LTP purification from tomato peel

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As concerns the chromatographic conditions, they were set as follows:

5 µL of each sample were injected each time, at a 0.20 mL/min flow rate, for C18 column, and at a 0.15 mL/min flow rate for C8 column, because of the higher back pressure. The column oven was kept at 35 °C. Gradient:

7’ isocratic elution with 100% A, 43’ linear gradient from 0% to 50% of B, 2.60’

isocratic elution with 50% A and 50% B, 0.4’ linear gradient to reach 100% B, 5.20’

isocratic elution with 100% B, 0.8’ linear gradient from 100% to 0% of B and 13’ of reconditioning with 100% of eluent A.

ESI-MS spectrometer conditions were the following: positive ion mode, capillary voltage 1.93 kV, cone voltage 150 V, source temperature 100 °C, desolvation temperature 200 °C, spraying gas (N2) 100 L/h, desolvation gas (N2) 650 L/h, full scan acquisition from 100 to 2000 m/z in continuum mode and 1 sec of scan time.

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0 0,5 1 1,5 2 2,5 3

0 5 10 15 20 25 30 35

OD  at  28 0n m

N° Fractions

Fig 2. Graphical representation of UV absorbance values of protein fractions off the flash HPLC step of purification.

Fractions from 13 to 33 were pooled together and the whole sample was concentrated about 5 times by diafiltration system, reducing the volume from 220 mL to 46 mL through a 1 kDa nominal molecular weight limit (NMWL) membrane.

ii. Size Exclusion Chromatography

Size exclusion chromatography, also called gel filtration, allows the separation of proteins with differences in molecular size, under mild conditions. Separation is based on differences in the size and/or shape of the analyte molecules, which determines the analytes’ access to the pore volume inside the column packing particles. According to their size, smaller analytes have partial to complete access to the pore volume. Among the analytes that partially or fully enter the pore volume, larger molecules with less access to the pore volume elute first, while the smallest molecules elute last.

Thus, protein molecular weight determination by gel filtration can be made by comparing the elution volume of the substance of interest with the ones obtained for several known calibration standards run in the same buffer.

Following this principles, a preparative gel filtration analysis was performed on the LTP enriched extract using a Superdex™ 75 column (16 mmL x 600 mmD). Since the sample does not have to be in exactly the same buffer as that used to equilibrate and run through the column, a low concentration of salt (25 mM phosphate and 150 mM NaCl) was including in the buffer composition, also to avoid nonspecific ionic interactions with the matrix which can be seen as delays in peak elution.

Both samples and buffer were 0.22-µm filtered before being applied to the column, to avoid the risk of blockage due to small particles. A super-loop was loaded with 46 mL of sample and 11 runs of 4 mL each were performed.

The graph showed in Fig 3a represents the overlapped chromatograms related to each run, compared to the chromatogram obtained for the molecular standards in the same conditions.

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‐50 0 50 100 150 200 250 300

‐20 0 20 40 60 80 100 120 140

Protein Extract MW Standards



◊ ∆ ○ ▲

z

A 280 (nm)

Volume (ml)

3 6 14 M

28 MrkDa

Fig 3. a, chromatogram related to the size exclusion chromatography of the LTP enriched extract.

Molecular weight standards were: , Bovine thyroglobulin (Mr 670 kDa); z, Bovine gamma globulin (Mr

158 kDa); ◊, Chicken ovalbumin (Mr 44 kDa); ∆, Horse myoglobin (Mr 17 kDa); ○, Aprotinin (Mr 6.5 kDa);

▲, Vitamin B12 (Mr 1.35 kDa). b, SDS PAGE analysis of fractions containing proteins with molecular weight ranging between 17 kDa and 6.5 kDa. Lane marked ‘M’ corresponds to molecular weight markers and their relative molecular masses are reported on the right side.

As it can observed from the chromatogram, several peaks were obtained, indicating the presence of several proteins. In order to identify fractions containing LTP, an SDS PAGE analysis was performed on those containing proteins with molecular weight ranging from 17 kDa to 6.5 kDa.

