Mutants of monomeric red fluorescent protein mRFP1 at residue 66: structure modeling by molecular dynamics and search for correlations with spectral properties.

To study the interrelation between the spectral and structural properties of fluorescent proteins, structures of mutants of monomeric red fluorescent protein mRFP1 with all possible point mutations of Glu66 (except replacement by Pro) were simulated by molecular dynamics. A global search for correlations between geometrical structure parameters and some spectral characteristics (absorption maximum wavelength, integral extinction coefficient at the absorption maximum, excitation maximum wavelength, emission maximum wavelength, and quantum yield) was performed for the chromophore and its 6 A environment in mRFP1, Q66A, Q66L, Q66S, Q66C, Q66H, and Q66N. The correlation coefficients (0.81-0.87) were maximal for torsion angles in phenolic and imidazolidine rings as well as for torsion angles in the regions of connection between these rings and chromophore attachment to beta-barrel. The data can be used to predict the spectral properties of fluorescent proteins based on their structures and to reveal promising positions for directed mutagenesis.

[A method for determining the individual optical characteristics of posttranslational fluorescent forms of fluorescent proteins with the use of nonlinear laser fluorimetry].

A method for determining the individual optical characteristics (fluorescence quantum yield, the rate constant and quantum yield of singlet-triplet conversion, excitation of fluorescence cross-section, extinction coefficient) and concentration correlations between the fluorescent forms of fluorescent proteins arising in the reaction of posttranslational chromophore formation has been developed, which is based on combined application of absorption spectroscopy and classical and nonlinear laser fluorimretry. The method allows one to determine the share of fluorescent forms in the mixture of chromoproteins. The individual optical characteristics of the red form of the fluorescent protein mRFP1 has been determined: the fluorescence quantum yield eta = 0.24 +/- 0.03; the extinction coefficient in the maximum of absorbance band (584 nm) epsilon = 213 +/- 40 mM(-1) cm(-1) (the cross-section of absorbance sigma = (8.2 +/- 1.5).10(-16) cm2); the constant of singlet-triplet conversion rate K32 = (0 +/- 0.6)-10970 s(-1). The part of the red form in the mixture of chromoproteins is 26 +/- 6%.

Red fluorescent protein DsRed: parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force field.

Topology of the neutral form of the DsRed fluorescent protein chromophore as a residue of [(4-cis)-2-[(1-cis)-4-amino-4-oxobutanimidoyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid was calculated with OPLS-AA force field. Use of this topology and molecular dynamics simulation allows calculating the parameters of proteins that contain such residue in their polypeptide chains. The chromophore parameters were obtained by ab initio (RHF/6-31G**) quantum chemical calculations applying density functional theory (B3LYP). Using this chromophore, we have calculated the molecular dynamics trajectory of tetrameric fluorescent protein DsRed in solution at 300 K (4 nsec). Correctness of the chromophore parametrization was revealed by comparison of quantitative characteristics of the chromophore structure obtained from the molecular dynamic simulations of DsRed protein with the quantitative characteristics of the chromophore based on the crystallographic X-ray data of fluorescent protein DsRed (PDB ID: 1ZGO, 1G7K, and 1GGX), and also with the quantitative characteristics of the chromophore obtained by quantum chemical calculations. Inclusion of the neutral form of DsRed protein chromophore topology into the OPLS-AA force field yielded the extended force field OPLS-AA/DsRed. This force field can be used for molecular dynamics calculations of proteins containing the DsRed chromophore. The parameter set presented in this study can be applied for similar extension in any other force fields.