Amino Acid Insertion Energetics in a POPC Bilayer from Unbiased Molecular Dynamics

Membrane association is governed by the thermodynamics of amino acid partitioning between water and the lipid bilayer. Here, we quantified amino acid side-chain insertion energetics in a 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) bilayer using unbiased molecular dynamics simulations. Equilibrium depth distributions of 28 analogs, including multiple protonation states, were converted into potentials of mean force (PMFs) by Boltzmann inversion. The resulting PMFs reproduced the main features of bilayer partitioning. Hydrophobic analogs favored the bilayer core, aromatic analogs were stabilized in interfacial regions, and polar or charged analogs remained unfavorable in the hydrophobic interior. A diglycine analog representing the peptide backbone behaved similarly to uncharged polar residues. Depth-dependent pK _a profiles and orientational analyses further showed how protonation equilibria and aromatic-ring alignment influence insertion energetics. Agreement with experimental hydrophobicity scales supports the robustness of the approach. These results provide an efficient and internally consistent framework for characterizing bilayer insertion energetics and establish a reference for future studies in more complex lipid environments.