Structure of the fibrinogen binding sequence: arginylglycylaspartic acid (RGD)

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Abstract
The crystal structure of a tetrahydrated form of l-arginyl-glycyl-l-aspartic acid (RGD), the consensus sequence for binding of fibrinogen to cell surface receptors, has been determined from diffractometer data. The tripeptide was crystallized in double zwitterionic form via hanging drop vapor diffusion experiments at a pH near 6.5. The orthorhombic unit cell contains four formula units in space group P2121 21 with lattice parameters a = 4.852(4), b = 11.376(3), c = 34.083(8) Å at RT. The structure was solved by direct methods and refined to a final R = 0.067 based upon 1345 observations with I 2σ(1). Peptide bonds both are trans, ω2= 174.2(6)° and ω3= - 169.3(6)°. The backbone bends at glycine with ρ2= -85.5(8)°. One of the water molecules sits between the arginyl side chain and the C-terminal carboxylate, forming an intramolecular hydrogen bond to the glycyl carboxyl and linking adjacent molecules through two other H-bond interactions. Comparison of the structure to RGD sequences extracted from 3-D protein structures reveals a diversity of conformations for this tripeptide sequence.