Paper Citing NAMD - Abstract
Bravaya, Ksenia B.; Khrenova, Maria G.; Grigorenko, Bella L.; Nemukhin, Alexander V.; Krylov, Anna I.
Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8296-8303, JUN 30 2011
The effect of the protein environment on the electronic structure of the gas phase green fluorescent protein (GFP) chromophore is investigated by QM/MM (quantum mechanics/molecular mechanics) calculations. The protein has very small effect on the excitation energy of the bright absorbing and the lowest triplet states of the anionic GFP chromophore, deprotonated 4-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anion, however, it increases vertical detachment energy from 2.5 eV (gas-phase deprotonated HBDI anion) to 5.0 eV (solvated protein). We also investigated possible existence of the charge-transfer-to-solvent (CTTS) states associated with the GFP chromophore. Although precursors of such states appear in cluster calculations, a tightly packed structure of the protein prevents the formation of the CTTS states in this system. Motivated by a recently discovered new type of photoconversion, oxidative redding, we characterized the redox properties of GFP. The computed standard reduction potential of the anionic form of GFP is 0.47 V (for the GFP(center dot) + le -> GFP(-) reaction), and the reduction potential at physiological conditions (pH 7, T = 25 degrees C) is 0.06 V.
