DFT/MM description of flavin IR spectra in BLUF domains.

A class of photoreceptors occurring in various organisms consists of domains that are blue light sensing using flavin (BLUF). The vibrational spectra of the flavin chromophore are spectroscopically well characterized for the dark-adapted resting states and for the light-adapted signaling states of BLUF domains in solution. Here we present a theoretical analysis of such spectra by applying density functional theory (DFT) to the flavin embedded in molecular mechanics (MM) models of its protein and solvent environment.

IR spectra of flavins in solution: DFT/MM description of redox effects.

The functional reactions in blue light photoreceptors generally involve transiently reduced flavins exhibiting characteristic infrared (IR) spectra. To approach a theoretical understanding, here we apply density functional theory (DFT) to flavin radicals embedded in a molecular mechanics (MM) model of an aqueous solution. Combining a DFT/MM approach with instantaneous normal-mode analyses (INMA), we compute the IR solution spectra of anionic and neutral flavin radicals.

Density functional theory combined with molecular mechanics: the infrared spectra of flavin in solution.

The photophysics and photochemistry of flavin dyes determine the functional dynamics of a series of blue light photoreceptors that include the so-called BLUF (blue light sensors using flavin) domains. To enable molecular dynamics (MD) simulation studies of such signaling processes, we derived molecular mechanics (MM) models of flavin chromophores from density functional theory (DFT). Two 300 K ensembles of lumiflavin (LF) in aqueous solution were generated by extended MM-MD simulations using different MM potentials for the water.

Relaxation time prediction for a light switchable peptide by molecular dynamics.

We study a monocyclic peptide called cAPB, whose conformations are light switchable due to the covalent integration of an azobenzene dye. Molecular dynamics (MD) simulations using the CHARMM22 force field and its CMAP extension serve us to sample the two distinct conformational ensembles of cAPB, which belong to the cis and trans isomers of the dye, at room temperature. For gaining sufficient statistics we apply a novel replica exchange technique.