Active site models

PLE catalyzes the hydrolysis of a wide range of meso-diesters (Table 2). This reaction is interesting from both theoretical and practical standpoints. Indeed, the analysis of a large range of kinetic data provided sufficient information to create a detailed active site model of PLE (31). From a practical standpoint, selective hydrolysis of y j (9-cyclo-I,2-dicarboxylates leads to chiral synthons that are valuable intermediates for the synthesis of a variety of natural products. 

Two types of sulfoximinocarboxylates (analogous to sulfinylcarboxylates 16), namely 5 -aryl-5 -methoxycarbonylmethyl-A(-methyl sulfoximine 36 and -methyl-5 -phenyl-A(-ethoxycarbonyl sulfoximine 37, were subjected to hydrolysis in the presence of PLE in a phosphate buffer. As a result of a kinetic resolution, both the enantiomerically enriched recovered substrates and the products of hydrolysis and subsequent decarboxylation 38 and 39, respectively, were obtained with moderate to good ees (Equations 20 and 21). Interestingly, in each case the enantiomers of the substrates, having opposite spatial arrangement of the analogous substituents, were preferentially hydrolysed. This was explained in terms of the Jones PLE active site model. ... 

Andreaus B, Eikerling M. 2007. Active site model for CO adlayer electrooxidation on nanoparticle catalysts. J Electroanal Chem 607 121-132. 

When comparing different computational approaches to enzyme systems, several different factors have to be considered, e.g., differences in high-level (QM) method, QM/MM implementation, optimization method, model selection etc. This makes it very difficult to compare different QM/MM calculations on the same system. Even comparisons with an active-site model are not straightforward. It can be argued that adding a larger part of the system into calculaton always should make the calculation more accurate. At the same time, introducing more variables to the calculation also increases the risk of artificial effects. 

Figure 2-5. Geometries of the 02-bound state optimized using the active-site model (left) and an ONIOM model (right). Note the large differences in geometry of the two calculations, especially the hydrogen bonds donated to O2 in the ONIOM model (marked in grey) (Adapted from Hoffman et al. [25]. Reprinted with permission. Copyright 2004 Wiley Periodicals, Inc.)...

The active-site model (and the ONIOM model system) includes Fe, one aspartate and two histidine ligands, a water ligand and selected parts of the substrate (see Figure 2-6). The 2-histidine-1-carboxylate ligand theme is shared by several other non-heme iron enzymes [59], For the protein system, we used two different... 

Figure 2-7. Origins of the increased O2 binding energy in IPNS when the protein is included in an ONIOM model. (A) A comparison of the optimized geometries from an active-site model (silver) and an ONIOM protein model (dark grey), show that the artificial structural relaxation of the active-site model is more pronounced for the reactant state than for the product state. (B) Contributions to O2 binding from the surrounding protein, evaluated only at the MM level (Adapted from Lundberg and Morokuma [26], Reprinted with permission. Copyright 2007 American Chemical Society.)...

One reason for the relatively large RMS deviations, compared to the active sites of MMO and RNR, is that the active-site residues are not coordinated to the selenium (see Figure 2-8). The lack of a structural anchor leads to a relatively unstable active-site geometry. An alternative formulation is that the presence of a metal center with strong ligand interactions is one reason the active-site model works comparatively well for many metal enzymes. 

To understand the effect of the protein on this modeled reaction mechanism, we selected the first reaction step, H2O2 reduction by a glutathione molecule for further investigations using the ONIOM (QM MM) method [28], The computational setup was similar to the structural study, but the effects of the additional water molecules were added from the active-site model. It is assumed that the reaction coordinate is the same as in the active-site study and no additional reaction pathways were investigated. An important point of the present ONIOM study is the full optimization of QM MM transition states using the novel ONIOM algorithms [9],... 

Figure 2-9. Reaction scheme for the complete catalytic cycle in glutathione peroxidase (left). Numbers represent calculated reaction barriers using the active-site model. The detailed potential energy diagram for the first elementary reaction, (E-SeH) + H2O2 - (E-SeOH) + H2O, calculated using both the active-site (dashed line) and ONIOM model (grey line) is shown to the right (Adapted from Prabhakar et al. [28, 65], Reprinted with permission. Copyright 2005, 2006 American Chemical Society.)...

Selection of an active-site model almost always leads to truncations of the hydrogen-bond network. Upon optimization of the active-site structure, this may lead to the formation of artificial hydrogen bonds that disrupt the structure. Freezing selected coordinates in the active-site model can prevent some of these hydrogen bonds to form. Another remedy could be to include more residues around the metal center, but larger QM models are much more expensive and there will probably still be truncated hydrogen bonds, although further away from the reaction center. 

Figure 2-14. Illustration of the different hydrogen bonding patterns for an iron-bound peroxide in IPNS using an active-site model (left) and an ONIOM QM MM model (right)...

When looking at the reaction mechanisms of glutathione peroxidase and isopenicillin N synthase, we did not find any reaction step where the transition state is significantly stabilized by long-range electrostatic interactions (i.e. electrostatic interactions outside the active-site model). However, it is should be added that most transition states have been calculated using ONIOM-ME. 

Quantum mechanics is essential for studying enzymatic processes [1-3]. Depending on the specific problem of interest, there are different requirements on the level of theory used and the scale of treatment involved. This ranges from the simplest cluster representation of the active site, modeled by the most accurate quantum chemical methods, to a hybrid description of the biomacromolecular catalyst by quantum mechanics and molecular mechanics (QM/MM) [1], to the full treatment of the entire enzyme-solvent system by a fully quantum-mechanical force field [4-8], In addition, the time-evolution of the macromolecular system can be modeled purely by classical mechanics in molecular dynamicssimulations, whereas the explicit incorporation... 

Coordinatodathrates in Active Site Modelling of Protease Enzymes Associates... 

Aizman, A., and D. A. Case. 1982. Electronic Structure Calculations on Active Site Models for 4-FE,4-S Iron-Sulfur Proteins. J. Am. Chem. Soc. 104, 3269. 

Bray, M. R., and R. J. Deeth. 1996. A density functional study of active site models of xantine oxidase. Inorganic Chemistry 35, 5720. 

Dive, G., D. Dehareng, and J. M. Ghuysen. 1994. Detailed Study of a Molecule in a Molecule N-Acetyl-L-tryptophanamide in an Active Site Model of a-Chymotrypsin. J. Am. Chem. Soc. 116, 2548-2556. 

Fig. 63 The Eyring reduced time model involves the activated site model for plastic and viscoelastic shear deformation of adjacent chains...

Synergy Between Theory and Experiment as Applied to H/D Exchange Activity Assays in [Fe]H2ase Active Site Models Jesse W. Tye, Michael B. Hall,... 

---