Purification of the Sarco-Endoplasmic Reticulum Ca2+-ATPase from Rabbit Muscle

Summary

This protocol describes an improved SERCA purification method, which includes the disaccharide trehalose in the final centrifugation step. This carbohydrate stabilizes proteins under harsh conditions. The purified SERCA was catalytically active and displayed high purity, making it suitable for structural and functional studies.

Abstract

Some P-type ATPases, such as sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA), are inherently labile membrane proteins that require specific physicochemical conditions during purification to obtain them with high purity and structural quality and in a catalytically active form. The disaccharide trehalose is a compatible solute that is synthesized and accumulated in high concentrations in the yeast cytoplasm to stabilize the membranes and proteins. The use of trehalose as an additive in the protocol for the purification of plasma membrane H⁺-ATPase results in a high-quality preparation, the hexameric structure of which is shown by biochemical analytical methods. Trehalose can, therefore, be used as a stabilizing additive for the purification of membrane proteins (P-ATPases). This protocol describes the modification of the classical protocol for SERCA purification by subjecting SERCA to centrifugation on a trehalose concentration gradient. The inclusion of this carbohydrate led to the purification of SERCA in a catalytically active form with high purity and, importantly, in a stable form. Partial biochemical characterization of the purified SERCA (SDS-PAGE, enzyme kinetics, FITC labeling, circular dichroism spectroscopy) showed that the enzyme is suitable for functional and structural studies. The use of trehalose in the purification protocol of P-type ATPases and other labile membrane (and cytosolic) proteins is suggested.

Introduction

Membrane proteins/enzymes are essential biological components of cells as they play critical roles in various processes^1,2,3. Some of the functions may include transport of ions and molecules in and out of the cell/internal compartments (either active/passive), cell-cell recognition, intercellular binding, anchorage/attachment, and sensing of the external environment through integration with the signal transduction machinery under normal and harsh physical and chemical conditions (high salt, low water, high temperature, drug resistance, etc.)³ Therefore, the determination of the three-dimensional (3D) structure of membrane proteins and/or enzymes has become of great importance for both basic and applied research^4,7,6. Importantly, membrane proteins/enzymes have been extensively used as targets for drug discovery (whether natural or by design)^7,8,9. That is, membrane proteins have an inherent importance in health^9,10,11.

The hydrophobic character of membrane proteins/enzymes is the most technically challenging physicochemical property for the experimental laboratory^12,13,14, even more so when working with oligomeric and/or highly labile integral membrane proteins^15,16. The isolation of appropriate amounts of the membrane protein/enzyme with the highest possible quality for functional experimental assays and structural studies is highly desirable¹⁷. Membrane proteins, being inherently hydrophobic, are very difficult to purify, and the choice of detergent is usually one of the most important issues to be considered^17,18,19,20. In this regard, the laboratory methods used to isolate membrane proteins typically cause some degree of damage to the 3D structural arrangement of the protein²¹. Some of these methods include the use of (a) sonication (high frequency/energy ultrasonic waves), (b) protein-solubilizing detergents (either harsh, medium, or gentle)²², (c) relatively high pressures in column chromatography and high-speed ultracentrifugation²³, (d) precipitating molecules, (e) digestive enzymes, and others²¹. All these processes can contribute to or be the main cause of protein destabilization during purification²¹. In this respect, some protocols seem to work relatively well for a given membrane protein. However, optimization is always welcome when using new modern assays or methods that require a higher quality of membrane protein preparation to obtain satisfactory results²⁴. Optimization steps may include, but are not limited to, improving construct design, finding optimal conditions for membrane protein expression, establishing better handling conditions (i.e., pH, temperature, etc.), finding the best compatible detergent, adjusting purification steps such as sonication time, centrifugation speed, reformulating buffer solutions by adding stabilizing agents, etc.^25,26,27. Therefore, any change in the purification methodology that leads to an increase in the quality (purity) and activity of the purified membrane protein/enzyme is important.

