Structure and dynamics of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus

Abstract

Understanding the behavior of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus in different concentrations of EmimAc.

Activity and stability of hyperthermostable cellulases and xylanases in ionic liquids

“…Such mechanisms include competitive inhibition of substrate binding, alteration of enzyme dynamics, protein denaturation and/or aggregation, and stripping of surface water molecules (Ferdjani et al 2011;Li et al 2013;Summers et al 2017;Manna and Ghosh 2020;Summers et al 2020). Competitive inhibition of substrate binding by the IL molecules was observed by the increase of K m as a factor in decreasing the activity of endoglucanases and xylanases (Li et al 2013;Chawachart et al 2014;Anbarasan et al 2017;Johnson and Snow 2017;Summers et al 2017;Manna and Ghosh 2020). The competitive inhibition effect was also suggested by binding of IL cation and anion to the enzyme active site by molecular simulation and docking studies (Jaeger and Pfaendtner 2013;Chawachart et al 2014;Hebal et al 2020).…”

“…ILs appear to negatively affect the dynamic behaviour of enzymes. Reduction of the endoglucanase Cel12A activity in 60% [EMIM]OAc was attributed to the loss of essential dynamic motions, notably the opening and closing motion of the protein (Manna and Ghosh 2020). In the same way, IL molecules caused the dampening of the dynamic protein motion in GH11 xylanase (Jaeger and Pfaendtner 2013).…”

“…Studies on the activity and stability of hyperthermostable cellulases and xylanases have led to proposals for molecular mechanisms of IL-dependent inactivation of these enzymes. Such mechanisms include competitive inhibition of substrate binding, alteration of enzyme dynamics, protein denaturation and/or aggregation, and stripping of surface water molecules (Ferdjani et al 2011;Li et al 2013;Summers et al 2017;Manna and Ghosh 2020;Summers et al 2020). Competitive inhibition of substrate binding by the IL molecules was observed by the increase of K m as a factor in decreasing the activity of endoglucanases and xylanases (Li et al 2013;Chawachart et al 2014;Anbarasan et al 2017;Johnson and Snow 2017;Summers et al 2017;Manna and Ghosh 2020).…”

“…Some insight into details on how ILs perturb the activity of hyperthermostable cellulases and xylanases have come from molecular dynamic (MD) simulations and molecular docking. Most of these studies were done with imidazolium ILs (Chawachart et al 2014;Johnson and Snow 2017;Summers et al 2017;Manna and Ghosh 2020;Konar et al 2020), but other docking studies included superbase ILs (Hebal et al 2020). The charge of the active site seems to contribute to the extent of competitive inhibition by the IL ions.…”

“…During simulations, Manna and Ghosh (2020) noted that as the concentration of [EMIM]OAc increases, an increase in the cumulative retention time of [EMIM] þ cation is seen related to the active site catalytic residues of the endoglucanase RmCel12A. In 20 and 40% [EMIM]OAc, the interactions were observed to be mostly transient, whereas in 60% concentration they were stable.…”