Linked Life Data

11266593

Source:http://linkedlifedata.com/resource/pubmed/id/11266593

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2001-3-27
pubmed:abstractText
The formation of alpha(2) dimer in Escherichia coli core RNA polymerase (RNAP) is thought to be the first step toward the assembly of the functional enzyme. A large number of evidences indicate that the alpha-subunit dimerizes through its N-terminal domain (NTD). The crystal structures of the alpha-subunit NTD and that of a homologous Thermus aquaticus core RNAP are known. To identify the stabilizing interactions in the dimer interface of the alpha-NTD of E. coli RNAP, we identified side-chain clusters by using the crystal structure coordinates of E. coli alpha-NTD. A graph spectral algorithm was used to identify side-chain clusters. This algorithm considers the global nonbonded side-chain interactions of the residues for the clustering procedure and is unique in identifying residues that make the largest number of interactions among the residues that form clusters in a very quantitative way. By using this algorithm, a nine-residue cluster consisting of polar and hydrophobic residues was identified in the subunit interface adjacent to the hydrophobic core. The residues forming the cluster are relatively rigid regions of the interface, as measured by the thermal factors of the residues. Most of the cluster residues in the E. coli enzyme were topologically and sequentially conserved in the T. aquaticus RNAP crystal structure. Residues 35F and 46I were predicted to be important in the stability of the alpha-dimer interface, with 35F forming the center of the cluster. The predictions were tested by isolating single-point mutants alpha-F35A and alpha-I46S on the dimer interface, which were found to disrupt dimerization. Thus, the identified cluster at the edge of the dimer interface seems to be a vital component in stabilizing the alpha-NTD.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-10413117, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-10493887, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-10499798, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-1153006, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-2067014, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-7015808, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-7490753, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-7613089, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-8089834, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-8347567, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-8744570, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-9078382, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-9299342, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-9562553, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-9653027, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-9657722, http://linkedlifedata.com/resource/pubmed/commentcorrection/11266593-9973571
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
0961-8368
pubmed:author
pubmed:issnType
Print
pubmed:volume
10
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
46-54
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.
pubmed:affiliation
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't