Molecular Dynamics Study of the Ribosomal A-Site

Abstract

Many aminoglycosidic antibiotics target the A-site of 16S RNA in the small ribosomal subunit and affect the fidelity of protein translation in bacteria. Upon binding aminoglycosides displace two adenines (A1492 and A1493 for E. coli numbering) that are involved in tRNA anticodon loop recognition. The major difference in the aminoglycosidic binding site between the prokaryota and eukaryota is an adenine into guanine substitution in the position 1408. This mutation likely affects the dynamics of near A1492 and A1493 and hinders the binding of aminoglycosides to eukaryotic ribosomes. With multiple 20 ns long all-atom molecular dynamics simulations we study the flexibility of a 22-nucleotide RNA fragment which mimics the aminoglycosidic binding site. Simulations are carried out for both, native and A1408G mutated RNA, as well as for their complexes with aminoglycosidic representative -paromomycin. We observe intra-and extrahelical configurations of A1492 and A1493, which differ between the prokaryotic and the mutated structure. We obtained configurations of the A-site that were also observed in the NMR and crystal structures. Our studies show the differences in the internal mobility of the A-site, as well as in ion and water density distributions inside the binding cleft, between the prokaryotic and mutated RNA. We also compare the performance of two force field parameters for RNA -Amber and Charmm.

Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome

“…Since most of the decoding activity in the A-site involves helix 44 of the 16S rRNA, several simulation studies on A-site containing 16S rRNA fragments in the presence and absence of antibiotics have been performed. (Reblova et al 2006;Vaiana et al 2006;Meroueh and Mobashery 2007;Romanowska et al 2008) These include classical MD as well as enhanced sampling simulations using replica exchange or targeted MD protocols. These studies have revealed changes in mobility of residues 1492 and 1493 when antibiotics are bound or when the nearby residue 1408 is changed from the prokaryotic adenine to the eukaryotic guanine.…”

Electrostatic Interactions in Aminoglycoside-RNA Complexes

“…This happens even though the neamine core is stably bound, in contrast to rings III, IV, and V, as shown in MD studies (20,23); the contacts formed by the other rings with the A-site were more transient than the contacts formed by neamine.…”

“…On average, ring IV gives high electrostatic contribution, similar to rings I and II. MD simulations of the complex of the A-site with PAR (20) and the superposition shown in Fig. 3 suggest that ring IV is flexible, so its high E el is somewhat surprising.…”

“…In two complexes (PAR and JSP4), an additional, third interaction is present between the water oxygen and the O3 0 hydroxyl group of PAR and JS4P. Although the bonding distance for this third hydrogen bond is longer (~3.6 Å ), this water molecule was previously shown to be stable in MD simulations of a PAR-A-site complex (20,23,46). The next common water mediation of ring II is conserved in four analyzed structures, PAR, NMY, RIO, and LIV (Pattern 2; Fig.…”

“…All-atom molecular dynamics (MD) simulations of the A-site concentrated on the functional flexibility of A1492 and A1493 (20,21). MD studies of the A-site with paromomycin (20) and amikacin (22) confirmed that the neamine core ( Fig. 1, rings I and II) is an anchor in the binding cleft.…”