PMID: 9552157Apr 29, 1998Paper

Recognition and interaction of small rings with the ricin A-chain binding site

Proteins
X YanS Wang

Abstract

Ricin A-chain is an N-glucosidase that attacks ribosomal RNA at a highly conserved adenine residue. Our recent crystallographic studies show that not only adenine and formycin, but also pterin-based rings can bind in the active site of ricin. For a better understanding of the means by which ricin recognizes adenine rings, the geometries and interaction energies were calculated for a number of complexes between ricin and tautomeric modifications of formycin, adenine, pterin, and guanine. These were studied by molecular mechanics, semi-empirical quantum mechanics, and ab initio quantum mechanical methods. The calculations indicate that the formycin ring binds better than adenine and pterin better than formycin, a result that is consistent with the crystallographic data. A tautomer of pterin that is not in the low energy form in either the gas phase or in aqueous solution has the best interaction with the enzyme. The net interaction energy, defined as the interaction energy calculated in vacuo between the receptor and an inhibitor minus the solvation energy of the inhibitor, provides a good prediction of the ability of the inhibitor to bind to the receptor. The results from experimental and molecular modeling work suggest that the...Continue Reading

References

Dec 1, 1992·Journal of Computer-aided Molecular Design·C J Cramer, D G Truhlar
Oct 20, 1992·Journal of Molecular Biology·A F Monzingo, J D Robertus
Jan 1, 1991·Proteins·E RutenberJ D Robertus
Jan 1, 1991·Proteins·B J KatzinJ D Robertus
Jun 1, 1995·Journal of Computer-aided Molecular Design·M A OlsonD C Hack
Dec 9, 1994·Journal of Molecular Biology·S A WestonR A Pauptit
Mar 14, 1997·Journal of Molecular Biology·X YanJ D Robertus

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Citations

Oct 21, 2009·Journal of Computer-aided Molecular Design·Yvonne Connolly Martin
Jun 7, 2011·European Journal of Medicinal Chemistry·Jeff M PruetJon D Robertus
May 25, 2010·Toxicon : Official Journal of the International Society on Toxinology·Yan BaiJon D Robertus
Jan 7, 2005·Journal of Peptide Science : an Official Publication of the European Peptide Society·Roland WackerWolfgang Voelter
Jun 10, 2003·Journal of Applied Toxicology : JAT·Brian M Paddle
Jun 1, 2013·Molecular Informatics·Nikolay T KochevNina Jeliazkova
Dec 10, 1999·Protein Engineering·H G LiY C Dong
Mar 27, 2012·Chemistry : a European Journal·Mirta RubčićVladislav Tomišić
Feb 3, 2004·Journal of Receptor and Signal Transduction Research·Pavel PospisilGerd Folkers
Apr 29, 2004·Journal of Peptide Science : an Official Publication of the European Peptide Society·Roland WackerWolfgang Voelter
Oct 1, 2013·Journal of Computational Chemistry·Thorsten WillVolkhard Helms
Apr 12, 2012·The Journal of Physical Chemistry. B·Bin WangBingqian Xu
Jul 10, 2020·Journal of Chemical Information and Modeling·Christopher M BakerAlan Dowling

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