title: Functional linkages can reveal protein complexes for structure determination.
abstract: In the study of protein complexes, is there a computational method for inferring which combinations of proteins in an organism are likely to form a crystallizable complex? Here we attempt to answer this question, using the Protein Data Bank (PDB) to assess the usefulness of inferred functional protein linkages from the Prolinks database. We find that of the 242 nonredundant prokaryotic protein complexes shared between the current PDB and Prolinks, 44% (107/242) contain proteins linked at high confidence by one or more methods of computed functional linkages. Similarly, high-confidence linkages detect 47% of known Escherichia coli protein complexes, with 45% accuracy. Together these findings suggest that functional linkages will be useful in defining protein complexes for structural studies, including for structural genomics. We offer a database of inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archaea.
authors.affiliation: Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Sul-Min
authors.initials: SM
authors.lastname: Kim
authors.forename: Peter M
authors.initials: PM
authors.lastname: Bowers
authors.forename: Debnath
authors.initials: D
authors.lastname: Pal
authors.forename: Michael
authors.initials: M
authors.lastname: Strong
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Terwilliger
authors.forename: Markus
authors.initials: M
authors.lastname: Kaufmann
authors.forename: David
authors.initials: D
authors.lastname: Eisenberg
mesh_terms: D030562:Databases, Protein; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D011487:Protein Conformation
chemical_list: D029968:Escherichia coli Proteins