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This study investigates the photocleavage activity of two anthraquinone derivatives isolated from T. harzianum ETS 323, chrysophanol and pachybasin, upon proteins. Pachybasin and chrysophanol exhibited different abilities to degrade BSA with UV 365 nm radiation. Between the two, pachybasin was shown to be a better reagent in the degradation of proteins as exhibited on the SDS-PAGE. The action mode of these compounds to proteins was found to be random cleavage by an oxygen-derived radical. The resulting binding constants of chrysophanol to lysozyme and BSA were 6.9 ± 0.5 × 104 M−1 (ΔGo = −27.62 kJ/mol at 25°C) and 6.6 ± 0.4 × 105 M−1 (ΔGo = −33.22 kJ/mol), and of pachybasin to lysozyme and BSA were 5.0 ± 0.2 × 104 M−1 (ΔGo = −26.82 kJ/mol) and 1.1 ± 0.1 × 104 M−1(ΔGo = −23.07 kJ/mol), respectively.