Computational studies of iron dependent dioxygenases

Brkić, Hrvoje (2014) Computational studies of iron dependent dioxygenases. Doctoral thesis, Faculty of Science > Department of Physics.

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Abstract

Subject of this doctoral thesis is theoretical study of dioxygenasis, non-hem iron dependent enzymes that incorporate both molecular oxygen atoms into substrate. Two enzymes were studied: Acetylacetone dioxygenasis form Acinetobacter Jonsoii (Dke1), and human 3,4-dioxygenasis of 3-hydroxyanthranilic acid (3HAO). Three dimensional structures of these enzymes, determined by x-ray crystallography and stored to the Protein Data Bank (www.ebi.ac.uk/pdbe ; codes 3BAL and 2QNK respectively), were used as starting points in the molecular modelling. Parameters required in MD simulations of the systems, but missing in the AMBER force field (i.e. charge distribution on iron ion and coordinating residues, bond lengths, angles, dihedrals and their barriers), were determined using quantum mechanical (QM) calculations. Stability and behaviour of the enzymes in nearly physiological conditions were studied by applying empirical methods of molecular modelling. Results of these simulations revealed: water population in the active site, hydrogen bond networks, amino acid residues interactions, protein flexibility… Besides, the pathways for trafficking different ligands (water, reactants, products and metal cofactor) from the enzyme environment to the active site were determined. Impact of point mutations to the hydrogen bond network and to the active site water accessibility was determined in Dke1. The reduced enzyme activity of the mutants was studied in correlation with trafficking of the metal ion, water, substrate and reactants to the enzyme active site, as well as in corelation with the amino acid residues interactions. Using hybrid quantum-mechanics/molecular-mechanics (QM/MM) calculations the reaction mechanism for 3HAO was determined. On the basis of the MD results, we proposed explanation of the reduced enzyme activity of the mutants.

Item Type: Thesis (Doctoral thesis)
Keywords: metalloenzymes ; molecular dynamics ; force field ; semiempirical calculations ; quantum mechanical calculations ; diketon dioxygenases ; dioxygenasis of 3-hydroxy anthranilic acid ; dioxygenase reaction mechanism ; quantum mechanics/molecular mechanics calculations
Supervisor: Tomić, Sanja
Date: 21 March 2014
Number of Pages: 117
Subjects: NATURAL SCIENCES > Physics
Divisions: Faculty of Science > Department of Physics
Depositing User: Gordana Stubičan Ladešić
Date Deposited: 07 Apr 2014 15:52
Last Modified: 07 Apr 2014 15:52
URI: http://digre.pmf.unizg.hr/id/eprint/783

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