QPNC-PAGE

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Folding funnel: By minimizing its free energy an unfolded polypeptide chain assumes its native structure. To protect the native state from unfolding, the conditions of native GE must be precisely adjusted for subsequent 3D structure determination. Folding funnel schematic.svg
Folding funnel: By minimizing its free energy an unfolded polypeptide chain assumes its native structure. To protect the native state from unfolding, the conditions of native GE must be precisely adjusted for subsequent 3D structure determination.

QPNC-PAGE, or QuantitativePreparativeNativeContinuousPolyacrylamideGel Electrophoresis, is an advanced bioanalytical, high-resolution and high-precision zone electrophoresis technique applied in biochemistry and bioinorganic chemistry to separate water-soluble proteins or protein isoforms by isoelectric point and by continuous elution from a gel column for further characterization. This standardized 1D hybrid variant of native gel electrophoresis and preparative polyacrylamide gel electrophoresis is used to resolve physiological concentrations of macromolecules with high recovery, for example, into active or native metalloproteins in biological samples or into properly and improperly folded metal cofactor-containing proteins in complex protein mixtures.

Contents

QPNC-PAGE reduces the concentration of contaminating metal ions and dipolar compounds in a sample, thereby preventing the misidentification of apometalloproteins (without cofactor) as holometalloproteins (with cofactor) and interfering metal exchange reactions. This is crucial for the study of diseases associated with protein misfolding, such as Alzheimer's disease, which are significantly influenced by metal ion cofactors. The gel used in this technique has been optimized through specific modifications to its polymerization process and chemical composition to ensure complete polymerization and large, homogeneous pore sizes. This eliminates the limitations of other native protein gel electrophoresis methods, where incomplete polymerization can lead to artifacts, denaturation or semi-quantitative results.

The QPNC-PAGE multi-platform experimental design for metalloproteomics can be used with a variety of samples, including purified, partially purified, and raw biological samples, collected from living organisms for purposes such as diagnosis, research, or the production of therapeutics. Complex protein solutions from these samples typically behave physically similarly to colloidal suspensions. Quantitative analytical results from this approach transform the management of Alzheimer from a subjective, symptom-based approach to an objective, biology-based one, which is fundamental for effective and safe therapy in a complex disease. [1] [2] [3]

Method and methodology

Biochemical basis

Proteins perform several functions in living organisms, including catalytic reactions and transport of molecules or ions within the cells, the organs or the whole body. The understanding of the metabolic processes in human organisms, which are mainly driven by biochemical reactions and protein-protein interactions, depends to a great extent on the ability to isolate active proteins in biological extracts or fluids for more detailed examination of chemical structure and physiological function. This essential information can imply an important indication of a patient's state of health. [4]

As about 30–40% of all known proteins contain one or more metal ion cofactors (e.g., ceruloplasmin, ferritin, amyloid-beta precursor protein, matrix metalloproteinase, or metallochaperones), especially native and denatured metalloproteins have to be isolated, identified and quantified after liquid biopsy or tissue extraction in physiological buffer. Many of these cofactors (e.g., iron, copper, or zinc) play a key role in vital enzymatic catalytic processes, such as electron transport and redox transformations, or stabilize globular protein molecules driven by protein-cofactor interactions. [5] Therefore, the high-precision gel electrophoresis and other complementary separation techniques are highly relevant as initial step of protein and trace metal speciation analysis of biological specimen, subsequently, followed by advanced mass spectrometric and magnetic resonance methods for quantifying and identifying the soluble proteins of interest. [6]

Separation and buffering mechanisms

Equipment for bioanalytical continuous-elution GE: electrophoresis chamber, peristaltic pump, fraction collector, buffer recirculation pump and UV detector (in the refrigerator), power supply and recorder (on the table). Electrphoresis Tools.TIF
Equipment for bioanalytical continuous-elution GE: electrophoresis chamber, peristaltic pump, fraction collector, buffer recirculation pump and UV detector (in the refrigerator), power supply and recorder (on the table).

