In silico molecular modelling and design of heme-containing peroxidases for industrial applications
- Autores: Marina Cañellas Fontanilles
- Directores de la Tesis: Victor Guallar Tasies (dir. tes.), Maria Fatima Lucas Lucas BSC (codir. tes.), Josefa Badia Palacín (tut. tes.)
- Lectura: En la Universitat de Barcelona ( España ) en 2018
- Idioma: español
- Tribunal Calificador de la Tesis: Jean-Didier Maréchal (presid.), Sílvia Osuna Oliveras (secret.), Volker Sieber (voc.)
- Programa de doctorado: Programa de Doctorado en Biotecnología por la Universidad de Barcelona
- Materias:
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- Resumen
It is widely known that the development of modern chemistry and the consequent world industrialization have improved our quality of life to unimaginable levels. However, these advances have come with a high cost, causing environmental, health and societal concerns. As a consequence, during the past two decades a growing need has appeared to update the traditional chemistry industry processes towards greener and efficient alternatives. Along these lines, the use of enzymes has shown to be a suitable alternative to conventional industrial chemical processes. Enzymes are life-essential proteins that catalyze biochemical reaction and show several advantages over conventional chemical catalysts: they work under milder conditions, which decrease the energy requirements and consequently the capital costs of reactions; They show a high degree of selectivity and catalytic efficiency; and in addition, they are inherently non-hazardous, reusable and biodegradable catalysts, making them ideal environmentally friendly reagents. However, the main bottleneck for taking more benefit of enzymes in an industrial context is the lack of biocatalysts with the required selectivity, availability, and compatibility with industrial rigorous process conditions, and because of this, the development of enhanced enzymes by means of enzyme engineering is a main research field nowadays. Along these lines, in silico methodologies have progressively turned into highly valuable tools for the study and design of enzymatic systems, due to their unique potential to offer atomic and electronic-level insights into biocatalysts’ activity. Moreover, the continuous software and hardware improvements, and the cost-effectiveness and rapidness generally associated with these methods, make them very appealing for their application to the real problems that face the industry.
Motivated by the advances on computational techniques and by the ease of obtaining valuable experimental data, which has been provided by our collaborators, the main goal of this thesis has been to understand the mechanisms of reaction of the heme-containing peroxidases under study (Auricularia auricula-judae DyP and Agrocybe aegerita UPO). Moreover, the acquired knowledge has been used to evaluate experimentally obtained enzyme variants and to guide the design of new ones towards desired properties. In this way, distinct computational techniques at different levels of accuracy (e.g. PELE, QM/MM or MD calculations) have been used to unravel the atomic and electronic mechanistic details under peroxidases mechanisms (e.g. long range electron transfer pathways, peroxidation and peroxygenation mechanisms) and to rationalize the molecular determinants that guide yield and selectivity in both natural occurring and experimentally designed peroxidases. Furthermore, the better understanding of the molecular principles under enzyme activity, along with the use of in silico semi-rational redesign methods, has enabled us to tailor UPO enzyme towards the enhanced production of high-value chemicals.
