Naslov
Computational approach to substrate promiscuity: a case study of selected phospholipase and lipase enzymes

Autori
Maršavelski, Aleksandra ; Sabljić, Igor ; Kojić- Prodić, Biserka

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, ostalo

Skup
Tiselius Symposium 2019

Mjesto i datum
Uppsala, Švedska, 28.08.2019

Vrsta sudjelovanja
Predavanje

Vrsta recenzije
Podatak o recenziji nije dostupan

Ključne riječi
Phospholipase ; lipase ; substrate specificity

Sažetak
Two highly homologous extracellular enzymes of the SGNH hydrolase supefamily-lipase from Streptomyces rimosus (SrLip)1, 2 and phospholipase A1 from Streptomyces albidoflavus (SaPLA1)3, 4 revealed the catalytic dyad Ser and His instead of common triad Ser-His-Asp. Their different substrate specificity has intrigued us to examine closely characteristic modes of ligand binding into corresponding pockets available in the enzyme interiors, and the influence of the phosphate polar head in the case phospholipid activity. SaPLA1 is preferably phospholipase with a preference towards long acyl chains, showing no detectable lipase activity towards triacylglycerol 1- palmitoyl-2-oleoyl-3-linoleoyl-glycerol (POL). The maximum activity SaPLA1 shows towards 1- palmitoyl-2-oleoyl-glycerol-3-phosphate (POPA) whereas half of the activity is observed with 1-palmitoyl-2-oleoyl-glycerol-3-phosphocholine (POPC).4 On the other hand, SrLip shows both phospholipase and lipase activity, as well as thioesterase, and Tweenase activities, however it prefers shorter acyl chains.1 To understand this substrate promiscuity, we performed docking using both AutoDock Vina and SwissDock to obtain complexes of POPA, POPC, POL and SaPLA. We then performed classical molecular dynamics simulations of apo SaPLA and SaPLA in complex with POPA, POPC and POL to understand the stability and conformational changes in binding. Each structure was simulated in triplicates for 150 ns giving in total 450 ns per structure. Cluster analysis using dihedral angles of amino acids that line the hydrophobic pocket revealed that chi1 dihedral angle of Tyr142 with the average value of -170 degrees is characteristic for productive binding of POPA. The value of -60 degrees is characteristic for apo SaPLA and for non- productive complex with POL. The analysis of the hydrogen bonds has revealed a network that extends from Tyr142 located in the hydrophobic pocket towards the surface of the enzyme. It was shown that when the substrate is productively bound, this network is broken, and Tyr142 does not interact with the side chain of Asp10, but rather forms T-shaped stacking interaction with Phe145. This extensive research requires systematic comparison of ligand binding into interior of these two studied enzymes based on: i) aliphatic chains lengths, ii) saturated vs unsaturated chains and iii) phospholipase vs lipase substrates.

Izvorni jezik
Engleski

Znanstvena područja
Kemija

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