A time-dependent DFT/molecular dynamics study of the proton-wire responsible for the red fluorescence in the LSSmKate2 protein

Randino, Carlos; Nadal-Ferret, Marc; Gelabert, Ricard; Moreno, Miquel; Lluch, José M.

doi:10.1007/s00214-012-1327-3

Cited by 11 publications

(13 citation statements)

References 45 publications

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“…Given that the X-ray data indicate that the chromophore adopts a mix of cis and trans configurations (with a proportion variable as a function of the pH) we performed MD simulations for both configurations at any given pH using a protocol previously applied with success to the mKeima and LSSmKate2 proteins. 17,18 From the full MD results we are able to theoretically reproduce the absorption spectra of TagRFP675 at three different pHs (4.5, 7.5 and 10) that roughly cover the experimental range (from 3.5 to 10.5). This study will provide a considerable insight at a molecular level into the intricate chemistry operating in these kinds of FPs.…”

Section: Introductionmentioning

confidence: 91%

“…For the sake of clarity the cumulative results are presented as convoluted spectra as was already done in our previous studies on other red FPs. 17,18 A similar procedure could be used to theoretically reproduce the fluorescence spectrum of TagRFP675. To do so a long enough MD simulation should be carried out for the excited electronic state.…”

Section: Electronic Excited State Calculationsmentioning

confidence: 99%

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Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein

Randino

Gelabert

Moreno

et al. 2015

Phys. Chem. Chem. Phys.

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Classical molecular dynamics (MD) simulations are carried out for the recently developed TagRFP675 fluorescent protein (FP), which is specifically designed to fully absorb and emit in the near infrared (NIR) region of the electromagnetic spectrum. Since the X-ray data of TagRFP675 reveal that the chromophore exists in both the cis and trans configuration and it can also be neutral (protonated) or anionic (deprotonated) depending on the pH of the media, a total of 8 molecular dynamic simulations have been run to simulate all the possible states of the chromophore. Time-dependent DFT (TDDFT) single point calculations are performed at selected points along the simulation to theoretically mimic the absorption spectrum of the protein. Our simulations compare well (within the expected error of the computational method) with the experimental results. Our theoretical procedure allows for an analysis of the molecular orbitals involved in the lowest energy electronic excitations of the chromophore and, more interestingly, for a full analysis of the H-bond interactions between the chromophore and its surrounding residues and solvent (water) molecules. This study does not support the hypothesis, exclusively based on the analysis of X-ray data, that the isomerization of nearby residues provokes the rearrangement of the hydrogen bonds in the chromophore's immediate environment leading to the observed red shift of the absorption bands at higher pHs. Instead, we attribute this shift mainly to the superposition of bands of the neutral and anionic chromophores that are expected to coexist at almost the full range of pHs experimentally analyzed. An additional factor that could contribute to this shift is the experimentally observed increase of the cis configuration of the chromophore at higher pHs.

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Section: Introductionmentioning

confidence: 91%

Section: Electronic Excited State Calculationsmentioning

confidence: 99%

Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein

Randino

Gelabert

Moreno

et al. 2015

Phys. Chem. Chem. Phys.

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“…This kind of approach has been used earlier for the calculation of absorption spectra of proteins with notable success. [47][48][49][50] In our case, we have taken 500 structures equally spaced (1 structure every 2 ps) from our MD simulations and performed TD-DFT excited state calculations (including the effect of the polarization caused by the environment by means of the MM charges) to average the electronic transitions calculated weighting them by its oscillator strength, which is a measure of how strong the transition will be.…”

Section: Absorption Spectra Calculationmentioning

confidence: 99%

New insights into the structure–spectrum relationship in S65T/H148D and E222Q/H148D green fluorescent protein mutants: a theoretical assessment

et al. 2014

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The green fluorescent protein (GFP) variant S65T/H148D recovers the A-band fluorescence lost in the single mutant S65T, and it has been established that Asp148 is the alternate proton acceptor for the excited state proton transfer (ESPT). This mutant has been widely studied and presents unique spectroscopic properties, such as an ultrafast rise in the fluorescence (<50 fs). Also it exhibits a red-shift of the A absorption band of 20 nm with respect to wt-GFP's. The double mutant E222Q/H148D presents a very similar behaviour, at least within the experimental data available (which is scarcer than those of S65T/H148D). By means of dynamic theoretical studies we have been able to (1) reproduce and thoroughly analyse the red-shifted absorption spectra of both mutants and (2) predict the structure that the variant E222Q/H148D (for which there is no X-ray-resolved structure available) most probably adopts in water at room temperature. Our results deepen the understanding of the way GFP variants work and give some new insights into the rational design of fluorescent proteins and biological photosystems in general.

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“…However, a study on the emission process of the whole protein is still missing. Similarly, Randino and coworkers 53 focused on the LSSmKate2 protein and carried out an MD simulation in which a series of excited states were calculated and analyzed on the basis of different snapshots. The final spectrum is obtained as an average of all individual spectra.…”

Section: Introductionmentioning

confidence: 99%

Characterizing the Structures, Spectra, and Energy Landscapes Involved in the Excited-State Proton Transfer Process of Red Fluorescent Protein LSSmKate1

et al. 2016

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By applying molecular dynamics (MD) simulations and quantum chemical calculations, we have characterized the states and processes involved in the excited-state proton transfer (ESPT) of LSSmKate1. MD simulations identify two stable structures in the electronic ground state of LSSmKate1, one with a protonated chromophore and the other with a deprotonated chromophore, thus leading to two separate low-energy absorption maxima with a large energy spacing, as observed in the calculated and experimentally measured absorption spectra. Proton transfer is induced by electronic excitation. When LSSmKate1 is excited, the electrons in the chromophore are transferred from the phenol ring to the N-acylimine moiety; the acidity of a phenolic hydroxyl group is thus enhanced. The calculated potential energy curves (PECs) exhibit energetic feasibility in the generation of the fluorescent species in LSSmKate1, and the exact agreement between the calculated and experimentally measured values of the large Stokes shift further provides solid theoretical evidence for the ESPT process taking place in photoexcited LSSmKate1. The molecular environments play a significant role in the geometries and absorption/emission energies of the chromophores. Overall, TD-ωB97X-D/molecular mechanics (MM) provides a better description of the optical properties of LSSmKate1 than TD-B3LYP/MM, although it always overestimates the excitation energies.

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A time-dependent DFT/molecular dynamics study of the proton-wire responsible for the red fluorescence in the LSSmKate2 protein

Cited by 11 publications

References 45 publications

Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein

Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein

New insights into the structure–spectrum relationship in S65T/H148D and E222Q/H148D green fluorescent protein mutants: a theoretical assessment

Characterizing the Structures, Spectra, and Energy Landscapes Involved in the Excited-State Proton Transfer Process of Red Fluorescent Protein LSSmKate1

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