In gel electrophoresis (GE), ampholytes or zwitterions, such as proteins and peptides, are normally separated by charge, size, or shape. [8] The aim of isoelectric focusing (IEF), for example, is to separate proteins according to their isoelectric point (pI), thus, according to their net charge at different pH values using immobilized pH gradient gels. [9] Here, a similar mechanism is accomplished in a commercially available electrophoresis chamber with integrated elution chamber for separating charged biomolecules, for example, superoxide dismutase (SOD) [10] or allergens, [11] at constantly higher pH conditions and different migration rates depending on different isoelectric points in an optimized resolving gel. [12]

The aqueous samples are stabilized in glycerol prior to separation. Small impurities in the form of non-protein-like dipolar molecules (e.g., vitamins, carbohydrates, metabolic intermediates, and nucleotides) do not migrate through the gel because they lack the net charge required for migration in an electric field. Free metal ions (cations) migrate to the cathode and are thus separated from the proteins in the sample. Small, negatively charged molecular ions (anions) are removed by electrophoretic migration and initially eluted through the continuous buffer system. Subsequently, the separated (metal) proteins elute sequentially, almost independently of their molecular mass, current folding state or hydrodynamic volume, starting with the lowest (pI > 2–4) and ending with the highest isoelectric point (pI < 10.0) of the dissolved protein molecules to be analyzed. [12]

Due to the specific properties of the prepared gel and electrophoresis buffer solution which is basic and contains Tris-HCl and NaN3, [7] most proteins of a biological system (e.g., Helicobacter pylori [13] ) are charged negatively in the solution, and will migrate almost frictionlessly as anions from the cathode to the anode due to the electric field. In general, reaction equation (1) shows that the carboxyl side group of a proteinogenic amino acid is negatively charged, equation (2) that the amino side groups are electrically neutral under these conditions:

(1) R-COOH + OH− → R-COO− + H2O

(2) R-NH3+ + OH− → R-NH2 + H2O

Thus, the net charge of a protein molecule is determined by the pH of the electrophoresis buffer.

At the anode, electrochemically-generated hydrogen ions react with Tris molecules to form monovalent Tris ions (3). The positively charged Tris ions migrate through the gel to the cathode where they neutralise hydroxide ions to form Tris molecules and water (4):

(3) (HOCH2)3CNH2 + H+ → [(HOCH2)3CNH3]+

(4) [(HOCH2)3CNH3]+ + OH− → (HOCH2)3CNH2 + H2O

Thus, the Tris-based buffering mechanism causes a constant pH in the continuous buffer system with a high buffer capacity. [14]

At 25 °C Tris buffer has an effective pH range between 7.5 and 9.0. Under the conditions given here (addressing the concentration of buffer components, buffering mechanism, pH and temperature) the effective pH is shifted in the range of about 10.0 to 10.5. Native buffer systems all have low conductivity and range in pH from 3.8 to 10.2. Continuous native buffer systems are thus used to separate proteins according their pI. [15]

Although the constant pH value (10.00) of the electrophoresis buffer does not correspond to a physiological pH value within a cell or tissue type, the separated ring-shaped protein bands (zones) are continuously eluted from the gel column into a physiological buffer solution (pH 8.00) and isolated in different fractions. [7] Provided that irreversible denaturation cannot be demonstrated by an independent procedure, most protein molecules are stable in aqueous solution, at pH values from 3 to 10 if the temperature is below 50 °C. [16] As the Joule heat and temperature generated during electrophoresis may exceed 50 °C, [17] and thus, have a negative impact on the stability and migration behavior of proteins in the gel, the separation system, consisting of the electrophoresis chamber, fraction collector and other devices, is cooled in a refrigerator at 4 °C, thus, greatly reducing the risk of heat convection currents. [18] Overheating of the gel is prevented by an additional internal cooling circuit as an integrated part of the electrophoresis chamber and by generating a low, constant power by the power supply. [19]

Gel properties and polymerization time

Best polymerization conditions for polyacrylamide gels (PAG) are obtained at 25–30 °C [20] and polymerization seems terminated after 20–30 min of reaction although residual monomers (10–30%) are detected after this time. [21] The co-polymerization of acrylamide (AA) monomer/N,N'-Methylenebisacrylamide (Bis-AA) cross-linker initiated by ammonium persulfate (APS)/tetramethylethylenediamine (TEMED) reactions, is most efficient at alkaline pH of the acrylamide solution. Thereby, acrylamide chains are created and cross-linked at a time. Due to the properties of the electrophoresis buffer, the gel polymerization is conducted at pH 10.00 making sure an efficient use of TEMED and APS as catalysts of the polymerization reaction, and concurrently, suppressing a competitive hydrolysis of the produced acrylamide polymer network (gel matrix). Polymer networks are three-dimensionally linked polymer chains. Otherwise, proteins could be modified by reaction with unpolymerized monomers of acrylamide, forming covalent acrylamide adduction products that may result in multiple bands. [22]

