PMID- 10835286
OWN - NLM
STAT- MEDLINE
DCOM- 20000711
LR  - 20131121
IS  - 0022-2836 (Print)
IS  - 0022-2836 (Linking)
VI  - 299
IP  - 3
DP  - 2000 Jun 9
TI  - Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.
PG  - 813-25
AB  - Our current understanding of Mg(2+) binding to RNA, in both thermodynamic and 
      structural terms, is largely based on classical studies of transfer RNAs. Based 
      on these studies, it is clear that magnesium ions are crucial for stabilizing the 
      folded structure of tRNA. We present here a rigorous theoretical model based on 
      the nonlinear Poisson-Boltzmann (NLPB) equation for understanding Mg(2+) binding 
      to yeast tRNA(Phe). We use this model to interpret a variety of experimental 
      Mg(2+) binding data. In particular, we find that the NLPB equation provides a 
      remarkably accurate description of both the overall stoichiometry and the free 
      energy of Mg(2+) binding to yeast tRNA(Phe) without any fitted parameters. In 
      addition, the model accurately describes the interaction of Mg(2+) with localized 
      regions of the RNA as determined by the pK(a) shift of differently bound 
      fluorophores. In each case, we find that the model also reproduces the univalent 
      salt-dependence and the anticooperativity of Mg(2+) binding. Our results lead us 
      to a thermodynamic description of Mg(2+) binding to yeast tRNA(Phe) based on the 
      NLPB equation. In this model, Mg(2+) binding is simply explained by an ensemble 
      of ions distributed according to a Boltzmann weighted average of the mean 
      electrostatic potential around the RNA. It appears that the entire ensemble of 
      electrostatically bound ions superficially mimics a few strongly coordinated 
      ions. In this regard, we find that Mg(2+) stabilizes the tertiary structure of 
      yeast tRNA(Phe) in part by accumulating in regions of high negative electrostatic 
      potential. These regions of Mg(2+) localization correspond to bound ions that are 
      observed in the X-ray crystallographic structures of yeast tRNA(Phe). Based on 
      our results and the available thermodynamic data, there is no evidence that 
      specifically coordinated Mg ions have a significant role in stabilizing the 
      native tertiary structure of yeast tRNA(Phe) in solution.
CI  - Copyright 2000 Academic Press.
FAU - Misra, V K
AU  - Misra VK
AD  - Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, 
      Baltimore, MD, 21218, USA.
FAU - Draper, D E
AU  - Draper DE
LA  - eng
GR  - GM58545/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - Netherlands
TA  - J Mol Biol
JT  - Journal of molecular biology
JID - 2985088R
RN  - 0 (Fluorescent Dyes)
RN  - 0 (Ions)
RN  - 0 (RNA, Fungal)
RN  - 0 (RNA, Transfer, Phe)
RN  - 0 (Salts)
RN  - 0 (Solutions)
RN  - I38ZP9992A (Magnesium)
SB  - IM
MH  - Binding Sites
MH  - Crystallography, X-Ray
MH  - Fluorescent Dyes/metabolism
MH  - Ions
MH  - Magnesium/*metabolism
MH  - Models, Molecular
MH  - *Nucleic Acid Conformation
MH  - Poisson Distribution
MH  - *RNA Stability
MH  - RNA, Fungal/chemistry/genetics/metabolism
MH  - RNA, Transfer, Phe/*chemistry/genetics/*metabolism
MH  - Salts/metabolism
MH  - Solutions
MH  - Static Electricity
MH  - Thermodynamics
MH  - Yeasts/*genetics
EDAT- 2000/06/03 09:00
MHDA- 2000/07/15 11:00
CRDT- 2000/06/03 09:00
PHST- 2000/06/03 09:00 [pubmed]
PHST- 2000/07/15 11:00 [medline]
PHST- 2000/06/03 09:00 [entrez]
AID - S0022-2836(00)93769-0 [pii]
AID - 10.1006/jmbi.2000.3769 [doi]
PST - ppublish
SO  - J Mol Biol. 2000 Jun 9;299(3):813-25. doi: 10.1006/jmbi.2000.3769.