Recognition and interaction of small rings with the ricin A-chain binding site.
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 ricin binding site is not flexible and may only recognize a limited range of adenine-like rings.
Yan
X
X
Department of Chemistry and Biochemistry, University of Texas, Austin, USA.
Day
P
P
Hollis
T
T
Monzingo
A F
AF
Schelp
E
E
Robertus
J D
JD
Milne
G W
GW
Wang
S
S
D000225:Adenine / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D004791:Enzyme Inhibitors; D005573:Formycins / Q000737:chemistry / Q000378:metabolism; D005959:Glucosidases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D006147:Guanine / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D008024:Ligands; D008956:Models, Chemical; D011485:Protein Binding; D011622:Pterins / Q000737:chemistry / Q000378:metabolism; D012276:Ricin / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity
D004791:Enzyme Inhibitors; D005573:Formycins; D008024:Ligands; D011622:Pterins; D006147:Guanine; C034550:formycin; D012276:Ricin; D005959:Glucosidases; D000225:Adenine