Linked Life Data

15850388

Source:http://linkedlifedata.com/resource/pubmed/id/15850388

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
17
pubmed:dateCreated
2005-4-26
pubmed:abstractText
The local geometry of a DNA helix can influence protein recognition, but the sequence-specific features that contribute to helix structure are not fully understood, and even less is known about how RNA helix geometry may affect protein recognition. To begin to understand how local or global helix structure may influence binding in an RNA model system, we generated a series of DNA analogues of HIV and BIV TAR RNAs in which ribose sugars were systematically substituted in and around the known binding sites for argininamide and a BIV Tat arginine-rich peptide, respectively, and measured their corresponding binding affinities. For each TAR interaction, binding occurs in the RNA major groove with high specificity, whereas binding to the all-DNA analogue is weak and nonspecific. Relatively few substitutions are needed to convert either DNA analogue of TAR into a high-affinity binder, with the ribose requirements being restricted largely to regions that directly contact the ligand. Substitutions at individual positions show up to 70-fold differences in binding affinity, even at adjacent base pairs, while two base pairs at the core of the BIV Tat peptide-RNA interface are largely unaffected by deoxyribose substitution. These results suggest that the helix geometries and unique conformational features required for binding are established locally and are relatively insulated from effects more than one base pair away. It seems plausible that arginine-rich peptides are able to adapt to a mosaic helical architecture in which segments as small as single base steps may be considered as modular recognition units.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
0006-2960
pubmed:author
pubmed:issnType
Print
pubmed:day
3
pubmed:volume
44
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
6547-58
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed-meshheading:15850388-Amino Acid Motifs, pubmed-meshheading:15850388-Amino Acid Sequence, pubmed-meshheading:15850388-Animals, pubmed-meshheading:15850388-Arginine, pubmed-meshheading:15850388-Base Pairing, pubmed-meshheading:15850388-Boric Acids, pubmed-meshheading:15850388-Cattle, pubmed-meshheading:15850388-Circular Dichroism, pubmed-meshheading:15850388-DNA, Viral, pubmed-meshheading:15850388-Edetic Acid, pubmed-meshheading:15850388-Electrophoresis, Polyacrylamide Gel, pubmed-meshheading:15850388-Gene Products, tat, pubmed-meshheading:15850388-HIV Long Terminal Repeat, pubmed-meshheading:15850388-Humans, pubmed-meshheading:15850388-Hydroxyl Radical, pubmed-meshheading:15850388-Immunodeficiency Virus, Bovine, pubmed-meshheading:15850388-Molecular Sequence Data, pubmed-meshheading:15850388-Nucleic Acid Conformation, pubmed-meshheading:15850388-RNA, Viral, pubmed-meshheading:15850388-RNA-Binding Proteins, pubmed-meshheading:15850388-Tromethamine
pubmed:year
2005
pubmed:articleTitle
Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove.
pubmed:affiliation
Department of Biochemistry and Biophysics, University of California, San Francisco 94143-2280, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural