Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Analysis of Hydrogen Bonds Involving Backbone Atoms in Ribosomal RNA

High-resolution crystal structures of ribosomal particles solved in the past decade provide a wealth of information for understanding principles of organization of complex RNA structures. Indeed, the availability of such information has spurred in-depth analyses of base-centered RNA structural motifs and backbone conformations, see, e.g. [1-4]. Less appreciated remain hydrogen bonds involving backbone acceptor atoms of RNA; nevertheless, such hydrogen bonds are common in tertiary interactions. We have analyzed hydrogen bonds in rRNA from the 2.20 Å-resolution structure of the large ribosomal subunit of Haloarcula marismortui [5]. In 2426 pairs of RNA residues connected with at least one hydrogen bond, there are 509 hydrogen bonds involving phosphorus oxygens OP1/OP2, and 120 and 28 hydrogen bonds involving phosphodiester oxygens O3? and O5?, respectively. The most common donor atoms for such hydrogen bonds are the hydroxyl proton of riboses and amino and imino protons of guanines, although the amino protons of adenines and cytosines and imino protons of uracils are also observed. Geometric parameters of such hydrogen bonds will be presented.

References and Footnotes
  1. S.R. Holbrook, Annu. Rev. Biophys. 37, 445-64 (2008).
  2. Y. Xin, C. Laing, N.B. Leontis & T. Schlick, RNA 14, 2465-77 (2008).
  3. W.K. Olson, M. Esguerra, Y. Xin, X-J. Lu, Methods 47, 177-86 (2009).
  4. J.S. Richardson, B. Schneider, L.W. Murray, G.J. Kapral, R.M. Immormino, L.D. Williams, K.S. Keating, A.M. Pyle, D. Micaliff, J. Westbrook & H.M. Berman, RNA 14, 465-81 (2008).
  5. T.M. Schmeing, K.S. Huang, D.E. Kitchen, S.A. Strobel & T.A. Steitz, Mol. Cell 20, 437-48 (2005).

Nikolai B. Ulyanov*
Thomas L. James

University of California
San Francisco, CA 94158-2517

Tel.: 415-476-0707