On the physical basis of the amino acid polar requirement.

Journal of Molecular Evolution
Damien C Mathew, Zaida Luthey-Schulten

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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Citations

Jul 23, 2013·Nucleic Acids Research·Anton A Polyansky, Bojan Zagrovic
Jul 24, 2013·Journal of Molecular Evolution·Harry BuhrmanLeen Stougie
Feb 28, 2014·RNA Biology·Bojan Zagrovic
Mar 11, 2015·Nucleic Acids Research·Mario Hlevnjak, Bojan Zagrovic
Jul 30, 2015·Physical Chemistry Chemical Physics : PCCP·Matea HajnicBojan Zagrovic
Jul 28, 2017·PLoS Computational Biology·Lukas Bartonek, Bojan Zagrovic
Aug 31, 2017·Annual Review of Genetics·Eugene V Koonin, Artem S Novozhilov
Jun 1, 2018·FEBS Letters·Bojan ZagrovicAnton A Polyansky
Aug 8, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Thomas ButlerZaida Luthey-Schulten
Apr 14, 2017·Royal Society Open Science·Marco V JoséEberto R Morgado
Nov 13, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Thomas Butler, Nigel Goldenfeld
Sep 15, 2019·Bio Systems·Stefan Wichmann, Zachary Ardern
Jan 25, 2021·Journal of Molecular Evolution·Michael Yarus
Jan 25, 2021·Journal of Molecular Evolution·Michael Yarus
Jan 8, 2021·Journal of Molecular Evolution·Michael Yarus
Mar 31, 2021·Annual Review of Biochemistry·Charles W Carter, Peter R Wills
Jun 18, 2021·Physical Review. E·John-Antonio ArgyriadisDjordje Minic
Sep 1, 2021·Proceedings of the National Academy of Sciences of the United States of America·Michael Yarus
Sep 1, 2021·Bio Systems·Paško Konjevoda, Nikola Štambuk
Sep 24, 2021·Scientific Reports·Georgina I López-CortésMarco V José

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