title: Simulating Substrate Recognition and Oxidation in Laccases: From Description to Design.
abstract: To meet the very specific requirements demanded by industry, proteins must be appropriately tailored. Engineering laccases, to improve the oxidation of small molecules, with applications in multiple fields, is, however, a difficult task. Most efforts have concentrated on increasing the redox potential of the enzyme, but in recent work, we have pursued an alternate strategy to engineering these biocatalysts. In particular, we have found that redesigning substrate binding at the T1 pocket, guided by in silico methodologies, to be a more consistent option. In this work, we evaluate the robustness of our computational approach to estimate activity, emphasizing the importance of the binding event in laccase reactivity. Strengths and weaknesses of the protocol are discussed along with its potential for scoring large numbers of protein sequences and thus its significance in protein engineering.
authors.affiliation: Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , Jordi Girona 29, E-08034 Barcelona, Spain.|Anaxomics Biotech , Balmes 89, E-08008 Barcelona, Spain.
authors.forename: Maria Fátima
authors.identifier: http://orcid.org/0000-0001-8672-9940
authors.initials: MF
authors.lastname: Lucas
authors.affiliation: Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , Jordi Girona 29, E-08034 Barcelona, Spain.
authors.forename: Emanuele
authors.identifier: http://orcid.org/0000-0002-3443-9447
authors.initials: E
authors.lastname: Monza
authors.affiliation: Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, C., Denmark.
authors.forename: Lise J
authors.identifier: http://orcid.org/0000-0003-0279-8653
authors.initials: LJ
authors.lastname: Jørgensen
authors.affiliation: Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, C., Denmark.
authors.forename: Heidi A
authors.identifier: http://orcid.org/0000-0001-5458-2454
authors.initials: HA
authors.lastname: Ernst
authors.affiliation: University of Freiburg , Albertstraße 21, D-79104 Freiburg im Breisgau, Germany.
authors.forename: Klaus
authors.initials: K
authors.lastname: Piontek
authors.affiliation: Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, C., Denmark.
authors.forename: Morten J
authors.identifier: http://orcid.org/0000-0002-8410-627X
authors.initials: MJ
authors.lastname: Bjerrum
authors.affiliation: Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain.
authors.forename: Ángel T
authors.identifier: http://orcid.org/0000-0002-1584-2863
authors.initials: ÁT
authors.lastname: Martinez
authors.affiliation: Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain.
authors.forename: Susana
authors.identifier: http://orcid.org/0000-0002-2812-895X
authors.initials: S
authors.lastname: Camarero
authors.affiliation: Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , Jordi Girona 29, E-08034 Barcelona, Spain.|ICREA , Passeig Lluís Companys 23, E-08010 Barcelona, Spain.
authors.forename: Víctor
authors.identifier: http://orcid.org/0000-0002-4580-1114
authors.initials: V
authors.lastname: Guallar
mesh_terms: D007700:Kinetics; D042845:Laccase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D019800:Phenol / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering
chemical_list: D019800:Phenol; D042845:Laccase