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Project Progress

It has been shown by Hsiao and coworkers^1,2 that three Mg²⁺-microsclusters (Mg²⁺-μc’s), each containing two Mg²⁺ ions, provide a rigid framework surrounding the peptidyl transferase center of the ribosome. A schematic representation of a generic Mg²⁺-μc is shown in Figure 1. A Mg²⁺-μc extracted from ribosomal structures is shown in Figure 2. We have initiated a high level theoretical evaluation of the contribution of Mg²⁺-μc’s to the energetics of ribosomal RNA assembly, using NASA supercomputing facilities. We will deconvolve the energy of interaction into fundamental components. Initial calculations using Gaussian30 were performed on ten-membered ring complexes (shaded yellow in Figures 1 and 2)

consisting of a nucleic acid fragment with a sugar (ribose or deoxyribose), two phosphate groups, a Mg²⁺ ion coordinated by two phosphate oxygens, and four water molecules (waters not shown in Figure 1). Geometry was optimized in the gas phase using Density Functional Theory. We incorporated solvent effects using the polarized continuum models (PCMs) at the BLYP/6-311++(d,p) level of theory. Ultimately we will characterize intact Mg²⁺-μc’s consisting of 120 atoms, including hydrogen atoms and multiple ions.

We have computed the interaction energy of the ten-membered ring complex, for both ribose and deoxyribose analogs, and found that formation of such complexes is energetically favorable (-5.6 kcal/mol for ribose and -3.4 kcal/mol for deoxyribose). We found a very high energetic penalty associated with the closing the sugar-phosphate backbone (~ 45 kcal/mol) to form the ring. We are repeating the simulations for complexes in which the same nucleic acid fragments are bound to Na^/ins>, Ca²⁺ and Fe²⁺ in place Mg²⁺. Our hypothesis is that Mg²⁺ is can be replaced by Fe²⁺ but not Na⁺ or Ca²⁺ in forming a stable ribosomal core.