Linked Life Data

18330543

Source:http://linkedlifedata.com/resource/pubmed/id/18330543

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4-6
pubmed:dateCreated
2008-6-19
pubmed:abstractText
We applied the fragment molecular orbital (FMO) method, which enables total electronic calculations of large molecules at ab initio level, to the evaluation of binding affinities between the human progesterone receptor ligand-binding domain (PR LBD) and various steroidal ligands. The FMO calculations were performed on the entire structure of the PR LBD, which is composed of approximately 4,100 atoms. Our computational binding energies of PR LBD/ligand complexes agreed well with experimental binding affinities (r=0.909). Interaction energies between each ligand and specific amino acid residues were also obtained from the FMO calculations. The principal residues involved in the interactions with these ligands were Arg766 and Asn719, with some additional contribution by Gln725. The main factor determining differences in binding affinity of the various ligands was not interactions with particular residues, but with the binding-site residues closest to the ligand. The interfragment interaction energy analysis is proving to be a useful method for gaining detailed information on ligand binding.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
0028-1298
pubmed:author
pubmed:issnType
Print
pubmed:volume
377
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
607-15
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Ab initio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain.
pubmed:affiliation
Research Information Center for Extremophile, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't