RNA-magnesium-protein interactions in large ribosomal subunit

Anton S. Petrov, Chad R. Bernier, Chiaolong Hsiao, C. Denise Okafor, Emmanuel Tannenbaum, Joshua Stern, Eric Gaucher, Dana Schneider, Nicholas V. Hud, Stephen C. Harvey, Loren Dean Williams

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


Some of the magnesium ions in the ribosome are coordinated by multiple rRNA phosphate groups. These magnesium ions link distal sequences of rRNA, primarily by incorporating phosphate groups into the first coordination shell. Less frequently, magnesium interacts with ribosomal proteins. Ribosomal protein L2 appears to be unique by forming specific magnesium-mediated interactions with rRNA. Using optimized models derived from X-ray structures, we subjected rRNA/magnesium/water/rProtein L2 assemblies to quantum mechanical analysis using the density functional theory and natural energy decomposition analysis. The combined results provide estimates of energies of formation of these assemblies, and allow us to decompose the energies of interaction. The results indicated that RNA immobilizes magnesium by multidentate chelation with phosphate, and that the magnesium ions in turn localize and polarize water molecules, increasing energies and specificities of interaction of these water molecules with L2 protein. Thus, magnesium plays subtle, yet important, roles in ribosomal assembly beyond neutralization of electrostatic repulsion and direct coordination of RNA functional groups.

Original languageEnglish (US)
Pages (from-to)8113-8120
Number of pages8
JournalJournal of Physical Chemistry B
Issue number28
StatePublished - Jul 19 2012

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry


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