Literature DB >> 27571168

On the Driving Force of the Excited-State Proton Shuttle in the Green Fluorescent Protein: A Time-Dependent Density Functional Theory (TD-DFT) Study of the Intrinsic Reaction Path.

Alessio Petrone1, Paola Cimino2, Greta Donati1, Hrant P Hratchian3, Michael J Frisch4, Nadia Rega1,5.   

Abstract

We simulated the intrinsic reaction path of the Green Fluorescent Protein (GFP) proton shuttle in both the ground state (S0) and first singlet excited state (S1), accounting for the main energetic and steric effects of the protein in a convenient model including the chromophore, the crystallographic water, and the residues directly involved in the proton transfer event. We adopted density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels to define the potential energy surfaces of the two electronic states, and we compared results obtained by the Damped Velocity Verlet and the Hessian-based Predictor-Corrector integrators of the intrinsic reaction coordinate, which gave a comparable and consistent picture of the mechanism. We show that, at S1, the GFP proton transfer becomes favored, with respect to S0, as suggested by the experimental evidence. As an important finding, this change is strictly related to the rearrangement of the hydrogen bond network composing the reaction path, which, in S1, relaxes to a tighter and planar configuration, as a consequence of the photoinduced relaxation in the GFP chromophore structure, thus prompting more effectively for the proton shuttle. Therefore, we give an unprecedented direct proof of the key role played by the photoinduced structural relaxation of the GFP on the chromophore photoacidity, validating, in particular, the hypothesis of Fang and co-workers [Nature 2009, 462, 200].

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Year:  2016        PMID: 27571168     DOI: 10.1021/acs.jctc.6b00402

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  6 in total

1.  Exploring free energy profile of petroleum thermal cracking mechanisms.

Authors:  Feng Wang; Peng Tao
Journal:  J Mol Model       Date:  2019-12-19       Impact factor: 1.810

2.  Nuclear quantum effect and H/D isotope effect on Cl· + (H2O) n → HCl + OH·(H2O) n-1 (n = 1-3) reactions.

Authors:  Keita Sugiura; Masanori Tachikawa; Taro Udagawa
Journal:  RSC Adv       Date:  2018-05-10       Impact factor: 4.036

3.  The mechanism of a green fluorescent protein proton shuttle unveiled in the time-resolved frequency domain by excited state ab initio dynamics.

Authors:  Greta Donati; Alessio Petrone; Pasquale Caruso; Nadia Rega
Journal:  Chem Sci       Date:  2018-01-02       Impact factor: 9.825

4.  Simulation of self-heating process on the nanoscale: a multiscale approach for molecular models of nanocomposite materials.

Authors:  Greta Donati; Antonio De Nicola; Gianmarco Munaò; Maksym Byshkin; Luigi Vertuccio; Liberata Guadagno; Ronan Le Goff; Giuseppe Milano
Journal:  Nanoscale Adv       Date:  2020-05-18

5.  A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics.

Authors:  Federico Coppola; Fulvio Perrella; Alessio Petrone; Greta Donati; Nadia Rega
Journal:  Front Mol Biosci       Date:  2020-10-27

6.  Modeling Excited-State Proton Transfer to Solvent: A Dynamics Study of a Super Photoacid with a Hybrid Implicit/Explicit Solvent Model.

Authors:  Umberto Raucci; Maria Gabriella Chiariello; Nadia Rega
Journal:  J Chem Theory Comput       Date:  2020-10-28       Impact factor: 6.006

  6 in total

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