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

Abstract

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 coexistence of two conformers which 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 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 initial increase of fluorescence yield only for relatively floppy fluorescent proteins, whereas the fluorescent proteins that have more rigid structures have quantum yield close to their maximum. The results suggest that 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.

Pressure-Induced Changes in the Fluorescence Behavior of Red Fluorescent Proteins

“…The observed drastic change in the fluorescence spectrum of mStrawberry at intermediate pressure can be traced to changes in the population of two conformers with different H-bonding environments of the chromophore (while retaining the overall conformation of the chromophore itself). 23 …”

“…An accompanying paper by Laurent et al 23 describes molecular dynamics (MD) and QM/MM (quantum mechanics-molecular mechanics) simulations performed on mStrawberry and mCherry that shed light on the molecular origins of the observed pressure induced changes in fluorescence behavior.…”

Effect of chromophore encapsulation on linear and nonlinear optical properties: the case of “miniSOG”, a protein-encased flavin

“…Such analyses have previously been useful in the interpretation of the one-and two-photon properties of fluorescent proteins. 19,77,78 First, note that the electrostatic potentials generated by the two distinct environments exhibit a similar general shape across the atomic sites. The potential is highest at the pteridine end and gradually decreases toward the nonpolar end of FMN, corresponding to an electric field along the long axis of the molecule (minus x-direction).…”

Intriguing cysteine induced improvement of the emissive property of carbon dots with sensing applications

“…As the pH increases, the keto form predominates. 50 The long chain thiols cannot undergo such rigid interaction. 45,46 This polymer is capable of anchoring on suitable surfaces.…”