PMID- 9745889
OWN - NLM
STAT- MEDLINE
DCOM- 19990112
LR  - 20131121
IS  - 0739-1102 (Print)
IS  - 0739-1102 (Linking)
VI  - 16
IP  - 1
DP  - 1998 Aug
TI  - Ion-RNA interactions in the RNA pseudoknot of a ribosomal frameshifting site: 
      molecular modeling studies.
PG  - 1-11
AB  - The three-dimensional (3-D) structure of a RNA pseudoknot that causes the 
      efficient ribosomal frameshifting in the gag-pro region of mouse mammary tumor 
      virus (MMTV) has been determined recently by nuclear magnetic resonance (NMR) 
      studies. But since the structure refinement in the studies did not use metal ions 
      and waters, it is not clear how metal ions participate in the stabilization of 
      the pseudoknot, and what kind of ion-RNA interactions dominate in the tertiary 
      contacts for the RNA pseudoknotting. Based on the reported structure data of the 
      pseudoknot VPK of MMTV, we gradually refined the structure by restrained 
      molecular dynamics (MD) using NMR distance restraints. Restrained MD simulation 
      of the RNA pseudoknot was performed with sodium ions and water molecules. Our 
      results are in good agreement with known NMR data and delineate the importance of 
      the metal ion coordination in the stability of the pseudoknot. In the 
      non-coaxially stacking pseudoknot, stem 1 (S1), stem 2 (S2), and the intervening 
      A14 involves unconventional stacking of base pairs coordinated by Na+ and/or 
      bridging water molecules. A6 and G7 of loop L1 make a perfect base stacking in 
      the major groove and are further stabilized by coordinated Na+ ions and water 
      molecules. The first 4-nucleotide (nt) ACUC of loop L2 form a sharp turn and the 
      following 4-nt AAAA cross the minor groove of S1 and are steadied by interactions 
      with the nucleotides of S , bridging water molecules and coordinated Na+ ions. 
      Our studies suggest that the metal ion plays a crucial role in the RNA 
      pseudoknotting of VPK. In the stacking interior of S1 and S2, the Na+ ion is 
      positioned in the major groove and interacts directly with the carbonyl group O6 
      of G28 and carbonyl group O4 of U13 in the wobble base pair U13:G28. The ion-RNA 
      interactions in MMTV VPK not only stabilize the RNA pseudoknot but also modify 
      the electrostatic properties of the nucleotides at the critical parts of the 
      pseudoknot VPK.
FAU - Le, S Y
AU  - Le SY
AD  - Laboratory of Experimental and Computational Biology, DBS, FCRDC, National Cancer 
      Institute, NIH, Frederick, MD 21701, USA. shuyun@orleans.ncifcrf.gov
FAU - Chen, J H
AU  - Chen JH
FAU - Pattabiraman, N
AU  - Pattabiraman N
FAU - Maizel, J V Jr
AU  - Maizel JV Jr
LA  - eng
PT  - Journal Article
PL  - England
TA  - J Biomol Struct Dyn
JT  - Journal of biomolecular structure & dynamics
JID - 8404176
RN  - 0 (Ions)
RN  - 0 (RNA, Viral)
RN  - 9NEZ333N27 (Sodium)
SB  - IM
MH  - Animals
MH  - *Frameshifting, Ribosomal
MH  - Ions
MH  - Mammary Tumor Virus, Mouse/*genetics
MH  - Mice
MH  - Models, Molecular
MH  - Nucleic Acid Conformation
MH  - RNA, Viral/*chemistry
MH  - Sodium
EDAT- 1998/09/24 02:03
MHDA- 2001/03/28 10:01
CRDT- 1998/09/24 02:03
PHST- 1998/09/24 02:03 [pubmed]
PHST- 2001/03/28 10:01 [medline]
PHST- 1998/09/24 02:03 [entrez]
AID - 10.1080/07391102.1998.10508221 [doi]
PST - ppublish
SO  - J Biomol Struct Dyn. 1998 Aug;16(1):1-11. doi: 10.1080/07391102.1998.10508221.