In the P-type ATPase family, the yeast plasma membrane H⁺-ATPase appears to be one of the most labile members^28,29. The H⁺-ATPase loses its ATP hydrolyzing activity upon dehydration (freeze-drying), heat shock, etc.^28,29. The use of trehalose as a protein stabilizer was tested in the isolation of the plasma membrane H⁺-ATPase from the yeast K. lactis^30,31; the H⁺-ATPase preparation obtained was of high purity and catalytically active. Importantly, this allowed the oligomeric state of the enzyme to be resolved by biochemical methods, revealing it to be a hexamer and later confirmed by cryo-electron microscopy^{31,32,33,34,35}. Therefore, it seems likely that the delicate three-dimensional (3D) arrangement of membrane proteins can be lost under relatively harsh conditions during purification³⁶. Biphasic inactivation kinetic is observed for H⁺-ATPase during heat-mediated inactivation²⁹. In yeast cells, as in many other organisms, the disaccharide trehalose accumulates at high concentrations under environmental stress conditions^37,38,39. Trehalose maintains membrane integrity and transport function by stabilizing proteins (both membrane-embedded and cytosolic) and cell membranes^40,41. The stabilizing mechanism of trehalose has been extensively studied by several groups and by our laboratory^42,43,44,45. Experiments with the H⁺-ATPase and other enzymes have shown that trehalose is the most effective protein stabilizer among mono- and disaccharides^28,29. This led to its inclusion in the H⁺-ATPase purification protocol³⁰. Recently, trehalose has also been used in the purification of the sarcoplasmic reticulum Ca²⁺-ATPase (SERCA) from rabbit fast-twitch muscle with good results in protein purity and activity⁴⁶. Therefore, trehalose seems to be a good and appropriate additive for the purification of P-type ATPases and probably other membrane and cytosolic proteins.

For P-ATPases, the existence of structural cytoplasmic domains is an experimental advantage, especially for substrate/ligand interaction studies⁴⁷; ATP binding has been studied in highly pure recombinant N-domains^47,48,49, thus eliminating the technical considerations for purification of whole membrane enzymes^47,48,50, among others⁵¹. Unfortunately, some functional (catalytic/energy conversion) and structural (subunit arrangement and interaction with other proteins) studies still require the whole P-ATPase^52,53. In this regard, the purification of SERCA has been achieved by several research groups^{54,55,56,57,58}. However, improvements can still be implemented⁴⁶, for example, increasing the intactness of the purified ATPase⁵⁹, avoiding protein denaturation/disruption of protein complexes²⁵, increase solubilization without denaturation of the membrane protein (i.e., avoiding formation of macromolecular aggregates)⁶⁰, lead to better compatibility with assays and other downstream analytical methods⁶¹ Furthermore, as new experimental strategies, additives, enzyme inhibitors, etc. appear in the scientific literature^{61,62,63,64,65,66}, they sometimes need to be tested with the whole P-ATPase. This work describes the protocol for the purification of SERCA and the use of trehalose as an additive to stabilize the protein structure and the ATPase activity; i.e., in addition to increasing the enzyme (structural) quality, trehalose helps to prevent the loss of enzyme structure and activity during enzyme isolation and storage, which helps to save biological material and thus reduce the number of enzyme purifications.

Protocol

All animal procedures were performed in accordance with international and local (NORMA Oficial Mexicana NOM-062-ZOO-1999) guidelines for the handling of animals in experimental laboratories^51,67,68. Muscle tissue was obtained from wild-type Oryctolagus cuniculus from a local animal handling unit (INE/CITES/DGVS-ZOO-E0055-SLP-98)⁴⁶. A veterinarian with expertise in laboratory animal management performed the initial muscle dissection and processing. The details of the reagents and the equipment used in this study are listed in the Table of Materials.

1. Isolation of sarcoplasmic reticulum from fast-twitch rabbit muscle (Timing, 7 - 9 h)

NOTE: For details on the procedure, refer to Champeil et al.⁶⁹.

1. Obtain fast-twitch muscle tissue (~70 g from both hind legs per animal) from wild-type Oryctolagus cuniculus.
   NOTE: Prior visual identification of the muscles to be dissected is required^70,71.
2. Macerate the fast-twitch muscle in a blender by suspending it in three volumes of 100 mM of KCl, with 1 min on and 1 min in ice-cold rest, repeat three times⁷².
3. Remove the tissue debris by centrifugation (1500 × g) at 4 °C for 5 min; a second centrifugation (4200 × g) is performed if necessary.
4. Collect the supernatant and homogenize it using a tissue grinder (10 strokes at low velocity, i.e., 500-1,500 rpm)^72,73. Centrifuge the homogenate (10,000 × g) at 4 °C for 15 min.
   NOTE: Care must be taken when homogenizing, as the use of a relatively high speed can result in damage to the system and the operator.
5. Centrifuge the supernatant (containing the sarcoplasmic reticulum) (33,000 × g) at 4 °C for 120 min.
6. Suspend the pellets in 40 mL of 0.5 M of sucrose and centrifuge (12,000 × g) at 4 °C for 15 min. Dilute the supernatant (0.6 M of KCl and 0.15 M of sucrose) and centrifuge the suspension (34,000 × g) at 4 °C for 165 min.
7. Suspend the pellet containing the sarcoplasmic reticulum vesicles (SRVs) sheets in 0.3 M of sucrose, 0.1 M of KCl, and 5 mM of Tris-HCl, pH 7.0. Determine the protein concentration by using the Lowry assay⁷⁴ and human serum albumin as the protein standard.
8. Aliquot the SRVs (30-32 mg/mL) in 1 mL volume. Store the SRVs samples at -72 °C for further processing.
   NOTE: Protein yield is 100-110 mg SRVs per animal.

