Thursday, April 10, 2014

Post Transition State Dynamics in Enzyme Catalysis

Dynamics simulations performed on the DFT potential energy surface reveal the role of post-transition state dynamics in natural product biosynthesis, and point towards another role for enzymatic control over product selectivity.

Multiple cyclization and rearrangement steps are involved in the biosynthesis of terpenoid natural products, each providing the possibility for the generation of a number of isomeric products, and so it is necessary for enzymatic control over which product is eventually formed. While selectivity in kinetically-controlled reactions is well known to result from differences in the relative (free) energies of the competing transition states, there appear to be a growing number of reactions in which reactions isomeric products (and hence selectivity) may also arise following a single transition state, due to a bifuration of the reaction pathway into two downhill pathways toward products. In fact, in a recent Chemistry and Engineering News piece on reaction path bifurcations in organic and bioorganic chemistry, Dan Singleton has estimated the proportion of such reactions to be around 20%, much higher than previously imagined.


Idealized potential energy surface featuring a bifurcation after the saddle point; the point at which the pathway splits into two is a valley ridge inflection (VRI).

In their recent article in Nature Chemistry Hong and Tantillo use quasiclassical dynamics calculations to interrogate the enzymatic biosynthesis of militradiene, applying Newtonian equations of motion with the forces that result from the (Born-Oppenheimer) potential energy surface obtained from density functional theory (B3LYP/6-31+G(d,p)) calculations on-the-fly. These calculations utilise energy/ gradient evaluations with standard quantum chemistry software, propagating the trajectory with Singeton's Progdyn code.  In this study hundreds of trajectory calculations were performed, each initiated in the region of the rate-limiting transition structure (i.e. the dynamical bottleneck). This is necessary since quantum chemical calculations reveal the underlying potential energy surface to be remarkably complex, with multiple, sequential bifurcations along the reaction path all occurring after an initial rate-limiting transition state. This initial TS is connected to several isomeric intermediates via steepest-descent pathways on the potential energy surface without any intervening minima, such that the redistribution of intramolecular vibrational energy is not significantly faster than the passage towards product(s) - the  assumptions underlying classical transition state theory are clearly inadequate for such a reaction mechanism.

Even though there a large number of stationary points on the underlying energy surface, each of which corresponds to isomeric carbocationic intermediates, the dynamics simulations reveal that only two constitutionally distinct carbocation structures are formed in appreciable amounts. While one of these structures corresponds to the natural product’s direct precursor, the other possesses a diterpene skeleton previously unknown in nature. Thus, to ensure selective formation of miltiradiene it appears that the enzyme must exert control over the dynamical preferences of the substrate in traversing the underlying potential energy surface once it has passed through the transition state. Due to the computational demands the simulations have yet to be performed in the presence of the enzyme active site, so we must wait further exploration of the specific interactions which influence the dynamics of this reaction. However, we can expect that the electrostatic environment of the active site, which include the dissociated pyrophosphate counterion, will play an important role in dynamical steering towards the natural product as has been shown for bornyl diphosphate synthase