STRUCTURAL RESILIENCY OF AN EGF-LIKE SUBDOMAIN BOUND TO ITS TARGET PROTEIN, THROMBIN

The thrombin-bound structures of native peptide fragments from the fif th EGF-like domain of thrombomodulin were determined by use of NMR and transferred NOE spectroscopy. The bound peptides assume an EGF-like s tructure of an antiparallel beta-sheet, a novel structural motif obser ved for a bound peptide in protein-peptide complexes. There is a remar kable structural resiliency of this structure motif manifested in its ability to accommodate a different number of residues within the disul fide loop. Docking experiments revealed that the key contacts with thr ombin are hydrophobic interactions between the side chains of residues Ile 414 and Ile 424 of thrombomodulin and a hydrophobic pocket on the thrombin surface. Residues Leu 415, Phe 419, and lie 420, which would have been buried in intact EGF-like domains, are unfavorably exposed in the complex of thrombin with the EGF-like thrombomodulin fragment, thus providing a rationale for the enhancement of binding affinity upo n the deletion of Ile 420. The unique beta-sheet structures of the bou nd peptides are specified by the presence of disulfide bridges in the peptides because a corresponding linear thrombomodulin fragment folds into a sheet structure with a different backbone topology. The differe nt bound conformations for the linear and the cyclized peptides indica te that side-chain interactions within a specific environment may dict ate the folding of bound peptides in protein-peptide complexes.