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Roberto Improta

Publications and source records attributed to Roberto Improta.

At least 19 recordsLinked to original sources
PubMed2007

Does tetracycline bind helix 2 of prion? An integrated spectroscopical and computational study of the interaction between the antibiotic and alpha helix 2 human prion protein fragments.

We demonstrate here that tetracycline (TC) can strongly interact (KD' = 189 +/- 7 nM) with model peptides derived from the C-terminal globular domain of the prion protein, hPrP [173-195], and that interaction concerns residues within the C-terminal half of the helix 2, a short region previously indicated as endowed with ambivalent conformational behavior and implicated in PrP conversion to the beta-sheet-rich, infective scrapie variant. Data have been confirmed by binding studies with the N-terminal truncated 180-195 variant that displays a dissociation constant of 483 +/- 30 nM. Remarkably, TC does not influence the structure of the N-terminally fluoresceinated peptides that both show alpha-helical conformations. Docking calculations and molecular dynamics simulations suggest a direct, strong interaction of the antibiotic with exposed side chain functional groups of threonines 190-193 on the solvent-exposed surface of helix 2.

Amino Acid Sequence↗
PubMed2006

Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water.

The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck-Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/pi* excited state. This finding provides the first unifying explanation for the experimental trend of 5-fluorouracil excited-state lifetime in different solvents. The microscopic mechanisms underlying solvent effects on the excited-state behavior of nucleobases are discussed.

Absorption↗
PubMed2006

A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution.

An effective state specific (SS) model for the inclusion of solvent effects in time dependent density functional theory (TD-DFT) computations of excited electronic states has been developed and coded in the framework of the so-called polarizable continuum model (PCM). Different relaxation time regimes can be treated thus giving access to a number of different spectroscopic properties together with solvent relaxation energies of paramount relevance in electron transfer processes. SS and conventional linear response (LR) models have been compared for two benchmark systems (coumarin 153 and formaldehyde in different solvents) and in the limiting simple case of a dipolar solute embedded in a spherical cavity. The results point out the complementarity of LR and SS approaches and the advantages of the latter model especially for polar solvents. The favorable scaling properties of PCM-TD-DFT models in both SS and LR variants and their availability in effective quantum mechanical codes pave the route for the computation of reliable spectroscopic properties of large molecules of technological and/or biological interest in their natural environments.

Biophysics↗
PubMed2006

Femtosecond study on the isomerization dynamics of NK88. I. Ground-state dynamics after photoexcitation.

Recently, optimal control of a photoisomerization reaction in the liquid phase was demonstrated for the first time on the system 3,3(')-diethyl-2,2(')-thiacyanine (NK88). Additionally, the class of cyanines to which the molecule NK88 belongs draws a lot of attention in different recent theoretical publications. Therefore, a better understanding of the molecular dynamics of this molecular system is of special interest. Experiments using the femtosecond pump-supercontinuum probe technique with an excitation wavelength of 400 nm and a spectral range from 370 to 620 nm for the probe beam have been performed. In order to analyze the dynamics properly the time window has been chosen to comprise the characteristic times of the contributing processes, additionally we have employed two solvents, methanol and ethylene glycol, and have conducted anisotropy measurements. The spectroscopic data have been assigned to different molecular states with the help of density functional theory and second-order Moller-Plesset perturbation theory calculations. The analysis of the data has revealed in the most likely model that three different isomers exist with different lifetimes. On the basis of experimental and theoretical data, a conclusive scheme of the isomerization reaction is presented.

Anisotropy↗
PubMed2006

Femtosecond study on the isomerization dynamics of NK88. II. Excited-state dynamics.