2. SERCA purification (Timing, 18 - 20 h)

NOTE: For details on the procedure, refer to Rivera-Morán et al.⁴⁶.

1. Dilute the SRVs suspension to 2 mg protein/mL using ice-cold 75 mM of Tris-HCl, pH 7.2, 0.6 M of KCl, 6 mM of EDTA, 1 mM of EGTA, and 0.1% (w/v) deoxycholate (DOC). Incubate the SRVs suspension on ice for 10 min and gentle agitation. Centrifuge the SRVs suspension (100,000 × g) at 4 °C for 60 min.
   NOTE: DOC should be added drop by drop.
2. Suspend the pellets in <3 mL of 25 mM of Tris-HCl, pH 7.5, 0.3 M of KCl, 45% glycerol (v/v), and 2 mM EDTA. Homogenize the suspension and adjust to a final volume of 10 mL. Determine protein concentration and then, adjust it to 6.5 mg/mL. Add azolectin at 5 mg/mL and 0.85 (w/w) Zwittergent 3-14.
   NOTE: Azolectin and Zwittergent 3-14 should be added drop by drop.
3. Homogenize the suspension and centrifuge (100,000 × g) at 4 °C for 60 min. Collect the supernatant and dilute 1:2 with 2 mM of EGTA (pH 7.2).
4. Pour the suspension gently onto a discontinuous trehalose concentration gradient (45, 40, 35, and 30% w/v) in 10 mM of Tris-HCl, pH 7.0, 1 mM of EDTA, 0.1% deoxycholate and 1 mg/mL azolectin. Centrifuge (100,000 × g) at 4 °C for 14 h. Collect the transparent, slightly yellowish pellet formed at the bottom of the tubes.
   NOTE: Both the formation of the trehalose gradient and the addition of the sample suspension must be performed using appropriate techniques. Overnight centrifugation is recommended.
5. Suspend gently the pellet in a small volume (<1.5 mL) of 25 mM of Tris-HCl, pH 7.5, 0.3 of M KCl, 45% glycerol, and 2 mM of EDTA. Determine protein concentration. Adjust the protein concentration by dilution to 2 mg/mL. Take aliquots (~50 µL) of the suspension and store the purified SERCA at −72 °C until its use.
6. Perform SDS-PAGE of the purified SERCA⁷², and of protein samples taken at different steps of purification. Stain the gel with Coomassie Blue⁷².
   NOTE: The use of 0.6 M trehalose instead of glycerol in the suspension buffer increases the stability of the enzyme during storage and freeze-thaw cycles^28,29.

3. Assay for ATPase activity (Timing, 1 - 2 h)

1. Enzyme-coupled assay: ATPase-Piruvate kinase-lactate dehydrogenase
   1. Prepare the reaction mixture (1 mL): 50 mM MOPS (pH 7.0), 1 mM EGTA, 80 mM KCl, 5 mM MgCl₂, 3 mM CaCl₂, 5 mM phosphoenolpyruvate, 250 µM NADH. Include variable ATP concentrations (0.001 to 0.25 mM).
   2. Homogenize carefully the reaction assay by vortexing. Incubate the reaction assay at 37 ◦C for 10 min. Add 0.9 U L-lactate dehydrogenase (LDH) and 1.5 U pyruvate kinase (PK).
   3. Initiate the ATPase reaction by the addition of 10 µg of SERCA.
   4. Determine the formation of NADH. Follow the change in absorbance intensity every second for 600 s at a wavelength (λ) of 340 nm over time using a spectrophotometer with a thermostatted cell holder.
      NOTE: The time interval for the absorbance measurement can vary, but try to record as many data points as possible to draw the initial straight line of the ATPase reaction.
2. Determine the rate of ATP hydrolysis
   NOTE: For details on the procedure, refer to Rivera-Morán et al.⁴⁶.
   1. Calculate the slope value (Δabs/min) of the linear portion in each curve formed. Use the molar extinction coefficient (ε) of NADH (λ = 6,220 M⁻¹·cm⁻¹) to determine the ATPase activity (µmoles ATP hydrolyzed/min.mg prot.)
3. Determine the kinetics parameters K_m and V_max
   1. Plot the velocity data versus ATP concentration using data analysis and graphing software.
   2. Fit the data by non-linear regression to the Michaelis-Menten Equation (Eq. 1)⁴⁶:
      
      where v is the velocity, V_max is the maximum velocity, [S] is the ATP concentration, and K_m is the Michaelis-Menten constant.
   3. Determine K_m and V_max by iteration.
      NOTE: The inclusion of DOC may increase the ATPase rate response; testing different concentrations of DOC is recommended to find the optimum.

