title: F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations.
abstract: The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization.
authors.affiliation: Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126, Pisa, Italy, and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127, Pisa, Italy.
authors.forename: Giordano
authors.initials: G
authors.lastname: Mancini
authors.affiliation: Università degli Studi di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185, Roma, Italy.
authors.forename: Costantino
authors.initials: C
authors.lastname: Zazza
mesh_terms: D000838:Anions; D001189:Aryl Hydrocarbon Hydroxylases / Q000737:chemistry* / Q000235:genetics*; D055162:Biocatalysis; D016000:Cluster Analysis; D000072467:Cytochrome P450 Family 2; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics*; D010545:Peroxides / Q000737:chemistry; D025341:Principal Component Analysis; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry
chemical_list: D000838:Anions; D010545:Peroxides; D014867:Water; D001189:Aryl Hydrocarbon Hydroxylases; D000072467:Cytochrome P450 Family 2; C465241:cytochrome P-450 CYP2B4 (rabbit)