Using Modified Long Chain Fatty Acids to Explore Protein Dynamics in an Intracellular-Lipid Binding Protein

Document Type

Book Chapter

Publication Date


Publication Title

Physical Chemistry Research at Undergraduate Institutions: Innovative and Impactful Approaches, Volum


Intracellular lipid-binding proteins (iLBPs) play a critical role in lipid availability and in signaling pathways making them possible therapeutic targets. One specific iLBP of interest is FABP5, a fatty acid binding protein that binds to naturally-occurring retinoic acid and activates the peroxisome proliferator-activated receptor β/δ causing cell growth and proliferation. Competitive-binding to FABP5 by other long-chain fatty acid ligands may reduce unwanted overgrowth of cells. Recently, an increase in computational studies of FABP5 has provided insight into the binding process. The focus of this chapter is the role of ligand starting conformation on protein dynamics. A series of nine ~1 μs molecular dynamics (MD) simulations were conducted on two modified long-chain fatty acids docked into FABP5. The ways in which undergraduate students performed the research in this project will also be discussed.