Free-energy landscapes and insertion pathways for peptides in membrane environment

• Published in: arXiv.org 2022-07
• Main Authors: Sharma, Ganga P, Meyer, Aaron C, Habeeb, Suhail, Karbach, Michael, Müller, Gerhard
• Format: Article
• Language: English
• Subjects: Aqueous environments; Backbone; Cell membranes; Elementary excitations; Free energy; Hydrophobicity; Insertion; Lipids; Peptides; Polar environments; Polypeptides; Protonation; Residues
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.2204.10404

Free-energy landscapes for short peptides -- specifically for variants of the pH Low Insertion Peptide (pHLIP) -- in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant interactions and the conformational preferences of the peptide backbone. Our methodology interprets broken internal H-bonds along the backbone of a polypeptide as statistically interacting quasiparticles, activated from the helix reference state. The favored conformation depends on the local environment (ranging from polar to nonpolar), specifically on the availability of external H-bonds (with \(\mathrm{H_2O}\) molecules or lipid headgroups) to replace internal H-bonds. The dominant side-chain contribution is accounted for by residue-specific transfer free energies between polar and nonpolar environments. The free-energy landscape is sensitive to the level of pH in the aqueous environment surrounding the membrane. For high pH, we identify pathways of descending free energy that suggest a coexistence of membrane-adsorbed peptides with peptides in solution. A drop in pH raises the degree of protonation of negatively charged residues and thus increases the hydrophobicity of peptide segments near the C terminus. For low pH, we identify insertion pathways between the membrane-adsorbed state and a stable trans-membrane state with the C terminus having crossed the membrane.