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Microcystin-LR (MC-LR) is a toxin produced by cyanobacteria that can bloom in freshwater supplies. This study describes a new strategy for remediation of MC-LR that combines linearization of the toxin using microcystinase A, MlrA, enzyme with rejection of linearized byproducts using membrane filtration. The MlrA enzyme was expressed in Escherichia coli (E. coli) and purified via a His-tag with 95% purity. Additionally, composite membranes made of 95% polysulfone and 5% sulfonated polyether ether ketone (SPEEK) were fabricated and used to filter a solution containing cyclic and linearized MC-LR. Tests were also performed to measure the adsorption and desorption of MC-LR on polysulfone/SPEEK membranes. Liquid chromatography-mass spectrometry (LC-MS) was used to characterize the progress of linearization and removal of MC-LR. Results indicate that the MlrA was successful at linearizing MC-LR. Membrane filtration tests showed rejection of 97% of cyclic MC-LR and virtually all linearized MC-LR, with adsorption to the membranes being the main rejection mechanism. Adsorption/desorption tests indicated that methanol could be used to strip residual MC-LR from membranes to regenerate them. This study demonstrates a novel strategy of remediation of microcystin-tainted water, combining linearization of MC-LR to a low-toxicity byproduct along with removal by membrane filtration.