Structure-function relationships of thrombin based on the computer-generated three-dimensional model of the B chain...

The advent of sophisticated computer graphics systems that permit the representation of macromolecular structure has made it possible to examine protein structure in detail. We have used one aspect of this technology to develop a model of thrombin. The model is based on structural and functional similarities this enzyme exhibits with respect to proteins found in the family of serine proteinases. This review has covered interpretations of the structure of the model based on analyses of data that had been collected before and after the model was developed. On one hand, the conceptualization of primary and secondary features in the model of the active site of thrombin has for the most part been preceded by data from experiments on the interaction of thrombin with naturally occurring substrates and inhibitors. The features of the model explain these data adequately. On the other hand, the model has been more recently used in an interactive way to derive information about the bioregulatory aspects of thrombin. The realization that the amino-terminus portion of the cyanogen-bromide fragment was probably not part of the chemotactic activity, because it was probably internalized in the native protein, has suggested that synthetic analogs should focus more on the carboxyterminus of the peptide. It is hoped that in the future the model will continue to serve more in this function and that it can be used to explore further other aspects about the structural and functional relationships of this enzyme.