method. Here, we have employed biophysical techniques to characterize the refolding mechanism of denatured BSA after 200 times of dilution in the presence of cationic, anionic surfactants and their catanionic mixture, separately. We have found that minimum refolding of diluted BSA in the presence of 1:1 rational mixture of CTAB and SDS (CTAB/SDS = 50/50), it may be due to the micelles formation which is responsible for the unordered microstructure aggregate formation. Other mixtures (CTAB/SDS = 20/80 and 80/20) slightly played an effective role during refolding process in the presence of methyl-ß-cyclodextrin. On other hand, CTAB and SDS are more effective and reflect a good renaturation tendency of denatured BSA solution separately and in existence of methyl-ß-cyclodextrin as compare to their mixture compositions. But overall, CTAB has the better renaturation tendency as compare to SDS in the existence of methyl-ß-cyclodextrin. These results ascribed the presence of charge head group and length of hydrophobic tail of CTAB surfactant that plays an important task during electrostatic and hydrophobic interactions at pH 7.4 at which BSA carries negative charge on their surface. These biophysical parameters suggest that, CTAB surfactant assisted artificial chaperone protocol may be utilized in the protein renaturation/refolding studies, which may address the associated problems of biotechnological industries for the development of efficient and inexpensive folding aides, which may also be used to produced genetically engineered cells related diseases, resulting from protein misfolding/aggregation.

A High-Throughput Automated Protein Folding System.

In vitro protein folding can be employed to produce complex proteins expressed as insoluble inclusion bodies in E. coli from laboratory to commercial scale. Often the most challenging step is identification of renaturation conditions that will enable the denatured protein to form the native structure at an acceptable yield. Generally this requires screening a matrix of buffers and stabilizers to find an appropriate solution. Herein, we describe an automated and quantitative method to identify optimal in vitro protein folding parameters with a high rate of success.

Use of Recombinant Fusion Proteins in a Fluorescent Protease Assay Platform and Their In-gel Renaturation.

Proteases are intensively studied enzymes due to their essential roles in several biological pathways of living organisms and in pathogenesis; therefore, they are important drug targets. We have developed a magnetic-agarose-bead-based assay platform for the investigation of proteolytic activity, which is based on the use of recombinant fusion protein substrates. In order to demonstrate the use of this assay system, a protocol is presented on the example of human immunodeficiency virus type 1 (HIV-1) protease. The introduced assay platform can be utilized efficiently in the biochemical characterization of proteases, including enzyme activity measurements in mutagenesis, kinetic, inhibition, or specificity studies, and it may be suitable for high-throughput substrate screening or may be adapted to other proteolytic enzymes. In this assay system, the applied substrates contain N-terminal hexahistidine (His6) and maltose-binding protein (MBP) tags, cleavage sites for tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein. The substrates can be efficiently produced in Escherichia coli cells and easily purified using nickel (Ni)-chelate-coated beads. During the assay, the proteolytic cleavage of bead-attached substrates leads to the release of fluorescent cleavage fragments, which can be measured by fluorimetry. Additionally, cleavage reactions can be analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A protocol for the in-gel renaturation of assay components is also described, as partial renaturation of fluorescent proteins enables their detection based on molecular weight and fluorescence.

Investigating Mechanisms that Control Ubiquitin-Mediated DAF-16/FOXO Protein Turnover.

Protein turnover of FOXO family transcription factors is regulated by the ubiquitin-proteasome system. A complex interplay of factors that covalently attach certain types of ubiquitin chains (E3-ubiquitin ligases), and enzymes that are able to remove ubiquitin conjugates (deubiquitylases), regulate the degradation of FOXO proteins by the proteasome. Here, we describe methods to characterize candidate E3-ubiquitin ligases and deubiquitylases as regulators of the FOXO ubiquitylation status. Our protocol can be utilized to purify and enrich a ubiquitylated FOXO pool from cultured cells under denaturing conditions, which inactivates cellular deubiquitylases and thereby protects ubiquitin conjugates on FOXO proteins. In addition, our method describes how ubiquitylated FOXO proteins can be renatured in a stepwise fashion to serve as substrates for in vitro deubiquitylation (DUB) assays.

Self-Organization of Recombinant Membrane Porin OmpF from Yersinia pseudotuberculosis in Aqueous Environments.

Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8 M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation. In aqueous solutions, rOmpF undergoes conformational changes, reversible self-association, and aggregation. When transferred from 8 M urea into water, PBS (containing 0.15 M NaCl, pH 7.4), or buffer containing 0.8 M urea (pH 8.0), fully unfolded rOmpF forms relatively compact monomeric intermediates prone to self-association with formation of multimers. The oligomeric intermediates have high content of native protein-like secondary structure and pronounced tertiary structure. In acidic media (pH 5.0, close to the protein isoelectric point), rOmpF undergoes rapid irreversible aggregation. Therefore, we found that medium composition significantly affects both porin folding and processes of its self-association and aggregation.

ZEITLUPE Contributes to a Thermoresponsive Protein Quality Control System in Arabidopsis.

