Thursday, January 22, 2015

Quantum protons in enzymes

A number of proteins involve short strong hydrogen bonds [also known as low-barrier bonds] and there is considerable debate about how important or relevant they are for functionality. A particularly interesting enzyme is KetoSteroid Isomerase (KSI) which features such bonds. Its structure and mechanism has recently been elucidated by some beautiful experiments using mutants near the active site.

There is a nice paper
Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site
Lu Wang, Stephen D. Fried, Steven G. Boxer, and Thomas E. Markland

This is a combined experimental and theoretical study of isotope substitution effects where the protons are replaced with deuterium. This allows one to probe the effects of the zero-point motion of the protons in hydrogen bonds. You can see zero-point energy with a pH meter.

The authors measure the change in the pKa [acidity] with H/D substitution of the different amino acid residues in the active site of KSI. Significantly, they find that for one of the KSI tyrosine's the pKa change is much larger than the change in water. Furthermore, they calculate this change using an ab initio path integral molecular dynamics simulation, obtaining a value in reasonable agreement with experiment.

The large isotope effect arises because of the significant quantum delocalisation of the protons in the H-bond network near the tyrosine's. This is illustrated in the figure below, showing the probability of finding a proton along the co-ordinate associated with proton transfer between the two different tyrosine's [when nu_16=0 the proton is equidistant between the Tyr16 and Tyr57 residues].

The simulation is a real tour de force. It uses a "force field" calculated "on the fly" from density functional theory with the B3LYP-D3 functional.
These simulations treat both the nuclear and electronic degrees of freedom quantum mechanically in the active-site QM region and also incorporate the fluctuations of the protein and solvent environment in the MM region. The simulations consisted of between 47 and 68 QM atoms and more than 52,000 MM atoms describing the rest of the protein and solvent. 
These simulations, which until recently would have been computationally prohibitive, were made possible by 
accelerating the path integral molecular dynamics convergence using a generalized Langevin equation, 
using new methods to accelerate the extraction of isotope effects, and 
exploiting graphical processing units (GPUs) to perform efficient electronic structure theory evaluations through an interface to the TeraChem code. 
Such a combination yielded almost three orders of magnitude speedup compared with existing AI-PIMD approaches.
Being able to perform such detailed stimulations will allow critical examination of controversial claims that short hydrogen bonds and proton tunnelling is a key ingredient in the functionality of specific enzymes.

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