The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations.
The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined.
Vidossich
Pietro
P
Laboratori de Simulació Computacional i Modelització (CoSMoLab), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
Alfonso-Prieto
Mercedes
M
Carpena
Xavi
X
Fita
Ignacio
I
Loewen
Peter C
PC
Rovira
Carme
C
D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D006418:Heme / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D056004:Molecular Dynamics Simulation; D010544:Peroxidases / Q000737:chemistry* / Q000378:metabolism*
D001426:Bacterial Proteins; D005656:Fungal Proteins; D006418:Heme; D010544:Peroxidases