All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer

Abstract

Protein–protein interactions between transmembrane helices are essential elements for membrane protein structures and functions. To understand the effects of peptide sequences and lipid compositions on these interactions, single-molecule experiments using model systems comprising artificial peptides and membranes have been extensively performed. However, their dynamic behavior at the atomic level remains largely unclear. In this study, we applied the all-atom molecular dynamics (MD) method to simulate the interactions of single-transmembrane helical peptide dimers in membrane environments, which has previously been analyzed by single-molecule experiments. The simulations were performed with two peptides (Ala- and Leu-based artificially designed peptides, termed “host peptide”, and the host peptide added with the GXXXG motif, termed “GXXXG peptide”), two membranes (pure-POPC and POPC mixed with 30% cholesterols), and two dimer directions (parallel and antiparallel), consistent with those in the previous experiment. As a result, the MD simulations with parallel dimers reproduced the experimentally observed tendency that introducing cholesterols weakened the interactions in the GXXXG dimer and facilitated those in the host dimer. Our simulation suggested that the host dimer formed hydrogen bonds but the GXXXG dimer did not. However, some discrepancies were also observed between the experiments and simulations. Limitations in the space and time scales of simulations restrict the large-scale undulation and peristaltic motions of the membranes, resulting in differences in lateral pressure profiles. This effect could cause a discrepancy in the rotation angles of helices against the membrane normal.

Effects of Gly Residue and Cholesterol on the GXXXG‐Mediated Parallel Association of Transmembrane Helices: A Single‐Pair FRET Study

“…However, we did not observe any helix associations for GXXXG3 in POPC or POPC/cholesterol membranes (Figure 2). This discrepancy between the prediction and experiment was attributed to the higher flexibility of the helical secondary structure for GXXXG3 because of an increase in the number of Gly residues, [9b,11b] which may abolish stable helix‐helix associations. Consistently, the halfwidth of the amide I’ band for GXXXG3 (19.3±0.8 cm −1 ) was slightly larger than that for GXXXG2 (17.7±0.4 cm −1 ) ( p =0.07, two‐tailed t ‐test) in POPC membranes (Supporting Information, Figure S7).…”

Effects of Membrane Cholesterol on Stability of Transmembrane Helix Associations

“…23,[30][31][32][33][34][35] Transmembrane helices are also useful in computer simulation studies to examine the effects of membrane physicochemical properties on the associations of transmembrane helices at the molecular level. [36][37][38][39] My collaborators and I used three types of model transmembrane helices (1TM, GXXXG, and 2TM) to examine the effects of cholesterol (Fig. 5).…”