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A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle

Authors

  • Péter Hudáky,

    1. Department of Theoretical Chemistry, Eötvös Loránd University, Budapest 112, Hungary
    2. Department of Organic Chemistry, Eötvös Loránd University, Budapest 112, Hungary
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  • András Perczel

    Corresponding author
    1. Department of Organic Chemistry, Eötvös Loránd University, Budapest 112, Hungary
    • Department of Organic Chemistry, Eötvös Loránd University, H-1518 Budapest 112, Hungary
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Abstract

A model of the catalytic triad of chymotrypsin is built assuring the arrangement and properties as they are within the complete enzyme. The model contains 18 amino acid residues of chymotrypsin and its substrate. A total of 135 atoms (including 70 heavy atoms) were subjected to full ab initio geometry optimizations through 127 individual steps along the reaction coordinate of the complete catalytic mechanism. It was shown that the described model of the catalytic apparatus forms a self-stabilized molecule ensemble without the rest of the enzyme and substrate. According to the calculations, the formations of the first and second tetrahedral intermediates in the model have 20.3 and 15.7 kcal/mol activation energy barriers, respectively. Removing elements of the catalytic apparatus such as the (1) catalytic aspartate or (2) the anion hole, as well as (3) inserting a water molecule “early” in the catalytic process, or (4) introducing conformational rigidity of the substrate, results in an increase of the above energy barrier of the first catalytic step in the model by 6.4, 13.7, 3.7, and 4.1 kcal/mol, respectively. Based on the calculated process one can conclude that the catalytic reaction in this model is much more similar to the reaction in the enzyme than to the reference reaction. To our knowledge, this is the first model system that mimics the complete catalytic mechanism. Proteins 2006. © 2005 Wiley-Liss, Inc.

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