On the physical basis of the amino acid polar requirement

Damien C. Mathew, Zaida Luthey-Schulten

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

Understanding how codons became associated with their specific amino acids is fundamental to deriving a theory for the origin of the genetic code. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and nucleobases that may have played a role in establishing the genetic code. Through these experiments it was found that a property of amino acids called the polar requirement (PR) is correlated with the organization of the codon table. No other property of amino acids has been found that correlates with the codon table as well as PR, indicating that PR is uniquely related to the modern genetic code. Using molecular dynamics simulations of amino acids in solutions of water and dimethylpyridine used to experimentally measure PR, we show that variations in the partitioning between the two phases as described by radial distribution functions correlate well with the measured PRs. Partition coefficients based on probability densities of the amino acids in each phase have the linear behavior with base concentration as suggested by PR experiments.

Original languageEnglish (US)
Pages (from-to)519-528
Number of pages10
JournalJournal of Molecular Evolution
Volume66
Issue number5
DOIs
StatePublished - May 1 2008

Keywords

  • Genetic code
  • Molecular dynamics simulation
  • Nucleobase
  • Partition coefficient
  • Radial distribution function

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