Thursday, June 28, 2012

Refuting the dynamic hypothesis for enzymes

How do enzymes work? Are they any different from other catalysts?
The traditional view is no. They simply lower the energy barrier of the transition state between the reactants and products. The only difference from man-made catalysts is that due to their complexity (and evolution) enzymes can lower this barrier by more than
an eV leading to an increase in reaction rate by tens of orders of magnitude.

In the traditional view the only role of the dynamics of the nuclei in the enzyme is that statistical thermal fluctuations provide access to the transition state. Furthermore, quantum dynamics of the nuclei does not play any significant role. Tunneling below the barrier may provide small corrections to the reaction rate for light nuclei such in proton, hydrogen, or hydride (hydrogen anion) transfer reactions.

Over the past decade some people have been advocating a radical non-traditional view of how (some) enzymes work. They claim that non-trivial (and non-local) dynamics plays
a key role. I think it should be emphasized that this is a radical point of view.
Proponents of this view include Steven Schwartz and Judith Klinman.
They also emphasize the role of quantum tunneling and suggest that enzymes have evolved to enhance it.
I have a paper which is skeptical of quantum tunneling playing a significant role.
A disparaging opponent of dynamical effects is Arieh Warshel.

At the worshop yesterday Tom Miller gave a stimulating talk based on a recent PNAS paper Dynamics and dissipation in enzyme catalysis. He addresses this controversy considering the specific case of hydride transfer in dihydrofolate reductase. This has attracted interest because double mutants (very distant from the active site) lead to non-additive effects on the rate activation energy.

Boekelheide, Salomón-Ferrer, and Miller calculated the reaction rate using a path integral approach (ring polymer molecular dynamics = RPMD)  for which it is claimed
In contrast to mixed quantum-classical and transition state theory methods, RPMD yields reaction rates and mechanisms that are formally independent of the choice of dividing surface or any other reaction coordinate assumption 
They compared both statistical and dynamical correlations in the enzyme nuclei in the reactant state, transition state, and product state. The former were sizeable over different parts of the enzyme as one might expect from its rigidity. However, the dynamical correlations were only significant close to the hydride donor and acceptor.

This talk led to the most animated discussion in the workshop so far. I got the impression (perhaps wrongly) that some people were concerned
  • whether one could make a clear division between statistical and dynamical correlations
  • whether the RPMD is really as assumption free as claimed
  • one should not be surprised the claimed dynamical correlations do not exist
  • transition state theory is very robust.
A recent PNAS paper from Steve Boxer's group addressed the issue (on a different enzyme) from an experimental view. It concluded that simple electrostatics (as advocated by Warshel) rather than dynamics were determinant.

A recent Nature Chemistry Perspective argues that transition state theory is adequate to describe enzymes.

Similar issues about protein dynamics are also relevant for claims of quantum coherent effects in photosynthetic proteins (an earlier post discussed work showing that the claimed dynamical correlations did not exist.)

1 comment:

  1. I was always confused by claims of dynamical catalysis, because they seem to imply very severe constraints on the boundary conditions. Isn't this the only way that dynamics could matter?