Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins

Molecular dynamics calculations of pressure effects on
mStrawberry
and mCherry fluorescent proteins are reported. The simulations reveal
that mStrawberry has much floppier structure at atmospheric pressure,
as evidenced by larger backbone fluctuations and the coexistence of
two conformers that differ by Ser146 orientation. Consequently, pressure
increase has a larger effect on mStrawberry, making its structure
more rigid and reducing the population of one of the conformers. The
most significant effect of pressure increase is in the hydrogen-bonding
network between the chromophore and the nearby residues. The quantum-mechanics/molecular
mechanics calculations of excitation energies in mStrawberry explain
the observed blue shift and identify Lys70 as the residue that has
the most pronounced effect on the spectra. The results suggest that
pressure increase causes an initial increase of fluorescence yield
only for relatively floppy fluorescent proteins, whereas the fluorescent
proteins that have more rigid structures have quantum yields close
to their maximum. The results suggest that a low quantum yield in
fluorescent proteins is dynamic in nature and depends on the range
of thermal motions of the chromophore and fluctuations in the H-bonding
network rather than on their average structure.