Fluorescent proteins are widely used as markers for visualization of processes in intact biological systems. The family of fluorescent proteins includes proteins of various representatives of Coelenterata that are able to absorb light and emit in the visible spectral range. All flu orescent proteins have similar structure represented by 11 strand β barrel with α helix inside, which contains a chromophore in the middle. The chromophore is a het erogroup formed by an autocatalytic posttranslational reaction between three adjacent amino acid residues. The presence of the chromophore imparts color to the protein and induces its possible fluorescence [1].Fluorescence of proteins of this family is influenced by external conditions: pH [2,3], temperature [1], and ionic content of the medium [4,5], but structures of the chromophore and its nearest environment [1,6] are the key factors. The representatives of this family in matura tion rate, stability, spectral properties (absorption and flu orescence spectra, fluorescence quantum yield, photo bleaching, etc.) are described in [1,7]. Theoretical, experimental, and computational studies are carried out to investigate the mechanism of fluorescence of these proteins [8 11].Green fluorescent protein (GFP) was discovered in the early 1960s [12], but its active study began only after cloning of the GFP gene in 1992 [13] and demonstration of its heterologic expression in other organisms. In 1999, another family of colored proteins including the red pro tein DsRed was cloned from corals [14]. However, DsRed is a tetramer, and its use as a fluorescent marker is limit ed because of possible effects of its large molecular mass ISSN 0006 2979, Biochemistry (Moscow), 2008, Vol. 73, No. 10, pp. 1085 1095. © Pleiades Publishing, Ltd., 2008. Original Russian Text © E. E. Khrameeva, V. L. Drutsa, E. P. Vrzheshch, D. V. Dmitrienko, and P. V. Vrzheshch, 2008, published in Biokhimiya, 2008, Vol. 73, No. 10, pp. 1355 1367. Originally published in Biochemistry (Moscow) On Line Papers in Press, as Manuscript BM08 038, September 21, 2008 1085 Abbreviations: DsRed) red fluorescent protein drFP583 from coral Discosoma sp.; GFP) green fluorescent protein from Aequorea victoria; MD) molecular dynamics; mRFP1) monomeric red fluorescent protein, mutant of DsRed; Q66X) mutants of mRFP1 with replacement of residue 66 by residue X. * To whom correspondence should be addressed. Abstract-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, Q...
