Study of Thermal Stability of Riboflavin Synthase of Eremothecium gossypii Through Molecular Dynamics Approach

Study of Thermal Stability of Riboflavin Synthase of Eremothecium gossypii Through Molecular Dynamics Approach

Syarifuddin Idrus, Usman S.F. Tambunan
Departement of Chemistry, Faculty of Mathematics and Science, University of Indonesia, Depok 16424 Indonesia.

Eremothecium gossypii has the enzymes that able to produce riboflavin naturally. The enzyme that responsible for the final production of riboflavin is riboflavin synthase. Riboflavin synthase catalyzes conversion of two molecules of 6,7-dimethyl-8-ribityllumazine into each one molecule riboflavin and 4-ribitylamino-5-aminouracil. In this study, we determined the interaction of riboflavin synthase isolated from Eremothecium gossypii with 6,7-dimethyl-8-ribityllumazine. We performed a computational approach to see the active sites of riboflavin synthase that play a role in the production of riboflavin. We designed riboflavin synthase isolated from Eremothecium gossypii as a model in PDB format. As a template, the structure of riboflavin synthase isolated from Schizosaccharomyces pombe with 1KZL PDB code was used. The thermal stability of enzyme had been conducted on the molecular dynamics simulation approach at 300K, 310K, 315K, 325K, 335K, and 350K. The results showed that amino acid residues which interact include Thr154, Ile169, Thr172, Val6, and Gly102 at the C-terminal domain and Thr56, Gly68, Ala70, Val109, and His108 at the N-terminal domain. Residue Thr154 was from the C-terminal domain and His108 was from the N-terminal domain, represents two-subunit of the enzyme that acts as an early stage at riboflavin catalysis reaction. These results shown that only one of active sites of the enzyme  (N-terminal domain) catalyze riboflavin formation. Molecular dynamics simulation showed the calculation of RMSD values at 300 K and 315 were fluctuated in the range of 2226 Ǻ from the initial state. At 320 K and 335 K, fluctuation occurred in the range of 29-34 Ǻ. At 350 K, fluctuation occurred in 38-45 Ǻ and the domains structure had separated.

Keywords: Thermal stability, riboflavin, riboflavin synthase, 6,7-dimethyl-8-ribityllumazine, molecular dynamics, Eremothecium gossypii.

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