Book of Abstracts: Albany 2009

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

Structural Insight into RNA Catalysis Revealed by Molecular Dynamics Simulations and QM/MM Calculation

The hepatitis delta virus (HDV) ribozyme is a representative example of RNA catalyst. This functional RNA segment is embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the HDV ribozyme, although its exact catalytic role in the process remains debated. Based on the available structural data, we have carried out extensive explicit solvent molecular dynamics (MD) simulations of HDV ribozyme, followed by hybrid quantum/classical (QM/MM) analysis of the possible reaction mechanisms. Combination of long-scale MD simulations and robust electronic structure QM/MM techniques can provide new structural insight into mechanism of RNA catalysis, including direct atomic-level analysis of the reaction mechanism. Our QM/MM calculations of the C75 general base pathway utilize the available structural data for the wild type HDV genomic ribozyme as a starting point. We found that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. On the other hand, even during long scale MD simulations we were not able to identify any plausible arrangements of the active site with protonated C75H+ positioned in a proper orientation for general acid catalysis. Thus general acid pathway seems to be inconsistent with available crystal structures of HDV ribozyme. Since most biochemical studies rather suggest that the catalytic mechanism of HDV ribozyme stems from C75 acting as general acid, we have an interesting case of possible nontrivial conflict between structural and mechanistic data, which will be discussed.

Reference and Footnotes
  1. Banas, P., Rulisek, L., Hanosova, V., Svozil, D., Walter, N. G., Sponer, J., & Otypeka, M. J Phys Chem B 112, 11177-11187 (2008)

Pavel Banas1
Nils G. Walter2
Jiri Sponer1,3
Michal Otyepka1,3

1Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems
Palacky University
tr. Svobody 26, 771 46
Olomouc, Czech Republic
2Department of Chemistry
Single Molecule Analysis Group
University of Michigan
930 N. University Avenue
Ann Arbor, MI 48109-1055, USA
3Institute of Biophysics
Academy of Science of the Czech Republic
Kralovopolska 135
61265 Brno, Czech Republic

*Phone/Fax: +420 585634756
Email: ribicka.neonka@email.cz