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

Abstract

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. SECTION: Biophysical Chemistry and Biomolecules

Experimental Detection of the Intrinsic Difference in Raman Optical Activity of a Photoreceptor Protein under Preresonance and Resonance Conditions

“…We observe aclose similarity between the shape of the RR spectrum and the resonance ROA spectrum of PYP.F urthermore,w ee xperimentally verify the theoretical prediction concerning the ratio of the amplitudes of the ROAa nd Raman spectra. [7][8][9] Since Raman scattering is ar elatively weak effect and the CID value is small (D < 10 À3 ), resonance enhancement is of great importance in ROAs tudies.H owever,e xperimental [10][11][12][13] and theoretical [14,15] ROAs tudies under resonance conditions have so far been very limited. In the case that molecules embedded in proteins exhibit an electronic transition, resonance Raman (RR) spectroscopy allows the enhancement of the vibrational modes of these chromophores with an excitation wavelength in resonance with this electronic transition.…”

“…This greatly increases the amplitude of the detected Raman bands and depends strongly on the energy difference between the position of the electronic transition and the excitation wavelength. [8,9] TheR OA signals measured in these studies are dominated by vibrational modes originating from the two distinct chromophores of these two photoreceptors.W es uggested that the ROAs pectra of the chromophore are enhanced by ap reresonance Raman effect. The difference in Raman scattered intensity between right (I R ) and left (I L )circularly polarized incident light holds information on molecular chirality [3][4][5][6] and is called Raman optical activity (ROA).…”

“…The difference in Raman scattered intensity between right (I R ) and left (I L )circularly polarized incident light holds information on molecular chirality [3][4][5][6] and is called Raman optical activity (ROA). [17] Additionally,the shape of the ROAspectra, including the sign of the detected bands,isquite distinct from Raman spectra for these proteins.In ROAs tudies on PYP, [8,9] the availability of its highresolution crystal structures [18,19] allows quantum chemical calculations based on density functional theory (DFT) to simulate the ROAspectra. [7][8][9] Since Raman scattering is ar elatively weak effect and the CID value is small (D < 10 À3 ), resonance enhancement is of great importance in ROAs tudies.H owever,e xperimental [10][11][12][13] and theoretical [14,15] ROAs tudies under resonance conditions have so far been very limited.…”

“…[7][8][9] Since Raman scattering is ar elatively weak effect and the CID value is small (D < 10 À3 ), resonance enhancement is of great importance in ROAs tudies.H owever,e xperimental [10][11][12][13] and theoretical [14,15] ROAs tudies under resonance conditions have so far been very limited. [7][8][9] Since Raman scattering is ar elatively weak effect and the CID value is small (D < 10 À3 ), resonance enhancement is of great importance in ROAs tudies.H owever,e xperimental [10][11][12][13] and theoretical [14,15] ROAs tudies under resonance conditions have so far been very limited.…”

“…In ROAs tudies on PYP, [8,9] the availability of its highresolution crystal structures [18,19] allows quantum chemical calculations based on density functional theory (DFT) to simulate the ROAspectra. Such combined experimental and computational studies established the high sensitivity of the ROAs pectra to out-of-plane deformations of the chromophore.T hese studies demonstrated that the near-infrared excitation allows accurate measurement of structurally infor-mative preresonance ROAs pectra of ac hromophore embedded in aprotein.…”