Additionally, the time of polymerization of a gel can directly affect the peak-elution times of separated metalloproteins in the electropherogram due to the compression and dilatation of the gels and their pores if the incubation times for the reaction mixture used to prepare a gel are not optimized. In order to ensure maximum reproducibility in gel pore size and to obtain a fully polymerized and non-restrictive large pore gel for a PAGE run, the polyacrylamide gel is polymerized for a time period of 69 hr at room temperature (RT) in a graduated glass column (gel tube) enclosing the cooling core on the casting stand. Atmospheric oxygen is excluded during this process. [19] The exothermic heat generated by the polymerization processes is dissipated constantly while the temperature may rise rapidly to over 75 °C in the first minutes, after which it falls slowly. [23] According to empirical studies, the gel reaches room temperature after exactly 69 hours and is then in a state of lowest energy, as the basic chemical reactions and gelation are complete. [19] Gelation means that the solvent (water) gets immobilized within the polymer network by means of hydrogen bonds and also van der Waals forces. As a result, the prepared gel is homogeneous (in terms of homogeneous distribution of cross-links throughout the gel sample [24] ), inherently stable and free of monomers or radicals. Fresh polyacrylamide gels are further hydrophilic, electrically neutral and do not bind proteins. [25] Sieving effects due to gravity-induced compression of the gel column can be excluded for stability reasons. Thus, in a medium without molecular sieving properties a high-resolution can be expected. [26]

Before an electrophoretic run is started the prepared 4% T (total polymer content (T)), 2.67% C (cross-linker concentration (C)) resolving gel, which has the shape of a hollow cylinder (gel column) and encapsulates the cooling core, is pre-run to equilibrate it. [7] It is essentially non-sieving and optimal for electrophoresis of proteins greater than or equal to 200 ku. Proteins migrate in it more or less on the basis of their free mobility. [27] For these reasons interactions of the gel with these biomolecules are negligibly low, and thus, the proteins separate cleanly and predictably in a cooled anticonvective medium with a polymerization time of 69 hr. [7] The separated metalloproteins including biomolecules ranging from approximately < 1 ku to greater than 30 ku (e.g., metal chaperones, normal prions, metal transport proteins (plasma proteins), globular metalloenzymes, globular hydrophilic metallopeptides, metallothionein, phytochelatins) are not dissociated into apoproteins and metal ion cofactors. [28]

Reproducibility and recovery

Electropherogram showing four runs of a high molecular weight plant model protein (m [?] 200 kDa, LRR) as a function of the polymerization time of PAG. Detection method of Cd cofactor concentrations (in mg/L): GF-AAS. Preparative Electroph.TIF
Electropherogram showing four runs of a high molecular weight plant model protein (m ≈ 200 kDa, LRR) as a function of the polymerization time of PAG. Detection method of Cd cofactor concentrations (in μg/L): GF-AAS.

The bioactive structures (native or 3D conformation or shape) of the isolated protein molecules do not undergo any significant conformational changes. Thus, active metal cofactor-containing proteins can be isolated reproducibly in the same fractions after a PAGE run. [12] A shifting peak in the respective electropherogram indicates that the standardized time of gel polymerization (69 hr, RT) is not implemented in a PAGE experiment. A shortening of the standardized polymerization time (< 69 hr) stands for incomplete polymerization, and thus, for inherent instability due to gel softening during the cross-linking of polymers as the material reaches swelling equilibrium, [29] whereas exceeding this time limit (> 69 hr) is an indicator of gel aging. [30] The phenomenon of gel aging is closely connected to long-term viscosity decrease of aqueous polyacrylamide solutions [31] and increased swelling of hydrogels. [32]

Under these standard conditions, metalloproteins with different molecular mass ranges and isoelectric points have been recovered in biologically active form at a quantitative yield of more than 95%. [19] By preparative SDS-PAGE standard proteins (cytochrome c, aldolase, ovalbumin and bovine serum albumin) with molecular masses of 14–66 ku can be recovered with an average yield of about 73.6%. [33] Preparative isotachophoresis (ITP) is applied for isolating palladium-containing proteins with molecular masses of 362 ku (recovery: 67%) and 158 ku (recovery: 97%). [34]

