Book of Abstracts: Albany 2009

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

All-Atom RNA Tertiary Structure Prediction

We used steered molecular dynamics and simulated annealing to predict the complete tertiary structure of several different RNAs. Our restraints are derived only from secondary structure, covariation analysis, ideal A-form values, multibranch coaxial stacking predictions, and, when necessary for larger systems, biochemical data [1,2]. The calculations are performed using the AMBER molecular dynamics package and the AMBER 99 forcefield. We applied this methodology to the Alu domain of the mammalian SRP RNA, yeast tRNAPhe, the full hammerhead ribozyme, the hairpin ribozyme, the group I intron, and the group IIc intron [3-7]. We accelerated these calculations by running without non-bonded forces while restraints were being applied, followed by their restoration using a novel application of ?soft core? van der Waals potentials [8]. We compare our results both with current crystal structures and with past modeling attempts and find that our simple ab initio approach is sufficient to make good predictions of the global topology of the molecules [9].

References and Footnotes
  1. Tyagi, R., Mathews, D. H. 2007. RNA 13:939-51
  2. Heckman JE, Lambert D, Burke JM. 2005. Biochemistry. 44: 4148-56.
  3. Weichenrieder, O., Wild, K., Strub, K., Cusack, S. 2000. Nature 408: 167-173.
  4. Shi, H., Moore, P.B. 2000. RNA 6: 1091-1105.
  5. Martick, M., Scott, W.G. 2006. Cell , 126: 309-320.
  6. Guo, F., Gooding, A.R., Cech, T.R. 2004. Mol.Cell , 16: 351-362
  7. Toor, N., Keating, K.S., Taylor, S.D., Pyle, A.M. 2008. Science, 320: 77-82.
  8. Steinbrecher, T., Mobley, D. L., Case, D. A. 2007. J Chem Phys. 127: 214108
  9. Michel, F., Westhof, E. 1990. J Mol. Biol. 216: 585-610

Matthew G. Seetin
David H. Mathews

Department of Biochemistry and Biophysics
University of Rochester Medical Center
601 Elmwood Ave. Box 712
Rochester, NY 14642

Phone: 585-275-1754
Fax: 585-275-6007
email: Matthew Seetin