Fig. 2: Computational design and experimental verification results from first-round design.
From: Targeting Ras-binding domain of ELMO1 by computational nanobody design
a Overall design workflow in first-round design. b Superposition of first-round nanobody designs revealed the stabilization of two clusters of binding poses on two distinct epitopes on ELMO1-RBD. c Rosetta energy scores and buried solvent accessible area comparisons between designs Nb01, Nb02 and pose-5855. d SPR single-cycle kinetics of Nb01 binding to ELMO1-RBD. Nb01 was tested at concentrations of 0.5, 1, 2, 4, and 8 μM from left to right (n = 2 independent experiments). e Comparison of side chain interactions at position 29 and 59 between Nb01 and Nb02 at their interfaces with ELMO1-RBD. f Comparison of design mutations between Nb01 and Nb02 with reference to the sequence of parent nanobody PDB 5 LMW. Dots represent the same residue type as the parent nanobody at the aligned positions.
