124 research outputs found

    Turismo acessível para todos, um paradigma emergente e um desafio para a oferta turística. O caso dos espaços museológicos e empreendimentos turísticos de Cascais.

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    Reflexão sobre o turismo acessível para todos, como modelo que se revela cada vez mais essencial para todo o sistema turístico, que se afirma não só pela sua relevância social, cívica e demográfica mas também pelas potencialidades económicas associadas. Todavia, o turismo acessível constitui um desafio de adaptação para a oferta turística instalada há vários anos, em destinos turísticos mais antigos, como é o caso de Cascais.Reflection on accessible tourism for all, as an increasingly essential model for the touristic system, that claims not only for its social, civic and demographic significance, but also for the economic potential associated. However, the accessible tourism is an adaptation challenge for the elderly tourism supply, at long-established tourism destinations, such as Cascais

    History of allostery.

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    <p>History of allostery.</p

    Identifying Key Residues for Protein Allostery through Rigid Residue Scan

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    Allostery is a ubiquitous process for protein regulatory activity in which a binding event can change a protein’s function carried out at a distal site. Despite intensive theoretical and experimental investigation of protein allostery in the past five decades, effective methods have yet to be developed that can systematically identify key residues involved in allosteric mechanisms. In this study, we propose the rigid residue scan as a systematic approach to identify important allosteric residues. The third PDZ domain (PDZ3) in the postsynaptic density 95 protein (PSD-95) is used as a model system, and each amino acid residue is treated as a single rigid body during independent molecular dynamics simulations. Various indices based on cross-correlation matrices are used, which allow for two groups of residues with different functions to be identified. The first group is proposed as “switches” that are needed to “turn on” the binding effect of protein allostery. The second group is proposed as “wire residues” that are needed to propagate energy or information from the binding site to distal locations within the same protein. Among the nine residues suggested as important for PDZ3 intramolecular communication in this study, eight have been reported as critical for allostery in PDZ3. Therefore, the rigid residue scan approach is demonstrated to be an effective method for systemically identifying key residues in protein intramolecular communication and allosteric mechanisms

    2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes

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    Cytochrome P450 (CYP) 3A4, 2D6, 2C9, 2C19, and 1A2 are the most important drug-metabolizing enzymes in the human liver. Knowledge of which parts of a drug molecule are subject to metabolic reactions catalyzed by these enzymes is crucial for rational drug design to mitigate ADME/toxicity issues. SMARTCyp, a recently developed 2D ligand structure-based method, is able to predict site-specific metabolic reactivity of CYP3A4 and CYP2D6 substrates with an accuracy that rivals the best and more computationally demanding 3D structure-based methods. In this article, the SMARTCyp approach was extended to predict the metabolic hotspots for CYP2C9, CYP2C19, and CYP1A2 substrates. This was accomplished by taking into account the impact of a key substrate-receptor recognition feature of each enzyme as a correction term to the SMARTCyp reactivity. The corrected reactivity was then used to rank order the likely sites of CYP-mediated metabolic reactions. For 60 CYP1A2 substrates, the observed major sites of CYP1A2 catalyzed metabolic reactions were among the top-ranked 1, 2, and 3 positions in 67%, 80%, and 83% of the cases, respectively. The results were similar to those obtained by MetaSite and the reactivity + docking approach. For 70 CYP2C9 substrates, the observed sites of CYP2C9 metabolism were among the top-ranked 1, 2, and 3 positions in 66%, 86%, and 87% of the cases, respectively. These results were better than the corresponding results of StarDrop version 5.0, which were 61%, 73%, and 77%, respectively. For 36 compounds metabolized by CYP2C19, the observed sites of metabolism were found to be among the top-ranked 1, 2, and 3 sites in 78%, 89%, and 94% of the cases, respectively. The computational procedure was implemented as an extension to the program SMARTCyp 2.0. With the extension, the program can now predict the site of metabolism for all five major drug-metabolizing enzymes with an accuracy similar to or better than that achieved by the best 3D structure-based methods. Both the Java source code and the binary executable of the program are freely available to interested users

    Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

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    <div><p>Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2) in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier’s principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.</p></div

    Key residues recognized based on protein entropic response to rigid body perturbation.

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    <p>Key residues recognized based on protein entropic response to rigid body perturbation.</p

    Distributions of density of states for unperturbed unbound and bound states.

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    <p>Distributions of density of states for unperturbed unbound and bound states.</p

    Distribution of unperturbed states projected onto a 2D surface using two PC1 modes.

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    <p>Only one set of 30 ns trajectories are used for sake of consistency with RRS simulations.</p

    Heat maps of individual residue entropic contribution under rigid residue perturbation for unbound (left) and bound (right) states.

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    <p>The entropic contribution from each residue in unperturbed simulations (with index as 0 in both plots) is set as reference.</p

    Unsigned average dot products of five lowest frequency quasi-harmonic modes (PC1 through 5) between each 30 ns trajectory and whole 210 ns trajectory.

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    <p>Unsigned average dot products of five lowest frequency quasi-harmonic modes (PC1 through 5) between each 30 ns trajectory and whole 210 ns trajectory.</p
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