Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures

Figures & data

Figure 1. (a) Free energy surface of the CDR-L1 loop with a loop length of 11 residues including the projected canonical cluster median representatives. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles and the respective color-coding is shown on the left. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-L1 loop in solution. We obtained four macrostates, in which all canonical cluster medians are present, and we are even able to suggest two additional dominant solution structures

Figure 2. (a) Free energy surface of the CDR-L2 loop with a loop length of eight residues including the projected canonical cluster median representatives. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles and the respective color-coding is shown on the left. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-L2 loop in solution. We obtained two macrostates, in which all canonical cluster medians are present and the highest populated cluster representative directly lies in the global free energy minimum in solution

Figure 3. (a) Free energy surface of the CDR-L2 loop with a loop length of 12 residues including the projected canonical cluster median representatives. The canonical cluster representative used as the starting structure for simulations is shaped as triangle, while the other available canonical cluster median X-ray structure is visualized as circle and the respective color-coding is shown on the left. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-L2 loop in solution. We obtained five macrostates, in which all canonical cluster medians are present

Figure 4. (a) Free energy surface of the CDR-L3 loop with a loop length of nine residues including the projected six available canonical cluster median representatives. The legend and color-coding of all canonical cluster representatives are shown on the left. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-L3 loop in solution. We obtained four macrostates, in which all canonical cluster medians are present

Figure 5. (a) Free energy surface of the CDR-H1 loop with a loop length of 13 residues including the projected 13 available canonical cluster median representatives. The legend and color-coding of all canonical cluster representatives are shown on the left. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-H1 loop in solution. We obtained four macrostates, in which all canonical cluster medians are present

Figure 6. (a) Free energy surface of the CDR-H1 loop with a loop length of 13 residues including the projected 13 available canonical cluster median representatives. The legend and color-coding of all canonical cluster representatives are shown on the left. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-H1 loop in solution. We obtained four macrostates, in which 12 of 13 canonical cluster medians are present. We also identify a potentially relevant conformation in solution

Figure 7. (a) Free energy surface of the CDR-H2 loop with a loop length of 10 residues including the projected available canonical cluster median representatives. The legend and color-coding of all canonical cluster representatives are shown on the left. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-H2 loop in solution. We obtained four macrostates, in which all canonical cluster medians are present

Figure 8. (a) Free energy surface of the CDR-H2 loop with a loop length of ten residues including the projected available canonical cluster median representatives. The legend and color-coding of all canonical cluster representatives are shown on the left. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-H2 loop in solution. We obtained four macrostates, in which eight of nine canonical cluster medians are present

Figure 9. (a) Free energy surface of the CDR-H3 loop with a loop length of seven residues including the projected available canonical cluster median representatives. The legend and color-coding of all canonical cluster representatives are shown on the left. The canonical cluster representative used as starting structure for simulations is shaped as triangle, while all the other available canonical cluster median X-ray structures are visualized as circles. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives were colored independent of the canonical cluster representatives in (a) and summarize the kinetically relevant conformations of the CDR-H3 loop in solution. We obtained four macrostates, in which all canonical cluster medians are present

Figure 10. (a) Free energy surface of the CDR-H3 loop with a loop length of 13 residues. As for this specific loop length, no canonical cluster could be assigned no projections of X-ray structures are shown. (b) Contours of the free energy surface are displayed in the background of the Markov-state model. The macrostate representatives with the respective macrostate ensemble and transition kinetics are also included. The macrostate representatives summarize the kinetically relevant conformations of the CDR-H3 loop in solution. We obtained five macrostates and identified potentially relevant solution structures