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bioRxiv · 10.1101/2023.05.30.542930

Computational Assessment on Catalytic Activity of PET Hydrolase

Cruz, I. N.·Ramos, R. B.
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Abstract

BackgroundPET hydrolase from Ideonella sakaiensis might provide a response for PET accumulation in the environment. In this project some previously studied mutations were implemented and their performance was evaluated via computational methods with tools such as Modeller, HADDOCK, PyMOL and Gromacs. One possible mutation that could lead to improved catalytic activity was proposed. ResultsPET hydrolase DM S209F W130H and I179 provide interesting binding results with studied ligands, however a solution that combines both mutations does not seem viable, since the binding cleft becomes occluded. Following the same rationale, the triple mutant S209F W130H I179Q is proposed but instead leaves space in the binding cleft for ligand to enter and might bond with the oxygen at the ester group. The experiments conducted with triple mutant S209F W130H I179Q failed to beat HADDOCK score for DM, however its experimental results could still increase PET degradation. Results from surface charge may indicate an increase in stability and binding affinity for the protein. ConclusionsAmong models implemented, DM S209F W130H seems the best model studied regarding BHET or PET binding. Despite Protein Engineering is a complex process, computational tools might provide a way of studying binding sites of hypothetical proteins. Supplementary informationSupplementary data is available in annexes.

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Cruz, I. N., Ramos, R. B.. 2023-06-01. Computational Assessment on Catalytic Activity of PET Hydrolase. https://doi.org/10.1101/2023.05.30.542930

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