pH-Responsive peptide nanopores are stabilized by lipid and water-mediated hydrogen bonding networksBondar, Ana-Nicoleta (Avtor) Lešnik, Samo (Avtor) Hristova, Kalina (Avtor) Wimley, William C. (Avtor) nanoporesmacromolecular cargobiomedical applicationsMembrane-spanning nanopores that allow controlled passage of macromolecular cargo across cell membranes can empower many biomedical applications. Such nanopores are formed, in a pH-responsive manner, by the synthetically evolved “pHD peptide” family. pHD peptides fold into amphipathic α-helices, but have many charged and polar residues and are thus not predicted by classical hydropathy analyses to fold into membrane-spanning structures. Yet, when the pH is below ∼6, pHD peptides readily self-assemble into nanopores, even at low concentration. Knowledge of the molecular structure of the pHD peptide pore is needed for further rational design and optimization of nanopore-forming activity targeted to specific membranes and pH conditions. To this end, we have carried out extensive atomistic molecular dynamics simulations to explore the protonation-dependent structure and dynamics of nanopores created by the peptide pHD108. Simulations and graph-based analyses of hydrogen bonding reveal that, in the nanopore, the numerous carboxylate and carboxyamide sidechains form a dense, water-bridged H-bond network across the bilayer. In this network, direct H-bonds between neighboring peptides are few. Instead, the network is dominated by water-bridged intrapeptide interactions and by water-bridged interactions with the headgroups of many lipid molecules with unusual conformations and orientations. The lipids in the H-bond network make critical contributions to nanopore stabilization. These studies reveal a non-classical means of stabilizing nanopores in bilayers formed by highly charged peptides, creating an avenue towards engineering of membrane-embedded structures. Royal society of chemistry20262026-03-31 07:10:19Članek v reviji97665UDK: 577COBISS_ID: 272733699DOI: 10.1039/D5NR03276HISSN pri članku: 2040-3372sl