Molecular Basis of Filtering Carbapenems by Porins from β-Lactam-resistant Clinical Strains of Escherichia coli

Integral membrane proteins known as porins are the major pathway by which hydrophilic antibiotics cross the outer mem- brane of Gram-negative bacteria. Single point mutations in porins can decrease the permeability of an antibiotic, either by reduction of channel size or modification of electrostatics in the channel, and thereby confer clinical resistance. Here, we inves- tigate four mutant OmpC proteins from four different clinical isolates of Escherichia coli obtained sequentially from a single patient during a course of antimicrobial chemotherapy. OmpC porin from the first isolate (OmpC20) undergoes three consec- utive and additive substitutions giving rise to OmpC26, OmpC28, and finally OmpC33. The permeability of two zwitte- rionic carbapenems, imipenem and meropenem, measured using liposome permeation assays and single channel electro- physiology differs significantly between OmpC20 and OmpC33. Molecular dynamic simulations show that the antibiotics must pass through the constriction zone of porins with a specific ori- entation, where the antibiotic dipole is aligned along the electric field inside the porin. We identify that changes in the vector of the electric field in the mutated porin, OmpC33, create an addi- tional barrier by “trapping” the antibiotic in an unfavorable ori- entation in the constriction zone that suffers steric hindrance for the reorientation needed for its onward translocation. Iden- tification and understanding the underlying molecular details of such a barrier to translocation will aid in the design of new anti- biotics with improved permeation properties in Gram-negative bacteria.