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.
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Acknowledgments
This work was funded by NSF-FIBR Grant SBCSF0526747. Some simulations were performed at the National Center for Supercomputing Applications through Teragrid LRAC No. MCA03S027S and through the University of Illinois School of Chemical Sciences computational resource NSF CRIF 05-41659. We wish to thank Carl Woese, Patrick O’Donoghue, and members of the Luthey-Schulten group for helpful discussions. Jordi Cohen provided analysis software for the occupancy probability studies, and Elijah Roberts assisted in parallelizing the RDF analysis software. Nigel Goldenfeld and Tom Butler provided helpful discussions on genetic code optimality. NAMD and VMD were developed by the Theoretical and Computational Biophysics Group of the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.
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Mathew, D.C., Luthey-Schulten, Z. On the Physical Basis of the Amino Acid Polar Requirement. J Mol Evol 66, 519–528 (2008). https://doi.org/10.1007/s00239-008-9073-9
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DOI: https://doi.org/10.1007/s00239-008-9073-9