A conserved interaction with the chromophore of fluorescent proteins

Choudhary, Amit; Kamer, Kimberli J.; Raines, Ronald T.

doi:10.1002/pro.762

Cited by 10 publications

(11 citation statements)

References 53 publications

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“…The results from the calculations indicate that the H-O···C=O interaction has a significant role in stabilizing the excited state via an n (OH) →π* (CO) interaction, which results in a low-lying LUMO state and a red-shifted fluorescence. The results are consistent with those reported by Raines and co-workers30, in which theoretical calculations and high-resolution structures of green fluorescent proteins revealed the existence of a n→π* interaction between the chromophore of fluorescent proteins and a main-chain oxygen, and this interaction could contribute to the photophysical properties of the chromophore. Based on the above-mentioned results, the EDF behaviour can be explained by the electronically excited state manifold of the carbonyl groups due to the oscillating HO···C=O interactions caused by the collective proton motion system.…”

Section: Resultssupporting

confidence: 92%

Excitation-dependent visible fluorescence in decameric nanoparticles with monoacylglycerol cluster chromophores

et al. 2013

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Organic fluorescent nanoparticles, excitation-dependent photoluminescence, hydrogen-bonded clusters and lysobisphosphatidic acid are four interesting individual topics in materials and biological sciences. They have attracted much attention not only because of their unique properties and important applications, but also because the nature of their intriguing phenomena remained unclear. Here we report a new type of organic fluorescent nanoparticles with intense blue and excitation-dependent visible fluorescence in the range of 410–620 nm. The nanoparticles are composed of ten bis(monoacylglycerol)bisphenol-A molecules and the self-assembly occurs only in elevated concentrations of 2-monoacylglycerol via radical-catalysed 3,2-acyl migration from 3-monoacylglycerol in neat conditions. The excitation-dependent fluorescence behaviour is caused by chromophores composed of hydrogen-bonded monoacylglycerol clusters, which are linked by an extensive hydrogen-bonding network between the ester carbonyl groups and the protons of the alcohols with collective proton motion and HO···C=O (n→π*) interactions.

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Section: Resultssupporting

confidence: 92%

Excitation-dependent visible fluorescence in decameric nanoparticles with monoacylglycerol cluster chromophores

et al. 2013

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“…In natural fluorescent proteins, such as green fluorescent protein (GFP), an n →π* interaction forms between a backbone oxygen and the imidazolidine chromophore ( 14 ). 92 The presence of this n →π* interaction is consistent with the red shift in the vibrational frequency of the imidazolidine carbonyl group in the protein-bound chromophore relative to small-molecule mimics in solution. Moreover, analyses of protein crystal structures with premature chromophores suggest that this n →π* interaction preorganizes the chromophore for cyclization and precludes bond rotations that would lower the quantum yield.…”

Section: Contributions To Small Moleculessupporting

confidence: 52%

The n→π* Interaction

2017

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ConspectusThe carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly.These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found that by modulating the distance between two carbonyl groups in the peptide backbone, one could alter the conformational preferences of a peptide bond to proline. Specifically, only the trans conformation of a peptide bond to proline allows for an attractive interaction with an adjacent carbonyl group, so when one increases the proximity of the two carbonyl groups, one enhances their interaction and promotes the trans conformation of the peptide bond, which increases the thermostability of collagen.More recently, attention has been paid to the nature of these interactions. Some have argued that rather than resulting from electron donation, carbonyl interactions are a particular example of dipolar interactions that are well-approximated by classical mechanics. However, experimental evidence has demonstrated otherwise. Numerous examples now exist where an increase in the dipole moment of a carbonyl group decreases the strength of its interactions with other carbonyl groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation.Although individual n→π* interactions are relatively weak (∼0.3–0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affect...

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“…An additional interaction between the C 2 atom and the carbonyl O atom of Thr62 can be regarded as a lone pair-* interaction [Figs. 8(b) and 8(c)] (Choudhary et al, 2012), which actually weakens the C 2 -O 2 bond, as indicated from the bond order shown in Supplementary Fig. S5(c).…”

Section: Nonbonded Interactions Around the Chromophorementioning

confidence: 83%

Subatomic resolution X-ray structures of green fluorescent protein

Takaba

Tai

Eki

et al. 2019

IUCrJ

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Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair–π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.

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A conserved interaction with the chromophore of fluorescent proteins

Cited by 10 publications

References 53 publications

Excitation-dependent visible fluorescence in decameric nanoparticles with monoacylglycerol cluster chromophores

Excitation-dependent visible fluorescence in decameric nanoparticles with monoacylglycerol cluster chromophores

The n→π* Interaction

Subatomic resolution X-ray structures of green fluorescent protein

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