Paper Citing NAMD - Abstract
Khrenova, Maria G.; Nemukhin, Alexander V.; Domratcheva, Tatiana
Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5176-5183, APR 23 2015
The iLOV protein is one of the most promising members of the family of engineered flavin-based fluorescent proteins (FbFPs), considered as an alternative to the green fluorescent protein family. We modeled the spectral properties of iLOV using quantum chemistry, quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics approaches. Computational results predict that the conserved Gln489 side chain in iLOV adopts two almost equally populated conformations, Gln(in) and Gln(out), altering hydrogen bonding near the flavin chromophore. Formation of the flavinN5-Gln489 and flavinO4-Gln489 hydrogen bonds in the case of Gln(in) accounts for the pronounced shifts of the flavin absorption and fluorescence maxima to the longer wavelengths. Following these results, we propose to introduce a point mutation in iLOV, Q489K, with the aim to obtain a more red-shifted variant. According to our simulations, this mutation should lead to a considerable, about 50 nm, red shift of the absorption and emission band maxima, thus introducing a new color in the FbFP palette.
