Linked Life Data

12654263

Source:http://linkedlifedata.com/resource/pubmed/id/12654263

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2003-3-25
pubmed:abstractText
Sequence-specific protein-nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid side-chains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen bond to unpaired bases, such as those found in RNA bulges and loops, or to the 53 possible RNA base-pairs. We find 32 possible interactions that involve two or more hydrogen bonds to the six unpaired bases (including protonated A and C), 17 of which have been observed. We find 186 "spanning" interactions to base-pairs in which the amino acid hydrogen bonds to both bases, in principle allowing particular base-pairs to be selectively targeted, and nine of these have been observed. Four calculated interactions span the Watson-Crick pairs and 15 span the G:U wobble pair, including two interesting arrangements with three hydrogen bonds to the Arg guanidinum group that have not yet been observed. The inherent donor-acceptor arrangements of the bases support many possible interactions to Asn (or Gln) and Ser (or Thr or Tyr), few interactions to Asp (or Glu) even though several already have been observed, and interactions to U (or T) only if the base is in an unpaired context, as also observed in several cases. This study highlights how complementary arrangements of donors and acceptors can contribute to base-specific recognition of RNA, predicts interactions not yet observed, and provides tools to analyze proposed contacts or design novel interactions.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
4
pubmed:volume
327
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
781-96
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed-meshheading:12654263-Amino Acids, pubmed-meshheading:12654263-Arginine, pubmed-meshheading:12654263-Asparagine, pubmed-meshheading:12654263-Base Composition, pubmed-meshheading:12654263-Base Pairing, pubmed-meshheading:12654263-Computer Simulation, pubmed-meshheading:12654263-Crystallography, X-Ray, pubmed-meshheading:12654263-DNA, pubmed-meshheading:12654263-Databases, Factual, pubmed-meshheading:12654263-Hydrogen Bonding, pubmed-meshheading:12654263-Magnetic Resonance Spectroscopy, pubmed-meshheading:12654263-Models, Molecular, pubmed-meshheading:12654263-Models, Structural, pubmed-meshheading:12654263-Nucleic Acid Conformation, pubmed-meshheading:12654263-Nucleic Acids, pubmed-meshheading:12654263-Protein Binding, pubmed-meshheading:12654263-Protein Structure, Secondary, pubmed-meshheading:12654263-Protons, pubmed-meshheading:12654263-Purines, pubmed-meshheading:12654263-Pyrimidines, pubmed-meshheading:12654263-RNA, pubmed-meshheading:12654263-Serine
pubmed:year
2003
pubmed:articleTitle
Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains.
pubmed:affiliation
Department of Biochemistry and Biophysics, University of California, 513 Parnassus Avenue, San Francisco, CA 94143-0448, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.