Method For Purification Of Proteins Research Articles

Expression in Escherichia coli, Refolding, and Purification of Plant Aspartic Proteases.

Aspartic proteases (APs) are widely distributed in plants. The large majority of genes encoding putative APs exhibit distinct features when compared with the so-called typical APs, and have been grouped as atypical and nucellin-like APs. Remarkably, a diverse pattern of enzymatic properties, subcellular localizations, and biological functions are emerging for these proteases, illustrating the functional complexity among plant pepsin-like proteases. However, many key questions regarding the structure-function relationships of plant APs remain unanswered. Therefore, the expression of these enzymes in heterologous systems is a valuable strategy to unfold the unique features/biochemical properties among members of this family of proteases. Here, we describe our protocol for the production and purification of recombinant plant APs, using a procedure where the protein is refolded from inclusion bodies by dialysis. This method allows the production of untagged versions of the target protease, which has revealed to be critical to disclose differences in processing/activation requirements between plant APs. The protocol includes protein expression, washing and solubilization of inclusion bodies, refolding by dialysis, and a protein purification method. Specific considerations on critical aspects of the refolding process and further suggestions for evaluation of the final recombinant product are also provided.

Protein Purification and Digestion Methods for Bacterial Proteomic Analyses.

Reproducible protein extraction is critical for the quantitative analysis of bacterial proteomes. While a wide range of techniques exist, there is no one-size-fits-all solution that will be suitable for all applications. In this report, we describe a set of standard extraction methods that have been adapted for a range of bacterial proteome analyses.

Towards an enhanced control of protein crystallization: Seeded batch lysozyme crystallization in a meso oscillatory flow reactor

Protein crystallization has been shown as a viable alternative to conventional protein purification methods. However, the stochastic and spontaneous nature of the primary nucleation process makes protein crystallization difficult to control. An approach often used in the crystallization of small organic and inorganic molecules to improve the reproducibility of the process and better control the crystallization outcome is seeding. This study presents for the first time the investigation of seeding on batch protein crystallization in a meso oscillatory flow reactor (meso-OFR). Seeded and unseeded lysozyme batch crystallization experiments were carried out, where the influence of the initial lysozyme concentration (initial supersaturation) and the seed quantity on the onset of nucleation, crystal properties and yield was assessed. No major influence of the seed quantity on the product crystal size was verified for the initial lysozyme concentration of 20 mg·mL−1 (below the secondary nucleation threshold - SNT), while for the initial lysozyme concentration of 25 mg·mL−1 (above the SNT) the onset of nucleation and mean crystal size significantly decrease with increasing seed quantity. Further, crystal yield increases with both the initial lysozyme concentration and seed quantity. Overall, the results highlight seeding as a promising technique to improve control over the crystallization time and product crystal size.

Mem-iLID, a fast and economic protein purification method.

Protein purification is the vital basis to study the function, structure and interaction of proteins. Widely used methods are affinity chromatography-based purifications, which require different chromatography columns and harsh conditions, such as acidic pH and/or adding imidazole or high salt concentration, to elute and collect the purified proteins. Here we established an easy and fast purification method for soluble proteins under mild conditions, based on the light-induced protein dimerization system improved light-induced dimer (iLID), which regulates protein binding and release with light. We utilize the biological membrane, which can be easily separated by centrifugation, as the port to anchor the target proteins. In Xenopus laevis oocyte and Escherichia coli, the blue light-sensitive part of iLID, AsLOV2-SsrA, was targeted to the plasma membrane by different membrane anchors. The other part of iLID, SspB, was fused with the protein of interest (POI) and expressed in the cytosol. The SspB-POI can be captured to the membrane fraction through light-induced binding to AsLOV2-SsrA and then released purely to fresh buffer in the dark after simple centrifugation and washing. This method, named mem-iLID, is very flexible in scale and economic. We demonstrate the quickly obtained yield of two pure and fully functional enzymes: a DNA polymerase and a light-activated adenylyl cyclase. Furthermore, we also designed a new SspB mutant for better dissociation and less interference with the POI, which could potentially facilitate other optogenetic manipulations of protein–protein interaction.

Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts

Protein crystallization can function as an effective method for protein purification or formulation. Such an application requires a comprehensive understanding of the intermolecular protein–protein interactions that drive and stabilize protein crystal formation to ensure a reproducible process. Using alcohol dehydrogenase from Lactobacillus brevis (LbADH) as a model system, we probed in our combined experimental and computational study the effect of residue substitutions at the protein crystal contacts on the crystallizability and the contact stability. Increased or decreased contact stability was calculated using molecular dynamics (MD) free energy simulations and showed excellent qualitative correlation with experimentally determined increased or decreased crystallizability. The MD simulations allowed us to trace back the changes to their physical origins at the atomic level. Engineered charge–charge interactions as well as engineered hydrophobic effects could be characterized and were found to improve crystallizability. For example, the simulations revealed a redesigning of a water mediated electrostatic interaction (“wet contact”) into a water depleted hydrophobic effect (“dry contact”) and the optimization of a weak hydrogen bonding contact towards a strong one. These findings explained the experimentally found improved crystallizability. Our study emphasizes that it is difficult to derive simple rules for engineering crystallizability but that free energy simulations could be a very useful tool for understanding the contribution of crystal contacts for stability and furthermore could help guide protein engineering strategies to enhance crystallization for technical purposes.

An Economical and Versatile High-Throughput Protein Purification System Using a Multi-Column Plate Adapter.

Protein purification is imperative to the study of protein structure and function and is usually used in combination with biophysical techniques. It is also a key component in the development of new therapeutics. The evolving era of functional proteomics is fueling the demand for high-throughput protein purification and improved techniques to facilitate this. It was hypothesized that a multi column plate adaptor (MCPA) can interface multiple chromatography columns of different resins with multi-well plates for parallel purification. This method offers an economical and versatile method of protein purification that can be used under gravity or vacuum, rivaling the speed of an automated system. The MCPA can be used to recover milligram yields of protein by an affordable and time efficient method for subsequent characterization and analysis. The MCPA has been used for high-throughput affinity purification of SH3 domains. Ion exchange has also been demonstrated via the MCPA to purify protein post Ni-NTA affinity chromatography, indicating how this system can be adapted to other purification types. Due to its setup with multiple columns, individual customization of parameters can be made in the same purification, unachievable by the current plate-based methods.

An Economical and Versatile High-Throughput Protein Purification System Using a Multi-Column Plate Adapter

A multi-column plate adapter allows chromatography columns to be interfaced with multi-well collection plates for parallel affinity or ion exchange purification providing an economical high throughput protein purification method. It can be used under gravity or vacuum yielding milligram quantities of protein via affordable instrumentation.

Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues.

To elucidate cancer pathogenesis and its mechanisms at the molecular level, the collecting and characterization of large individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardized methods of formalin fixation and paraffin embedment, these archived FFPE tissues are important collections of pathology material that include patient metadata, such as medical history and treatments. FFPE blocks can be stored under ambient conditions for decades, while retaining cellular morphology, due to modifications induced by formalin. However, the effect of long-term storage, at resource-limited institutions in developing countries, on extractable protein quantity/quality has not yet been investigated. In addition, the optimal sample preparation techniques required for accurate and reproducible results from label-free LC-MS/MS analysis across block ages remains unclear. This study investigated protein extraction efficiency of 1, 5, and 10-year old human colorectal carcinoma resection tissue and assessed three different gel-free protein purification methods for label-free LC-MS/MS analysis. A sample size of n = 17 patients per experimental group (with experiment power = 0.7 and α = 0.05, resulting in 70% confidence level) was selected. Data were evaluated in terms of protein concentration extracted, peptide/protein identifications, method reproducibility and efficiency, sample proteome integrity (due to storage time), as well as protein/peptide distribution according to biological processes, cellular components, and physicochemical properties. Data are available via ProteomeXchange with identifier PXD017198. The results indicate that the amount of protein extracted is significantly dependent on block age (p < 0.0001), with older blocks yielding less protein than newer blocks. Detergent removal plates were the most efficient and overall reproducible protein purification method with regard to number of peptide and protein identifications, followed by the MagReSyn® SP3/HILIC method (with on-bead enzymatic digestion), and lastly the acetone precipitation and formic acid resolubilization method. Overall, the results indicate that long-term storage of FFPE tissues (as measured by methionine oxidation) does not considerably interfere with retrospective proteomic analysis (p > 0.1). Block age mainly affects initial protein extraction yields and does not extensively impact on subsequent label-free LC-MS/MS analysis results.