The molecule 3,3(')-diethyl-2,2(')-thiacyanine isomerizes after irradiation with light of the proper wavelength. After excitation, it undergoes a transition, in which one or more conical intersections are involved, back to the ground state to form different product photoisomers. The dynamics before and directly after the transition back to the ground state is investigated by transient absorption spectroscopy in a wavelength region of 360-950 nm, as well as by fluorescence upconversion. It is shown that the excited-state dynamics are governed by two time scales: a short one with a decay time of less than 2 ps and a long one with about 9 ps. A thorough comparison of the experimental results with those of configuration interaction singles and time-dependent density functional theory calculations suggests that these dynamics are related to two competing pathways differing in the molecular twisting on the excited surface after photoexcitation. From the experimental point of view this picture arises taking into account the time scales for ground-state bleach, excited-state absorption, stimulated emission, fluorescence, and assumed hot ground-state absorption both in the solvent methanol and ethylene glycol.

Absorption↗
PubMed2006

Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water.

The excited-state dynamics of 5-fluorouracil in acetonitrile has been investigated by femtosecond fluorescence upconversion spectroscopy in combination with quantum chemistry TD-DFT calculations ((PCM/TD-PBE0). Experimentally, it was found that when going from water to acetonitrile solution the fluorescence decay of 5FU becomes much faster. The calculations show that this is related to the opening of an additional decay channel in acetonitrile solution since the dark n/pi* excited state becomes near degenerate with the bright pi/pi* state, forming a conical intersection close to the Franck-Condon region. In both solvents, a S1-S0 conical intersection, governed by the out-of-plane motion of the fluorine atom, is active, allowing an ultrafast internal conversion to the ground state.

Acetonitriles↗
PubMed2006

Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pK(a) calculations and molecular dynamics simulations.

A thorough study of the acid-base behavior of the four histidines and the other titratable residues of the structured domain of human prion protein (125-228) is presented. By using multi-tautomer electrostatic calculations, average titration curves have been built for all titratable residues, using the whole bundles of NMR structures determined at pH 4.5 and 7.0. According to our results, (1) only histidine residues are likely to be involved in the first steps of the pH-driven conformational transition of prion protein; (2) the pK(a)'s of His140 and His177 are approximately 7.0, whereas those of His155 and His187 are < 5.5. 10-ns long molecular dynamics simulations have been performed on five different models, corresponding to the most significant combinations of histidine protonation states. A critical comparison between the available NMR structures and our computational results (1) confirms that His155 and His187 are the residues whose protonation is involved in the conformational rearrangement of huPrP in mildly acidic condition, and (2) shows how their protonation leads to the destructuration of the C-terminal part of HB and to the loss of the last turn of HA that represent the crucial microscopic steps of the rearrangement.

Amino Acid Sequence↗
PubMed2006

Dissociative electron transfer in donor-peptide-acceptor systems: results for kinetic parameters from a density functional/polarizable continuum model.

The main structural and electronic factors playing a role in intramolecular dissociative electron transfer of a simple donor-peptide-acceptor (D-peptide-A) model have been investigated by an integrated computational protocol based on the density functional theory, its time-dependent extension, and the polarizable continuum model. Our results allow us to elucidate the electronic states involved in the process and how they are perturbed by the orientation of the donor and the acceptor with respect to the peptide chain and by the presence of the solvent. We also report a semiquantitative estimation of the rate constant governing electron transfer obtained by a direct quantum mechanical evaluation of all the terms entering the kinetic expressions based on the Marcus theory and its extensions.

Electron Transport↗
PubMed2006

A polarizable continuum approach for the study of heterogeneous dielectric environments.

We present a computational method, exploiting some features of the polarizable continuum model (PCM) to describe heterogeneous media; it belongs to the family of electrostatic embedding mixed methods, such as the more common quantum-mechanical (QM)/molecular mechanics approaches, with the electrostatic long range effects accounted for by a polarized continuum instead of atomic point charges. Provided effective dielectric constants are determined for the various parts of the system, the method is much faster than its atomistic counterpart, and allows for high-level QM calculations on the fragment of interest, using all the highly efficient computational tools developed for homogeneous PCM. Two case studies (the calculation of the pKa of solvent exposed acidic residues in a model protein, and the calculation of the electron spin resonance spectrum of a typical spin probe partially embedded in a membrane) are analyzed in some detail, to illustrate the application of the method to complex systems.

