Chorismate computation studies

Experimental results for the CM-catalyzed and uncatalyzed reaction, as weU as structural information for chorismate mutase, have been extensively discussed in two previous reviews [2, 3]. There has been a rapid growth of literature in computational studies of chorismate mutase in the last few years. In this chapter, we shall begin by summarizing some key experimental data related to the Claisen rearrangement along with existing structural information for chorismate mutase. We will then review the results of computational studies of chorismate mutase and discuss different proposals that have been suggested for the mechanism of the CM[Pg.1]

Chorismate mutase catalyzes the Claisen rearrangement of chorismate to prephenate at a rate 106 times greater than that in solution (Fig. 5.5). This enzyme reaction has attracted the attention of computational (bio)chemists, because it is a rare example of an enzyme-catalyzed pericyclic reaction. Several research groups have studied the mechanism of this enzyme by use of QM/MM methods [76-78], It has also been studied with the effective fragment potential (EFP) method [79, 80]. In this method the chemically active part of an enzyme is treated by use of the ab initio QM method and the rest of the system (protein environment) by effective fragment potentials. These potentials account... 

Bruice s contention that there is very little stabilization of the TS by CM, rather it is a favorable binding of the NAC that accounts for its catalytic activity, has been met with much skepticism. An early study by Wiest and Houk" looked at chorismate models with coordinated waters and aminidium cations in positions that matched interacting groups found in the crystal structure of CM with a coordinated substrate. These model computations suggested that the neighboring amino acid residues could be stabilizing the TS. 

COMT is, for many of the same reasons as with chorismate mutase, well suited for the study with computational techniques. The reaction mechanism it catalyzes is the same mechanism that operates in the absence of the enzyme, specifically, the S 2 mechanism, facilitating comparison of the bare solution-phase reaction with the catalyzed reaction. The subsfiate and cofactor do not covalendy bind to the enzyme, so that defining the QM region and the MM region should be relatively uncomplicated. Lasdy, the X-ray crystal structure of COMT bound with the inhibitor 3,5-dinitrocatechol has been determined with a resolution of 2 kP An interesting twist to this enzyme is that the active site includes a metal cation, Mg " ". This crystal structure allows for a natural starting point for computational exploration of the means of the catalytic action of COMT. The rate acceleration provided by COMT is substantial the reaction is 10 times faster within the enzyme than in solution. " ... 

Chorismate mutase (CM) catalyzes the Claisen rearrangement of chorismate to prephenate in the shikimic acid pathway used in the biosynthesis of aromatic amino acids. It represents a reference enzyme to explore the fundamentals of catalysis and has been the subject of extensive experimental and computational research. These have shown both that catalysis proceeds without covalent binding of the substrate to the enzyme, and that the uncatalyzed reaction in water proceeds by the same mechanism. This makes CM a particularly convenient target for QM/MM studies. 

This suggests that care must be excised in choosing proper computational methods for the study of the Claisen rearrangement of chorismate. 

The discussions given in this chapter have shown that although chorismate mutase has been a subject of extensive experimental and theoretical investigations, there are still considerable uncertainties concerning how the Claisen rearrangement from chorismate to prephenate is actually catalyzed by the enzyme. The computational investigations have led different possibilities, but experimental studies with modem techniques are necessary to identify the most likely mechanism of the CM catalysis. 

---