Examining the Vectorial Folding Pathway of the β-Helical Peptide, Pertactin, using Molecular Dynamics Simulations

Abstract

Gram-negative bacteria, lacking an energy source at the outer membrane (OM), have evolved a number of unique systems in order to carry out necessary exchange of molecules across the OM. An example is the export of so-called ”virulence factors“, the passenger domain of autotransporters (AT), >97% of which are predicted to adopt right-handed β-helical structures. Given that these passenger domains have a stable C-terminal core, and cross the OM C-terminus to N-terminus, a vectorial folding pathway could direct secretion of the passenger domain across the OM without the need for an external energy source. To better understand the proposed vectoral folding pathway, we calculate the free energy landscape for the first turn of the β-helical protein, pertactin (PDB: 1DAB). Using the radius of gyration, RG, and the number of native hydrogen bonds, QH, we performed 2D umbrella sampling with replica exchange (REMD-US) on residues 438 to 481, while restraining residues 482 to 539 to their crystal structure. We examine how kinetic traps may affect the folding rate in the unconstrained pathway, whereas the vectorial pathway avoids these traps, leading to faster folding rates for the latter, which has been observed experimentally.