How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme‐inhibitor complexes? Implications for enzyme design

Abstract

Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate-determining transition state plus the catalytic groups modeled by side-chain mimics was optimized using B3LYP/6-31G(d) or, in one case, HF/3-21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X-ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate-active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64Å from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42Å. The implications for computational enzyme design are discussed.Keywords: theozyme; active site structure; density functional theory; enzyme; biological catalysis Supplemental material: see www.proteinscience.orgThe computational investigation of mechanism and catalysis delivered by biomolecules is a rich and rapidly growing field of computational chemistry (Warshel and Levitt 1976;Sherwood 2000;Lin and Truhlar 2006;Senn and Thiel 2007). Progress in this area has been facilitated by the application of theoretical models representing a truncated active site. Such a model has been called a theozyme, short for theoretical enzyme, which embodies the predicted catalytic array of biological functionalities stabilizing a particular transition state (TS) Tantillo et al. 1998). The active site is limited to the necessary catalytic residues, which are then further reduced to include hydrogen-capped mimics for the sidechain or peptide backbone functionalities.Our group has utilized the theozyme model to gain valuable insights into the origin of catalysis and stereoselectivity delivered by catalytic antibodies

Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism

“…The initial state with Cu(II) is shown in Fig. 1C (blue) threaded onto the structure (pink), which closely agrees (rmsd = 0.37 Å for heavy atoms, which is quite good agreement for "theozyme" ASMs) (26). The coordinating nitrogen atoms in the histidine brace are within 1.97-2.08 Å to copper, with one equatorial water molecule.…”

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

“…Rational enzyme design is still considered to be an enormous challenge and often fails due to a limited understanding of the subtle interplay of the residues in the active site. Thus, rational design becomes a more tractable problem by combining a detailed knowledge of residue function with approaches such as the theoretical enzyme (the theozyme 32,33 ).…”

Computational Design of New Protein Catalysts

“…The functional groups are tuned to bind and stabilize the transition state (TS) (Figure 16.1a). It has been shown that these theoretical model calculations involving common enzymatic functionalities yield realistic and accurate active site geometries compared to X-ray crystal structures [27], and can also predict structural data for a potential active site [28]. Protein scaffolds capable of hosting the new catalytic machinery are selected from the Protein Data Bank (PDB) [29] (Figure 16.1b) and are used as templates into which the QM transition-state geometry is grafted (Figure 16.1c).…”

“…Theozymes have been found to recapitulate accurately the geometries of naturalistic active sites, despite the approximations that are inherent to truncated model systems [27]. They have been employed in mechanistic studies of both enzyme-and antibody-catalyzed reactions, examples of which include biocatalysts for the Diels-Alder reaction [8,[35][36][37][38], the Kemp elimination [39,40], a decarboxylation [41], and epoxide-ring openings [42].…”