Large scale production of synthetic spider silk proteins in Escherichia coli

Spider silk, which has remarkable mechanical properties, is a natural protein fiber produced by spiders. Spiders cannot be farmed because of their cannibalistic and territorial nature. Hence, large amounts of spider silk cannot be produced from spiders. Genetic engineering is an alternative approach to produce large quantities of spider silk. Our group has produced synthetic spider silk proteins in E. coli to study structure/function and to produce biomaterials comparable to the silks produced by orb-weaving spiders. Here we give a detailed description of our cloning, expression, and purification methods of synthetic spider silk proteins ranging from ~30 to ~200 kDa. We have cloned the relevant genes of the spider Nephila clavipes and introduced them into bacteria to produce synthetic spider silk proteins using small and large-scale bioreactors. We have optimized the fermentation process, and we have developed protein purification methods as well. The purified proteins are spun into fibers and are used to make alternative materials like films and adhesives with various possible commercial applications.

One-step purification and immobilization of recombinant proteins using SpyTag/SpyCatcher chemistry.

Based on the specific and spontaneous formation of isopeptide bonds by SpyCatcher/SpyTag, we have developed a one-step method for purification and immobilization of recombinant proteins. The procedure is to immobilize SpyCatcher on glyoxyl agarose gels, and then the SpyCatcher immobilisate can be used to immobilize the SpyTag-fused protein in the crude extract selectively. A mutant of SpyCatcher (mSC), in which a peptide (LysGlyLysGlyLysGly) was added to the C-terminus of SpyCatcher and three lysine residues around the SpyTag/SpyCatcher binding domain were replaced with arginine, was designed to improve the attachment of SpyCatcher to the support. Compared with wild-type SpyCatcher, mSC can be immobilized on the glyoxyl-agarose support more efficiently, which enables the obtained mSC derivative a high binding capacity of the SpyTag-fused protein. The results showed that the target proteins in the crude enzyme extract were purified and immobilized in one step, and the thermal stability of the immobilized target proteins was also remarkably improved.

A novel serum protein purification technique combined with surface-enhanced Raman spectroscopy for liver cancer detection

In this study, silver nanoparticles-based surface-enhanced Raman spectroscopy combined with a serum protein purification method was employed to screen liver tumors. The cellulose acetate membrane was used to separate proteins from human serum, and then the purified serum proteins were mixed with silver nanoparticles for surface-enhanced Raman spectroscopy detection. High-quality spectra were recorded from serum protein samples belonging to 45 healthy volunteers and 42 liver cancer patients, and the diagnostic sensitivity and specificity of liver cancer were 90.5% and 95.6%, respectively, indicating that this method has great application potential for the detection and screening of liver cancer.

Influence of Salts on the Adsorption of Lysozyme on a Mixed-Mode Resin

Mixed-mode chromatography (MMC), which combines features of ion exchange chromatography (IEC) and hydrophobic interaction chromatography (HIC), is an interesting method for protein separation and purification. The design of MMC processes is challenging as adsorption equilibria are influenced by many parameters, including ionic strength and the presence of different salts in solution. Systematic studies on the influence of those parameters in MMC are rare. Therefore, in the present work, the influence of four salts, namely, sodium chloride, sodium sulfate, ammonium chloride, and ammonium sulfate, on the adsorption of lysozyme on the mixed-mode resin Toyopearl MX-Trp-650M at pH 7.0 and 25°C was studied systematically in equilibrium adsorption experiments for ionic strengths between 0 mM and 3000 mM. For all salts, a noticeable adsorption strength was observed over the entire range of studied ionic strengths. An exponential decay of the loading of the resin with increasing ionic strength was found until approx. 1000 mM. For higher ionic strengths, the loading was found to be practically independent of the ionic strength. At constant ionic strength, the highest lysozyme loadings were observed for ammonium sulfate, the lowest for sodium chloride. A mathematical model was developed that correctly describes the influence of the ionic strength as well as the influence of the studied salts. The model is the first that enables the prediction of adsorption isotherms of proteins on mixed-mode resins in a wide range of technically interesting conditions, accounting for the influence of the ionic strength and four salts of practical relevance.

