title: Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen.
abstract: The 2'-fluoro/2'-O-methyl modified RNA aptamer Macugen is a potent inhibitor of the angiogenic regulatory protein, VEGF165. Macugen binds with high affinity to the heparin-binding domain (HBD) of VEGF165. 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA.
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
authors.forename: Fiona
authors.initials: F
authors.lastname: Jucker
authors.forename: Arthur
authors.initials: A
authors.lastname: Pardi
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000494:pharmacology*; D007097:Imines / Q000737:chemistry; D051379:Mice; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011522:Protons; D042461:Vascular Endothelial Growth Factor A / Q000037:antagonists & inhibitors* / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D007097:Imines; D011522:Protons; D042461:Vascular Endothelial Growth Factor A; C495058:pegaptanib