Assessment of the PETase Conformational Changes Induced by Poly(ethylene terephthalate) Binding

Abstract

Recently, a bacterium strain of Ideonella sakaiensis was identified with the uncommon ability to degrade the poly(ethylene terephthalate) (PET). The PETase from I. sakaiensis strain 201-F6 catalyzes the hydrolysis of PET converting it to mono(2-hydroxyethyl) terephthalic acid (MHET), bis(2-hydroxyethyl)-TPA (BHET), and terephthalic acid (TPA). Despite the potential of this enzyme for mitigation or elimination of environmental contaminants, one of the limitations of the use of PETase for PET degradation is the fact that it acts only at moderate temperature due to its low thermal stability. Besides, molecular details of the main interaction of PET in the active site of PETase remains unclear. Herein, molecular docking and molecular dynamics (MD) simulations were applied to analyze structural changes of PETase induced by PET binding. Results from the essential dynamics revealed that β1-β2 connecting loop is very flexible. This Loop is located far from the active site of PETase and we suggest that it can be considered for mutagenesis in order to increase the thermal stability of PETase. The free energy landscape (FEL) demonstrates that the main change in the transition between the unbounded to the bounded state is associated with β7-α5 connecting loop, where the catalytic residue Asp206 is located. Overall, the present study provides insights into the molecular binding mechanism of PET into the PETase structure and a computational strategy for mapping flexible regions of this enzyme, which can be useful for the engineering of more efficient enzymes for recycling the plastic polymers using biological systems.

Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants

“…The PCs were obtained from the diagonalization of the covariance matrix obtained from the Cartesian coordinates of the superposed Cα atoms of complex structure. To avoid an underestimate of the atomic displacement, an iterated superposition procedure was applied before the PCA, where residues displaying the largest positional differences were excluded at each round until only the invariant 'core' residues remained [76][77][78][79] .…”

Mechanistic studies of a lipase unveil a dramatic effect of pH on the selectivity toward the hydrolysis of PET oligomers

“…We recently studied the reaction mechanism of the PET degradation catalysed by IsPETase and IsMHETase, as well as by the metagenome-derived leaf-branch compost cutinase (LCC-ICCG variant) 15 by computational methods with predicted rate constants in agreement with the experimental observations. 16 The similar mechanism obtained in both systems suggested that the origin of the apparent better performance of LCC-ICCG protein over IsPETase must be due to its thermal stability and its intrinsic relationship with the crystallinity grade of the polymer, which was con rmed by our recent analysis of the structural changes of IsPETase induced by PET binding, 17 and by the results of Alper and co-workers who, based on the structure-based machine learning algorithm, engineered a robust and active PET hydrolase basically by improving its capability of working at a larger range of temperatures and pH levels. 18 The results derived from these computational studies represent the bedrock to understanding the molecular mechanism that rules the performance of PET degrading enzymes.…”

Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library

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