We apply a SCRF-PCM-CI calculation to elucidate the mechanism of spectral tuning in photoactive yellow protein (PYP). It is shown that the calculation well reproduces solvatochromic shifts observed for some model compounds of the PYP chromophore. By regression analysis, we obtain an empirical equation to predict solvatochromic shifts of these compounds for a given set of dielectric constant and refractive index. Next, using a classical electrostatic theory and the crystal structure of PYP, the value of refractive index is calculated for the chromophore-binding pocket. The value of the dielectric constant is estimated from the fact that the binding pocket is highly hydrophobic. On the basis of these results we predict the absorption maximum of PYP. In addition, the, spectral tuning mechanism in PYP is divided into three factors, that is, counterion effect, hydrogen-bonding effect, medium effect of,the protein matrix,and each contribution is quantitatively evaluated. It is shown that the electronic polarization effects of the protein matrix plays a nonnegligible role in tuning the absorption maximum of PYP as similar to the case of bacteriorhodopsin.