Unlocking the mystery behind the activation phenomenon of T1 lipase: A molecular dynamics simulations approach

Abstract

The activation of lipases has been postulated to proceed by interfacial activation, temperature switch activation, or aqueous activation. Recently, based on molecular dynamics (MD) simulation experiments, the T1 lipase activation mechanism was proposed to involve aqueous activation in addition to a double-flap mechanism. Because the open conformation structure is still unavailable, it is difficult to validate the proposed theory unambiguously to understand the behavior of the enzyme. In this study, we try to validate the previous reports and uncover the mystery behind the activation process using structural analysis and MD simulations. To investigate the effects of temperature and environmental conditions on the activation process, MD simulations in different solvent environments (water and water-octane interface) and temperatures (20, 50, 70, 80, and 100°C) were performed. Based on the structural analysis of the lipases in the same family of T1 lipase (I.5 lipase family), we proposed that the lid domain comprises a6 and a7 helices connected by a loop, thus forming a helix-loop-helix motif involved in interfacial activation. Throughout the MD simulations experiments, lid displacements were only observed in the water-octane interface, not in the aqueous environment with respect to the temperature effect, suggesting that the activation process is governed by interfacial activation coupled with temperature switch activation. Examining the activation process in detail revealed that the large structural rearrangement of the lid domain was caused by the interaction between the hydrophobic residues of the lid with octane, a nonpolar solvent, and this conformation was found to be thermodynamically favorable.

Isolation and characterization of a thermostable lipase from <i>Bacillus thermoamylovorans</i> NB501

“…Due to low sequence homology in a local region, one of the catalytic triad (His352) could not be placed in a correct position by the simple modeling method. In lipases, a prominent lid domain covers and protects the active site in a closed conformation, and opening the lid presumably exposes the active site at the lipid-water interface (Abdul Rahman et al, 2012). Helix a6 in the lid domain of NB501 lipase was shorter than that of L1 lipase by four amino acids (Fig.…”

Immobilization of lipases on hydrophobic supports: immobilization mechanism, advantages, problems, and solutions

“…For this reason, the resolution of racemic mixtures of acids, alcohols, esters, amines or amides, or rather the desymetrization of this type of compounds bearing a prochiral centre, is a very usual process catalyzed by lipases (Cunha et al, 2015;de Miranda et al, 2015;Hoyos et al, 2016;Patel, 2012;Rodríguez-Mata and Gotor-Fernández, 2015;Seddigi et al, 2017). It is worth mentioning that going deeper into the knowledge of the molecular basis explaining the stereochemical recognition of (pro)chiral substrates is also a very attractive research area (Colombo et al, 2000;Cygler et al, 1994;Juhl et al, 2009;Li et al, 2008Li et al, , 2015Park et al, 2009;Rahman et al, 2012;Sin et al, 2009;Toledo et al, 2016;Trodler et al, 2009;Trodler and Pleiss, 2008).…”

Typoselectivity of CrudeGeobacillussp. T1 Lipase Fused with a Cellulose‐Binding Domain and Its Use in the Synthesis of Structured Lipids

“…T1 lipase is an intrinsically stable enzyme, which has received a great deal of attention in recent years. There are several reports on T1 lipase [9][10][11][12][13], but few reports have discussed FA specificity or typoselectivity of T1 lipase and its potential for industrial applications. The FA specificity or typoselectivity concerns lipases that are specific to a particular FA or a group of FA.…”