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. 2022 Feb 24;298(4):101772. doi: 10.1016/j.jbc.2022.101772

Figure 6.

Figure 6

Effects of scFv-CDR mutations on binding with Fu-bc loop of dengue virus E.A, close-up view of the binding interface of DENV-Fubc and scFv-complementarity determining regions (CDRs) complex. Binding sites of Fu-bc and putative affinity-enhancing mutational sites in scFv-CDRs are rendered in ball and stick format. DENV EDII is colored in cyan, while Fusion and bc loops are colored in orange and yellow, respectively. Otherwise, scFv VH-CDR1, VH-CDR3, and VL-CDR3 are painted blue, green, and red, respectively. B, bonding effects of affinity-enhancing CDR mutations. C, bonding and steric effects of affinity-reducing CDR mutations. D, hydrophobic effects of affinity-enhancing CDR mutations. Using the Discovery Studio 3.0 program, the interaction interface was analyzed after substitution with each of the putative affinity-enhancing amino acids in Coot, with local energy minimization (within 10–20 Å). In silico mutagenesis was performed using the WNV/DENV-scFv complex model. Discontinuous lines with different colors between residues represent different types of nonbonds (i.e., green, H-bond; violet, electrostatic; pink, hydrophobic, orange, other non-bonds, and the red lines denoting the steric hindrances). EDII, envelope Domain II; Fu-bc, fusion and bc loop; scFv, single chain variable fragment antibody.