Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications

Abstract

Conformational changes occurring to the open form of five different lipases were studied by means of molecular dynamic simulations in explicit water. The conformational changes indicate remarkable differences among the lipases considered, not only in terms of accessibility of the active site but also of modification of the geometry of the catalytic machinery. Lipase B from Candida antarctica undergoes minor conformational change at either level, so that it appears to be the most suitable lipase for being applied and formulated in aqueous environments or other hydrophilic media. On the other side, lipase from Pseudomonas cepacia undergoes the most relevant conformational variations both at the level of the catalytic triad and the residues involved in the oxyanion stabilization, suggesting that its "interfacial activation" is not simply related to a variation of the accessibility of the active site. Indeed, preliminary experimental data here reported indicate that covalent immobilization of lipase from Pseudomonas cepacia performed in the presence of hydrophobic solvent allows one to achieve a more than 10-fold increase in immobilization yield as compared to similar protocols performed in simple aqueous buffer. On the contrary, the benefit coming from immobilizing lipase B from Candida antarctica in hydrophobic solvent appears more limited (two-fold higher immobilization yield).

Lipase from Pseudomonas stutzeri: Purification, homology modelling and rational explanation of the substrate binding mode

“…MIS38 [62] or lipase T1 from G. zalihae [63], therefore making these lipases very attractive for modelling studies to simulate lid movements upon solvent effects [64], which will be commented in next section.…”

Nature Inspired Solutions for Polymers: Will Cutinase Enzymes Make Polyesters and Polyamides Greener?

“…Unlike CaLB and most lipases, the catalytic Ser of cutinases is not buried into a deep funnel shape active site, rather the active site is superficial and accessible to solvents and substrates even in absence of any hydrophobic interface [10]. In addition, the active site accessibility of most lipases is regulated by conformational changes involving the lid domain which exposes the active site upon interfacial activation [54]. In this sense, cutinases appear to be more similar to C. antarctica lipase B (CaLB) (Figure 1) which is considered as an unconventional lipase also because it lacks the mobile lid which is not susceptible to any relevant structural rearrangements [54].…”

“…In addition, the active site accessibility of most lipases is regulated by conformational changes involving the lid domain which exposes the active site upon interfacial activation [54]. In this sense, cutinases appear to be more similar to C. antarctica lipase B (CaLB) (Figure 1) which is considered as an unconventional lipase also because it lacks the mobile lid which is not susceptible to any relevant structural rearrangements [54]. On that respect, the dynamic behavior of two cutinases, namely Humicola insolens cutinase (HiC) and cutinase 1 from Thermobifida cellulosilytica (Thc_cut1) were compared with CaLB by performing MD simulations in explicit water and toluene environments [10].…”

Thermomyces lanuginosus Lipase with Closed Lid Catalyzes Elimination of Acetic Acid from 11‐Acetyl‐Prostaglandin E2

“…[21] Lipases have different lid types, ranging from complex structures to having no lid at all. [22] Despite the fact that TLL has a short lid of simple structure, there is still no existing unequivocal understanding of the structure of the lid of TLL. Different researchers define it with variations as consisting of the following amino acid residues: either of 85-93, [23] 82-96, [24] or of 82-90.…”

“…Different researchers define it with variations as consisting of the following amino acid residues: either of 85-93, [23] 82-96, [24] or of 82-90. [22] In this work the definition of 82-96 residues has been preferred, because Trp89 would obviously be considered to belong to the central part of the lid, and Ser83 has to be involved. [21] Lipases can be activated in a hydrophobic organic solvent in the same manner as at the water/triglyceride interface.…”