CAN COORDINATE DRIVING DESCRIBE PROTON TRANSFER COUPLED TO COMPLEX PROTEIN MOTIONS?

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.