IMIDAZOANNELATED IMIDAZOLES: METHODS OF SYNTHESIS AND PRACTICAL APPLICATION

In recent decades, the chemistry of imidazoles, which are most likely due to their strong biological potential and practical application, has attracted more and more attention from scientists. The structural fragment of partially hydrogenated imidazoimidazole is an integral part of azamacrocycle precursors such as 1,4,7,10-tetraazacyclododecane and 1,4,7-triazacyclononane, important macrocycles for chelated compounds. The latter, being often paramagnetic materials, are used as contrast agents in magnetic resonance imaging (MRI), as sensitive MRI probes, are used in positron emission tomography (PET), as well as in radioimmunotherapy (RIT). Along with these uses of saturated imidazoimidazole derivatives, they have also been used as ligands in immobilized metal affinity chromatography (IMAC), the most universal method of protein purification. Analysis of the literature has shown that intermolecular cyclocondensations of amino derivatives with a nitrile moiety, intramolecular cyclocondensations of imidazole derivatives and metal-catalytic synthesis are most often used for the synthesis of imidazo[1,2-a]imidazoles. The article provides a comprehensive generalization of the known methods of obtaining imidazoimidazoles, reveals their practical application for both chemistry and medicine.

Protein Conformational Dynamics upon Association with the Surfaces of Lipid Membranes and Engineered Nanoparticles: Insights from Electron Paramagnetic Resonance Spectroscopy.

Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning from a solution environment to the states in which they are associated with the surfaces of biological membranes or engineered nanoobjects. In the former case these structural transitions generally underlie functional protein states. The latter case is mostly relevant to the application of protein immobilization in biotechnological industries, developing methods for protein purification, etc. Therefore, evaluating the stability of the protein functional state is particularly important. EPR spectroscopy in the form of continuous-wave EPR or pulse EPR distance measurements in conjunction with protein spin labeling provides highly versatile and sensitive tools to characterize the changes in protein local dynamics as well as large conformational rearrangements. The technique can be widely utilized in studies of both protein-membrane and engineered nanoobject-protein complexes.

Purification of Classical Swine Fever Virus E2 Subunit Vaccines Based on High Affinity Peptide Ligand.

The purification of expressed proteins is the most critical part of subunit-- vaccine production. Protein-purification methods such as affinity chromatography and ion exchange still have the shortcomings of being time consuming and complicated. With the rapid development of computational molecular-simulation technology, structure-based peptide-ligand design has become feasible. Objection: We aimed to apply molecular docking for a peptide ligand designed for classical swine fever virus (CSFV) E2 purification. Computational-derived peptides were synthesized, and the in vitro binding interaction with E2 was investigated. The effects of purification on E2 were also evaluated. The best peptide recognizing E2 was P6, which had a sequence of KKFYWRYWEH. Based on kinetic surface plasmon resonance (SPR) analysis, the apparent affinity constant of P6 was found to be 148 nM. Importantly, P6 showed suitable binding affinity and specificity for E2 purification from transgenic rice seeds. Evaluation of immune antibodies in mice showed that the antibody- blocking rate on day 42 after inoculation reached 86.18% and 90.68%. The computational-designed peptide in this study has high sensitivity and selectivity and is thus useful for the purification of CSFV E2. The novel method of design provided a broad platform and powerful tool for protein-peptide screening, as well as new insights into CSFV vaccine design.

Protein Purification Technologies.

Protein Biotechnology is an exciting and fast- growing areaof research, with numerous industrial applications. The growing demand for developing efficient and rapid protein purification methods is driving research and growth in this area. Advances and progress in the techniques and methods of protein purification have been such that one can reasonably expect that any protein of a given order of stability may be purified to currently acceptable standards of homogeneity. However, protein manufacturing cost remains extremely high, with downstream processing constituting a substantial proportion of the overall cost. Understanding of the methods and optimization of the experimental conditions have become critical to the manufacturing industry in order to minimize production costs while satisfying the quality as well as all regulatory requirements. New purification processes exploiting specific, effective and robust methods and chromatographicmaterials are expected to guide the future of the protein purification market.

An Orthogonal Fusion Tag for Efficient Protein Purification.

In this chapter, we present an efficient method for stringent protein purification facilitated by a dual affinity tag referred to as ABDz1, which is based on a 5kDa albumin-binding domain from Streptococcal Protein G. The small fusion tag enables an orthogonal affinity purification approach based on two successive and highly specific affinity purification steps. This approach is enabled by native binding of ABDz1 to human serum albumin and engineered binding to Staphylococcal Protein A, respectively. The ABDz1-tag can be fused to either terminus of a protein of interest and the purification steps can be carried out using standard laboratory equipment.

