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Agarase-producing bacteria, Bacillus sp. was isolated from Jindong located at South Korea. After 4-day culture of this strain, supernatant was obtained from culture broth by centrifugation. Crude enzyme was obtained by ammonium sulfate precipitation and membrane dialysis. Separation of agarase was performed by ion exchange chromatography on DEAE-Sepharose resin. Equilibrium pH and volume ratio of resine to the amount of protein were optimized for efficient adsorption of protein. Most of protein was adsorbed in 3 mL of resine per 410 mg of protein at
pH 7.5 ~ 8.0. The elution performances of bind proteins were compared at different concentrations of NaCl in elution buffer. The presence of agarase in eluted proteins was determined by Lugol’s staining technique. The total amount of eluted protein increased as NaCl concentration increased to 400 mM, in which condition agarase activity was observed in eluted fraction 3–8 and maximum recovery was found to be 41%. The size of agarase was determined by performing SDS-PAGE and zymography.