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study/management/literature/articles/Effects of threonine 203 replacements on excited-state dynamics and fluorescence properties of the green fluorescent protein (GFP) (@kummer2000effects).md

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+---
+tags:
+  - lit
+date: 2000-01-01
+---
+
+# Effects of threonine 203 replacements on excited-state dynamics and fluorescence properties of the green fluorescent protein (GFP)
+
+**Authors:** Andreas D Kummer, Jens Wiehler, Hermann Rehaber, Christian Kompa, Boris Steipe, Maria Elisabeth Michel-Beyerle
+
+**DOI:** [10.1021/jp9942522](https://doi.org/10.1021/jp9942522)
+
+<!-- more -->
+
+Takeaways:
+
+- 
+
+## Abstract
+
+> We report a comparative study of wild-type green fluorescent protein (GFP) and single-site mutants in which threonine at position 203 has been replaced by aliphatic and aromatic residues, i.e., by valine (V), isoleucine (I), phenylalanine (F), tyrosine (Y), and histidine (H). Steady-state absorption spectra reveal changes that reflect different charge distributions in the mutants as compared to wild-type GFP. While the absorption peak of the protonated fluorophore, RH, undergoes only a small red shift in all T203 mutants, a pronounced red shift is observed for the deprotonated form R-, ca. 1000 cm-1 for the aliphatic mutants T203V and T203I, ca. 1200 cm-1 for T203F, and 1360 cm-1 for T203Y. Thus, we conclude that a ground-state conformation higher in energy than the wild-type R- state is the predominant origin of the red shift in all the T203 mutants investigated. Furthermore, mutant-dependent changes in the ground-state equilibria of RH and R- result from at least two modes of electrostatic stabilization, one resting on hydrogen bonding as in T203 and the other one on π−π-stacking as in T203F and T203Y. Surprisingly, the deprotonation dynamics of RH* is only weakly affected by the mutations at position 203. Only in the most red-shifted mutant T203Y an additional ultrafast (1.7 ps) excited-state decay channel of RH* has been observed. The identical kinetics of both processes, decay of RH* and ground-state recovery of RH in T203Y, is discussed in terms of two mechanisms:  (i) rate-determining electron transfer from the protonated (or deprotonated) tyrosyl 203 residue to RH* followed by considerably faster recombination processes, which cannot occur in T203F for energetic reasons, and (ii) internal conversion in RH* favored by rotational motion around the exocyclic double bond.
+
+## Main
+
+> Owing to the missing hydroxy group of T203, there is less stabilization of R- and the corresponding absorption band is almost entirely lost.
+
+> Furthermore, the presence of threonine at position 203 is not required for ESPT to occur.
+

study/management/literature/articles/Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein (@brejc1997structural).md

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+---
+tags:
+  - lit
+date: 1997-01-01
+---
+
+# Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein
+
+**Authors:** Katjuša Brejc, Titia K. Sixma, Paul A. Kitts, Steven R. Kain, Roger Y. Tsien, Mats Ormö, S. James Remington
+
+**DOI:** [10.1073/pnas.94.6.2306](https://doi.org/10.1073/pnas.94.6.2306)
+
+<!-- more -->
+
+Takeaways:
+
+- 
+
+## Abstract
+
+> The 2.1-Å resolution crystal structure of wild-type green fluorescent protein and comparison of it with the recently determined structure of the Ser-65 → Thr (S65T) mutant explains the dual wavelength absorption and photoisomerization properties of the wild-type protein. The two absorption maxima are caused by a change in the ionization state of the chromophore. The equilibrium between these states appears to be governed by a hydrogen bond network that permits proton transfer between the chromophore and neighboring side chains. The predominant neutral form of the fluorophore maximally absorbs at 395 nm. It is maintained by the carboxylate of Glu-222 through electrostatic repulsion and hydrogen bonding via a bound water molecule and Ser-205. The ionized form of the fluorophore, absorbing at 475 nm, is present in a minor fraction of the native protein. Glu-222 donates its charge to the fluorophore by proton abstraction through a hydrogen bond network, involving Ser-205 and bound water. Further stabilization of the ionized state of the fluorophore occurs through a rearrangement of the side chains of Thr-203 and His-148. UV irradiation shifts the ratio of the two absorption maxima by pumping a proton relay from the neutral chromophore’s excited state to Glu-222. Loss of the Ser-205–Glu-222 hydrogen bond and isomerization of neutral Glu-222 explains the slow return to the equilibrium dark-adapted state of the chromophore. In the S65T structure, steric hindrance by the extra methyl group stabilizes a hydrogen bonding network, which prevents ionization of Glu-222. Therefore the fluorophore is permanently ionized, causing only a 489-nm excitation peak. This new understanding of proton redistribution in green fluorescent protein should enable engineering of environmentally sensitive fluorescent indicators and UV-triggered fluorescent markers of protein diffusion and trafficking in living cells.
+
+## Main

