Molecular dynamics simulations of Glycerol-3-Phosphate Acyltransferase protein from Chlorella sorokiniana with Glycerol-3-Phosphate and oleoyl-CoA: insights into the synergistic interactions

Microalgae have the potential to accumulate high amounts of neutral lipids, specifically triacylglycerol (TAG), which can serve as a feedstock for biofuel production. In Chlorella sp., TAG synthesis is initiated by the rate-limiting enzyme Glycerol-3-Phosphate Acyltransferase (GPAT), playing a critical role in the first step of acylation using Glycerol-3-Phosphate (G3P) and acetyl-CoA. However, compared to higher plants and other eukaryotes, the lipid synthesis pathway in microalgae is not as thoroughly studied. To effectively apply genetic engineering in improving algal biofuel, a deep understanding of the molecular behaviour of GPAT and its potential binding partners is crucial for comprehending the GPAT mechanism of action. In this study, molecular dynamics simulations were conducted to investigate the complexes of GPAT, GPAT-G3P and GPAT-oleoyl-CoA. Our results revealed that G3P formed nine hydrogen bonds and six hydrophobic bonds with GPAT, while oleoyl-CoA formed seven hydrogen bonds and nine hydrophobic bonds. Analysis of the MD simulation trajectory indicated that both G3P and oleoyl-CoA were predicted to be positioned synergistically to facilitate acylation of the fatty acyl moiety to the sn1 position of G3P. Moreover, the protein-ligand complexes remained stable throughout the MD simulation, suggesting that synergistic interactions between G3P and oleoyl-CoA may occur in the bound state with GPAT, promoting the formation of lysophosphatidic acid (LPA).