Marcela Ayala | Universidad Nacional Autónoma de México (original) (raw)

Papers by Marcela Ayala

Biocatalysis, 2016

The protein design toolbox has been greatly improved by the addition of enzyme computational simu... more The protein design toolbox has been greatly improved by the addition of enzyme computational simulations. Not only do they warrant a more ambitious and thorough exploration of sequence space, but a much higher number of variants and protein-ligand systems can be analyzed in silico compared to experimental engineering methods. Modern computational tools are being used to redesign and also for de novo generation of enzymes. These approaches are contingent on a deep understanding of the reaction mechanism and the enzyme’s three-dimensional structure coordinates, but the wealth of information produced by these analyses leads to greatly improved or even totally new types of catalysis.

Biochemical and Biophysical Research Communications, 2002

Tip Revista Especializada En Ciencias Quimico Biologicas, May 20, 2015

PLOS ONE, 2016

Fungal laccases are enzymes that have been studied because of their ability to decolorize and det... more Fungal laccases are enzymes that have been studied because of their ability to decolorize and detoxify effluents; they are also used in paper bleaching, synthesis of polymers, bioremediation, etc. In this work we were able to express a laccase from Trametes (Pycnoporus) sanguineus in the filamentous fungus Trichoderma atroviride. For this purpose, a transformation vector was designed to integrate the gene of interest in an intergenic locus near the blu17 terminator region. Although monosporic selection was still necessary, stable integration at the desired locus was achieved. The native signal peptide from T. sanguineus laccase was successful to secrete the recombinant protein into the culture medium. The purified, heterologously expressed laccase maintained similar properties to those observed in the native enzyme (Km and kcat and kcat/km values for ABTS, thermostability, substrate range, pH optimum, etc). To determine the bioremediation potential of this modified strain, the laccase-overexpressing Trichoderma strain was used to remove xenobiotic compounds. Phenolic compounds present in industrial wastewater and bisphenol A (an endocrine disruptor) from the culture medium were more efficiently removed by this modified strain than with the wild type. In addition, the heterologously expressed laccase was able to decolorize different dyes as well as remove benzo[α]pyrene and phenanthrene in vitro, showing its potential for xenobiotic compound degradation.

Revista Mexicana De Micologia, 2010

Chloroperoxidase from Caldariomyces fumago was immobilized in Eupergit® C, a commercial mesoporou... more Chloroperoxidase from Caldariomyces fumago was immobilized in Eupergit® C, a commercial mesoporous acrylic-based material. Due to low stability of the enzyme under neutral and basic pH, the usual covalent immobilization procedures cannot be applied to this enzyme. Several strategies were followed in order to achieve a stable interaction between the protein and the support. The support was efficiently functionalized with different reactive groups such as aromatic and aliphatic amines, glutaraldehyde, diazonium ions, and maleimide moieties; solvent-exposed amino acid residues in chloroperoxidase were identified or created through chemical modification, so that they were reactive under conditions where the enzyme is stable. Enzyme load and retained activity were monitored, obtaining biocatalysts with specific activity ranging from 200 to 25,000 U/g. The highest load and activity was obtained from the immobilization of a chemically-modified CPO preparation bearing a solvent-exposed free...

Si pudiéramos describir nuestra existencia en términos de reacciones químicas, usaríamos la palab... more Si pudiéramos describir nuestra existencia en términos de reacciones químicas, usaríamos la palabra “autocatalítica”. A cada instante, dentro de nuestro organismo ocurren cientos de reacciones químicas necesarias para la vida, que deben ocurrir en una escala de tiempo razonable.

Applied Biochemistry and Biotechnology, 2015

The ability of poly(ethylene glycol) (PEG) to protect enzymatic peroxidase activity was determine... more The ability of poly(ethylene glycol) (PEG) to protect enzymatic peroxidase activity was determined for horseradish peroxidase (HRP), versatile peroxidase (VP), commercial Coprinus peroxidase (BP), and chloroperoxidase (CPO). The operational stability measured as the total turnover number was determined for the four peroxidases. The presence of PEG significantly increased the operational stability of VP and HRP up to 123 and 195 %, respectively, and dramatically increased the total turnover number of BP up to 597 %. Chloroperoxidase was not protected by PEG, which may be due to the different oxidation mechanism, in which the oxidation is mediated by hypochlorous ion instead of free radicals as in the other peroxidases. The presence of PEG does not protect the enzyme when incubated only in the presence of H2O2 without reducing substrate. The catalytic constants (k cat) are insensitive to the presence of PEG, suggesting that the protection mechanism is not due to a competition between the PEG and the substrate as electron donors. On the other hand, PEG showed to have a significant antioxidant capacity. Thus, we conclude that the protection mechanism for peroxidases of PEG is based in its antioxidant capacity with which it is able scavenge or drain radicals that are harmful to the protein.

Petroleum Science and Technology, 2015

ABSTRACT Asphaltenes are considered the most recalcitrant fraction of oils. Nevertheless, there a... more ABSTRACT Asphaltenes are considered the most recalcitrant fraction of oils. Nevertheless, there are reports with rigorous experimental procedures that clearly demonstrate the capacity of enzymes and few microor- ganisms to transform asphaltenes. These microorganisms, fungi and bacteria, may contain a unique or very versatile enzymatic system that allows the transformation and mineralization of the highly com- plex asphaltene molecules. For enzymatic reactions, the biotransformation may occur only when the asphaltenes and the enzyme are in the same phase, reducing the mass transfer limitations. In this work, literature on the biotransformations of asphaltene fraction is critically reviewed.

Handbook of Hydrocarbon and Lipid Microbiology, 2010

Studies in Surface Science and Catalysis, 2004

Handbook of Hydrocarbon and Lipid Microbiology, 2010

ABSTRACT Bacteria which are able to transform sulfur-containing compounds, for utilization of eit... more ABSTRACT Bacteria which are able to transform sulfur-containing compounds, for utilization of either the sulfur or the carbon skeleton, are widely spread in nature. In this chapter, we focus on those bacteria able to degrade heterocyclic hydrocarbons by extracting the sulfur atom without major disruption of the hydrocarbon moiety. Benzothiophene and dibenzothiophene are present in crude oil, and have been utilized as models of thiocyclic sulfur-containing species present in real fractions. These compounds are difficult to desulfurize through conventional desulfurization processes. Here we present information on the desulfurization of these sulfur heterocyles by bacteria. The different metabolic pathways are described with emphasis on the 4S pathway, including the genes and enzymes involved. Research opportunities are identified and novel approaches to deepen our comprehension of these metabolic pathways are proposed.