The three-dimensional solution structure of a nonspecific lipid transfer protein extracted from maize seeds determined by ' H NMR spectroscopy is described. This cationic protein consists of 93 amino acid residues. Its structure was determined from 1,091 NOE-derived distance restraints, including 929 interresidue connectivities and 197 dihedral restraints (4,$, x,) derived from NOES and 3J coupling constants. The global fold involving four helical fragments connected by three loops and a C-terminal tail without regular secondary structures is stabilized by four disulfide bridges. The most striking feature of this structure is the existence of an internal hydrophobic cavity running through the whole molecule. The global fold of this protein, very similar to that of a previously described lipid transfer protein extracted from wheat seeds (Gincel E et al., 1994, Eur J Biochem 226:413-422) constitutes a new architecture for a-class proteins. 'H NMR and fluorescence studies show that this protein forms well-defined complexes in aqueous solution with lysophosphatidylcholine. Dissociation constants, K d , of 1.9 f 0.6 x M and M were obtained with lyso-C,, and -Clz, respectively. A structure model for a lipidprotein complex is proposed in which the aliphatic chain of the phospholipid is inserted in the internal cavity and the polar head interacts with the charged side chains located at one end of this cavity. Our model for the lipidprotein complex is qualitatively very similar to the recently published crystal structure (Shin DH et al., 1995, Structure 3:189-199).

The nucleophilic reactivities (N, s ) of peroxide anions (generated from aromatic and aliphatic peroxy acids or alkyl hydroperoxides) were investigated by following the kinetics of their reactions with a series of benzhydrylium ions (Ar CH ) in alkaline aqueous solutions at 20 °C. The second-order rate constants revealed that deprotonated peroxy acids (RCO ), although they are the considerably weaker Brønsted bases, react much faster than anions of aliphatic hydroperoxides (ROO ). Substitution of the rate constants of their reactions with benzhydrylium ions into the linear free energy relationship lg k=s (N+E) furnished nucleophilicity parameters (N, s ) of peroxide anions, which were successfully applied to predict the rates of Weitz-Scheffer epoxidations. DFT calculations with inclusion of solvent effects by means of the Integral Equation Formalism version of the Polarizable Continuum Model were performed to rationalize the observed reactivities.

The three-dimensional solution structure of maize nonspecific lipid transfer protein (nsLTP) obtained by nuclear magnetic resonance (NMR) is compared to the X-ray structure. Although both structures are very similar, some local structural differences are observed in the first and the fourth helices and in several side-chain conformations. These discrepancies arise partly from intermolecular contacts in the crystal lattice. The main characteristic of nsLTP structures is the presence of an internal hydrophobic cavity whose volume was found to vary from 237 to 513 A3 without major variations in the 15 solution structures. Comparison of crystal and NMR structures shows the existence of another small hollow at the periphery of the protein containing a water molecule in the X-ray structure, which could play an important structural role. A model of the complexed form of maize nsLTP by alpha-lysopalmitoylphosphatidylcholine was built by docking the lipid inside the protein cavity of the NMR structure. The main structural feature is a hydrogen bond found also in the X-ray structure of the complex maize nsLTP/palmitate between the hydroxyl of Tyr81 and the carbonyl of the lipid. Comparison of 12 primary sequences of nsLTPs emphasizes that all residues delineating the cavities calculated on solution and X-ray structures are conserved, which suggests that this large cavity is a common feature of all compared plant nsLTPs. Furthermore several conserved basic residues seem to be involved in the stabilization of the protein architecture.

The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported. These functionals have been chosen among those belonging to three different families of hybrid functionals, namely global, range separated, and double hybrids. Other computational parameters have also been considered, such as basis set and solvent effects. The selected parameters, namely bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) allow a mechanistic evaluation of the antioxidant activities of free radical scavengers. Our results show that all the selected functionals provide a coherent picture of these properties, predicting the same order of BDEs and PDEs. However, with respect to the reference values, the errors found at CBS-Q3 level significantly vary with the functional. Although it is difficult to evidence a global trend from the reported data, it clearly appears that LC-ωPBE, M05-2X, and M06-2X are the most suitable approaches for the considered properties, giving the lowest cumulative mean absolute errors. These methods are therefore suggested for an accurate and fast evaluation of energetic parameters related to an antioxidant activity via free radical scavenging.

Aiming at developing an affordable and easily implementable computational protocol for routine prediction of spectral properties of rigid molecular dyes, density functional theory, and time-dependent density functional theory were used in conjunction with a vibronic coupling scheme for band shape estimate. To predict the perceived color of molecules in solution, a model has been setup linking the UV-vis spectra predicted at ab initio level to the L*a*b* colorimetric parameters. The results show that a mixed protocol, implying the use of a global hybrid functional for the prediction of adiabatic energy differences and a range separated hybrid for the prediction of potential energy curvature, allows perceived colors to be quantitatively predicted, as demonstrated by the comparison of L*a*b* colorimetric parameters obtained from computed and experimental spectra. © 2017 Wiley Periodicals, Inc.

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The combination of a Monte Carlo (MC) sampling of the configurational space with time dependent‐density functional theory (TD‐DFT) to estimate vertical excitations energies has been applied to compute the absorption spectra of a family of merocyanine dyes in both their monomeric and dimeric forms. These results have been compared to those obtained using a static DFT/TD‐DFT approach as well as to the available experimental spectra. Though suffering of the limitations related to the use of DFT and TD‐DFT for this type of systems, our data clearly show that the classical MC sampling provides a suitable alternative to classical molecular dynamics to explore the structural flexibility of these donor‐acceptor (D‐π‐A) chromophores enabling a realistic description of the potential energy surface of both their monomers and aggregates (here dimers) and thus of their spectra. Overall, the combination of MC sampling with quantum mechanics (TD‐DFT) calculations, carried out in implicit dioxane solvent on random snapshots, provides a workable compromise to solve the combined challenge of accuracy and time‐consuming problem not only for merocyanines momers, but also for their dimers, up to now less investigated. Indeed, the simulated absorption spectra fairly agree with the experimental ones, suggesting the general reliability of the method.

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