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Katz A.,Computational Chemistry and Biology Group | Saenz-Mendez P.,Computational Chemistry and Biology Group | Saenz-Mendez P.,Physical Organic Chemistry and Bioprocesses Group | Cousido-Siah A.,Computational Chemistry and Biology Group | And 2 more authors.
Biophysical Reviews and Letters | Year: 2012

Protein tyrosine phosphorylation is a post-translational modification mechanism, crucial for the regulation of nearly all aspects of cell life. This dynamic, reversible process is regulated by the balanced opposing activity of protein tyrosine kinases and protein tyrosine phosphatases. In particular, the protein tyrosine phosphatase 1B (PTP1B) is implicated in the regulation of the insulin-receptor activity, leptin-stimulated signal transduction pathways and other clinically relevant metabolic routes, and it has been found overexpressed or overregulated in human breasts, colon and ovary cancers. The WPD loop of the enzyme presents an inherent flexibility, and it plays a fundamental role in the enzymatic catalysis, turning it into a potential target in the design of new efficient PTP1B inhibitors. In order to determine the interactions that control the spatial conformation adopted by the WPD loop, complexes between the enzyme and halide ions (Br- and I- in particular) were crystallized and their crystallographic structure determined, and the collective movements of the aforementioned complexes were studied through Molecular Dynamics (MD) simulations. Both studies yielded concordant results, indicating the existence of a relationship between the identity of the ion present in the complex and the strength of the interactions it establishes with the surrounding protein residues. © 2012 World Scientific Publishing Company.

Bermudez E.,Computational Chemistry and Biology Group | Ventura O.N.,Computational Chemistry and Biology Group | Mendez P.S.,Computational Chemistry and Biology Group | Mendez P.S.,Physical Organic Chemistry and Bioprocesses Group
Journal of Physical Chemistry A | Year: 2010

We have investigated important intermediates and key transition states of the organocatalyzed Knoevenagel condensation using density functional theory and two different basis sets (6-31 G(d,p) and 6-311++G(2df,2pd)), both in gas phase and simulating the bulk solvent (pyridine) using the PCM method. Calculated structures for reactants, intermediates, and key transition states suggest that the secondary amine catalyst is essential, both for activating the aldehyde for nucleophilic attack, and in the possible decarboxylation pathways. The calculated results are shown to agree with available experimental information. On the basis of the results obtained, the studied mechanism may be important in the understanding of vinylphenol production during malting and brewing of wheat and barley grains. © 2010 American Chemical Society.

Ventura O.N.,Computational Chemistry and Biology Group | Saenz-Mendez P.,Computational Chemistry and Biology Group | Saenz-Mendez P.,Physical Organic Chemistry and Bioprocesses Group | Bottinelli F.,Computational Chemistry and Biology Group
Theoretical Chemistry Accounts | Year: 2011

Density functional and MP2 calculations with extended basis sets were performed on the species participating in both the previously suggested and a newly proposed mechanisms of partial dechlorination of chloropicrin by simple sulfur species, both in gas phase and in a simulated water environment. Thermochemistry of both mechanisms in the gas phase was also studied using the chemical models G3 and G4. It is shown that the previously proposed reductive dehalogenation is not thermodynamically feasible at room temperature, as it should be according to the experimental evidence. Although inclusion of the solvent improves the results with respect to gas phase, the thermodynamics of the proposed mechanism by Zheng et al. is still unfavorable for obtaining the experimental products. An alternative mechanism is then proposed, involving the formation of HSCl, which is the intermediate that then undergoes redox reactions. Such a mechanism is exothermic and spontaneous, according to the computational results, and produces elementary sulfur in agreement with the experimental facts. © 2011 Springer-Verlag.

Dos Santos D.J.V.A.,University of Lisbon | Saenz-Mendez P.,Physical Organic Chemistry and Bioprocesses Group | Eriksson L.A.,National University of Ireland | Guedes R.C.,University of Lisbon
Physical Chemistry Chemical Physics | Year: 2011

Allopsoralens are angular psoralen derivatives presenting advantages over the parent compound because of monofunctional DNA-photobinding and consequent lower toxicity. Allopsoralen molecules with three different substituents and different protonation states were studied using the molecular dynamics technique. The location of these molecules when inside the lipid bilayer is of major importance because their photochemical properties can change with the environment. Also, the ability of psoralens to form photoadducts with unsaturated phospholipids depends on the preference of the molecules to locate themselves closer to the bilayer middle were the double bond functionality can be found. Herein we show that the allopsoralens tend to accumulate inside the lipid bilayer closer to the water interface when protonated or closer to the interface middle otherwise. Allopsoralens containing one amine terminated carbon chain tend to have different rotational and orientational behaviour and an orientation preference close to the ones shown by the lipids. The size and chemical nature of the substituent also affect the molecular mobility and capacity to interact with water molecules and the nitrogen or phosphorus atoms of the lipids. © 2011 the Owner Societies.

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