Internal Electric Field of GRAM- Unspecific Porins Directs the Choreography of Antibiotic Translocation

Abstract

The number of multiple drug resistant pathogens is ever increasing. The impact on healthcare systems is urgently demanding for novel classes of antibiotics, especially against Gram-negative bacteria. Their first line of defense is the outer membrane, where unspecific protein channels, called porins, modulate passive diffusion of nutrients. Porins are considered today the main path for entry of polar antibiotics into the bacterial cell. Down-regulation and/or mutation of porins are very common in drug resistant strains.1 The inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features for better penetration. This can be obtained with molecular dynamics simulations, an atomic level microscope for detailed investigation of molecules’ translocation choreography through protein channels.In this work, a series of unspecific porins were selected, including also clinical mutant isolates. As their size is comparable1, structural comparison was focused on lumen electrostatics. Serial modifications of the internal electric field was found moving from wild-type porins to resistant mutants. Water molecules were used as an intrinsic molecular probe and the electric field variations inside the channels matched with charged residues distribution.2 Translocation free energy surface was reconstructed for β-lactams antibiotics from different families with multiple-walkers metadynamics simulations.The choreography followed by the molecular electric dipole was analyzed in terms of spherical coordinates to distinguish the influence of different components of the internal electric field. The direction perpendicular to the channel axis is the most important in the absence of an externally applied voltage. The antibiotic has to fit both shape and electrostatics of the channel constriction region to minimize the main energy barrier to translocation.1Lou et al., PloS ONE 6 (2011) e25825.2Acosta-Gutierrez et al., J. Phys. Chem. Lett. 6 (2015) 1807-1812.