THE STRUCTURE OF A DESIGNED PEPTIDOMIMETIC INHIBITOR COMPLEX OF ALPHA-THROMBIN

Thrombin displays remarkable specificity, effecting the removal of fib rinopeptides A and B of fibrinogen through the selective cleavage of t wo Arg-Gly bonds between the 181 Arg/Lys - Xaa bonds in fibrinogen. Si gnificant advances have been made in recent years towards understandin g the origin of the specificity of cleavage of the Arg16 - Gly17 bond of the Aalpha-chain of human fibrinogen. We have previously proposed a model for the bound structure of fibrinopeptide A7-16 (FpA), based up on NMR data, computer-assisted molecular modeling and the synthesis an d study of peptidomimetic substrates and inhibitors of thrombin. We no w report the structure of the ternary complex of an FPA mimetic (FPAM) , hirugen and thrombin at 2.5 angstrom resolution (R-factor = 0. 138) and specificity data for the inhibition of thrombin and related trypsi n-like proteinases by FPAM. The crystallographic structures of FPA and its chloromethyl ketone derivative bound to thrombin were determined. Although there are differences between these structures in the above modeled FPA structure and that of the crystal structure of FPAM bound to thrombin, the phi, psi angles in the critical region of P1 - P2 - P 3 in all of the structures are similar to those of bovine pancreatic t rypsin inhibitor (BPTI) in the BPTI - trypsin complex and D - Phe - Pr o - Arg (PPACK) in the PPACK-thrombin structure. A comparison between these and an NMR-derived structure is carried out and discussed.