Modeling spectral tuning in monomeric teal fluorescent protein mTFP1

Topol, Igor A.; Collins, Jack; Nemukhin, Alexander V.

doi:10.1016/j.bpc.2010.04.002

Cited by 18 publications

(23 citation statements)

References 12 publications

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“…For the systems with carefully optimized geometry parameters, ZINDO has been found to be very efficient in computing bands in optical spectra. As shown in our previous applications for several classes of fluorescent proteins [19,21,24], such a strategy in fact leads to accurate results that are comparable to the experimenttal values. In this work we show that an elaborate selection of model clusters in the coordinate-locking scheme and an application of fairly inexpensive quantum chemistry methods allow us to calculate bands both in the absorption and in the emission spectra of proteins.…”

Section: Introductionsupporting

confidence: 64%

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

Topol

Collins²,

Nemukhin³

2012

CMB

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An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large-and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments.

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Section: Introductionsupporting

confidence: 64%

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

Topol

Collins²,

Nemukhin³

2012

CMB

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“…Finally, we comment that the structure and charge of the nearby residues play a strong role in shifting the absorption wavelength to the red, compared to that in the isolated chromophore—from 408 to 437 nm. In previous studies of green and blue fluorescent proteins,23–25 we usually observed such shifts within 10–15 nm.…”

Section: Resultsmentioning

confidence: 69%

“…Following our previous experience in simulation structure and spectra of fluorescent proteins,23–25 we optimized ground state equilibrium geometry parameters in the large molecular cluster, mimicking a chromophore‐containing pocket by using density functional theory (DFT) approximations. We believe that the QM part considered in Ref 14.…”

Section: Introductionmentioning

confidence: 99%

Initial report of the cancer Patient‐Reported Outcomes Measurement Information System (PROMIS) sexual function committee

Jeffery

Tzeng

Keefe

et al. 2009

Cancer

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For this report, the authors described the initial activities of the Cancer Patient-Reported Outcomes Measurement Information System (PROMIS)-Sexual Function domain group, which is part of the National Institutes of Health Roadmap Initiative to develop brief questionnaires or individually tailored assessments of quality-of-life domains. Presented are a literature review of sexual function measures used in cancer populations and descriptions of the domains found in those measures. By using a consensus-driven approach, an electronic bibliographic search was conducted for articles that were published from 1991 to 2007, and 486 articles were identified for in-depth review. In total, 257 articles reported the administration of a psychometrically evaluated sexual function measure to individuals who were diagnosed with cancer. Apart from the University of CaliforniaLos Angeles Prostate Cancer Index, the International Index of Erectile Function, and the Female Sexual Function Index, the 31 identified measures have not been tested widely in cancer populations. Most measures were multidimensional and included domains related to the sexual response cycle and to general sexual satisfaction. The current review supports the need for a flexible, psychometrically robust measure of sexual function for use in oncology settings and strongly justifies the development of the PROMIS-Sexual Function instrument. When the PROMIS-Sexual Function instrument is available publicly, cancer clinicians and researchers will have another measure with which to assess patient-reported sexual function outcomes in addition to the few legacy measures that were identified through this review.

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“…To compute vertical excitation energies from the respective minima on the S 0 potential surfaces of the model systems we applied the semiempirical ZINDO method [9]. As shown previously [5][6][7][8], this strategy to estimate the S 0 -S 1 excitation energies at the DFT-optimized equilibrium geometry parameters performs quite well for these model systems.…”

Section: Calculation Methodsmentioning

confidence: 99%

“…Kindling phenomenon of KFP was successfully used for the development of novel subdiffraction method of fluorescent microscopy with resolution up to 50-100 nm As demonstrated in our previous simulations for GFP and blue fluorescent proteins [5][6][7][8], we can rely on ab initio and semiempirical methods of quantum chemistry to calculate equilibrium geometry configurations of the molecular cluster mimicking the chromophore molecule and the immediate protein environment in the ground electronic state and to estimate vertical excitation energies of the S 0 -S 1 optical transitions. The latter may be compared to the observed bands in absorption spectra of the fluorescent proteins.…”

Section: Introductionmentioning

confidence: 95%

Modeling structure and spectra of the kindling fluorescent protein asFP595

et al. 2011

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Modern computational approaches based on quantum mechanical methods to characterize structures and optical spectra of biological chromophores in proteins are intensively used to gain knowledge of events occurring upon of their photoexcitation. Primary attention is paid to the species from the family of the green fluorescent protein applied as biomarkers in living cells. We apply quantum chemical approaches for accurate calculations of the structures of the chromophore binding pockets and to estimate spectral bands corresponding to the S 0 -S 1 optical transitions of the intriguing kindling protein asFP595. Its precursor, the chromoprotein asCP from the sea anemony Anemonia sulcata is characterized by distinctive spectral properties: at low light intensities the wild-type protein is weakly fluorescent with the very low quantum yield, however, high intensity irradiation with green light leads to a drastic increase of quantum yield. This phenomenon is now termed ''kindling''. In simulations, the model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S 0 -S 1 transitions are computed by using the semiempirical ZINDO technique. A special attention is paid to evaluate effects of point mutations in the vicinity of the chromophore group. Theoretical data provide important information on the chromophore properties aiming to interpret the results of experimental studies and applications of this fluorescent protein.

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Modeling spectral tuning in monomeric teal fluorescent protein mTFP1

Cited by 18 publications

References 12 publications

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

Initial report of the cancer Patient‐Reported Outcomes Measurement Information System (PROMIS) sexual function committee

Modeling structure and spectra of the kindling fluorescent protein asFP595

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