NMR Backbone Assignment of Fibronectin Extradomain B in the Free State and in Complex with the Specific Binding Aptide

Abstract

The extra domain B (EDB) of fibronectin, a naturally occurring marker of tissue remodeling and angiogenesis, is expressed in the majority of aggressive solid human tumors, whereas it is not detectable in normal vessels and tissues. Aptides based on the tryptophan zipper scaffold with variable target-binding arms were shown to recognize diverse target proteins with high affinity and specificity. I employed NMR spectroscopy in order to characterize the binding mode of EDB and its specific aptide. Performed three-dimensional triple resonance NMR experiments to assign the backbone resonances of free EDB and EDB:aptide complex using double labeled (13C/15N) and triple labeled (2H/13C/15N) samples. 3D CBCACONH, HNCACB, and HBHA(CO)NH were recorded and analyzed, yielding a total of 97% of the 1Hα, 13Cα, and 13Cβ chemical shift assignment. After that I calculated the Chemical Shift Index (CSI) using the backbone chemical shifts. The results indicated that six β-strand secondary structures were found between residues 5-15, 20-28, 34-42, 51-55, 62-64, and 7280 and also a α-helical turn between residues 5659. Comparison of the CSI between free EDB and the EDB:aptide complex revealed a dramatic change in the secondary structures upon the complex formation. Based on the backbone chemical shift assignment, side chain assignment and distance restraint measurement are underway to determine the three-dimensional structure of the complex.