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PEDS Advance Access published online on February 3, 2006
Protein Engineering Design and Selection, doi:10.1093/protein/gzj014
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received September 20, 2005
Revised December 16, 2005
Accepted December 18, 2005

Article

Stabilization of the autoproteolysis of TNF-alpha converting enzyme (TACE) results in a novel crystal form suitable for structure-based drug design studies

Richard N. Ingram 1, Peter Orth 1, Corey L. Strickland 1, Hung V. Le 1, Vincent Madison 1, and Brian M. Beyer 1 *

1 Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA

* To whom correspondence should be addressed.
Brian M. Beyer, E-mail: brian.beyer{at}spcorp.com


  Abstract

The crystallization of TNF-alpha converting enzyme (TACE) has been useful in understanding the structure-activity relationships of new chemical entities. However, the propensity of TACE to undergo autoproteolysis has made enzyme handling difficult and impeded the identification of inhibitor soakable crystal forms. The autoproteolysis of TACE was found to be specific (Y352-V353) and occurred within a flexible loop that is in close proximity to the P-side of the active site. The rate of autoproteolysis was found to be proportional to the concentration of TACE, suggesting a bimolecular reaction mechanism. A limited specificity study of the S1' subsite was conducted using surrogate peptides and suggested substitutions that would stabilize the proteolysis of the loop at positions Y352-V353. Two mutant proteases (V353G and V353S) were generated and proved to be highly resistant to autoproteolysis. The kinetics of the more resistant mutant (V353G) and wild-type TACE were compared and demonstrated virtually identical IC50 values for a panel of competitive inhibitors. However, the kcat/Km of the mutant for a larger substrate (P6 - P'6) was ~5-fold lower than that for the wild-type enzyme. Comparison of the complexed wild-type and mutant structures indicated a subtle shift in a peripheral P-side loop (comprising the mutation site) that may be involved in substrate binding/turnover and might explain the mild kinetic difference. The characterization of this stabilized form of TACE has yielded an enzyme with similar native kinetic properties and identified a novel crystal form that is suitable for inhibitor soaking and structure determination.

Keywords: autoproteolysis; protein engineering; soakable crystal form; structure-based drug design; TACE.
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