Mg2+ vs Ca2+ bound active site of group II intron– A MD study

Divalent-Metal-Ion Selectivity of the CRISPR-Cas System-Associated Cas1 Protein: Insights from Classical Molecular Dynamics Simulations and Electronic Structure Calculations

“…A spherically truncated biomacromolecular system is advantageous because (1) it reduces the computational cost and (2) considerably improves the convergence of free energy calculations (requires multiple independent MD simulations). The methodology adopted in the work (spherically truncated biomolecule in a water box) was successful in various contexts, including ion selectivity by RNA and protein–RNA recognition. − The objective of our adopted MD model (spherically truncated protein in a box of water) was to ensure (1) the protein is immersed in bulk water. The standard requirement is that there must be at least five water molecules (i.e., 15 Å) between any protein atom and the box boundary. , (2) The box should be large enough so that the protein does not interact with its image in the next cell.…”

“…Positive ΔΔ G refers to favorable Mg 2+ binding relative to Ca 2+ (Table S3). The same approach has been adopted recently for quantifying the Mg 2+ vs Ca 2+ preference at various stages of the splicing process of group II intron …”

Structure-based thermodynamics of ion selectivity (Mg2+versus Ca2+ and K+versus Na+) in the active site of the eukaryotic lariat group II intron from algae Pylaiella littoralis

“…Previously, we reported the metal-ion selectivity for the linear group II intron of bacterium (O. iheyensis), and the estimated strength of divalent metal-ion selectivity (DDG: between Mg 2+ and Ca 2+ , favoring the former) for the prehydrolytic and post-hydrolytic states was E12 kcal mol À1 and E10 kcal mol À1 , respectively. 18,19 Thus, the discriminatory power of the lariat intron (favoring Mg 2+ relative to Ca 2+ binding) was found to be higher than the linear intron in bacteria, particularly in the post-hydrolytic state. On the other hand, the pre-hydrolytic state of the linear group II intron of O. iheyensis was found to be strongly selective between K + and Na + (DDG E 6 kcal mol À1 in favor of K + ) compared with the lariat group II intron of P. littoralis (DDG E À2 kcal mol À1 in favor of Na + ).…”

“…The spherically truncated biomolecule in a box of water was studied in various contexts, including protein-RNA recognition and metal-ion selectivity by RNA. 18,19,[24][25][26][27] MD simulations were carried out using the Particle Mesh Ewald method 28 for long-range electrostatics. The temperature and pressure were kept at 310 K and 1 bar, respectively, using Langevin dynamics 29 for non-hydrogen atoms with a coupling coefficient of 5 ps and the Nose ´-Hoover method for Langevin pistons.…”

“…Thus, metal-ion selectivity is crucial for splicing in group II introns. [15][16][17] Previously, we have reported 18,19 structure-based computational studies and estimated the strength of the metal-ion selectivity (K + versus Na + , Mg 2+ versus Ca 2+ ) in the active site of the bacterial group IIC intron (O. iheyensis) at various stages of the hydrolytic splicing process. The results showed that the group IIC intron was strongly selective for monovalent (K + favored over Na + ) as well as divalent (Mg 2+ favored over Ca 2+ ) metal ions in the active site.…”