1,313 research outputs found
Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace
No full textWe address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412-425]. We discuss how modelling protocols can be improved in order to solve this problem
On the use of the quasi-Gaussian entropy theory in the study of simulated dilute solutions
No full textIn a recent paper [M. D'Alessandro, M. D'Abramo, G. Brancato, A. Di Nola, and A. Amadei, J. Phys. Chem. B 106, 11843 (2002)] we showed how to combine molecular dynamics simulations with the quasi-Gaussian entropy theory, in order to model the statistical mechanics and thermodynamics of ionic (water) solutions. In this paper we extend the method to treat nonspherical solutes, describe more thoroughly its theoretical basis and apply it to a set of more complex solute molecules in water (i.e., water, methane, ethane, methanol, and ethanol). Results show that this approach can really provide an excellent theoretical description of solute-solvent systems over a wide range of temperatures. (C) 2004 American Institute of Physics
Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions
No full textHere, we extend a recently introduced theoretical-computational procedure [M. D'Alessandro, M. Aschi, C. Mazzuca, A. Palleschi, and A. Amadei, J. Chem. Phys. 139, 114102 (2013)] to include quantum vibrational transitions in modelling electronic spectra of atomic molecular systems in condensed phase. The method is based on the combination of Molecular Dynamics simulations and quantum chemical calculations within the Perturbed Matrix Method approach. The main aim of the presented approach is to reproduce as much as possible the spectral line shape which results from a subtle combination of environmental and intrinsic (chromophore) mechanical-dynamical features. As a case study, we were able to model the low energy UV-vis transitions of pyrene in liquid acetonitrile in good agreement with the experimental data
Restauro e Ampliamento Banca d'Albania.
No full textM. Petreschi (capogruppo), N. Valentin, G. Amadei, M. Pascucci (gruppo di progettazione) importante edifico storico a Tirana, Albani
Essential dynamics: foundation and applications
No full textCollective coordinates, as obtained by a principal component analysis of atomic fluctuations, are commonly used to predict a low-dimensional subspace in which essential protein motion is expected to take place. The definition of such an essential subspace allows to characterize protein functional, and folding, motion, to provide insight into the (free) energy landscape, and to enhance conformational sampling in molecular dynamics simulations. Here, we provide an overview on the topic, giving particular attention to some methodological aspects, such as the problem of convergence, and mentioning possible new developments. (c) 2012 John Wiley & Sons, Ltd
The motet Aspice Domine from the collection Motecta liber secundus by Michelangelo Amadei (1615): critical edition and analysis
No full textopenIl secondo libro dei mottetti da una a cinque voci (Motecta singulis, binis, ternis, quaternis, quinisque vocibus [...] liber secundus) di Michelangelo Amadei (1615), maestro di Cappella della Cattedrale di Cortona, è una raccolta il cui unico esemplare oggi noto è mancante del secondo volume. Per questa ragione la raccolta non è stata mai pubblicata in edizione moderna. Dopo una breve introduzione sulla vita e delle opere dell’autore, il presente lavoro si concentra sull’analisi e sulla trascrizione del primo mottetto a voce sola del volume, Aspice Domine, l’unico pervenutoci completo
Modelling vibrational relaxation in complex molecular systems
No full textIn this paper we show how it is possible to treat the quantum vibrational relaxation of a chromophore, embedded in a complex atomic-molecular environment, via the explicit solution of the time-dependent Schroedinger equation once using a proper separation between quantum and semiclassical degrees of freedom. The rigorous theoretical framework derived, based on first principles and making use of well defined approximations/assumptions, is utilized to construct a general model for the kinetics of the vibrational relaxation as obtained by the direct evaluation of the density matrix for all the relevant quantum state transitions. Application to (deuterated) N-methylacetamide (the typical benchmark used as a model for the amino acids) shows that the obtained theoretical-computational approach captures the essential features of the experimental process, unveiling the basic relaxation mechanism involving several vibrational state transitions
A Theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra
No full textInfrared spectroscopy has long provided a means to estimate the secondary structure of proteins and peptides. In particular, the vibrational spectra of the amide I' band have been widely used for this purpose as the frequency positions of the amide I' bands are related to the presence of specific secondary structures. Here, we calculate the amide I' IR spectra of polylysine in aqueous solution in its three secondary structure states, i.e., alpha-helix, beta-sheet, and random coil, by means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical computational methodology based on the perturbed matrix method (PM/vI). The computed spectra show a good agreement with the experimental ones. Although our calculations confirm the importance of the excitonic coupling in reproducing important spectral features (e.g., the width of the absorption band), the frequency shift due to secondary-structure changes is also well reproduced without the inclusion of the excitonic coupling, pointing to a role played by the local environment. Concerning the beta-conformation spectrum, which is characterized by a double-peak amide I' band due to excitonic coupling, our results indicate that it does not correspond to a generic antiparallel beta-sheet (e.g., of the typical size present in native proteins) but is rather representative of extended beta-structures, which are common in beta-aggregates. Moreover, we also show that the solvent has a crucial role in the shape determination of the beta-conformation amide I' band and in particular in the disappearance of the high-frequency secondary peak in the case of small sheets (e.g., 6-stranded)
The unfolding effects on the protein hydration shell and partial molar volume: A computational study
No full textIn this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process
A theoretical model for the folding/unfolding thermodynamics of single-domain proteins, based on the quasi-Gaussian entropy theory
No full textThe quasi-Gaussian entropy (QGE) theory was used to formulate a statistical mechanical model describing the thermodynamics of the folding/unfolding process of single-domain proteins. The model was parametrized using experimental data obtained from differential scanning calorimetry (DSC) of a set of proteins. The results showed that the model is able to reproduce the experimental behavior in the usual temperature range, for all the analyzed proteins. Furthermore, a remarkable similarity of some parameters of the model, when normalized per residue and corresponding to well-defined physical properties, was found. Interestingly, at low temperature, the model provides cold denaturation features for all the proteins. Finally, a general description of the folding/unfolding process and stability, based on the physical view provided by the model, is discussed
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