These fractions (Fig 3b) showed a protein band with a relative molecular mass of 6 kDa, which could be an LTP, together with other high molecular weight proteins.

In order to purify the potential LTP, a further chromatographic step was performed, exploiting another chemical features of proteins: the charge.

iii. Ion exchange chromatography

Ion exchange chromatography separates proteins with differences in surface charge to give high-resolution separation. The partition is based on the reversible interaction between a charged protein and an oppositely charged chromatography medium.

Typically, when below their isoeletric points, as in this case, proteins will bind to a negatively charged, cation exchanger. Proteins bind as they are loaded onto the column at low ionic strength (20 mM MES buffer pH 6.0). The conditions are then altered so that bound substances are desorbed differentially. Elution is usually performed by increasing salt concentration (from 0 to 0.4 M of 1 M NaCl), so that the presence of Na⁺ ions competes with the bound proteins for the binding to the column.

In this way, unbound molecules are eluted before the gradient begins, while tightly bound molecules are eluted in a high-salt wash. All the other proteins will elute according to the ion strength during the gradient.

Since the proteins have to be loaded onto the POROS^® 20 HS column (4.6 mmD x 100 mmL) at low ionic strength, a dialysis of pooled fractions off the gel filtration was

a

b

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0 20 40 60 80 100 120

‐500 0 500 1000 1500 2000 2500 3000

0 5 10 15 20 25 30 35 40 45

220nm 280nm Conductivity

Volume (ml)

Absorbance(nm)

3 6 14 17 28 38 49 62 98 188 M Mr kDa

* **

carried out. After 2 hours of dialysis in 20 mM MES buffer, the conductivity of the sample lowered to 5.86 mS/cm, low enough to be analyzed by a cation exchange chromatography.

5 mL of dialyzed sample were injected onto the column and the injections were repeated until the whole volume (150 mL) was depleted.

Since LTPs are low abundant in aromatic amino acid residues, the eluent was monitored also following the absorbance at 220 nm, in order to detect peptide bounds.

Fig 4. Ion exchange chromatogram of pooled fractions off the gel filtration containing the protein of interest. Stars indicate the range of fractions which were further analyzed by SDS PAGE.

After ion exchange chromatography (Fig 4), peaks eluting during the linear gradient of salt were further investigated by SDS PAGE, in order to understand whether the protein with the expected molecular weight had been purified.

Fig 5. SDS PAGE of fractions off ion exchange chromatography. Stars indicate fractions as referred to in Fig 4. The lane marked as ‘M’ represents the molecular weight standards and their relative molecular masses are reported on the right side.

As showed by the electrophoresis analysis reported in Fig 5, fractions constituting the peak indicated with ‘**’ revealed the presence of an unique protein band with the

*

**

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mg/ml

A 562 nm

expected molecular weight. So they were pooled and used for purified protein characterization.

Also fractions referred to ‘*’ showed the protein of interest but some other bands, with both higher and lower molecular weights, were also present. Due to their different behavior during the ion exchange chromatography, it was supposed that different tomato LTP isoforms had been detected but, because of their different interactions with the stationary phase, one of them couldn’t be purified, since it still co-eluted with other proteins.

iv. Purified protein quantitation

Purified protein was quantified by the bicinchoninic acid (BCA) assay. The principle is similar to the Lowry procedure, since both rely on the formation of a Cu²⁺-protein complex under alkaline conditions, followed by reduction of the Cu²⁺ to Cu¹⁺. The amount of reduction is proportional to the protein present. It has been shown that cysteine, tryptophan, tyrosine, and the peptide bond are able to reduce Cu²⁺ to Cu¹⁺. BCA forms a purple-blue complex with Cu¹⁺ in alkaline environments, thus providing a basis to monitor the reduction of alkaline Cu²⁺ by proteins at absorbance maximum 562 nm.

A calibration curve was obtained by using Bovine Serum Albumine (BSA) standard at increasing concentration, from 0 µg/mL to 1000 µg/mL. The net absorbance at 562 nm was calculated as mean between the three repeats for each standard and sample. A standard curve (Fig 6) was obtained by plotting the net absorbance at 562 nm versus the protein standard concentrations.

