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Conformational and structural changes of lentil seedlings amine oxidase (LSAO) were studied in the presence of trifluoroethanol (TFE) by spectroscopic and analytical techniques. At TFE concentrations up to 5%, the induction of a structural transition from β-sheet to α-helix and up to 10% TFE a structural transition from α-helix to β-sheet as well as inactivation of the enzyme are observed. At TFE concentrations between 10-35%, LSAO proves to be prone to aggregation and beyond 35% TFE leads to a non-native protein structure with a high α-helix content. The obtained results revealed that the aggregation of LSAO is strongly linked to the nature of secondary structures.