Literature DB >> 15471344

Conical intersection dynamics in solution: the chromophore of Green Fluorescent Protein.

A Toniolo1, S Olsen, L Manohar, T J Martínez.   

Abstract

We use ab initio results to reparameterize a multi-reference semiempirical method to reproduce the ground and excited state potential energy surfaces (PESs) for the chromophore of Green Fluorescent Protein (GFP). The validity of the new parameter set is tested, and the new method is combined with a quantum mechanical/molecular mechanical (QM/MM) treatment so that it can be applied in the solution phase. Solvent effects on the energetics of the relevant conical intersections are explored. We then combine this representation of the ground and excited state PESs with the full multiple spawning (FMS) nonadiabatic wavepacket dynamics method to simulate the photodynamics of the neutral GFP chromophore in both gas and solution phases. In these calculations, the PESs and their nonadiabatic couplings are evaluated simultaneously with the nuclear dynamics, ie. "on-the-fly". The effect of solvation is seen to be quite dramatic, resulting in an order of magnitude decrease in the excited state lifetime. We observe a correlated torsion about a double bond and its adjacent single bond in both gas and solution phases. This is discussed in the context of previous proposals about minimal volume isomerization mechanisms in protein environments.

Mesh:

Substances:

Year:  2004        PMID: 15471344     DOI: 10.1039/b401167h

Source DB:  PubMed          Journal:  Faraday Discuss        ISSN: 1359-6640            Impact factor:   4.008


  16 in total

1.  The gas-phase absorption spectrum of a neutral GFP model chromophore.

Authors:  L Lammich; M Axman Petersen; M Brøndsted Nielsen; L H Andersen
Journal:  Biophys J       Date:  2006-10-13       Impact factor: 4.033

2.  Ultrafast Electronic and Vibrational Dynamics of Stabilized A State Mutants of the Green Fluorescent Protein (GFP): Snipping the Proton Wire.

Authors:  Deborah Stoner-Ma; Andrew A Jaye; Kate L Ronayne; Jerome Nappa; Peter J Tonge; Stephen R Meech
Journal:  Chem Phys       Date:  2008-06-23       Impact factor: 2.348

3.  Coupling of pressure-induced structural shifts to spectral changes in a yellow fluorescent protein.

Authors:  Buz Barstow; Nozomi Ando; Chae Un Kim; Sol M Gruner
Journal:  Biophys J       Date:  2009-09-16       Impact factor: 4.033

4.  Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.

Authors:  Ganglong Cui; Weitao Yang
Journal:  J Chem Phys       Date:  2011-05-28       Impact factor: 3.488

5.  Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs).

Authors:  Chi-Yun Lin; Johan Both; Keunbong Do; Steven G Boxer
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-27       Impact factor: 11.205

6.  COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.

Authors:  Oliver Weingart; Artur Nenov; Piero Altoè; Ivan Rivalta; Javier Segarra-Martí; Irina Dokukina; Marco Garavelli
Journal:  J Mol Model       Date:  2018-09-03       Impact factor: 1.810

7.  Machine Learning for Electronically Excited States of Molecules.

Authors:  Julia Westermayr; Philipp Marquetand
Journal:  Chem Rev       Date:  2020-11-19       Impact factor: 60.622

8.  Computer modeling of the structure and spectra of fluorescent proteins.

Authors:  A V Nemukhin; B L Grigorenko; A P Savitsky
Journal:  Acta Naturae       Date:  2009-07       Impact factor: 1.845

9.  Hydrogen bonding controls excited-state decay of the photoactive yellow protein chromophore.

Authors:  Martial Boggio-Pasqua; Michael A Robb; Gerrit Groenhof
Journal:  J Am Chem Soc       Date:  2009-09-30       Impact factor: 15.419

10.  Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein.

Authors:  Colleen M Megley; Luisa A Dickson; Scott L Maddalo; Gabriel J Chandler; Marc Zimmer
Journal:  J Phys Chem B       Date:  2009-01-08       Impact factor: 2.991

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.