title: Catalase evolved to concentrate H2O2 at its active site.
abstract: Catalase is a homo-tetrameric enzyme that has its heme active site deeply buried inside the protein. Its only substrate, hydrogen peroxide (H2O2), reaches the heme through a 45 A-long channel. Large-subunit catalases, but not small-subunit catalases, have a loop (gate loop) that interrupts the major channel. Two accesses lead to a gate that opens the final section of the channel to the heme; gates from the R-related subunits are interconnected. Using molecular dynamic simulations of the Neurospora crassa catalase-1 tetramer in a box of water (48,600 molecules) or 6M H2O2, it is shown that the number of H2O2 molecules augments at the surface of the protein and in the accesses to the gate and the final section of the channel. Increase in H2O2 is due to the prevalence and distribution of amino acids that have an increased residency for H2O2 (mainly histidine, proline and charged residues), which are localized at the protein surface and the accesses to the gate. In the section of the channel from the heme to the gate, turnover rate of water molecules was faster than for H2O2 and increased residence sites for water and H2O2 were determined. In the presence of H2O2, the exclusion of water molecules from a specific site suggests a mechanism that could contend with the competing activity of water, allowing for catalase high kinetic efficiency.
authors.affiliation: Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Circuito interior s/n, Ciudad Universitaria, Copilco, México D. F. CP 04510, Mexico.
authors.forename: Laura
authors.initials: L
authors.lastname: Domínguez
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sosa-Peinado
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Hansberg
mesh_terms: D002374:Catalase / Q000737:chemistry* / Q000378:metabolism*; D020134:Catalytic Domain; D006861:Hydrogen Peroxide / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009492:Neurospora crassa / Q000201:enzymology*; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D014867:Water; D006861:Hydrogen Peroxide; D002374:Catalase