Cellular proteins undergo denaturation and oxidative damage under heat stress, forming insoluble aggregates that are toxic to cells. Plants possess versatile mechanisms to deal with insoluble protein aggregates. Denatured proteins are either renatured to their native conformations or removed from cellular compartments; these processes are often referred to as protein quality control. Heat shock proteins (HSPs) act as molecular chaperones that assist in the renaturation-degradation process. However, how protein aggregates are cleared from cells in plants is largely unknown. Here, we demonstrate that heat-induced protein aggregates are removed by a protein quality control system that includes the ZEITLUPE (ZTL) E3 ubiquitin ligase, a central circadian clock component in Arabidopsis thaliana ZTL mediates the polyubiquitination of aggregated proteins, which leads to proteasomal degradation and enhances the thermotolerance of plants growing at high temperatures. The ZTL-defective ztl-105 mutant exhibited reduced thermotolerance, which was accompanied by a decline in polyubiquitination but an increase in protein aggregate formation. ZTL and its interacting partner HSP90 were cofractionated with insoluble aggregates under heat stress, indicating that ZTL contributes to the thermoresponsive protein quality control machinery. Notably, the circadian clock was hypersensitive to heat in ztl-105 We propose that ZTL-mediated protein quality control contributes to the thermal stability of the circadian clock.

Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections.

Multiplexing, labeling for multiple immunostains in the very same cell or tissue section in situ, has raised considerable interest. The methods proposed include the use of labeled primary antibodies, spectral separation of fluorochromes, bleaching of the fluorophores or chromogens, blocking of previous antibody layers, all in various combinations. The major obstacles to the diffusion of this technique are high costs in custom antibodies and instruments, low throughput, and scarcity of specialized skills or facilities. We have validated a method based on common primary and secondary antibodies and diffusely available fluorescent image scanners. It entails rounds of four-color indirect immunofluorescence, image acquisition, and removal (stripping) of the antibodies, before another stain is applied. The images are digitally registered and the autofluorescence is subtracted. Removal of antibodies is accomplished by disulfide cleavage and a detergent or by a chaotropic salt treatment, this latter followed by antigen refolding. More than 30 different antibody stains can be applied to one single section from routinely fixed and embedded tissue. This method requires a modest investment in hardware and materials and uses freeware image analysis software. Multiplexing on routine tissue sections is a high throughput tool for in situ characterization of neoplastic, reactive, inflammatory, and normal cells.

Alumina nanoparticle-assisted enzyme refolding: A versatile methodology for proteins renaturation.

We present a high-yield method for the renaturation of negatively charged enzymes. The approach is based on the use of alumina nanoparticles, which after electrostatic interaction with denatured protein molecules, prevent their aggregation and make the process of refolding controllable. The method, demonstrated by the renaturation of several enzymes, is efficient, rapid, employs a minimal amount of reagents and even can be applied to renature mixture of the denatured enzymes.

Collagen type I from bovine bone. Effect of animal age, bone anatomy and drying methodology on extraction yield, self-assembly, thermal behaviour and electrokinetic potential.

Natural collagen is easily available from animal tissues such as bones. Main limitations reported in the use of natural collagen are heterogeneity and loss of integrity during recovery. However, its natural complexity, functionality and bioactivity still remain to be achieved through synthetic and recombinant ways. Variability of physicochemical properties of collagen extracted from bovine bone by acetic acid was then investigated taking into account endogenous and exogenous factors. Endogenous: bovine's bones age (4 and 7 years) and anatomy (femur and tibia); exogenous: thermal treatments (spray-drying and lyophilisation). Scanning electron microscopy, spectroscopy (EDS, FTIR, UV/Vis and CD), differential scanning calorimetry (DSC), centesimal composition, mass spectrometry, amino acids and zeta-potential analysis were used for the purpose. Age correlated negatively with yield of recovery and positively with minerals and proteoglycans content. Comparing the anatomy, higher yields were found for tibias, and higher stability of tibias collagen in solution was noticed. Whatever the age and the anatomy, collagens were able to renature and to self-assemble into tri-dimensional structures. Nonetheless thermal stability and kinetics of renaturation were different. Variability of natural collagen with bone age and anatomy, and drying methodology, may be a crucial advantage to conceive tailor-made applications in either the biological or technical sector.

Experimental Model System to Study pH Shift-Induced Aggregation of Monoclonal Antibodies Under Controlled Conditions.

PURPOSE: To present a convenient screening method for evaluating additive effects on the renaturation of an acid-exposed monoclonal antibody (mAb). METHODS: The assay involves brief incubation of a mAb at acidic pH and subsequent neutralization in the absence or presence of additive to induce mainly aggregation. An increase in absorbance depicted aggregation. The recorded aggregation data traces were fitted with a nucleation-autocatalytic growth model for the extraction of kinetic parameters. RESULTS: All kinetic data traces were fitted successfully with the selected model and the adjusted R square values were greater than 0.99. Trehalose had strongly stabilizing, proline mildly stabilizing and trimethylamine oxide had destabilizing effects on both the nucleation and growth phase of the reaction. Histidine was strongly stabilizing but was limited by its poor solubility. CONCLUSION: The results demonstrate the suitability of the experimental mAb aggregation system and the nucleation-autocatalytic growth fit in the screening and quantification of additive effects on the renaturation of an acid-exposed mAb respectively. This will aid the investigation and derivation of quantitative structure-activity relationships of additive effects on mAb solubility.

