|
rdf:type |
|
|
lifeskim:mentions |
|
|
pubmed:issue |
5
|
|
pubmed:dateCreated |
1998-12-4
|
|
pubmed:abstractText |
Eleven protein-DNA crystal structures were analyzed to test the hypothesis that hydration sites predicted in the first hydration shell of DNA mark the positions where protein residues hydrogen-bond to DNA. For nine of those structures, protein atoms, which form hydrogen bonds to DNA bases, were found within 1.5 A of the predicted hydration positions in 86% of the interactions. The correspondence of the predicted hydration sites with the hydrogen-bonded protein side chains was significantly higher for bases inside the conserved DNA recognition sequences than outside those regions. In two CAP-DNA complexes, predicted base hydration sites correctly marked 71% (within 1.5 A) of protein atoms, which form hydrogen bonds to DNA bases. Phosphate hydration was compared to actual protein binding sites in one CAP-DNA complex with 78% marked contacts within 2.0 A. These data suggest that hydration sites mark the binding sites at protein-DNA interfaces.
|
|
pubmed:grant |
|
|
pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-1062791,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-13054694,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-1387915,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-1557122,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-1682054,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-1977522,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-2028256,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-3187531,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-3359001,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-3419502,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-8133895,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-8312469,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-8355273,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-8599672,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-8757802,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-8836098,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9788911-9788937
|
|
pubmed:language |
eng
|
|
pubmed:journal |
|
|
pubmed:citationSubset |
IM
|
|
pubmed:chemical |
|
|
pubmed:status |
MEDLINE
|
|
pubmed:month |
Nov
|
|
pubmed:issn |
0006-3495
|
|
pubmed:author |
|
|
pubmed:issnType |
Print
|
|
pubmed:volume |
75
|
|
pubmed:owner |
NLM
|
|
pubmed:authorsComplete |
Y
|
|
pubmed:pagination |
2170-7
|
|
pubmed:dateRevised |
2009-11-18
|
|
pubmed:meshHeading |
pubmed-meshheading:9788911-Binding Sites,
pubmed-meshheading:9788911-Conserved Sequence,
pubmed-meshheading:9788911-DNA,
pubmed-meshheading:9788911-DNA-Binding Proteins,
pubmed-meshheading:9788911-Homeodomain Proteins,
pubmed-meshheading:9788911-Hydrogen Bonding,
pubmed-meshheading:9788911-Models, Molecular,
pubmed-meshheading:9788911-Molecular Conformation,
pubmed-meshheading:9788911-Nucleoproteins,
pubmed-meshheading:9788911-Repressor Proteins,
pubmed-meshheading:9788911-Water
|
|
pubmed:year |
1998
|
|
pubmed:articleTitle |
An analysis of the relationship between hydration and protein-DNA interactions.
|
|
pubmed:affiliation |
Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854-8087, USA.
|
|
pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.,
Research Support, Non-U.S. Gov't
|
