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Pablo M De Biase

Publications and source records attributed to Pablo M De Biase.

2 recordsLinked to original sources

Modeling heme proteins using atomistic simulations.

Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.

Computer Simulation↗

Mechanisms of NO release by N1-nitrosomelatonin: nucleophilic attack versus reducing pathways.

A new type of physiologically relevant nitrosamines have been recently recognized, the N(1)-nitrosoindoles. The possible pathways by which N(1)-nitrosomelatonin (NOMel) can react in physiological environments have been studied. Our results show that NOMel slowly decomposes spontaneously in aqueous solution, generating melatonin as the main organic product (k = (3.7 +/- 1.1) x 10(-5) s(-1), Tris-HCl (0.2 M) buffer, pH 7.4 at 37 degrees C, anaerobic). This rate is accelerated by acidification (k(pH 5.8) = (4.5 +/- 0.7) x 10(-4) s(-1), k(pH 8.8) = (3.9 +/- 0.6) x 10(-6) s(-1), Tris-HCl (0.2 M) buffer at 37 degrees C), by the presence of O(2) (k(o) = (9.8 +/- 0.1) x 10(-5) s(-1), pH 7.4, 37 degrees C, [NOMel] = 0.1 mM, P(O(2)) = 1 atm), and by the presence of the spin trap TEMPO (2,2,6,6-tetramethylpiperidine 1-oxyl; k(o) = (2.0 +/- 0.1) x 10(-4) s(-1), pH 7.4, 37 degrees C, [NOMel] = 0.1 mM, [TEMPO] = 9 mM). We also found that NOMel can transnitrosate to l-cysteinate, producing S-nitrosocysteine and melatonin (k = 0.127 +/- 0.002 M(-1) s(-1), Tris-HCl (0.2 M) buffer, pH 7.4 at 37 degrees C). The reaction of NOMel with ascorbic acid as a reducing agent has also been studied. This rapid reaction produces nitric oxide and melatonin. The saturation of the observed rate constant (k = (1.08 +/- 0.04) x 10(-3) s(-1), Tris-HCl (0.2 M) buffer, pH 7.4 at 37 degrees C) at high ascorbic acid concentration (100-fold with respect to NOMel) and the pH independence of this reaction in the pH range 7-9 indicate that the reactive species are ascorbate and melatonyl radical originated from the reversible homolysis of NOMel. Taking into account kinetic and DFT calculation data, a comprehensive mechanism for the denitrosation of NOMel is proposed. On the basis of our kinetics results, we conclude that under physiological conditions NOMel mainly reacts with endogenous reducing agents (such as ascorbic acid), producing nitric oxide and melatonin.

Ascorbic Acid↗