Can coordinate driving describe proton transfer coupled to complex protein motions?

Abstract

We have combined the Quantum Mechanical/Molecular Mechanical (QM/MM) computational approach with techniques that search for minimum energy reaction paths to investigate retinal deprotonation in the light-driven proton pump protein, bacteriorhodopsin. The calculations indicate that the commonly-used adiabatic mapping method can lead to misleading energy barriers when too simple reaction coordinates are selected. The use of a reaction search method that does not require the a priori definition of a reaction coordinate allows to find multiple low-energy retinal deprotonation pathways whose energy barriers are fully characterized.

Keywords:

• Bacteriorhodopsin
• Quantum mechanical/Molecular mechanical
• adiabatic mapping
• Conjugate peak refinement

Acknowledgements

This work has been supported by grants to N. B. from Deutsches Krebsforschungszentrum Heidelberg and by the Deutsche Forschungsgemeinschaft SM 63/7.