Linked Life Data

15001352

Source:http://linkedlifedata.com/resource/pubmed/id/15001352

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2004-3-5
pubmed:abstractText
Information readout in the DNA minor groove is accompanied by substantial DNA deformations, such as sugar switching between the two conformational domains, B-like C2'-endo and A-like C3'-endo. The effect of sugar puckering on the sequence-dependent protein-DNA interactions has not been studied systematically, however. Here, we analyzed the structural role of A-like nucleotides in 156 protein-DNA complexes solved by X-ray crystallography and NMR. To this end, a new algorithm was developed to distinguish interactions in the minor groove from those in the major groove, and to calculate the solvent-accessible surface areas in each groove separately. Based on this approach, we found a striking difference between the sets of amino acids interacting with B-like and A-like nucleotides in the minor groove. Polar amino acids mostly interact with B-nucleotides, while hydrophobic amino acids interact extensively with A-nucleotides (a hydrophobicity-structure correlation). This tendency is consistent with the larger exposure of hydrophobic surfaces in the case of A-like sugars. Overall, the A-like nucleotides aid in achieving protein-induced fit in two major ways. First, hydrophobic clusters formed by several consecutive A-like sugars interact cooperatively with the non-polar surfaces in proteins. Second, the sugar switching occurs in large kinks promoted by direct protein contact, predominantly at the pyrimidine-purine dimeric steps. The sequence preference for the B-to-A sugar repuckering, observed for pyrimidines, suggests that the described DNA deformations contribute to specificity of the protein-DNA recognition in the minor groove.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
12
pubmed:volume
337
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
65-76
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching.
pubmed:affiliation
Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bg. 12B, Rm. B116, Bethesda, MD 20892-5677, USA.
pubmed:publicationType
Journal Article