6533b851fe1ef96bd12a8e7d

RESEARCH PRODUCT

Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17

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A recently designed enzyme, HG3.17, obtained by directed evolution, has shown a catalytic activity close to natural enzymes. Hybrid QM/MM molecular dynamics simulations for the Kemp elimination in this new enzyme have provided a deep insight into the origin of its catalytic efficiency. In this case, we have first demonstrated the presence of different conformations with significantly different reactivity. The larger reactivity is related with a better electrostatic preorganization of the environment that creates a more favorable electrostatic potential for the reaction to proceed. In HG3.17, efforts to improve the catalytic properties must be focused in possible mutations increasing the preorganization and decreasing the reorganization around the oxyanion hole. Mutations should be considered not only in the first shell of residues but in further shells since protein electrostatics is a long-range property. The present work stresses the fact that not all features of catalysis can be revealed of a single structure derived from X-ray diffraction. This work was supported by the Spanish Ministerio de Economia y Competitividad for project CTQ2012-36253-C03, Universitat Jaume I (project P1·1B2011-23), Generalitat Valenciana (PROMETEOII/2014/022 and ACOMP/2014/277 projects), Polish National Center for Science (NCN)(grant 2011/02/A/ST4/00246, 2012−2017), the PolishMinistry of Science and Higher Education (“Iuventus Plus”program project no. 0478/IP3/2015/73, 2015-2016), and the USA National Institute of Health (ref NIH R01 GM065368).