Purification and Refolding to Amyloid Fibrils of (His)6-tagged Recombinant Shadoo Protein Expressed as Inclusion Bodies in E. coli.

The Escherichia coli expression system is a powerful tool for the production of recombinant eukaryotic proteins. We use it to produce Shadoo, a protein belonging to the prion family. A chromatographic method for the purification of (His)6-tagged recombinant Shadoo expressed as inclusion bodies is described. The inclusion bodies are solubilized in 8 M urea and bound to a Ni(2+)-charged column to perform ion affinity chromatography. Bound proteins are eluted by a gradient of imidazole. Fractions containing Shadoo protein are subjected to size exclusion chromatography to obtain a highly purified protein. In the final step purified Shadoo is desalted to remove salts, urea and imidazole. Recombinant Shadoo protein is an important reagent for biophysical and biochemical studies of protein conformation disorders occurring in prion diseases. Many reports demonstrated that prion neurodegenerative diseases originate from the deposition of stable, ordered amyloid fibrils. Sample protocols describing how to fibrillate Shadoo into amyloid fibrils at acidic and neutral/basic pHs are presented. The methods on how to produce and fibrillate Shadoo can facilitate research in laboratories working on prion diseases, since it allows for production of large amounts of protein in a rapid and low cost manner.

Enzyme renaturation to higher activity driven by the sol-gel transition: Carbonic anhydrase.

We describe a so-far unknown route for renaturing denatured enzymes, namely subjecting the denatured enzyme to an oxide sol-gel transition. The phenomenon was revealed in a detailed study of denatured carbonic anhydrase which was subjected to an alumina sol-gel transition, up to the thermally stabilizing entrapment in the final xerogel. Remarkably, not only that the killed enzyme regained its activity during the sol-gel process, but its activity increased to 180% of the native enzyme. To the best of our knowledge, this is the first report of enhanced activity following by renaturing (a "Phoenix effect"). Kinetic study which revealed a five-orders of magnitude (!) increase in the Arrhenius prefactor upon entrapment compared to solution. Circular dichroism analysis, differential scanning calorimetry, zeta potential analyses as well as synchronous fluorescence measurements, all of which were used to characterize the phenomenon, are consistent with a proposed mechanism which is based on the specific orienting interactions of the active site of the enzyme with respect to the alumina interface and its pores network.

On-Membrane Renaturation of Recombinant Ro60 Autoantigen by Calcium Ions.

Calcium plays an important role in many biochemical processes in different cell types. This divalent cation interacts with specific calcium-binding proteins that serve as calcium sensors and regulatory proteins to mediate its function. Previously, we found that calcium was involved in the protein-protein interaction observed between Ro60 multiple antigenic peptides and Ro60 autoantigen. Since calcium bound Ro60 multiple antigenic peptides, we hypothesized that it would renature human recombinant Ro60 on a protein blot. We found that anti-Ro60 antibodies bound significantly higher to the recombinant Ro60 antigen that was incubated with calcium compared to that incubated without calcium on a polyvinylidene fluoride (PVDF) blot. Since the immunological epitopes of Ro60 are mainly conformational, we believe that calcium induced a more native tertiary structure in recombinant Ro60 autoantigen following blotting to a PVDF membrane.

Early Days of Pressure Denaturation Studies of Proteins.

The denaturation of protein by pressure has been generally well known since the findings of the perfect coagulation of egg white by a pressure of 7,000 atm within 30 min by Bridgman (J Biol Chem 19:511-512, 1914), and Kiyama and Yanagimoto (Rev Phys Chem Jpn 21:41-43, 1951) confirmed that the coagulation occurs above 3,880 kg cm(-2). Grant et al. (Science 94:616, 1941) and Suzuki and Kitamura (Abstracts of 30th annual meeting of Japanese Biochemical Society, 1957) found that SH groups are detected at the compressed sample of ovalbumin. On the other hand, Johnson and Campbell (J Cell Comp Physiol 26:43-49, 1945), Tongur (Kolloid Zhur 11:274-279, 1949; Biokhimiya 17:495-503, 1952) and Suzuki et al. (Mem Res Inst Sci Eng Ritsumeikan Univ 3:1-4, 1958) reported that the thermal denaturation of proteins is retarded in a few examples by the low pressure of about 1,000 atm. Before 1960, the studies of denaturation under high pressure were, however, rare and almost qualitative compared with those by heat, acid, urea and so on, so that there was no theory for the influence of hydrostatic pressure on the mechanism of denaturation. Here I review how I started experiments and analysis on pressure denaturation of proteins in early days of 1950s and 1960s in my laboratory and others.