Quantification and identification

Physiological concentrations (ppb-range) of iron, copper, zinc, nickel, molybdenum, palladium, cobalt, manganese, platinum, chromium, cadmium and other metal cofactors can be identified and absolutely quantified in an aliquot of an analytical fraction by inductively coupled plasma mass spectrometry (ICP-MS) [35] or total reflection X-ray fluorescence (TXRF), [36] for example. In case of ICP-MS the structural information of the functionally associated metallobiomolecules is irreversibly lost due to ionization of the sample with plasma. [37] [38] Another established high sensitive detection method for the determination of trace elements in biological samples is graphite furnace atomic absorption spectroscopy (GF-AAS). [39] Because of high purity and optimized concentration of the separated properly folded metalloproteins, for example, therapeutic recombinant plant-made pharmaceuticals such as copper chaperone for superoxide dismutase (CCS) from medicinal plants, in a few specific PAGE fractions, the related 3D structures of these bioactive analytes can be quantitatively elucidated in an aliqot of a fraction by using solution NMR spectroscopy under non-denaturing conditions. [40]

Applications

Improperly folded metal proteins, for example, CCS or Cu-Zn-superoxide dismutase (SOD1) present in brain, blood or other clinical samples, are indicative of neurodegenerative diseases like Alzheimer's disease (AD) or amyotrophic lateral sclerosis (ALS). [41] Functional CCS or SOD molecules contribute to intracellular homeostatic control of essential metal ion species (e.g., Cu1+/2+, Zn2+, Fe2+/3+, Mn2+, Ni3+) in living organisms, and thus, these biomolecules can balance pro-oxidative and antioxidative processes in the cytoplasm. [42] Otherwise, free or loosely bound transition metal ions take part in Fenton-like reactions in which deleterious hydroxyl radical is formed, which unrestrained would be destructive to proteins. [43] The loss of active CCS increases the amyloid-β production in neurons which, in turn, is a major pathological hallmark of AD. [44] Therefore, copper chaperone for superoxide dismutase is proposed to be one of the most promising biomarkers of copper toxicity in these diseases. [45] CCS should be analysed primarily in blood because a meta-analysis of serum data showed that AD patients have higher levels of serum Cu than healthy controls. [46]

Limitations

The main limitations of Quantitative Preparative Native Continuous Polyacrylamide Gel Electrophoresis are its technical complexity, demanding protocol, technical expertise, specialized equipment, multi-platform experimental design, long runtime, sample capacity, sample loss due to multianalytical processing steps, manual operator intervention, co-migrating proteins, unsuitability for membrane proteins due to their water insolubility, and high cost, which may limit its availability for routine laboratory and high-throughput applications. [7]

History

In the late 1990s, QPNC-PAGE was developed at the Jülich Research Centre to optimize the chemical composition and physico-chemical properties of the acrylamide gel matrix, as incomplete polymerization processes during electrophoresis lead to dynamic compression and decompression effects in the gel, which impair the results of protein purification. [47] A new gel design made it possible to elucidate the relationships between gel properties and polymerization time on the one hand, and reproducibility and recovery on the other. For the first time in the history of electrophoresis, an independent method confirmed that physiological concentrations of proteins containing bioactive metal cofactors do not denature during preparative native gel electrophoresis runs. [12] Metal proteins of any size or folding state could be isolated in quantitative amounts for further analysis or structure determination in a combined procedure. [28] As a sophisticated technique compatible with sensitive downstream analyses, this was finally published in the Nature Portfolio in 2010 [7] and patented by the DPMA in 2014. [48]

Persons

This highly specialized electrophoretic technique for investigating the quantitative relationship between metal metabolism and protein folding in clinical research, as well as the structure-function relationships of fragile metal proteins, was invented by Bernd Kastenholz and was significantly influenced by the pioneering work of David E. Garfin and several other specialist authors from various fields, such as Jürgen Horst, Kerstin A. Nagel, and Klaus Günther. Building on existing findings in natural product pharmacology and metal-related neurobiology, Kastenholz, Garfin, Horst, and Nagel were among the first researchers to specifically propose the use of plant-made copper chaperones for Alzheimer's therapy by identifying therapeutic mechanisms to reduce the cellular toxicity of intracellular protein aggregates. [42]

See also

References

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  48. ↑ "Method of isolating metal cofactors from biological organic systems using preparative native polyacrylamide continuous gel electrophoresis (PNC-PAGE)". Google Patents. Retrieved 9 October 2025.

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