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Volume 272, Number 14, Issue of April 4, 1997 pp. 9204-9209
©1997 by The American Society for Biochemistry and Molecular Biology, Inc.

Substrate Specificity of the Hepatitis C Virus Serine Protease NS3

(Received for publication, November 11, 1995, and in revised form, January 19, 1997)

Andrea Urbani , Elisabetta Bianchi , Frank Narjes , Anna Tramontano , Raffaele De Francesco , Christian Steinkühler and Antonello Pessi

From the Istituto di Ricerche di Biologia Molecolare (IRBM) P. Angeletti, Pomezia, Rome, Italy

The substrate specificity of a purified protein encompassing the hepatitis C virus NS3 serine protease domain was investigated by introducing systematic modifications, including non-natural amino acids, into substrate peptides derived from the NS4A/NS4B cleavage site. Kinetic parameters were determined in the absence and presence of a peptide mimicking the protease co-factor NS4A (Pep4A). Based on this study we draw the following conclusions: (i) the NS3 protease domain has an absolute requirement for a small residue in the P1 position of substrates, thereby confirming previous modelling predictions. (ii) Optimization of the P1 binding site occupancy primarily influences transition state binding, whereas the occupancy of distal binding sites is a determinant for both ground state and transition state binding. (iii) Optimized contacts at distal binding sites may contribute synergistically to cleavage efficiency.


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