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Three dimensional structural models of the heavy chain of Factor Xa, the heavy chain of Factor IXa, and the B chain of thrombin have been developed using a computer molecular graphics display system. These models are based upon the sequence homology of these proteins with chymotrypsin and trypsin and the assumption that the three dimensional structures of the peptide backbones of these proteins are nearly identical to the known backbone structure of trypsin and chymotrypsin. Sequence alignments of each protein with the digestive proteases were based upon regions of sequence homology, location of disulfide bonds, and preservation of β-barrels. Regions of insertion and deletion relative to the chymotrypsin backbone were identified and incorporated into the backbone structure. Factor Xa (heavy chain) and Factor IXa (heavy chain) contain 5 insertions and 4 deletions. Thrombin (B chain) contains nine insertions and two deletions. Factor Xa, Factor IXa, and thrombin models were generated by substituting their respective amino acid sequences into the model of the peptide backbone. The molecular surfaces of these models each suggest unique topographical and physicochemical properties. In-contrast, the core of these proteins are nearly identical. One area of the molecular surface, the active site, is also highly conserved despite marked differences in substrate specificity among these enzymes. The extended substrate binding regions, surrounding the active site, are highly substituted and also contain areas of both insertions and deletions. These models predict that the functional differences that distinguish these serine proteases are manifestations of the molecular surface differences. It would appear that substrate recognition and specificity determinants of Factor Xa, Factor IXa, and thrombin reside in an extensive surface surrounding the active site, but not exclusively within the active site.

Three Dimensional Computer Graphics Models Of Bovine Factor Xa, Factor IXa And Thrombin