Manuel F. Ruiz-López

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Quantum chemical calculations are reported to provide new insights on plausible mechanisms leading to the deamidation of asparagine residues in proteins and peptides. Direct hydrolysis to aspartic acid and several succinimide-mediated mechanisms have been described. The catalytic effect of water molecules has been explicitly analyzed. Calculations have been(More)
We present an analysis of rare event trajectories for the nucleophilic displacement of a chloride anion of 1,2-dichloroethane by a carboxylate group in haloalkane dehalogenase from Xanthobacterautotrophicus (DhlA) and in aqueous solution. Differences in the transmission coefficient are rationalized on the basis of the electrostatic coupling between the(More)
This work examines the ability of semiempirical methods to describe the structure of liquid water. Particularly, the standard AM1 and PM3 methods together with recently developed PM3-PIF and PM3-MAIS parametrizations have been considered. We perform molecular dynamics simulations for a system consisting of 64 or 216 water molecules in a periodic cubic box.(More)
Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide(More)
OBJECTIVE Negative pressure therapy (VAC, vacuum assisted closure) is a method used still in our country. It consists of a system of aspirating a wound by means of a piece of foam and a few adhesive films. It allows the treatment of complex wounds, included (although this is still controversial) those with intestinal fistulas. We present 3 cases of(More)
Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to(More)
The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have(More)