The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation

Computational approaches have to date failed to fully capture the large (about 0.4 eV) excitation energy tuning displayed by the nearly identical anionic chromophore in different green fluorescent protein (GFP) variants. Here, we present a thorough comparative study of a set of proteins in this sub-family, including the most red- (phiYFP) and blue-shifted (mTFP0.7) ones. We employ a classical polarisable embedding through induced dipoles and combine it with time-dependent density functional theory and multireference perturbation theory in order to capture both state-specific induction contributions and the coupling of the polarisation of the protein to the chromophore transition density. The obtained results show that only upon inclusion of both these two effects generated by the mutual polarisation between the chromophore and the protein can the full spectral tuning be replicated. We finally discuss how this mutual polarisation affects the correlation between excitation energies, dipole moment variation, and molecular electrostatic field

Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation

We present the implementation of a fully coupled polarizable QM/MM/continuum model based on the AMOEBA polarizable force field and the domain decomposition implementation of the conductor-like screening model. Energies, response properties, and analytical gradients with respect to both QM and MM nuclear positions are available, and a generic, atomistic cavity can be employed. The model is linear scaling in memory requirements and computational cost with respect to the number of classical atoms and is therefore suited to model large, complex systems. Using three variants of the green-fluorescent protein, we investigate the overall computational cost of such calculations and the effect of the continuum model on the convergence of the computed properties with respect to the size of the embedding. We also demonstrate the fundamental role of polarization effects by comparing polarizable and nonpolarizable embeddings to fully QM ones

Quantum many-body dynamics in a Lagrangian frame: II. Geometric formulation of time-dependent density functional theory

We formulate equations of time-dependent density functional theory (TDDFT) in the co-moving Lagrangian reference frame. The main advantage of the Lagrangian description of many-body dynamics is that in the co-moving frame the current density vanishes, while the density of particles becomes independent of time. Therefore a co-moving observer will see the picture which is very similar to that seen in the equilibrium system from the laboratory frame. It is shown that the most natural set of basic variables in TDDFT includes the Lagrangian coordinate, $\bm\xi$, a symmetric deformation tensor $g_{\mu\nu}$, and a skew-symmetric vorticity tensor, $F_{\mu\nu}$. These three quantities, respectively, describe the translation, deformation, and the rotation of an infinitesimal fluid element. Reformulation of TDDFT in terms of new basic variables resolves the problem of nonlocality and thus allows to regularly derive a local nonadiabatic approximation for exchange correlation (xc) potential. Stationarity of the density in the co-moving frame makes the derivation to a large extent similar to the derivation of the standard static local density approximation. We present a few explicit examples of nonlinear nonadiabatic xc functionals in a form convenient for practical applications.Comment: RevTeX4, 18 pages, Corrected final version. The first part of this work is cond-mat/040835

Asymptotically exact dispersion relations for collective modes in a confined charged Fermi liquid

Using general local conservations laws we derive dispersion relations for edge modes in a slab of electron liquid confined by a symmetric potential. The dispersion relations are exact up to $\lambda^{2} q^{2}$, where $q$ is a wave vector and $\lambda$ is an effective screening length. For a harmonic external potential the dispersion relations are expressed in terms of the {\em exact} static pressure and dynamic shear modulus of a homogeneous liquid with the density taken at the slab core. We also derive a simple expression for the frequency shift of the dipole (Kohn) modes in nearly parabolic quantum dots in a magnetic field.Comment: RevTeX4, 4 pages. Revised version with new results on quantum qots and wires. Published in Phys.Rev.

Tolerance to coxibs in patients with intolerance to non-steroidal anti-inflammatory drugs (NSAIDs): a systematic structured review of the literature

Adverse events triggered by non-steroidal anti-inflammatory drugs (NSAIDs) are among the most common drug-related intolerance reactions in medicine; they are possibly related to inhibition of cyclooxygenase-1. Coxibs, preferentially inhibiting cyclooxygenase-2, may therefore represent safe alternatives in patients with NSAID intolerance. We reviewed the literature in a systematic and structured manner to identify and evaluate studies on the tolerance of coxibs in patients with NSAID intolerance. We searched MEDLINE (1966–2006), the COCHRANE LIBRARY (4th Issue 2006) and EMBASE (1966–2006) up to December 9, 2006, and analysed all publications included using a predefined evaluation sheet. Symptoms and severity of adverse events to coxibs were analysed based on all articles comprising such information. Subsequently, the probability for adverse events triggered by coxibs was determined on analyses of double-blind prospective trials only. Among 3,304 patients with NSAID intolerance, 119 adverse events occurred under coxib medication. All adverse events, except two, have been allergic/urticarial in nature; none was lethal, but two were graded as life-threatening (grade 4). The two non-allergic adverse events were described as a grade 1 upper respiratory tract haemorrhage, and a grade 1 gastrointestinal symptom, respectively. In 13 double-blind prospective studies comprising a total of 591 patients with NSAID intolerance, only 13 adverse reactions to coxib provocations were observed. The triggering coxibs were rofecoxib (2/286), celecoxib (6/208), etoricoxib (4/56), and valdecoxib (1/41). This review documents the good tolerability of coxibs in patients with NSAID intolerance, for whom access to this class of drugs for short-term treatment of pain and inflammation is advantageous

A Novel Coumarin Fluorescent Sensor to Probe Polarity Around Biomolecules

Polarity-sensitive (solvatochromic) probes are useful tools to investigate on subtle biochemical processes which occur at membrane and subcellular level (e.g., the uptake and cell targeting of a functionalized nanoparticle). In this paper, we describe the development of a new solvatochromic biosensor. The probe is structured as a "push-pull" system, bearing an electron-rich naphtyl ring and an electron poor benzothiazene group, conjugated to a central coumarin core. These features confer interesting spectroscopic and solvatochromic properties to the fluorophore. The dye was derivatized with a versatile sulfonyl chloride functional group. We also demonstrated that solvatochromic properties are nearly maintained when the fluorophore is covalently linked to proteins usually employed for nanoparticle coatings (bovine serum albumin or streptavidin). Finally, we proved the efficiency of our polarity-sensitive probe by obtaining a statistically significant difference between the fluorescence signals of fluorophore-labeled streptavidin before and after addition of BSA-labeled biotin

Main photophysical properties of oxyblepharismin

Oxyblepharismin is the photo-oxidized form of blepharismin, the chromophore responsible for the photophobic response of heterotrich ciliate Blepharisma joponicum, and represents a nice model for the study of phototransduction. In this work, we focused on the photophysical characterization of OxyBP, in view of highlighting the main features related to excitation and emission. By a combined experimental and computational approach we identified the main features of absorption and fluorescence emission of the molecule in solvents of different properties, identifying the nature of transitions as well as the possible heterogeneity at ground/excited state. The thorough photophysical characterization of OxyBP is meant to provide the starting point for the elucidation of the photo-transduction pathway in vivo