Ab initio study of molecular interactions in higher plant and Galdieria partita Rubiscos with the fragment molecular orbital method

Ribulose bisphosphate carboxylase/oxygenase (Rubisco) from one of the thermophilic red algae Galdieria partita with a high specificity factor shows a characteristic difference from higher plant Rubisco in structural change. We investigate such a difference by evaluating the inter-fragment interaction energy (IFIE) value with fragment molecular orbital (FMO) method in comparison to experimental structural studies. We found some important residues which determine the loop6 stability or which make difference in the structure between higher plant and G. partita Rubiscos. We found that amino acid change of LYS18 to ILE18 is important for the difference in location at which anion binding site is occupied, P1α or P1β, when inorganic anions are bound to the enzyme. Occupation of P2 anion binding site makes the stabilizing interaction between LYS128 and the loop6 stronger. Amino acid change of HIS386 to GLN386 contributed to the difference in the loop6 stability, while amino acid change of MET472 to THR472 did not contribute to it. It is confirmed that the patterns of interactions among THR65, THR67, and THR462 are consistent with previous experimental discussions. However, we found a case that THR65 was not stabilized with anion at P1α binding site in a closed-state structure of G. partita Rubisco.