Minimum-Energy Path for a U6 RNA Conformational Change Involving Protonation, Base-Pair Rearrangement and Base Flipping

JOURNAL OF MOLECULAR BIOLOGY

卷:391

Article

Venditti, Vincenzo^2,3  Clos, Lawrence, II¹  Niccolai, Neri^2,3  Butcher, Samuel E.^1,4 

[1] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA

[2] Univ Siena, Dipartimento Biol Mol, I-53100 Siena, Italy

[3] Univ Siena, Biol Struct Res Ctr, I-53100 Siena, Italy

[4] Univ Wisconsin, Nucl Magnet Resonance Facil Madison, Madison, WI 53706 USA

关键词: U6 RNA;    RNA structure;    NMR;    molecular dynamics;    nudged elastic band;   

DOI  :  10.1016/j.jmb.2009.07.003

来源: Elsevier

【 摘 要 】

The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a) =6.5). Lower pH favors formation of a protonated C-A(+) wobble pair and base flipping of the adjacent uracil. Higher pH favors stacking of the uracil and allows an essential metal ion to bind at this position. Here, we define the minimal-energy path for this conformational transition. To do this, we solved the U6 ISL structure at higher pH (8.0) in order to eliminate interference from the low-pH conformer. This structure reveals disruption pair and formation of a new C-U pair, which of the protonated C-A explains the preference for a stacked uracil at higher pH. Next, we used nudged elastic band molecular dynamics simulations to calculate the minimum-energy path between the two conformations. Our results indicate that the C-U pair is dynamic, which allows formation of the more stable C-A(+) pair upon adenine protonation. After formation of the C-A(+) pair, the unpaired uracil follows a minor-groove base-flipping pathway. Molecular dynamics simulations suggest that the extrahelical uracil is stabilized by contacts with the adjacent helix. (C) 2009 Elsevier Inc. All rights reserved.

【 授权许可】

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