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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Architecture of H-Type Pseudoknots and The Role Of Pseudknots in Frameshifting

We determined the three-dimensional structure of the frameshifting pseudoknot of simian retrovirus type-1 (SRV-1) using NMR spectroscopy.This is only the third structure of an H-type pseudoknot Ð which is omnipresent in RNA and plays a key role in various regulatory mechanisms Ð solved at sufficient resolution to provide detailed structural information - e.g. specific stem-loop interactions, mediated by hydrogen bonding - necessary to understand its function. The SRV-1 pseudoknot is especially interesting due to its involvement in a translational recoding mechanism that is ubiquitous in nature: A programmed Ð1 ribosomal frameshift, used by almost all retroviruses, several plantviruses, yeast and bacterial systems.

The pseudoknot is stabilized by coaxial stacking of the two stems and several loop-helix interactions. The major groove of stem 2 is spanned by the single nucleotide loop 1. Loop 2 is anchored in the minor groove of stem 1 by several base-base and base-sugar interactions and by a ribose-zipper motif, not observed in pseudoknots so far. The two base pairs at the junction have an overwound helical twist angle of 48¡ allowing an arrangement of the different strands such that the stems stack coaxially, while steric hindrance of individual strands at the junction is prevented. Additionally, a sharp bend at the 3Õ-end of loop 2 creates the necessary local adjustment of the backbone to accommodate stacking of the two helices and to position loop 2 in the minor groove of stem 1. These structural aspects will be discussed in relation to its role in ribosomal frameshifting.

Geometrical models are presented that reveal the importance of the magnitude of the helical twist at the junction in determining the overall architecture of classical H-type pseudoknots. In particular the opening of the minor groove of stem 1 and the orientation of stem 2, which determines the number of loop 1 nucleotides that span its major groove.

H.A. Heus(1), Paul J.A. Michiels(1), Alexandra A.M. Versleijen(1), Cornelis W.A. Pleij(2) & Cornelis W. Hilbers(1),

(1)NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld, 6525 ED Nijmegen, The Netherlands;
(2)BIOMAC, Gorlaeus Laboratories, Genexpress, University of Leiden, Einsteinweg 55, 2333 CC Leiden, The Netherlands