In silico identification of conserved amino acids within the resistance-nodulation-division efflux pump proteins of Pseudomonas aeruginosa

Membrane-bound efflux pumps are key physiological components used by bacteria to evade antibiotics. The resistance-nodulation-division (RND) efflux system is a tripartite complex containing an outer membrane protein, a periplasmic adaptor protein, and an RND antiporter protein. These efflux pumps have broad substrate specificity—from antibacterial compounds to dyes to detergents—due to the plasticity of the antiporter protein substrate binding pocket, which is influenced by the entire multiprotein assembly. Understanding the protein structure of each component of the RND complex and comparing their conserved amino acids will aid in understanding the residues essential for substrate selectivity, which can then guide the targeted disruption of antibiotic efflux and lead us to therapeutic solutions for antimicrobial-resistant bacteria. Using published protein structures, we used in silico techniques to compare RND efflux pump proteins from clinical and environmental isolates of Pseudomonas aeruginosa , a known multidrug-resistant pathogen. We also compared key amino acids already identified among all other P. aeruginosa PAO1 RND protein homologs to predict their homolog-wide distribution and function and found that although the amino acid identity between homologs is less than 50%, crucial amino acids are well conserved. • Pseudomonas aeruginosa efflux pump proteins are not distinct among varied isolates. • Amino acid conservation between efflux pump protein homologs differs with function. • Outer membrane proteins have crucial amino acids for efflux pump complex formation. • Periplasmic adaptor proteins join the pump complex via key domain-specific residues. • A phenylalanine-rich RND antiporter protein domain may guide substrate specificity.