Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF(165)-targeting aptamer, Macugen

Abstract

The 2'-fluoro/2'-O-methyl modified RNA aptamer Macugen is a potent inhibitor of the angiogenic regulatory protein, VEGF(165). Macugen hinds with high affinity to the heparin-binding domain (HBD) of VEGF(165). Hydrogen exchange rates of the imino protons were measured for free Macugen and Macugen bound to the HBD or full-length VEGF to better understand the mechanism for high affinity binding. The results here show that the internal loop and hairpin loop of Macugen are highly dynamic in the free state and are greatly stabilized and/or protected from solvent upon protein binding. (c) 2008 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.