1,721,215 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
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
Statistical Mechanics for Chemical Thermodynamics and Kinetics
No full textThis advanced textbook on theoretical chemistry includes all the fundamental concepts and theoretical approaches to be used when modelling a chemical system (i.e., a molecular system). Starting from the basic principles of quantum mechanics and specifically addressing the concepts and methods to treat quantum-classical systems, the authors derive from first principles the fundamental relations of statistical mechanics and then describe their application to chemical thermodynamics and kinetics. This book provides a rigorous description of the fundamental theoretical principles and derivations addressing sophisticated physical-mathematical issues of special interest in chemistry, thus bridging the gap between basic textbooks and up-to-date specialized publications in both quantum mechanics and statistical mechanics of molecular systems. This is a useful resource for all researchers and/or graduate students interested in the field of theoretical chemistry
Anthropologie et paléodemographie d'une classe socialement élevée de la Renaissance italienne: la série de momies de S. Domenico Maggiore à Naples (XVe-XVIe siècles)
No full textTheoretical-computational modelling of the electric field effects on protein unfolding thermodynamics
No full textIdentification of a pattern in protein structure based on statistical and energetical considerations
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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
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)
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