Unlocking the mystery behind the activation phenomenon of T1 lipase: a molecular dynamics simulations approach.
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 α6 and α7 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.
Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor.
Mohd Zulhilmi
MZ
Abdul Rahman
Abu Bakar
AB
Salleh
Raja Noor Zaliha Raja
RN
Abdul Rahman
Mohd Basyaruddin
MB
Abdul Rahman
Mahiran
M
Basri
Thean Chor
TC
Leow
D004789:Enzyme Activation; D056506:Geobacillus / Q000737:chemistry / Q000201:enzymology*; D008049:Lipase / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009795:Octanes / Q000737:chemistry; D011487:Protein Conformation; D013696:Temperature; D014867:Water / Q000737:chemistry
D009795:Octanes; D014867:Water; D008049:Lipase; C026728:octane