Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: A density functional study

Nifosı̀, Riccardo; Amat, Pietro; Tozzini, Valentina

doi:10.1002/jcc.20764

Cited by 46 publications

(63 citation statements)

References 68 publications

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“…Compared with the ab initio and the semiempirical methods, the TDDFT turns out to be a good compromise between accuracy, predictive power, and computational cost. This circumstance allowed systematic studies on the whole series of the FP chromophores 33 in different protonation states, revealing an inverse proportionality relationship between the excitation energy and the charge displacement upon excitation ( Figure 2). This roughly explains the variety of colors of the FPs: red-shifted chromophores are obtained from the green one by the progressive extensions of the electronic delocalization, while blue-shifted chromophores were obtained by artificially mutating the central tyrosine residue to effectively shorten the electron delocalization.…”

Section: Applicationsmentioning

confidence: 98%

Multiscale Modeling of Proteins

2009

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The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was recently confirmed by the assignment of two of the Nobel prizes in 2008: in chemistry for the discovery of GFP and in medicine for the discovery of HIV. Accordingly, these proteins were studied with essentially all of the available modeling techniques, making them ideal examples for studying the details of multiscale approaches in protein modeling.

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Section: Applicationsmentioning

confidence: 98%

Multiscale Modeling of Proteins

2009

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“…As already mentioned, chromophore structure is the principal determinant of the excitation energy. In term of the computed gas-phase vertical excitation energies, the most [71]. In the third column, pink (cyan) regions indicate charge depletion (increase) upon HOMO !…”

Section: Chromophores Of Fps: Computational Studiesmentioning

confidence: 98%

“…TD-DFT low computational cost makes it an affordable method for a systematic and homogeneous investigation of the large set of chromophore structures [71]. Using this technique, the trends among the various FPs are reproduced.…”

Section: Chromophores Of Fps: Computational Studiesmentioning

confidence: 99%

“…Attempts to include solvent effects were performed using implicit solvent methods [71] or by considering solvent-solute electronic interactions using liquid-structure simulations [72,77]. Despite being relatively small molecules (though not so small for the most sophisticated quantum chemistry methods), there are subtle issues to be considered when trying to reproduce FPs chromophore optical spectra [66].…”

Section: Chromophores Of Fps: Computational Studiesmentioning

confidence: 99%

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One-Photon and Two-Photon Excitation of Fluorescent Proteins

Nifosı̀

Tozzini

2011

Springer Series on Fluorescence

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Fluorescent proteins (FPs) offer a wide palette of colors for imaging applications. One purpose of this chapter is to review the variety of FP spectral properties, with a focus on their structural basis. Fluorescence in FPs originates from the autocatalytically formed chromophore. Several studies exist on synthetic chromophore analogs in gas phase and in solution. Together with the X-ray structures of many FPs, these studies help to understand how excitation and emission energies are tuned by chromophore structure, protonation state, and interactions with the surrounding environment, either solvent molecules or amino acids residues. The increasing use of FPs in two-photon microscopy also prompted detailed investigations of their two-photon excitation properties. The comparison with one-photon excitation reveals nontrivial features, which are relevant both for their implications in understanding multiphoton properties of fluorophores and for application purposes.

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“…Many theoretical studies on the absorption spectra of isolated FP chromophores have been performed in gas phase and in solution with semi-empirical methods (Voityuk et al,1997;Weber et al, 1999), a multireference approach (Martin et al, 2004;Bravaya et al, 2008;Epifanovsky et al, 2009) and at the ab initio level of theory (Nifosì et al, 2007). The influence of the protein environment is often neglected although it can induce drastic modifications of the spectra.…”

Section: Introductionmentioning

confidence: 99%

Effect of the Enhanced Cyan Fluorescent Protein framework on the UV/visible absorption spectra of some chromophores

Laurent

Assfeld

2010

Interdiscip Sci Comput Life Sci

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Mutation on Enhanced Cyan Fluorescent Protein (ECFP) has been investigated by means of a hybrid quantum mechanics and molecular mechanics (QM/MM) approach. A simple model, which represents the electronic response of the surroundings (ERS) by a polarizable continuum characterized by the relative dielectric constant extrapolated to infinite frequency, is used. For all mutations, this method (QM/MM+ERS) reproduces the experimental trend (shift) and is in correct agreement with experimental maximum absorption wavelength (between -10 and +10 nm). The effect of the ECFP on the optical properties is analyzed and decomposed into three major contributions (geometric deformation, electrostatic polarization and electronic response). It is shown that these three contributions have similar magnitude and one cannot neglect one with respect to the others. In addition, these contributions differ greatly from one chromophore to another showing that the same protein framework acts differently on different chromophores.

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Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: A density functional study

Cited by 46 publications

References 68 publications

Multiscale Modeling of Proteins

Multiscale Modeling of Proteins

One-Photon and Two-Photon Excitation of Fluorescent Proteins

Effect of the Enhanced Cyan Fluorescent Protein framework on the UV/visible absorption spectra of some chromophores

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