A Computational Study and Parameterisation of Phosphatidylinositol Phosphates for Lipid Simulations with AMBER

Abstract: Phosphatidylinositol phosphates (PIPs) are membrane phospholipids that play crucial roles in a wide range of cellular functions. However, there is a dearth of experimental data in the literature on PIPs because their investigations are not always feasible and often prohibitively expensive. Hence, there is great interest in using computational simulations to study the structures, transitions, and interactions of PIP-containing membranes. Assisted Model Building with Energy Refinement (AMBER) is a molecular dynamics program with validated force fields parameterized for a range of lipid types. The development of AMBER's Lipid force fields is a continuous process with ongoing work in both improving the accuracy of the simulated result and extending the force field with diverse lipid types. The research conducted for this work represents the first attempt to parameterize PIPs using the protocols of the latest Lipid21 force field.