Developing a 3D Physical Model of 16S rRNA m1A1408 Methyltransferase, NpmA to Enhance Student Understanding of the Mechanisms of Resistance to Aminoglycosides

Abstract

Aminoglycosides are broad‐spectrum antibiotics common in clinical, veterinary, and agricultural settings and are often reserved for treating severe bacterial infections. With antibiotic resistance becoming a global crisis, understanding the mechanisms by which bacteria attain such resistance is more urgent than ever. One such mechanism specific to aminoglycosides is ribosomal modification by methyltransferases (RMTases). RMTases pose a significant threat as they grant simultaneous resistance to various aminoglycosides and are transmitted between species. The purpose of this project was to develop a 3D physical model of NpmA, an RMTase that confers blanket resistance to aminoglycoside antibiotics by transferring a methyl group to the A1408 nucleotide in helix 44 of the 30S ribosomal subunit. Methylation of A1408 makes helix 44 unrecognizable to these antibiotics. Database searches and sequence alignments were performed to identify conserved amino acids and structural features important in the catalytic mechanism of NpmA. Details of the protein structure and its interaction with helix 44 were obtained by analyzing the Protein Databank File 4OX9. To construct the physical model, the structure file (4OX9) was imported into Jmol and modified into a format suitable for 3D printing using scripts created by undergraduate researchers. The 3D model features NpmA interacting with rRNA and S‐adenosyl‐L‐methionine, the methyl group donor for the methylation reaction. The physical model also highlights key amino acids such as Arg207, E146, Trp107 and Trp197, which are critical to flip A1408 from helix 44 and position it into the enzyme's active site prior to methylation. A Jmol tutorial was created to complement the 3D model and assess students' learning of the structure and function of NpmA. Initial assessment of this activity showed improvement of students' protein visualization abilities, and computational skills. Future work will focus on field‐testing the complete exercise in a microbiology course to evaluate the impact of the 3D model on students' understanding of the mechanisms of antimicrobial resistance.Support or Funding InformationThis project was supported by NSF‐DUE 1725940 awarded to the CREST (Connecting Researchers, Educators, and Students) ProjectThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.