| Abstract
| - The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light bychanging shape. After excitation by blue light, PYP undergoes several transformations, to partially unfoldinto its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid afterexcitation and isomerization of this chromophore. Experimentalists still debate on the nature of the protondonor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of themechanism, we studied this proton transfer using Car−Parrinello molecular dynamics, classical moleculardynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics,QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the proteinmeasured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumedproton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that thestabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequentlyoccurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acidscan easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMMsimulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bondrearrangements in this time span are not sufficient to stabilize the new protonation state. Force field moleculardynamics simulations on a much longer time scale have shown which internal rearrangements of the proteinare needed. Combining these simulations with more QMMM calculations enabled us to check the stability ofprotonation states and clarify the initial requirements for the proton transfer in PYP.
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