Paper Citing NAMD - Abstract
El-Hendawy, Morad M.; Garate, Jose-Antonio; English, Niall J.; O'Reilly, Stephen; Mooney, Damian A.
Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 145103, OCT 14 2012
Molecular dynamics (MD) at the molecular mechanical level and geometry optimisation at the quantum mechanical level have been performed to investigate the transport and fixation of oxygen and carbon dioxide in the cavity of ribulose-1,5-bisphosphate carboxylase/oxygenase, or Rubisco. Multiple MD simulations have been carried out to study the diffusive behaviour of O-2 and CO2 molecules from the Mg2+ cation in Rubisco at 298 K and 1 bar, being one step in the overall process of carboxylation/oxygenation in Rubisco. In addition to this work, in order to gain additional perspective on the role of chemical reaction rates and thermodynamics, oxygen, and carbon dioxide uptake mechanisms have also been investigated by the aid of quantum chemical calculations. The results indicate that the activation barrier for carboxylation is slightly lower than that of oxygenation. This agrees qualitatively with experimental findings, and rationalises the observed competition between both catalytic processes in nature. Finally, the longer-lived persistence of CO2 in the vicinity of the active centre (i.e., slower self-diffusion) may serve to explain, in part, why carboxylation is the more kinetically favoured on an overall basis compared to oxygenation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4757021]
