Chorismate transition state stabilization

The differences in the rate constant for the water reaction and the catalyzed reactions reside in the mole fraction of substrate present as near attack conformers (NACs).171 These results and knowledge of the importance of transition-state stabilization in other cases support a proposal that enzymes utilize both NAC and transition-state stabilization in the mix required for the most efficient catalysis. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively.172 The fact that the reaction occurred faster in water than in methanol was attributed to greater stabilization of the TS in water by specific interactions with first-shell solvent molecules. The Claisen rearrangements of chorismate in water and at the active site of E. coli chorismate mutase have been compared.173 It follows that the efficiency of formation of NAC (7.8 kcal/mol) at the active site provides approximately 90% of the kinetic advantage of the enzymatic reaction as compared with the water reaction. 

Szefczyk B, Mulholland AJ, Ranaghan KE, Sokalski WA (2004) Differential transition-state stabilization in enzyme catalysis Quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. J Am Chem Soc 126 16148—16159... 

QM/MM methods have proved their value for enzyme reactions in differentiating between alternative proposed mechanisms, and in analysing contributions to catalysis. A current example is the analysis of the contribution of conformational effects and transition state stabilization in the reaction catalysed by the enzyme chorismate mutase.98,99 QM/MM calculations can be performed with... 

Recent investigations of the enzyme chorismate mutase show how modelling can contribute to fundamental debates in enzymology, such as analysing the importance of transition state stabilization in catalysis, and alternative proposals to explain enzyme catalytic proficiency. 

Ranaghan KE, L Ridder, B Szefczyk, WA Sokalski, JC Hermann, AJ Mulholland (2004) Transition state stabilization and substrate strain in enzyme catalysis ab initio QM/MM modelling of the chorismate mutase reaction. Organic Biomolecular Chemistry 2 (7) 968-980... 

Strajbl M, A Shurki, M Kato, A Warshel (2003) Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. J. Am. Chem. Soc. 125 (34) 10228-10237... 

Guimaraes CRW, MP Repasky, J Chandrasekhar, J Tirado-Rives, WL Jorgensen (2003) Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase. J. Am. Chem. Soc. 125 (23) 6892-6899... 

Claeyssens F, KE Ranaghan, FR Manby, JN Harvey, AJ Mulholland (2005) Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase correlation of barrier height with transition-state stabilization. Chem. Comm. (40) 5068—5070... 

Andrews, P. R. Smith, G. D. Yonng, I. G. Transition-state stabilization and enzymic catalysis. Kinetic and molecular orbital studies of the rearrangement of chorismate to prephenate, Biochemistry 1973,12, 3492-3498. 

The calculated barrier to reaction in chorismate mutase was 17.8 kcal/mol, compared to 42 kcal/mol in the gas phase. Factors other than substrate distortion also play an important part in reducing the barrier to reaction in the enzyme important interactions were identified by a simple decomposition analysis (as described in sections 6.1 and 6.2 above). It was found that Glu78 and Arg90 specifically stabilize the transition state, relative to the bound substrate [8]. Overall, therefore, catalysis in chorismate mutase can be rationalized in terms of a combination of substrate strain and transition state stabilization. While it is possible to analyse all these catalytic effects as arising from maximal binding in the enzyme being achieved at the transition state, it appears useful to separate the different types of contribution. The possible role of substrate destabilization/distortion or strain in lowering the barrier to reaction in enzyme reactions, as put forward by Haldane [219], and invoked in... 

Figure 1 In a QM/MM calculation, a small region is treated by a quantum mechanical (QM) electronic structure method, and the surroundings treated by simpler, empirical, molecular mechanics. In treating an enzyme-catalysed reaction, the QM region includes the reactive groups, with the bulk of the protein and solvent environment included by molecular mechanics. Here, the approximate transition state for the Claisen rearrangement of chorismate to prephenate (catalysed by the enzyme chorismate mutase) is shown. This was calculated at the RHF(6-31G(d)-CHARMM QM-MM level. The QM region here (the substrate only) is shown by thick tubes, with some important active site residues (treated by MM) also shown. The whole model was based on a 25 A sphere around the active site, and contained 4211 protein atoms, 24 atoms of the substrate and 947 water molecules (including 144 water molecules observed by X-ray crystallography), a total of 7076 atoms. The results showed specific transition state stabilization by the enzyme. Comparison with the same reaction in solution showed that transition state stabilization is important in catalysis by chorismate mutase78.

It has been shown that both the catalyzed and the uncatalyzed reaction proceed through a chairlike transition state, stabilized in polar media59 60-143 262-263. Compound 1, an analog of the transition-state structure, proved to be a potent inhibitor of E. coli chorismate mutase-prephenate dehydrogenase204-255. For a discussion of the mechanism and structural requirements of the enzyme see refs 266 and 267. 

Schultz and coworkers (Jackson et a ., 1988) have generated an antibody which exhibits behaviour similar to the enzyme chorismate mutase. The enzyme catalyses the conversion of chorismate [49] to prephenate [50] as part of the shikimate pathway for the biosynthesis of aromatic amino acids in plants and micro-organisms (Haslam, 1974 Dixon and Webb, 1979). It is unusual for an enzyme in that it does not seem to employ acid-base chemistry, nucleophilic or electrophilic catalysis, metal ions, or redox chemistry. Rather, it binds the substrate and forces it into the appropriate conformation for reaction and stabilizes the transition state, without using distinct catalytic groups. 

Adamantane has an extra methylene bridge (the asterisk in the diagram) linked to the six-membered ring, thus stabilizing a cagelike structure. The authors indeed subsequently showed that some adamantane derivatives are potent inhibitors of chorismate mutase thus, these are examples of transition-state analogs. 

The transition state for the enzymatic reaction has been shown to have a chairlike geometry as well [61], and conformationally constrained compounds that mimic this structure, such as the oxabicyclic dicarboxylic acid 1 (Fig. 3.6), are good inhibitors of chorismate mutase enzymes [62 - 64], How a protein might stabilize this high-energy species has been a matter of some debate. Recently, heavy atom isotope effects were used to characterize the structure of the transition state bound to BsCM [65]. A very... 

Wiest, O. Honk, K. N. Stabilization of the transition state of the chorismate-prephenate rearrangement An ab initio study of enzyme and antibody catalysis, J. Am. Chem. Soc. 1995,117, 11628-11639. 

Kienhofo-, A. Kast, R Hilvert, D. Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor, J. Am. Chem. Soc. 2003, 125, 3206-3207. 

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