Active Site Structure of Photoactive Yellow Protein with a Locked Chromophore Analogue Revealed by Near-Infrared Raman Optical Activity

Many biological cofactors, such as light-absorbing chromophores in photoreceptors, are intrinsically planar molecules. A protein environment, however, causes structural distortions of the cofactor, and such structural changes can lead to a modulation of chemical properties of the cofactor to maximize its biological activity. Here, we investigate the active site structure of photoactive yellow protein (PYP), a blue light photoreceptor that contains a p-coumaric acid (pCA) chromophore, by a near-infrared excited Raman optical activity (ROA). Specifically, we measured the ROA spectra of PYP, whose chromophore is replaced with a locked pCA analogue. Furthermore, we show that a spectral analysis based on quantum mechanical/molecular mechanical (QM/MM) calculations of the whole protein molecule is useful to obtain structural information from the observed ROA spectra. The use of the near-infrared ROA combined with QM/MM calculations is a novel and generally applicable spectroscopic tool to study the chromophore distortions within a protein environment.