title: Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions.
abstract: Aminoglycosides are broad-spectrum antibiotics that bind to the 30S ribosomal subunit (30S) of bacteria and disrupt protein translation. NpmA, a structurally well-characterized methyltransferase identified in an E. coli clinical isolate, catalyzes methylation of 30S at A1408 of the 16S rRNA and confers aminoglycoside resistance. Using sucrose cushion centrifugation and isothermal titration calorimetry, we first confirmed the binding between NpmA and 30S. Next, we performed amide Hydrogen/Deuterium Exchange Mass Spectrometry (HDXMS) of apo NpmA and in the presence and absence of SAM/SAH. We observed that ligand binding resulted in time-dependent differences in deuterium exchange not only at the ligand-binding pocket (D25-D55 and A86-E112) but also in distal regions (F62-F82 and Y113-S144) of NpmA. These results provide insights into methylation group donor cofactor-mediated allostery in NpmA in the ligand-bound states, which could not be observed in the static endpoint crystal structures. We predict that the two distal sites in NpmA form part of the allosteric sites that importantly are part of the main 16S rRNA binding interface. Thus HDXMS helped uncover allosteric communication relays that couple SAM/SAH binding sites with the ribosome-binding site. This highlights how HDXMS together with X-ray crystallography can provide important allosteric insights in protein-ligand complexes.
authors.affiliation: Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543 Singapore.
authors.forename: Nilofer
authors.initials: N
authors.lastname: Husain
authors.affiliation: Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543 Singapore.
authors.forename: Nikhil Kumar
authors.initials: NK
authors.lastname: Tulsian
authors.affiliation: Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543 Singapore.
authors.forename: Wang Loo
authors.initials: WL
authors.lastname: Chien
authors.affiliation: Manipal College of Pharmaceutical Sciences, Manipal, 576104 India.
authors.forename: Sushant
authors.initials: S
authors.lastname: Suresh
authors.affiliation: Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543 Singapore.
authors.forename: Ganesh Srinivasan
authors.initials: GS
authors.lastname: Anand
authors.affiliation: Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543 Singapore.
authors.forename: J
authors.initials: J
authors.lastname: Sivaraman
mesh_terms: D001665:Binding Sites; D041961:Deuterium Exchange Measurement; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D013058:Mass Spectrometry; D008780:Methyltransferases / Q000737:chemistry* / Q000378:metabolism; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry / Q000378:metabolism; D012435:S-Adenosylhomocysteine / Q000737:chemistry* / Q000378:metabolism; D012436:S-Adenosylmethionine / Q000737:chemistry* / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D008024:Ligands; D012436:S-Adenosylmethionine; D012435:S-Adenosylhomocysteine; D008780:Methyltransferases; C554940:NpmA protein, E coli