Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Chemistry

Background:

• Glycerol-3-phosphate acyltransferase (GPAT) is crucial for triacylglycerol synthesis.
• Understanding GPAT substrate binding is vital for regulating cellular glycerol lipid production.
• GPAT4 is a key isoform involved in these pathways.

Purpose of the Study:

• To investigate the substrate recognition mechanism of human GPAT4.
• To elucidate how glycerol-3-phosphate (G3P) and palmitoyl-coenzyme A (CoA) bind to GPAT4.
• To provide insights for designing GPAT4 inhibitors.

Main Methods:

• Molecular dynamics (MD) simulations were employed to study GPAT4-substrate interactions.
• AlphaFold models were used to construct the GPAT4-substrate complex due to the lack of experimental structures.
• A validation study using GPAT1 demonstrated the reliability of the AlphaFold-based MD approach.

Main Results:

• MD simulations revealed that residue R427 plays a significant role in G3P recognition through a stable salt bridge.
• The flexibility of R427 allows G3P to interact with multiple binding sites on GPAT4.
• A unique flexible region in GPAT4, absent in GPAT1, contributes to this observed flexibility.

Conclusions:

• The study elucidates the substrate recognition mechanism of GPAT4.
• The findings highlight the importance of residue R427 and GPAT4's flexible regions in substrate binding.
• This research lays the groundwork for developing targeted GPAT4 inhibitors for therapeutic purposes.