COMP 399 |
| We have developed a coarse-grained description of the ribosome with activated rate processes to describe the rotational motion of the ternary complex EF-Tu(GTP)aa-tRNA towards the peptidyl-tRNA after matching of mRNA codon with anticodon of cognate ternary complex. We have determined the speed of sampling the space allowed by diffusion and the size of the spring constant and the damping associated with the rotational motion. We have carried out Grand Monte Carlo simulations to elucidate the role magnesium ion binding sites in the ternary complex EF-Tu(GTP)aa-tRNA and the sarcin ricin loop in Escherichia coli (E.coli) ribosome. Finally, we will discuss the nature of interactions of magnesium ions with RNA bases through high-level ab initio calculations. The results will be compared with single molecule experiment of the ribosome. (Work done in collaboration with A. Spasic and S. Sanyasi (Boston College) and Steve Chu (Stanford University and Berkeley). Work supported (UM) by NSF.) |
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Bold Predictions in Theoretical Chemistry: A Symposium in Honor of One of the Boldest, Bill Goddard, on the Occasion of his 70th Birthday
1:30 PM-5:15 PM, Wednesday, August 22, 2007 BCEC -- 160B, Oral
Division of Computers in Chemistry |