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two reduced cytochrome c molecules are produced per one converted GFP molecule).
The stability of the red form under the aerobic conditions points out that the mecha-nisms
of anaerobic and oxidative redding are, most likely, different13. Moreover, the
excitation spectra of the two forms are different: the maxima are 2.36 and 2.16 eV (525
and 575 nm) for anaerobic and oxidative redding forms of GFP, respectively. Bogdanov
et al.13 hypothesized that anaerobic redding proceeds by photoreduction producing a
stable radical (which will be sensitive to the presence of oxygen). Their findings suggest
that oxidative redding produces more stable species. Other GFP variants, i.e., AcGFP1,
TagGFP, zFP506, amFP486, and ppuGFP2 also undergo oxidative redding, however, the
blue and cyan mutants (that have notably different chromophores) of GFP (EBFP and
ECFP) do not13.
Theoretical modeling noticeably contributes to the studies of the GFP and related
model systems14–24 (for a recent review, see Ref. 25). In this chapter we charac-terize
the electronic structure of two different oxidized states of the deprotonated 4’-
hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anion (Fig. 3.1). We consider
singly and doubly oxidized forms and discuss excitation energies and oscillator strengths
of the electronic transitions in these species. To avoid confusion, it is important to clar-ify
the terminology. Here we refer to deprotonated HBDI as the HBDI anion, or simply
anion. The (neutral) species derived by removing one electron from the anion is called
the HBDI radical, and doubly oxidized deprotonated HBDI is called the HBDI cation.
We also present the relevant ionization energies and estimate standard reduction poten-tials
corresponding to these oxidation steps. The calculations are performed for the
isolated gas-phase chromophores, however, possible effects of the solvent on reduction
potentials are also discussed.
84
Object Description
| Title | Development of predictive electronic structure methods and their application to atmospheric chemistry, combustion, and biologically relevant systems |
| Author | Epifanovskiy, Evgeny |
| Author email | epifanov@usc.edu; epifanov@usc.edu |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Chemistry |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2011-03-21 |
| Date submitted | 2011 |
| Restricted until | Unrestricted |
| Date published | 2011-04-28 |
| Advisor (committee chair) | Krylov, Anna I. |
| Advisor (committee member) |
Wittig, Curt Johnson, Clifford |
| Abstract | This work demonstrates electronic structure techniques that enable predictive modeling of the properties of biologically relevant species. Chapters 2 and 3 present studies of the electronically excited and detached states of the chromophore of the green fluorescent protein, the mechanism of its cis-trans isomerization, and the effect of oxidation. The bright excited ππ∗ state of the chromophore in the gas phase located at 2.6 eV is found to have an autoionizing resonance nature as it lies above the electron detachment level at 2.4 eV. The calculation of the barrier for the ground-state cis-trans isomerization of the chromophore yields 14.8 kcal/mol, which agrees with an experimental value of 15.4 kcal/mol; the electronic correlation and solvent stabilization are shown to have an important effect. In Chapter 3, a one-photon two-electron mechanism is proposed to explain the experimentally observed oxidative reddening of the chromophore. Chapter 4 considers the excited states of uracil. It demonstrates the role of the one-electron basis set and triples excitations in obtaining the converged values of the excitation energies of the nπ∗ and ππ∗ states. The effects of the solvent and protein environment are included in some of the models.; Chapter 5 describes an implementation of the algorithm for locating and exploring intersection seams between potential energy surfaces. The theory is illustrated with examples from atmospheric and combustion chemistry. |
| Keyword | electronic structure theory; coupled clusters theory; equation of motion theory; organic chromophore; green fluorescent protein; uracil |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m3801 |
| Contributing entity | University of Southern California |
| Rights | Epifanovskiy, Evgeny |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@lib.usc.edu |
| Filename | etd-Epifanovskiy-4557 |
| Archival file | uscthesesreloadpub_Volume14/etd-Epifanovskiy-4557.pdf |
Description
| Title | Page 94 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | two reduced cytochrome c molecules are produced per one converted GFP molecule). The stability of the red form under the aerobic conditions points out that the mecha-nisms of anaerobic and oxidative redding are, most likely, different13. Moreover, the excitation spectra of the two forms are different: the maxima are 2.36 and 2.16 eV (525 and 575 nm) for anaerobic and oxidative redding forms of GFP, respectively. Bogdanov et al.13 hypothesized that anaerobic redding proceeds by photoreduction producing a stable radical (which will be sensitive to the presence of oxygen). Their findings suggest that oxidative redding produces more stable species. Other GFP variants, i.e., AcGFP1, TagGFP, zFP506, amFP486, and ppuGFP2 also undergo oxidative redding, however, the blue and cyan mutants (that have notably different chromophores) of GFP (EBFP and ECFP) do not13. Theoretical modeling noticeably contributes to the studies of the GFP and related model systems14–24 (for a recent review, see Ref. 25). In this chapter we charac-terize the electronic structure of two different oxidized states of the deprotonated 4’- hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anion (Fig. 3.1). We consider singly and doubly oxidized forms and discuss excitation energies and oscillator strengths of the electronic transitions in these species. To avoid confusion, it is important to clar-ify the terminology. Here we refer to deprotonated HBDI as the HBDI anion, or simply anion. The (neutral) species derived by removing one electron from the anion is called the HBDI radical, and doubly oxidized deprotonated HBDI is called the HBDI cation. We also present the relevant ionization energies and estimate standard reduction poten-tials corresponding to these oxidation steps. The calculations are performed for the isolated gas-phase chromophores, however, possible effects of the solvent on reduction potentials are also discussed. 84 |