The rapid \u201cteabag\u201d method for high-end purification of membrane proteins

Overproduction and purification of membrane proteins are generally challenging and time-consuming procedures due to low expression levels, misfolding, and low stability once extracted from the membrane. Reducing processing steps and shortening the timespan for purification represent attractive approaches to overcome some of these challenges. We have therefore compared a fast “teabag” purification method with conventional purification for five different membrane proteins (MraY, AQP10, ClC-1, PAR2 and KCC2). Notably, this new approach reduces the purification time significantly, and the quality of the purified membrane proteins is equal to or exceeds conventional methods as assessed by size exclusion chromatography, SDS-PAGE and downstream applications such as ITC, crystallization and cryo-EM. Furthermore, the method is scalable, applicable to a range of affinity resins and allows for parallelization. Consequently, the technique has the potential to substantially simplify purification efforts of membrane proteins in basic and applied sciences.

Selective protein purification via tangential flow filtration – Exploiting protein-protein complexes to enable size-based separations

Tangential flow filtration (TFF) is a size-based separation method conventionally used for buffer exchange, concentration, pathogen removal, and for coarse purification. In this study, we use TFF for selective purification of proteins in their complexed form. This process was demonstrated to recover human serum albumin (HSA) in its complexed form from an artificially produced mixture of hemoglobin (Hb) and HSA and from plasma using an anti-HSA polyclonal immunoglobulin G (IgG) as the target-protein binding molecule (TPBM). Moreover, haptoglobin (Hp) in its complexed form was recovered from human Cohn Fraction IV using Hb as the TPBM. Hb-Hp was then partially dissociated with 5 M urea to yield Hp. In the experiments performed here, the TP-TPBM had purities >95%, but recovery was low with >50% for HSA-IgG and 10–15% for Hb-Hp. However, a simple mathematical model used to describe the TFF purification process showed that product recovery could be increased without loss of purity by introducing TFF filters with the same MWCO in series. Taken together, this study presents a new method for selective purification of proteins using TFF and simple mathematical models to describe and predict the performance of TFF systems.

A Rapid and Facile Purification Method for Glycan-Binding Proteins and Glycoproteins.

Glycosylated proteins, namely glycoproteins and proteoglycans (collectively called glycoconjugates), are indispensable in a variety of biological processes. The functions of many glycoconjugates are regulated by their interactions with another group of proteins known as lectins. In order to understand the biological functions of lectins and their glycosylated binding partners, one must obtain these proteins in pure form. The conventional protein purification methods often require long times, elaborate infrastructure, costly reagents, and large sample volumes. To minimize some of these problems, we recently developed and validated a new method termed capture and release (CaRe). This method is time-saving, precise, inexpensive, and it needs a relatively small sample volume. In this approach, targets (lectins and glycoproteins) are captured in solution by multivalent ligands called target capturing agents (TCAs). The captured targets are then released and separated from their TCAs to obtain purified targets. Application of the CaRe method could play an important role in discovering new lectins and glycoconjugates. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of crude extracts containing the target proteins from soybean flour Alternate Protocol 1: Preparation of crude extracts from Jack bean meal Alternate Protocol 2: Preparation of crude extracts from the corms of Colocasia esculenta, Xanthosoma sagittifolium, and from the bulbs of Allium sativum Alternate Protocol 3: Preparation of Escherichia coli cell lysates containing human galectin-3 Alternate Protocol 4: Preparation of crude extracts from chicken egg whites (source of ovalbumin) Basic Protocol 2: Preparation of 2% (v/v) red blood cell suspension Basic Protocol 3: Detection of lectin activity of the crude extracts Basic Protocol 4: Identification of multivalent inhibitors as target capturing agents by hemagglutination inhibition assays Basic Protocol 5: Testing the capturing abilities of target capturing agents by precipitation/turbidity assays Basic Protocol 6: Capturing of targets (lectins and glycoproteins) in the crude extracts by target capturing agents and separation of the target-TCA complex from other components of the crude extracts Basic Protocol 7: Releasing the captured targets (lectins and glycoproteins) by dissolving the complex Basic Protocol 8: Separation of the targets (lectins and glycoproteins) from their respective target capturing agents Basic Protocol 9: Verification of the purity of the isolated targets (lectins or glycoproteins).