Molecular modeling, docking and dynamics analysis of lipid droplet associated enzyme Ypr147cp from Saccharomyces cerevisiae.

Naresh Kumar Manda

doi:10.6026/97320630017132

Abstract

Ypr147cp of Saccharomyces cerevisiae was localized to lipid droplets. The recombinant Ypr147cp showed both triacylglycerol lipase and ester hydrolase activities. Knock out of YPR147C led to accumulation of TAG in ypr147cΔ when compared to wild type (WT). Transmission electron microscopic analysis of ypr147cΔ cells show increased lipid bodies. Moreover, the lipid profiling confirmed the accumulation of fatty acids derived from neutral and phospholipids in ypr147cΔ cells. Sequence analysis of Ypr147cp show the presence of an a/b hydrolase domain with the conserved GXSXG lipase motif. The YPR147c homology model was built and the modeled protein was analysed using RMSD and root mean square fluctuation (RMSF) for a 100 ns simulation trajectory. Docking the acetate, butyrate and palmitate ligands with the model confirmed covalent binding of ligands with the Ser207 of the GXSXG motif. Thus, Ypr147cp is a lipid droplet associated triacylglycerol lipase having short chain ester hydrolyzing capacity.

Highlights

Knock out of YPR147C led to accumulation of TAG in ypr147cΔ when compared to wild type (WT)
Saccharomyces cerevisiae’s Ypr147cp, previously known as bifunctional enzyme which acts as triacylglycerol lipase and short chain ester hydrolase, null mutant results in the accumulation of both triacylglycerol and fatty acids derived from neutral lipids and phospholipids as well as an increase in the quantity of lipid droplets, contains an alpha/beta hydrolase domain with a conserved GXSXG lipase motif [1] localizes to lipid droplets [2]
We report the molecular modeling, docking and dynamics analysis of Saccharomyces cerevisiae lipid droplet associated enzyme Ypr147cp to confirm its activity as triacylglycerol (TAG) lipase and short chain ester hydrolase

Summary

Background

Saccharomyces cerevisiae’s Ypr147cp, previously known as bifunctional enzyme which acts as triacylglycerol lipase and short chain ester hydrolase, null mutant results in the accumulation of both triacylglycerol and fatty acids derived from neutral lipids and phospholipids as well as an increase in the quantity of lipid droplets, contains an alpha/beta hydrolase domain with a conserved GXSXG lipase motif [1] localizes to lipid droplets [2]. Activity of lipase has not been studied in any detail and there are no bioinformatics data to confirm the functionality, evolutionary relationship, substrate specificity and the role of this protein in lipid breakdown. We report the molecular modeling, docking and dynamics analysis of Saccharomyces cerevisiae lipid droplet associated enzyme Ypr147cp to confirm its activity as triacylglycerol (TAG) lipase and short chain ester hydrolase

Materials and Methods

Results and Discussion

Conclusion