Research on Mathematical Calculations of Bonds Betwen Amino Acid Residues and CO2 Molecules

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Cundari et al presented a powerful computational prediction system based on mathematical calculations of bonds between amino acid residues and CO2 molecule (Cundari et al. 2009). In their study, binding energies for CO2 and amino acid residues of Rubisco active site differ between different enzyme species that belongs to different organisms. It has been suggested that most of the hydrogen bonding in α-helices goes toward stabilizing the tightly coiled helix in loop 6 of Rubisco, whereas in contrast the edge of a β-sheet is open to hydrogen bonding, the binding energies are shown in table 1 (Cundari et al. 2009). Cundari also compared the residues binding energy to CO2 with other molecules such as methan, phenol, and benzen. Interestingly, amino acids with aromatic side-chain were found to have similar binding energies despite the difference in their structure. Other than Rubisco, molecular dynamic studies have shown that hydrophobic residues in the active sites of CO2 binding enzymes has similar characteristics in terms of using a specific ion and electrostatic forces. Domsic et al studied the entrapment of CO2 molecule in the active site of human Carbonic Anhydrase II, which shares the same mechanics of CO2 binding with Rubisco (Domsic et al. 2008), and found that the formation and release of the final product depends on the free energy of the amino acid residues, suggesting that altering or substituting the side-chains could alter the enzyme affinity and specificity in the same time. The acid/base interactions between the side-chains and substrate CO2 molecule are the major effective forces in determining enzyme specificity and affinity more than hydro-philicity/phobicity forces (Cundari et al. 2009). Therefore, using charged a... ... middle of paper ... ... C-terminal region of RCA, which contains the Sensor II domain, affects the substrate recognition and enhance the carboxylation turnover rate (Li et al. 2005). The C-terminal domain is detailed in figure XXX. Changing the residues in the region containing both Box VII and Sensor II domains can alter the interaction between Rubisco and RCA (Li et al. 2005), where it was shown that Rubisco N-terminus interacts with RCA C-terminus in two positions; (Rubisco-94 with RCA-311) and (Rubisco-89 with RCA-314). This interaction occurs through electrostatic forces to enhance the movement of RCA C-terminus towards Rubisco active site, allowing the Sensor II domain to recognize the RuBP. Kallis et al focused their research on ATP hydrolysis of RCA; they found that the mutants Q111E and Q111D had greater rates of ATP hydrolysis under high concentrations of ADP (Kallis et al. 2000).

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