4. Labeling assay of SERCA with Fluorescein Isothiocyanate (FITC ) (Timing, 30 - 45 min, only for FITC labeling)

NOTE: For details on the procedure, refer to^54,75,76.

1. Suspend SERCA (20 µg) in 50 µL (final volume) of labeling buffer (100 mM of KCl, 5 mM MgCl₂, and 30 mM of Tris-HCl, pH 8.9) containing 1 mM of FITC. Mix by vortexing.
2. Incubate the samples at different times (15 min, 10 min, 7 min, 5 min, and 2 min) in the dark and at room temperature.
3. Stop the labeling reaction by adding 1 volume of ice-cold stopping buffer (480 mM of sucrose and 48 mM of MOPS, pH 7.0), containing ATP (5 mM). Incubate on ice for 5 min in the dark.
4. Subject the FITC-labeled SERCA to SDS-PAGE⁷². Expose the clear gels to UV light (λ = 302 nm). Photo document the result.
5. Stain the gel with Coomassie blue. Photo document the result.
   NOTE: Performing FITC labeling in a dark room may improve the quality of the fluorescence signal.

5. Circular dichroism (CD) spectra (Timing, 30 min)

NOTE: For details on the procedure, refer to^11,77.

1. Suspend SERCA (3 µM) in 400 µL of 10 mM phosphate buffer (pH 7.0) at 25 °C.
2. Load the sample in a 0.1 cm path-length cell. Set far-UV spectra λ range between 190-260 nm. Set the internal resolution and the bandwidth to 1 nm.
3. Record the CD signal at 50 nm/min at 25 °C.

Results

SDS-PAGE of SERCA at different stages of purification (Figure 1). The Coomassie blue-stained gel shows the enrichment of the SERCA protein band (apparent molecular weight >100 kDa) as the purification protocol progresses. The protein band corresponding to SERCA shows a purity of >90% after centrifugation on a trehalose concentration gradient. Plot of ATP hydrolysis rate versus ATP concentration (Figure 2A). Michaelis-Menten ATPase kinetic (hyperbo...

Discussion

Most molecules and ions cannot freely cross the cell membranes, e.g., proton (H⁺) requires a membrane transporter in the plasma membrane of a variety of organisms and organelles such as mitochondria^83,84. Cell membranes are selective, and the molecules and ions that cross the cell membranes are diverse, so several types of membrane proteins can be found in the cell, such as (a) ABC transporters, (b) ion channels, (c) membrane-bound ATPases, (d) SLC tra...

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
ATP	Sigma-Aldrich Corp	A2383
Azolectin from soybean	Sigma-Aldrich Corp	44924
Benchtop UV transilluminator	Cole-Parmer	EW-97623-08	Dual intensity High setting is ideal for analytical documentation. Low setting reduces photonicking or photobleaching of gel samples while doing preparative work.
CaCl2 • 2H2O	Sigma-Aldrich Corp	223506
Coolpix B500 camera	Nikon Corp	S210
Coomassie brilliant blue G-250	Bio-Rad	1610406
Dodecyl maltoside	Sigma-Aldrich Corp	D4641
Ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid	Sigma-Aldrich Corp	E4378
Ethylenediaminetetraacetic acid tetrasodium salt dihydrate	Sigma-Aldrich Corp	E6511
Fluorescein isothiocyanate	Sigma-Aldrich Corp	F3651
KCl	JT Baker	7447-40-7
MgCl2 • 6H2O	Sigma-Aldrich Corp	M9272
MOPS	Sigma-Aldrich Corp	M1254
NADH	Chem-Impex International Inc	230
N-tetradecyl-N,N- dimethyl-3-ammonium-1-propanesulfonate	Sigma-Aldrich Corp	D0431
Phosphoenolpyruvate (PEP)	Chem-Impex International Inc	9711
Rabbit muscle lactate dehydrogenase	Roche	10003557103
Rabbit muscle pyruvate kinase	Sigma-Aldrich Corp	P1506
Sodium deoxycholate	Sigma-Aldrich Corp	D6750
Sodium dodecyl sulfate	Bio-Rad	1610302
Spectropolarimeter	Jasco Corp.	Jasco J1500
Sucrose	Sigma-Aldrich Corp	84100
Trehalose	Sigma-Aldrich Corp	T0167	Dihydrate
Tris(hydroxymethyl)aminomethane hydrochloride	Sigma-Aldrich Corp	857645
Ultracentrifuge	Beckman	Optima XPN
UV/VIS spectrophotometer	Agilent Technologies	8453	The Agilent 8453 UV-Vis Spectrophotometer uses a photodiode array for simultaneous measurement of the complete ultra-violet to visible light spectrum
WiseStir HS- 30E	Daihan Scientific Co.	DH.WOS01010	Ideal for all disperging and homogenizing applications, designed for tissue grinders.