Abstract
Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.
Highlights
Antibodies are proteins produced by the B cells of jawed vertebrates that play a central role in the adaptive immune system
We initially asked whether complementarity determining region (CDR)-H3 loop rigidification, having been observed in many past studies, was present in a large set of antibodies derived from human peripheral blood cells
Since de novo modeling of long loops is challenging, DeKosky et al limited their antibody set to the more tractable subset of antibodies with CDR-H3 loop lengths under 16 residues. They compared their models for seven human germline antibodies with solved crystal structures and found models had under 1.4 Å backbone root-mean-square deviation (RMSD) for the framework regions (FRs) and under 2.4 Å backbone RMSD for the CDR-H3 loop
Summary
Antibodies are proteins produced by the B cells of jawed vertebrates that play a central role in the adaptive immune system. In a process known as affinity maturation, iterations of somatic hypermutation are followed by selection to evolve the antibody in specific response to a particular antigen. This evolution results in the gradual accumulation of mutations across the entire antibody, with higher mutation rates in the six complementarity determining regions (CDRs) than in the framework regions (FRs) [4, 5]. To understand the role of B cells in adaptive immunity and how they evolve antibodies capable of binding specific antigens, we must first understand the effects of affinity maturation on the CDRs, and in particular on the CDR-H3
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