Abstract
During the affinity maturation process the immune system produces antibodies with higher specificity and activity through various rounds of somatic hypermutations in response to an antigen. Elucidating the affinity maturation process is fundamental in understanding immunity and in the development of biotherapeutics. Therefore, we analyzed 10 pairs of antibody fragments differing in their specificity and in distinct stages of affinity maturation using metadynamics in combination with molecular dynamics (MD) simulations. We investigated differences in flexibility of the CDR-H3 loop and global changes in plasticity upon affinity maturation. Among all antibody pairs we observed a substantial rigidification in flexibility and plasticity reflected in a substantial decrease of conformational diversity. To visualize and characterize these findings we used Markov-states models to reconstruct the kinetics of CDR-H3 loop dynamics and for the first time provide a method to define and localize surface plasticity upon affinity maturation.
Highlights
Since the identification of antibodies in the 19th century, the rise and importance of monoclonal antibodies as biotherapeutics over the past 30 years has been extraordinary (Carter, 2006, 2011; Reichert, 2017; Kaplon and Reichert, 2019)
On the right the number of complementary determining region (CDR)-H3 loop clusters of the naïve and matured antibody fragments are plotted against each other to visualize the substantial rigidification upon affinity maturation
The clustering been performed using different cut-off criteria to see if the results presented in Figure 1 are stable under variation of the cut-off and in all cases the native antibodies reveal a higher number of clusters, indicating a higher flexibility of the CDR-H3 loop before maturation
Summary
Since the identification of antibodies in the 19th century, the rise and importance of monoclonal antibodies as biotherapeutics over the past 30 years has been extraordinary (Carter, 2006, 2011; Reichert, 2017; Kaplon and Reichert, 2019). Each chain consists of a variable and a constant region. The variable domain contains six hypervariable loops, referred to as the complementarity determining regions (CDRs), which shape the antigen-binding site, the paratope (Nguyen et al, 2017). Five of the six CDR loops, except the CDR-H3 loop, can adopt a limited number of main-chain conformations and have been classified into canonical structures according to their length and sequence composition (Chothia and Lesk, 1987; Al-Lazikani et al, 1997). The highest variability in sequence, length and structure of an antibody can be observed in the CDRs, especially in the CDRH3 loop, while antibody frameworks are fairly well conserved (∼150 human germline framework sequences).
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