Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions.

Physical Chemistry Chemical Physics : PCCP
Matea HajnicBojan Zagrovic

Abstract

Despite the paramount importance of protein-nucleic acid interactions in different cellular processes, our understanding of such interactions at the atomistic level remains incomplete. We have used molecular dynamics (MD) simulations and 15 μs of sampling time to study the behavior of amino acids and amino-acid sidechain analogs in aqueous solutions of different mimetics of naturally occurring nucleobases, including dimethylpyridine (DMP) and unsubstituted purine and pyrimidine rings. By using structural and energetic analysis, we have derived preference scales for the interaction of amino acids and their sidechain analogs with different nucleobase mimetics and have exhaustively compared them with each other. A close correspondence with a standard hydrophobicity measure in the case of the pyrimidine mimetic DMP and purines suggests that the hydrophobic effect is the main defining factor behind such interactions. We analyze our findings in the context of the origin of the genetic code and the recently proposed cognate mRNA-protein complementarity hypothesis. Most importantly, we show that unsubstituted purine and pyrimidine rings alone cannot differentiate between predominantly purine- and pyrimidine-coded amino acids, suggestin...Continue Reading

References

Oct 1, 1973·Die Naturwissenschaften·C R Woese
Dec 1, 1965·Proceedings of the National Academy of Sciences of the United States of America·C R Woese
Jan 1, 1968·Proceedings of the National Academy of Sciences of the United States of America·C R Woese
Jul 14, 1969·Journal of Molecular Biology·C Woese
Aug 14, 2001·Journal of Molecular Recognition : JMR·M Treger, E Westhof
Aug 9, 2002·The Journal of Biological Chemistry·Christophe BiotMarianne Rooman
Dec 19, 2003·Nucleic Acids Research·Michael M HoffmanAndrew D Ellington
Jul 21, 2004·Journal of Computational Chemistry·Chris OostenbrinkWilfred F van Gunsteren
Apr 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·William R AtchleyTanja Drüke
Sep 29, 2006·The Journal of Physical Chemistry. B·Lesley R RutledgeStacey D Wetmore
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Jan 30, 2007·Nucleic Acids Research·Jason E DonaldEugene I Shakhnovich
Nov 14, 2007·Nucleic Acids Research·Shuichi KawashimaMinoru Kanehisa
Dec 1, 2007·Journal of the American Chemical Society·Martin C Stumpe, Helmut Grubmüller
Apr 30, 2008·Journal of Molecular Evolution·Damien C Mathew, Zaida Luthey-Schulten
Jan 9, 2010·The Journal of Physical Chemistry. B·Justin A Lemkul, David R Bevan
Aug 20, 2011·BMC Bioinformatics·Irina Tuszynska, Janusz M Bujnicki
Mar 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Stefan CanzarGunnar W Klau
Jul 23, 2013·Nucleic Acids Research·Anton A Polyansky, Bojan Zagrovic
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Dec 13, 2011·Journal of Chemical Theory and Computation·Alpeshkumar K MaldeAlan E Mark

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Citations

Nov 28, 2015·Biology Direct·Anatoly D Altstein
Apr 20, 2016·Journal of the American Chemical Society·Matea HajnicBojan Zagrovic
Jul 1, 2017·The Journal of Physical Chemistry. B·Michael FeigYuji Sugita
Jul 28, 2017·PLoS Computational Biology·Lukas Bartonek, Bojan Zagrovic
Jun 1, 2018·FEBS Letters·Bojan ZagrovicAnton A Polyansky
Mar 5, 2020·Proceedings of the National Academy of Sciences of the United States of America·Lukas BartonekBojan Zagrovic
Aug 3, 2017·Journal of Chemical Theory and Computation·Anita de RuiterBojan Zagrovic

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