study/management/literature/articles/Structural characterization of green fluorescent protein in the I-state (@takeda2024structural).md

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+---
+tags:
+  - lit
+date: 2024-01-01
+---
+
+# Structural characterization of green fluorescent protein in the I-state
+
+**Authors:** Ryota Takeda, Erika Tsutsumi, Kei Okatsu, Shuya Fukai, Kazuki Takeda
+
+**DOI:** [10.1038/s41598-024-73696-y](https://doi.org/10.1038/s41598-024-73696-y)
+
+<!-- more -->
+
+Takeaways:
+
+- 
+
+## Abstract
+
+> Green fluorescent protein (GFP) is widely utilized as a fluorescent tag in biochemical fields. Whereas the intermediate (I) state has been proposed in the photoreaction cycle in addition to the A and B states, until now the structure of I has only been estimated by computational studies. In this paper, we report the crystal structures of the I stabilizing variants of GFP at high resolutions where respective atoms can be observed separately. Comparison with the structures in the other states highlights the structural feature of the I state. The side chain of one of the substituted residues, Val203, adopts the _gauche-_ conformation observed for Thr203 in the A state, which is different from the B state. On the other hand, His148 interacts with the chromophore by ordinary hydrogen bonding with a distance of 2.85 Å, while the weaker interaction by longer distances is observed in the A state. Therefore, it was indicated that it is possible to distinguish three states A, B and I by the two hydrogen bond distances Oγ-Thr203···Oη-chromophore and Nδ1-His148···Oη-chromophore. We discuss the characteristics of the I intermediate of wild-type GFP on the bases of the structure estimated from the variant structures by quantum chemical calculations.
+
+## Main

study/management/literature/refs.bib

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+@article{takeda2024structural,
+  title={Structural characterization of green fluorescent protein in the I-state},
+   volume={14},
+   issn={2045-2322},
+   url={http://dx.doi.org/10.1038/s41598-024-73696-y},
+   doi={10.1038/s41598-024-73696-y},
+   number={1},
+   journal={Scientific Reports},
+   publisher={Springer Science and Business Media LLC},
+   author={Takeda, Ryota and Tsutsumi, Erika and Okatsu, Kei and Fukai, Shuya and Takeda, Kazuki},
+   year={2024},
+   month=oct 
+}
+
+@article{brejc1997structural,
+  title={Structural basis for dual excitation and photoisomerization of the
+            Aequorea victoria
+            green fluorescent protein},
+   volume={94},
+   issn={1091-6490},
+   url={http://dx.doi.org/10.1073/pnas.94.6.2306},
+   doi={10.1073/pnas.94.6.2306},
+   number={6},
+   journal={Proceedings of the National Academy of Sciences},
+   publisher={Proceedings of the National Academy of Sciences},
+   author={Brejc, Katjuša and Sixma, Titia K. and Kitts, Paul A. and Kain, Steven R. and Tsien, Roger Y. and Ormö, Mats and Remington, S. James},
+   year={1997},
+   month=mar, pages={2306–2311} 
+}
+
 @article{izadi2016accuracy,
   title={Accuracy limit of rigid 3-point water models},
   author={Izadi, Saeed and Onufriev, Alexey V},