Binding affinity and conformational change predictions for a series of inhibitors with RuBisCO in a carbon dioxide gas and water environment by multiple computational methods

Abstract

Ribulose 1, 5-bisphosphate carboxylase-oxygenase (RuBisCO), a Calvin cycle enzyme, is responsible for absorbing the majority of atmospheric CO2 into photosynthetic organisms (McKinlay and Harwood, 2010) [1]. RuBisCO has been the subject of a great deal of research over the years, but its progress is still constrained by the low activity of the RuBisCO enzyme (Timm et al., 2016) [2]. It has not yet been documented how tightly bound inhibitors induce decreased efficiency and how this is related to CO2. In our study, we investigated and validated the binding of five natural inhibitors and substrates to RuBisCO using a variety of analytical techniques such as accelerated molecular dynamics simulation (Perez et al., 2009) [3], binding free energy calculation (Sakae et al., 2020) [4], and protein interior analysis such as a dynamical cross-correlation matrix, a free energy landscape, a dictionary of secondary structure of proteins, and principal component analysis (Marelius et al., 1998) [5]. The results provided evidence in support of the tight binding and activity control of RuBisCO, in fact, The level of inhibitor binding ability calculated by us well echoes the level of inhibition (Frank et al., 1998; Zhu and Jensen, 1991; Keys et al., 1995; Pearce, 2006) [6–9] rate under physiological conditions, which reflects the accuracy of the calculation model. According to the results of the dynamic simulation, significant dynamic changes that occurred before and after the tight binding and were influenced by different aspects of the major and secondary structures were discovered. The analysis indicates that the close binding of the oxidation-produced inhibitor to RuBisCO was controlled by the interaction of key amino acids, the degree of bending of the inhibitor, and the critical LOOP area. Further, the CO2 simulation conditions (Tcherkez, 2016) [10] described the CO2 concentrating mechanism's carbon concentration mechanism and offered fresh insights into the RuBisCO enzyme (Andrews and Whitney, 2005) [11] (CCM). Analysis was done on CO2’s crucial function in the binding of RuBisCO.