Algorithms↗
PubMed2006

Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives.

The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.

Models, Molecular↗
PubMed2005

Understanding electron transfer across negatively-charged Aib oligopeptides.

The physicochemical effects modulating the conformational behavior and the rate of intramolecular dissociative electron transfer in phthalimide-Aibn-peroxide peptides (n = 0-3) have been studied by an integrated density functional/continuum solvent model. We found that three different orientations of the phthalimide ring are possible, labeled Phihel, PhiC7, and PhipII. In the condensed phase, they are very close in energy when the system is neutral and short. When the peptide chain length increases and the system is negatively charged, Phihel becomes instead the most stable conformer. Our calculations confirm that the 3(10)-helix is the most stable secondary structure for the peptide bridge. However, upon charge injection in the phthalimide end of the phthalimide-Aib3-peroxide, the peptide bridge can adopt an alpha-helix conformation as well. The study of the dependence of the frontier orbitals on the length and on the conformation of the peptide bridge (in agreement with experimental indications) suggests that for n = 3 the process could be influenced by a 3(10) --> alpha-helix conformational transition of the peptide chain.

Computer Simulation↗
PubMed2005

Building cavities in a fluid of spherical or rod-like particles: a contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model.

A general formalism for the calculation of cavitation energies in the framework of the scaled particle theory has been implemented in the Polarizable Continuum Model (PCM), contributing to the nonelectrostatic part of the molecular free energy in solution. The solute cavity and the solvent molecules are described as hard spherocylinders, whose radius and length are related to the actual molecular shape, while the solvent density is estimated from experimental data, or from the solvent molecular volume, suitably scaled. The present model can describe isotropic solutions of spherical and rod-like molecules in spherical or rod-like solvents, and also anisotropic solutions in which the solvent molecules are oriented in space: in this case, the cavitation energy also depends on the relative orientation of solute and solvent molecules. Test calculations have been performed on simple systems to evaluate the accuracy of the present approach, in comparison with other methods and with the available experimental estimates of the cavitation energy, giving encouraging results.

Journal Article↗
PubMed2004

Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TD-DFT quantum mechanical study.

Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.

Gases↗
PubMed2004

Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: effect of protonation of histidine residues.

The role of acidic pH in the conversion of human prion protein to the pathogenic isoform is investigated by means of molecular dynamics simulations, focusing the attention on the effect of protonation of histidine residues on the conformational behavior of human PrPC globular domain. Our simulations reveal a significant loss of alpha-helix content under mildly acidic conditions, due to destructuration of the C-terminal part of HB (thus suggesting a possible involvement of HB into the conformational transition leading to the pathogenic isoform) and a transient lengthening of the native beta-sheet. Protonation of His-187 and His-155 seems to be crucial for the onset of the conformational rearrangement. This finding can be related to the existence of a pathogenic mutation, H187R, which is associated with GSS syndrome. Finally, the relevance of our results for the location of a Cu2+-binding pocket in the C-terminal part of the prion is discussed.

Computer Simulation↗
PubMed2004

Assessing the reliability of density functional methods in the conformational study of polypeptides: the treatment of intraresidue nonbonding interactions.

The role of intraresidue interactions in determining the conformational behavior of polypeptides is analyzed by means of density functional and post-Hartree-Fock computations on the alanine dipeptide analog and other model compounds. Our computations show that the accuracy of current density functionals is sufficient for H-bond, electrostatic, inductive, and short-range repulsive interactions, whereas medium-range attractions between electron-rich atoms and/or bonds are underestimated. This leads, in turn, to an underestimation of the stability of helical structures w.r.t. extended or folded conformers involving H-bonds. Those results could pave the route for devising local ad hoc corrections able to significantly improve structural and dynamic predictions for polypeptides issuing from DFT computations.

Alanine↗