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

Dmitrienko, D. V.; Vrzheshch, E. P.; Друца, В. Л.; Vrzheshch, P. V.

doi:10.1134/s0006297906100129

Cited by 5 publications

(6 citation statements)

References 44 publications

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“…MD simulations for mRFP1 and all its possible mutants at residue 66 except for proline, for which chro mophore parameterization is still absent, were performed as described above [19]. Moreover, formation of the chro mophore in the proline mutant at residue 66 is hardly possible; this is supported by complete absence of data on the existence of such proline mutants in the family of flu orescent proteins.…”

Section: Methodsmentioning

confidence: 81%

“…The integrity of the β barrel is maintained by multiple hydrogen bonds with energy high enough (2 5 kcal/mol per bond) for β barrel to become a rather rigid system. Such rigid β barrel seems to influence the conformation of the chromophore, which is exactly planar in vacuum [19], but its structure is more tensive within the protein (torsion angle values vary from 0 and 180°).…”

Section: Resultsmentioning

confidence: 99%

“…In the case of fluorescent proteins, it is necessary to have such parameters also for atoms of the chromophore incorporated into the protein chain as an amino acid residue. The extended force field OPLS AA/DsRed1 was selected for MD calculations [19] because the chro mophore of red fluorescent protein DsRed is parameter ized in the OPLS AA/DsRed1 force field; this allows MD simulations of all proteins containing DsRed chro mophore, including simulations of mRFP1 mutants.…”

Section: Methodsmentioning

confidence: 99%

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

Khrameeva

Друца

Vrzheshch

et al. 2008

Biochemistry Moscow

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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...

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Section: Methodsmentioning

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Khrameeva

Друца

Vrzheshch

et al. 2008

Biochemistry Moscow

Self Cite

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“…Force field parameters for the mCherry, mPlum, and DsRed chromophores were those published in ( Dmitrienko et. al., 2006 ) with the exception of excluding the phenolic hydroxyl hydrogen in order to form the anionic chromophore.…”

Section: Methodsmentioning

confidence: 99%

Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins

Drobizhev

Molina

Callis

et al. 2021

Front. Mol. Biosci.

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Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.

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“…10 The CHARMM27 force field 31 has been used to describe the protein. The parameters for the mStrawberry and mCherry chromophore were taken from: (i) anionic GFP chromophore’s parameters for CHARMM22; 32 (ii) acylimine parameters of the DsRed chromophore for OPLS; 33, 34 and (iii) the retinal parameters (van der Waals parameters of acylimine nitrogen) for CHARMM27. The parameters are given in supporting information (SI).…”

Section: Computational Detailsmentioning

confidence: 99%

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

et al. 2012

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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.

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

Cited by 5 publications

References 44 publications

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

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

Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins

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

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