Chapter 12: Ribozymes
Published:16 Nov 2016
J. Bertran and A. Oliva, in Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, ed. I. Tunon and V. Moliner, The Royal Society of Chemistry, 2016, ch. 12, pp. 404-435.
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It has been found that RNA can act not only as a genetic carrier, but also as a biological catalyst. The concept of a ribozyme, created in 1982, and the hypothesis of a RNA world, reflect this dual behaviour. This chapter is devoted to studying the mechanisms of several reactions catalysed by natural ribozymes with the aim of detecting the main catalytic factors that intervene in this kind of enzyme. It has been shown that the dications Mg2+, which help to neutralise the large negative charge of the main chain, not only play the structural role that they have in the ribosome, but can also play a direct role in the catalytic process in some cases. The molecular dynamics (MD) simulations are very important in order to clarify the catalytic mechanism of natural ribozymes and are becoming basic for achieving the rational design of low-cost artificial ribozymes in the near future.