Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
7
pubmed:dateCreated
2002-4-3
pubmed:abstractText
Computational mapping places molecular probes--small molecules or functional groups--on a protein surface to identify the most favorable binding positions. Although x-ray crystallography and NMR show that organic solvents bind to a limited number of sites on a protein, current mapping methods result in hundreds of energy minima and do not reveal why some sites bind molecules with different sizes and polarities. We describe a mapping algorithm that explains the origin of this phenomenon. The algorithm has been applied to hen egg-white lysozyme and to thermolysin, interacting with eight and four different ligands, respectively. In both cases the search finds the consensus site to which all molecules bind, whereas other positions that bind only certain ligands are not necessarily found. The consensus sites are pockets of the active site, lined with partially exposed hydrophobic residues and with a number of polar residues toward the edge. These sites can accommodate each ligand in a number of rotational states, some with a hydrogen bond to one of the nearby donor/acceptor groups. Specific substrates and/or inhibitors of hen egg-white lysozyme and thermolysin interact with the same side chains identified by the mapping, but form several hydrogen bonds and bind in unique orientations.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-11287678, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-1313175, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-1583540, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-1624956, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-3186692, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-3892003, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-7541840, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-7663131, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-7761829, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-7947806, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-8254666, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-8340918, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-8510098, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-8929414, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-9062927, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-9126848, http://linkedlifedata.com/resource/pubmed/commentcorrection/11904374-9630949
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0027-8424
pubmed:author
pubmed:issnType
Print
pubmed:day
2
pubmed:volume
99
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
4290-5
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Computational mapping identifies the binding sites of organic solvents on proteins.
pubmed:affiliation
Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S.