On the Permeation by Dioxygen of the Cofactor‐Independent Unusual Oxygenase RhCC,in Complex with Substrate 4‐Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation |
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Authors: | Francesco Pietra |
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Affiliation: | Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, Lucca, Italy |
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Abstract: | This work deals with a trimeric bacterial protein, RhCC, which, although belonging to the tautomerase superfamily, shows oxygenase activity. A model of the complex from RhCC and substrate 4‐hydroxyphenylenolpyruvate (4HPP), fitting the observation of extra electron densities from X‐ray diffraction of the crystal, could be built by autodocking. When subjected to molecular dynamics (MD) aided by an external random force applied to a O2 molecule placed above 4HPP, this model evolved with O2 egressing toward the bulk solvent from two nearly opposite gates. These were located between the nearly parallel helices 75 – 91 and 15 – 33 of either chain C (gate SE) or chain B (gate FL). Alternatively, with four O2 molecules in the bulk solvent, unbiased MD led to O2 entering the protein from gate SE and getting to 4HPP, while forming a stabilizing salt bridge between the 4HPP carboxylate and P1.C +NH2, thus providing scientific ground for a refined model of the complex. |
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Keywords: | Oxygenases Tautomerases Molecular dynamics Random‐acceleration molecular dynamics Gas permeation of proteins |
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