Partitioning Charged Side Chains into Lipid Bilayer Membranes

Abstract

Hydrophobic amino acids are abundant in transmembrane (TM) helices of membrane proteins. Charged residues are sparse, apparently due to the unfavorable energetic cost of partitioning charges into non-polar phases. Nevertheless, conserved arginine residues within TM helices regulate vital functions, such as ion channel voltage gating and integrin receptor inactivation. The energetic cost of arginine in various positions along hydrophobic helices has been controversial. Potential of mean force (PMF) calculations from atomistic molecular dynamics simulations predict very large energetic penalties, while in vitro experiments with Sec61 translocons indicate much smaller penalties, even for arginine in the center of hydrophobic TM helices. Resolution of this conflict has proved difficult, because the in vitro assay utilizes the complex Sec61 translocon, while the PMF calculations rely on the choice of simulation system and reaction coordinate. Here we present the results of computational and experimental studies that permit direct comparison with the Sec61 translocon results. We find that arginine can be accommodated at the center of a hydrophobic TM helix without a significant energetic penalty for peptides designed using templates from the in vitro Sec61 experiments. Furthermore, the translocon assay seems to underestimate the probability of insertion compared to our computational results. We show that a combination of arginine snorkeling, bilayer deformation, and peptide tilting is sufficient to lower the penalty of arginine insertion, thus providing an explanation for the differences between PMF- and experiment-based burial penalties.This research was supported in part by the National Institute of General Medical Sciences (GM-74737 and GM-86685 to S.H.W) and a Marie Curie International Fellowship (to M.B.U).