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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
15
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pubmed:dateCreated |
2003-7-30
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pubmed:abstractText |
Interactions with magnesium (Mg2+) ions are essential for RNA folding and function. The locations and function of bound Mg2+ ions are difficult to characterize both experimentally and computationally. In particular, the P456 domain of the Tetrahymena thermophila group I intron, and a 58 nt 23s rRNA from Escherichia coli have been important systems for studying the role of Mg2+ binding in RNA, but characteristics of all the binding sites remain unclear. We therefore investigated the Mg2+ binding capabilities of these RNA systems using a computational approach to identify and further characterize their Mg2+ binding sites. The approach is based on the FEATURE algorithm, reported previously for microenvironment analysis of protein functional sites. We have determined novel physicochemical descriptions of site-bound and diffusely bound Mg2+ ions in RNA that are useful for prediction. Electrostatic calculations using the Non-Linear Poisson Boltzmann (NLPB) equation provided further evidence for the locations of site-bound ions. We confirmed the locations of experimentally determined sites and further differentiated between classes of ion binding. We also identified potentially important, high scoring sites in the group I intron that are not currently annotated as Mg2+ binding sites. We note their potential function and believe they deserve experimental follow-up.
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pubmed:grant |
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pubmed:commentsCorrections |
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Aug
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pubmed:issn |
1362-4962
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:day |
1
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pubmed:volume |
31
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
4450-60
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:12888505-Algorithms,
pubmed-meshheading:12888505-Animals,
pubmed-meshheading:12888505-Binding Sites,
pubmed-meshheading:12888505-Computational Biology,
pubmed-meshheading:12888505-Genomics,
pubmed-meshheading:12888505-Introns,
pubmed-meshheading:12888505-Magnesium,
pubmed-meshheading:12888505-Models, Molecular,
pubmed-meshheading:12888505-Models, Statistical,
pubmed-meshheading:12888505-Nucleic Acid Conformation,
pubmed-meshheading:12888505-RNA,
pubmed-meshheading:12888505-RNA, Ribosomal, 23S,
pubmed-meshheading:12888505-Static Electricity,
pubmed-meshheading:12888505-Tetrahymena
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pubmed:year |
2003
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pubmed:articleTitle |
Microenvironment analysis and identification of magnesium binding sites in RNA.
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pubmed:affiliation |
Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, CA 94305, USA.
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