Fig 6. Standard curve obtained by plotting the absorbance values versus the protein standard concentration. The calculated R² was 0.99.

Interpolating the values of absorbance obtained for the sample non diluted and diluted 1:1 in Phosphate Buffer Saline (PBS), the protein concentrations were found to be 0.13 mg/mL and 0.065 mg/mL respectively. Accounting for the dilution factor, also the diluted sample gave a value of 0.13 mg/mL for the protein concentration.

Considering that the volume of the pooled fraction containing purified proteins was 91 mL, 9.1 mg of pure protein were thus purified. As referred to the amount of starting material (3 kg of whole tomatoes), it can be estimated that the isolation

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strategy developed here allowed to obtain a yield for the purified proteins around 3 mg/kg of whole tomatoes.

v. Assessing protein purity

The bands obtained after a SDS PAGE analysis may contain more than a protein, if their molecular weights differ for few Daltons, since they can not be discriminated by gel electrophoresis.

Although a separation according to pH had already been performed, since only basic proteins could have interacted with the stationary phase during the ion exchange chromatography, further analytical checks were carried out in order to value the purity of the isolated protein.

400 µL of the solution containing the purified protein were then applied to a Superdex™ 75 analytical column (10 mmD x 300 mmL) and the run was performed as described in paragraph 3.11.

As shown in Fig 7a, the analytical size exclusion chromatography revealed the presence of two peaks: besides the expected one, between 17 kDa and 6.5 kDa, which was related to the protein of interest, another one was observed whose molecular weight ranged between 6.5 kDa and 1.35 kDa. The last one was proved to belong to the MES buffer by a blank run. So, the analytical gel filtration analysis confirmed the presence of only one protein.

Fig 7. Analytical gel filtration analysis. a, chromatogram of purified protein, the arrow indicates the peak related to the protein of interest; b, chromatogram of 20 mM MES buffer. Molecular weight standards were: , Bovine thyroglobulin (Mr 670 kDa); z, Bovine gamma globulin (Mr 158 kDa); ◊, Chicken ovalbumin (Mr 44 kDa); ∆, Horse myoglobin (Mr 17 kDa); ○, Aprotinin (Mr 6.5 kDa); ▲, Vitamin B12 (Mr 1.35 kDa).

To further check the purity of the isolated protein, the highest resolution chromatography technique available was applied: reversed phase chromatography.

In this chromatography, the separation of proteins depends on a reversible hydrophobic interaction between sample molecules in the eluent and the medium.

Initial conditions are primarily aqueous, favoring a high degree of organized water structure surrounding the sample molecule. Frequently, a small percentage of organic modifier, is present in order to achieve a “wetted” surface. As sample binds to the medium, the hydrophobic area exposed to the eluent is minimized. Separation relies on sample molecules existing in an equilibrium between the eluent and the surface of the medium. Initially, conditions favor an extreme equilibrium state where essentially 100% of the sample is bound. To bring about elution the amount of organic solvent is

a b

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increased so that conditions become more hydrophobic. Binding and elution occur continuously as sample moves through the column. The process of moving through the column is slower for those samples that are more hydrophobic. Consequently, samples are eluted in order of increasing hydrophobicity.

To test the efficiency of the method and of the column, a preliminary separation was performed using a β-lactoglobulin mixture, containing both A and B β-lactoglobulin genetic variants, which differ for two substitutions: 64th (Asp (A)→ Gly (b)) and 118th (Val(A) → Ala(B) (Fig 8a).

The presence of two resolved peaks, indicating the two isoforms of β-lactoglobulin which differ for 86.04 Da, indicated the efficiency of the developed method.

Afterwards, the same method was applied to the purified protein. As shown in Fig 8b, only a peak was obtained, again confirming the purity of the isolated protein.

Fig 8. chromatograms of a, β-lactoglobulin A and B variants and of b, purified protein separated by reversed phase chromatography.