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Updated: Aug 14, 2025

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
Published on: February 17, 2023
Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics
Mahroof Kalathingal1,2, Young Min Rhee2
1Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
Abstract:
Macugen is a therapeutic RNA aptamer against vascular endothelial growth factor (VEGF)-165, the VEGF isoform primarily responsible for angiogenesis. It has been reported that Macugen inhibits angiogenesis by specifically binding to the heparin binding domain (HBD) of VEGF165. The mechanism of the molecular recognition between HBD and Macugen is investigated here using all-atom molecular dynamics simulations. We find that Macugen recognizes HBD by an induced-fit mechanism with major conformational changes in Macugen and almost no changes in the structure of HBD, whereas HBD recognizes Macugen by a conformational selection mechanism.
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