Decoding the Rich Biological Properties of Noble Gases: How Well Can We Predict Noble Gas Binding to Diverse Proteins?

ChemMedChem
David A WinklerAaron Thornton

Abstract

The chemically inert noble gases display a surprisingly rich spectrum of useful biological properties. Relatively little is known about the molecular mechanisms behind these effects. It is clearly not feasible to conduct large numbers of pharmacological experiments on noble gases to identify activity. Computational studies of the binding of noble gases and proteins can address this paucity of information and provide insight into mechanisms of action. We used bespoke computational grid calculations to predict the positions of energy minima in the interactions of noble gases with diverse proteins. The method was validated by quantifying how well simulations could predict binding positions in 131 diverse protein X-ray structures containing 399 Xe and Kr atoms. We found excellent agreement between calculated and experimental binding positions of noble gases. 94 % of all crystallographic xenon atoms were within 1 Xe van der Waals (vdW) diameter of a predicted binding site, and 97 % lay within 2 vdW diameters. 100 % of crystallographic krypton atoms were within 1 Kr vdW diameter of a predicted binding site. We showed the feasibility of large-scale computational screening of all ≈60 000 unique structures in the Protein Data Bank. This...Continue Reading

References

Nov 20, 1986·Journal of Molecular Biology·R F TiltonD A Case
Dec 9, 1998·Nature·N P FranksW R Lieb
Jun 27, 2001·Medical Hypotheses·E L Altschuler
Dec 31, 2003·Methods in Enzymology·Marc SchiltzThierry Prangé
Mar 16, 2004·The Journal of Biological Chemistry·Mario MilaniMartino Bolognesi
Jun 6, 2006·Biophysical Journal·Jordi CohenKlaus Schulten
Apr 17, 2009·RNA·P Therese LangIrwin D Kuntz
Apr 29, 2009·Journal of Computational Chemistry·Garrett M MorrisArthur J Olson
Jun 6, 2009·European Journal of Anaesthesiology·Andrea Kopp LugliChristoph H Kindler
Mar 20, 2010·Physical Chemistry Chemical Physics : PCCP·Ryo AkiyamaAyako Yoshifuku
Jun 22, 2010·The Journal of Physical Chemistry. B·Lu Tian LiuPei Tang
Sep 15, 2010·Critical Care : the Official Journal of the Critical Care Forum·Robert Dickinson, Nicholas P Franks
Jun 22, 2012·The Journal of Physical Chemistry. B·Eiji YamamotoKenji Yasuoka
Feb 5, 2013·Biochimica Et Biophysica Acta·Ryan D Booker, Amadeu K Sum
Oct 8, 2013·PloS One·Ryan G ColemanBrian K Shoichet
Jan 1, 2014·Expert Opinion on Drug Discovery·Heping ZhengWladek Minor
Mar 27, 2015·Journal of Molecular Recognition : JMR·Elizabeth YurievPaul A Ramsland
Feb 21, 2016·Pharmacology & Therapeutics·David A WinklerIra Katz
Apr 12, 2017·Journal of Neurochemistry·Jérémie LavaurPatrick P Michel

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Citations

Oct 16, 2019·Journal of Chemical Information and Modeling·D A WinklerI Katz

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