Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy

Abstract

DsRed is a sort of red fluorescent protein (RFP) isolated from Discosoma coral. Previously, we successfully calculated the excitation and emission energies of DsRed, based on the CIS (D) type excited state method in conjunction with the multilayer version of fragment molecular orbital (MFMO) scheme [Mochizuki et al., Chem. Phys. Lett., 433, 360 (2007) & Taguchi et al., J. Phys. Chem. B, 113, 1153 (2009) ]. However, there have been no reports on the effects from water molecules, configurations of amino acid residues surrounding the DsRed chromophore. In the present work, we made a series of examinations on these effects on the excitation energy of DsRed. As a result, the following three factors were found to be important in obtaining quantitative correspondence to the experimental value; (1) two water molecules having hydrogen-bonds with the crucial pigment part, (2) orientation of the OH group of Ser69 to make a hydrogen-bond with CRQ66, and (3) configurational relaxation of neighboring amino acid residues (in particular, positively charged Lys163 as well as negatively charged Glu215). The present work could justify the reliability of protein modeling in our previous two papers.