title: Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases.
abstract: The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition because of its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B as a protein scaffold to redesign a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusions. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of a reactant complex that, in turn, would reduce the energy barrier.
authors.affiliation: Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland.|Departamento de Química Física y Analítica, Universitat Jaume I , 12071 Castellón, Spain.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Świderek
authors.affiliation: Departamento de Química Física y Analítica, Universitat Jaume I , 12071 Castellón, Spain.
authors.forename: Vicent
authors.initials: V
authors.lastname: Moliner
mesh_terms: D002175:Candida / Q000737:chemistry / Q000201:enzymology*; D061565:Cycloaddition Reaction; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism; D008049:Lipase / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D005656:Fungal Proteins; D008049:Lipase; C431349:lipase B, Candida antarctica