Unraveling the potential of uninvestigated thermoalkaliphilic lipases by molecular docking and molecular dynamic simulation: an in silico characterization study

Abstract

Thermoalkaliphilic lipase enzymes are mostly favored for use in the detergent industry. While there has been considerable research on Geobacillus lipases, a significant portion of these enzymes remains unexplored or undocumented in the scientific literature. This work performed in silico phylogeny, sequence alignment, structural and enzyme-substrate interaction analyses of the five thermoalkaliphilic lipases belonging to different Geobacillus species (Geobacillus stearothermophilus lipase = GsLip, Geobacillus sp. B4113_201601 lipase = Gb4Lip, Geobacillus kaustophilus HTA426 lipase = GkLip, Geobacillus sp. SP22 lipase = GspLip, Geobacillus sp. NTU 03 lipase = GntLip). For this purpose, unreviewed enzyme sequences of five Geobacillus thermoalkaliphilic lipases were analyzed at sequence and phylogeny levels. 3D homology enzyme models were built, validated, and investigated by different bioinformatics tools. The ligand interactions screening using seven para-nitrophenyl (pNP) esters and enzyme-ligand interactions were analyzed on Gb4Lip:pNP-C12 and BTL2:pNP-C12 by MD simulation. Biophysicochemical characteristic analysis showed that Gb4Lip had a theoretical T _m value of above 65 ºC, and a higher aliphatic index indicating greater thermal stability. Sequence alignment showed a hydrophilic threonine in the α6 helix of Gb4Lip, indicating high enzymatic activity. A normalized temperature factor B (B'-factor) analysis showed that the lid domains of five lipases significantly possessed lower B'-factor values, compared to G. thermocatenulatus lipase 2 (BTL2), indicating that they had higher rigidity. Molecular docking results indicated that the five lipases had the highest binding affinity toward pNP-C12. The RMSF investigation revealed that the thermostability of Gb4Lip is influenced by specific molecular elements: D202-S203 within the αB region of the lid domain, and E274-Q275 within the b3 strand, as well as W278 in the b3-b4 loop, and H282 in the b4 strand of the Ca²⁺-binding region. MD simulation analysis showed that catalytic residue S114 and at least one oxyanion hole residue (F17 and/or Q114) in Gb4Lip frequently formed hydrogen bonds with the pNP-C12 ligand at 343 K and 348 K throughout the simulation process, indicating that Gb4Lip might catalyze relatively long-chain ligand pNP-C12 with high performance. In conclusion, Gb4Lip might be a more suitable candidate as the detergent additive. In addition, this investigation can offer valuable perspectives on Family I.5 lipases such as Gb4Lip for future exploration in the field of protein engineering.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04023-5.

Keywords: Detergent additive; Geobacillus; MD simulation; Molecular docking; Thermoalkaliphilic lipase.

Fig. 1

The evolutionary tree of lipase families was obtained from 41 protein sequences. The UniProt or GeneBank accession numbers and the names of the microorganisms are provided

Fig. 2

Multiple sequence alignment of the five lipases, and BTL2 lipase from G. thermocatenulatus. The purpose of the red background in the figure is to draw attention to residues that are strictly conserved, while residues that are conservatively substituted are enclosed in boxes. The aligned sequences of Gb4Lip showed the secondary structural elements, such as α-helices (α) and β-strands (β), positioned above them. The conserved catalytic triad, specifically S114, D318, and H359, were indicated with green asterisks. Oxyanion hole residues F17 and Q115 were marked by the orange arrow. The figure was created utilizing ESPript (Gouet et al. ; Robert and Gouet 2014)

Fig. 3

Overall predicted three-dimensional homology models of the five thermoalkaliphilic lipase enzymes. The α-helices and β-strands in the lid domain are labeled and highlighted with orange color. a GsLip, b Gb4Lip, c GkLip, d GspLip, e GntLip

Fig. 4

The alignment of B’-factor distribution of the five thermoalkaliphilic lipase enzymes with the BTL2 lipase from G. thermocatenulatus a GsLip, b Gb4Lip, c GkLip, d GspLip, e GntLip. Position 1, position 2, and position 3 refer to Phe177, Arg180, and Leu/Trp278, respectively

Fig. 5

The RMSD profiles at 343 K (a) and 348 K (b) of Gb4lip (red line) and BTL2 (black line). RMSF profiles in Gb4Lip (c) and BTL2 (d) at 343 K (black line) and 348 K (red line) during the molecular dynamics simulation

Fig. 6

Schematical representation of the residues interacted with the pNP-C12. a Gb4Lip-343 K, b Gb4Lip-348 K, c BTL2-343 K, d BTL2-348 K

Fig. 7

Distance analysis of the Ser114 Cb–Asp318 Cb, Ser114 Cb–His359 Cb, Asp318 Cb–His359 Cb in Gb4Lip at 343 K (a, b, c) and 348 K (d, e, f), respectively

Fig. 8

Distance analysis of the Ser114 Cb–Asp318 Cb, Ser114 Cb–His359 Cb, and Asp318 Cb–His359 Cb in BTL2 at 343 K (a, b, c) and 348 K (d, e, f), respectively

Fig. 9

Distance analysis of the Arg93 NH2–Asp210 OD1, the Arg93 NH2–Asp210 OD2, Lys208 NZ–Glu24 OE1 in Gb4Lip at 343 K (a, b, c) and 348 K (d, e, f), respectively

Fig. 10

Distance analysis of the Arg93 NH2–Asp210 OD1, the Arg93 NH2–Asp210 OD2, Lys208 NZ–Glu24 OE1, Arg242 NH2–Asp179 OD2 in BTL2 at 343 K (a, b, c, d) and 348 K (e, f, g, h), respectively