Computational Modeling of 3’-Phosphoadenosine 5’- Phosphosulfate Synthase PAPSS

Rüdiger Ettrich1,2,3, Xichong Liu4, Chris Soha3, Plačková Lydie1,2, Dhiraj Sinha1, David Reha1,2 and Kallidaikurichi V. Venkatachalam3

1Center forNanobiology and Structural Biology, Institute of Microbiology Academy of Sciences of the Czech Republic, Zamek 136, CZ-37333 Nove Hrady, Czech Republic

2Faculty of Sciences, University of South Bohemia, Zamek 136, CZ-37333 Nove Hrady, Czech Republic

3College of Medical Sciences, NOVA Southeastern University, Fort Lauderdale, Florida, 33314-7796, USA

4Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544-1009, USA

The sulfur nucleotide PAPS (3’-phosphoadenosine 5’-phosphosulfate) is the universal sulfuryl donor of the cell. In mammals 3’- phosphoadenosine 5’-phosphosulfate Synthase (PAPSS), using ATP, converts biochemically inert inorganic sulfate to the metabolically active PAPS. It is a bi-functional enzyme and catalyzes the formation of PAPS in two sequential steps.1 In the first step, inorganic sulfate reacts with ATP to form APS and pyrophosphate. The resulting phosphoric-sulfuric anhydride bond has high energy that is the chemical basis of sulfate activation. The second step is catalyzed by the kinase domain of PAPSS and involves the reaction of APS with ATP to form PAPS and ADP. The proper function of PAPSS is essential for normal physiology in the human being. Although its overall mechanism and kinetics have been well studied in the past, more recent discoveries including the resolution of its crystal structure and research in its regulatory functions revealed previously unanticipated behaviors.2 As the ubiquitous sulfate donor in most biological systems, the product of the enzyme, PAPS, plays an essential role in ECM formation, embryonic development and biomolecule secretion.3 Moreover, PAPSS has also been shown to be involved with the pathophysiology of a number of diseases including HIV, hepatocellular carcinoma and non-small cell lung cancer.4,5,6 PAPSS deficiency in human results in osteochondrodysplasias or defective cartilage and bone metabolism as evidenced in the clinical condition of the recessively inherited, spondyloepimetaphyseal dysplasia (SEMD). Using a combination of homology modeling, molecular dynamics simulations and computational chemistry methods we try to understand how the three dimensional structure of PAPSS determines the enzyme function, focusing on the roles of specific amino acid residues/overall structures on the dynamics of the enzyme in aqueous solution and the related quaternary arrangements of the enzyme. Finally, enzymatic reactions are predicted/described in three-dimensional space and the reaction coordinate is explored through the lens of molecular dynamics simulations, hybrid QM/MM and quantum calculations. Results are discussed that give a realistic picture of the enzyme activity including molecular interactions, transition state structures and the reaction coordinate.

This work was supported by a Fulbright-Masaryk Scholarship to RE and a HPD grant by Nova Southeastern University to KVV and RE.

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