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Is there a weak H‐bond → LBHB transition on tetrahedral complex formation in serine proteases?
Author(s) -
Shokhen Michael,
Albeck Am
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10610
Subject(s) - diad , tetrahedral carbonyl addition compound , hydrogen bond , chemistry , low barrier hydrogen bond , covalent bond , proteases , active site , crystallography , tetrahedron , solvation , ionic bonding , serine protease , stereochemistry , computational chemistry , enzyme , molecule , catalysis , organic chemistry , protease , ion , copolymer , nucleophile , polymer
The transformation of a weak hydrogen bond in the free enzyme into a low‐barrier hydrogen bond (LBHB) in the tetrahedral intermediate has been suggested as an important factor facilitating catalysis in serine proteases. In this work, we examine the structure of the H‐bond in the Asp102–His57 diad of serine proteases in the free enzyme and in a covalent tetrahedral complex (TC) with a trifluoromethylketone inhibitor. We apply ab initio quantum mechanical calculations to models consisting of a large molecular fragment of the enzyme active site, and the combined effect of the rest of the protein body and the solvation by surrounding bulk water was simulated by a self‐consistent reaction field method in our novel QM/SCRF(VS) approach. Potential profiles of adiabatic proton transfer in the Asp102–His57 diad in these model systems were calculated. We conclude that the hydrogen bond in both the free enzyme and in the enzyme‐inhibitor TC is a strong ionic asymmetric one‐well hydrogen bond, in contrast to a previous suggestion that it is a weak H‐bond in the former and a double‐well LBHB in the latter. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.