title: 2.8 A crystal structures of recombinant fibrinogen fragment D with and without two peptide ligands: GHRP binding to the "b" site disrupts its nearby calcium-binding site.
abstract: We report two crystal structures, each at a resolution of 2.8 A, of recombinant human fibrinogen fragment D (rfD) in the absence and presence of peptide ligands. The bound ligands, Gly-Pro-Arg-Pro-amide and Gly-His-Arg-Pro-amide, mimic the interactions of the thrombin exposed polymerization sites, "A" and "B", respectively. This report is the first to describe the structure of fragment D in the presence of both peptide ligands. The structures reveal that recombinant fibrinogen is nearly identical to the plasma protein but with minor changes, like the addition of a proximal fucose to the carbohydrate linked to residue betaGln364, and slightly different relative positions of the beta- and gamma-modules. Of major interest in our structures is that a previously identified calcium site in plasma fibrinogen is absent when Gly-His-Arg-Pro-amide is bound. The peptide-dependent loss of this calcium site may have significant biological implications that are further discussed. These structures provide a foundation for the detailed structural analysis of variant recombinant fibrinogens that were used to identify critical functional residues within fragment D.
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000502:physiology; D016466:CHO Cells; D002118:Calcium / Q000378:metabolism*; D002241:Carbohydrates / Q000737:chemistry; D006224:Cricetinae; D018360:Crystallography, X-Ray; D005338:Fibrin Fibrinogen Degradation Products / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008024:Ligands; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary
chemical_list: D002241:Carbohydrates; D005338:Fibrin Fibrinogen Degradation Products; D008024:Ligands; D009842:Oligopeptides; C015214:fibrinogen D fragment; C048770:glycyl-histidyl-arginyl-proline; C034585:glycyl-prolyl-arginyl-proline; D002118:Calcium