title: Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides.
abstract: Chemical cross-linking, followed by identification of the cross-linked residues, is a powerful approach to probe the topologies and interacting surfaces of protein assemblies. In this work, we demonstrate a new bioinformatics approach using multiple program modules within the software package "Protein Prospector" that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies. Examples are given for how this approach has been used for defining interfaces in heterodimeric and homodimeric protein complexes, both of which provide results in close agreement with crystal structures, verifying the reliability of the approach.
authors.affiliation: Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
authors.forename: Feixia
authors.initials: F
authors.lastname: Chu
authors.forename: Peter R
authors.initials: PR
authors.lastname: Baker
authors.forename: Alma L
authors.initials: AL
authors.lastname: Burlingame
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D003432:Cross-Linking Reagents / Q000737:chemistry*; D018360:Crystallography, X-Ray; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D015394:Molecular Structure; D009154:Mutation; D033903:Periplasmic Proteins / Q000737:chemistry / Q000235:genetics; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000737:chemistry* / Q000235:genetics; D012984:Software
chemical_list: D001426:Bacterial Proteins; D003432:Cross-Linking Reagents; C039076:Eco protein, E coli; D029968:Escherichia coli Proteins; D033903:Periplasmic Proteins; D011993:Recombinant Fusion Proteins; C427216:glycyl-glycyl-histidyl-ecotin, recombinant