Table 1.

Computational design and experimental characterization of 2F5-epitope scaffolds

ES1ES2ES3ES4ES5MPER WTMPER cyc
Computational Design
PDB code of parent1LGYa1KU2a2MATa1IWLa1D3BbNANA
rmsd gp41660-667Cα (Å)0.70.70.80.91.4NANA
rmsd gp41660-667 MC (Å)0.70.80.81.01.3NANA
DDMP rmsd gp41660-6670.20.40.40.51.1NANA
Nonbound surface (Å2)18717610816079241193*
Experimental Characterization
ExpressionBacterialMammalianBacterialMammalianBacterialSyntheticSynthetic
Binding to antibody 2F5 Fab
on-rate (1/Ms) (x105)6.52 ± 0.0416.68 ± 0.041.56 ± 0.017.43 ± 0.029.70 ± 0.037.17 ± 0.048.48 ± 0.05
off-rate (1/s) (x10-3)3.50 ± 0.021.00 ± 0.000.547 ± 0.00413.90 ± 0.022.92 ± 0.014.62 ± 0.031.64 ± 0.02
KD (nM)5.38 ± 0.040.600 ± 0.0043.50 ± 0.0218.80 ± 0.033.01 ± 0.016.44 ± 0.031.93 ± 0.02
Thermodynamics (37 °C)
ΔG (kcal/mol)ND−12.8 ± 2.3ND−11.0 ± 0.2−10.8 ± 0.4−10.6 ± 0.1−11.8 ± 0.2
ΔH (kcal/mol)ND−2.7 ± 0.1ND−10.0 ± 0.2−17.6 ± 0.6−25.6 ± 0.5−18.7 ± 0.3
−TΔS (kcal/mol)ND−10.1 ± 2.3ND−0.9 ± 0.26.8 ± 0.715.0 ± 0.56.9 ± 0.3
Antigenic recognition by flexible MPER sera (mean EC50)
Flexible MPER A (serum dilution)45.6 ± 13.819.6 ± 16.456.0 ± 11.418.9 ± 3.190.9 ± 72.5155.3 ± 36.6ND
Flexible MPER B (serum dilution)20.0 ± 31.12.1 ± 0.619.0 ± 1.98.2 ± 8.685.2 ± 33.8357.4 ± 22.3ND
MPER flexible loop (serum dilution)59.2 ± 30.938.6 ± 0.938.4 ± 16.127.9 ± 0.9723.3 ± 611.49227.0 ± 1668.8ND
  • ES1-ES5 are 2F5-epitope scaffolds; MPER WT is a peptide composed of residues 656–670 of gp41 linked to a C9 tag; MPER cyc is a cyclized version of MPER WT. NA, not applicable; ND, not determined.

  • *Nonbound surface of MPER cyc is based on a structural model.