Volume 14 Number 3	July 1998

In Vivo Deployment of Palmaz-Schatz Stent Sparse Matrix Methods Fluid Phase Equilibria Modeling the Dynamics of RNA Seminar Synopsis Visitors Research Reports ne key step in biological synthesis of proteins is the translation of genetic code, as carried by messenger ribonucleic acid (mRNA), into the correct sequence of amino acids that defines a given protein. This translation is accomplished within cellular assemblies of RNA and proteins called ribosomes. Amino acids are delivered to the ribosome by transfer ribonucleic acid (tRNA) molecules that have anticodon regions complementary to the 3-base codon sequence of the mRNA. Therefore, a necessary aspect of translation includes ensuring that distinct tRNA molecules always carry their designated amino acid. University researchers in the Chemistry Department are studying the process by which tRNA molecules become charged with the proper amino acid (there are 20 amino acids commonly used in protein synthesis and each has its own unique tRNA). This charging is accomplished by enzymes called aminoacyl-tRNA synthetases, and one of the many questions with respect to their specificity is how they recognize their substrate tRNA molecules. Experimental studies in the laboratory of Professor Karin Musier-Forsyth have defined key atomic groups in the sequence of the tRNA that carries the amino acid alanine; in particular, substitution and/or modification of the first base pair in the amino acid acceptor stem eliminates alanine tRNA synthetase activity with respect to the mutant tRNA as a substrate. Average structures for RNA hairpins analoous to wild-type and mutant alanine tRNA over 1.5 nanosecons of simulation time in aqueous solution. Undergraduate researcher Stephanie Kerimo in the Musier-Forsyth group, working in collaboration with Professor Chris Cramer, has simulated the structure and dynamics of both a natural (wild-type) and a modified (mutant) RNA hairpin that mimics the amino acid acceptor stem of alanine tRNA. The former is experimentally recognized and charged by alanine tRNA synthetase while the latter, which differs only by interchange of a paired set of guanine (G) and cytosine (C) bases, is not recognized. Molecular dynamics simulations in aqueous solution using the AMBER simulation package indicate that the mutant RNA hairpin undergoes structural changes associated with base stacking. This is an important intramolecular interaction in RNA, particularly in the region of an adenine (A) base adjacent to the GC pair. This structural change may account for the enzyme’s inability to recognize the mutant RNA. Ongoing work has the goal of simulating structures for other mutants experimentally characterized as having various levels of activity and quantifying specific interaction energies of RNA with the synthetase.

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