Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

John I. Manchester, Masayuki Shibata, Robert F. Setlik, Rick L. Ornstein, Robert Rein

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on the system under investigation. In the preent study we assess the validity of the MNDO/PM3 method on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Original languageAmerican English
Pages (from-to)419-427
Number of pages9
JournalOrigins of life and evolution of the biosphere
Volume23
Issue number5-6
DOIs
StatePublished - Dec 1993
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Space and Planetary Science

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