Computional study of the spectral tuning and photoreaction of photoactive yellow protein

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In this study, we clarified the following points concerning the properties of photoactive yellow protein (PYP). 1) We developed a quantum chemical methodology that can evaluate the absorption maximum of a photoreceptor protein such as PYP and retinal proteins. In this method, the entire protein is decomposed into two parts : region I is treated quantum mechanically and includes only a chromophore, and region II (the surrounding protein part) is treated by classical electrostatics. A feature of this method is that the electronic polarization effect of the protein part can be explicitly taken into account. Using this method, we indicated that the electronic polarization of the protein matrix is a decisive role in spectral tuning of PYP and retinal proteins such as bacteriorhodopsin and halorhodopsin. 2) 10 ns molecular dynamics simulations were carried out for the dark state of PYP, and the PYP_L and PYP_M intermediates. It was indicated that among the three states PYP_M has the largest molecular fluctuation in solution. As a result, a channel is formed to allow water exchange between the exterior and interior of the protein. In addition, the results of principal component analysis indicated that the PYP_M has a characteristic low frequency vibrational motion, namely a hinge bending motion. It was inferred that this motion contributes to binding to transduction, in other words, to the activation of signal transduction. 3) We developed a full quantum chemical methodology of pKa calculation of ionizable groups in proteins and applied it to bacteriorhodopsin (bR). The calculation based on this method successfully reproduced the relative pKa values of retinal Schiff base to Asp85 in both the bR ground state and the M intermediate. It was concluded that Tbr89 is a key residue driving the first proton transfer step in bR.