Abstract
We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies in three pairs differing substantially in their individual promiscuity respectively specificity. For two pairs of antibodies crystal structures are available in different states of maturation and used as starting structures for the analyses. For a third pair we chose two antibody CDR sequences obtained from a synthetic library and predicted the respective structures. For all three pairs of antibodies we performed metadynamics simulations to overcome the limitations in conformational sampling imposed by high energy barriers. Additionally, we used classic molecular dynamics simulations to describe nano- to microsecond flexibility and to estimate up to millisecond kinetics of captured conformational transitions. The methodology represents the antibodies as conformational ensembles and allows comprehensive analysis of structural diversity, thermodynamics of conformations and kinetics of structural transitions. Referring to the concept of conformational selection we investigated the link between promiscuity and flexibility of the antibodies' binding interfaces. The obtained detailed characterization of the binding interface clearly indicates a link between structural flexibility and binding promiscuity for this set of antibodies.
Highlights
Antibodies have emerged as essential therapeutic agents in the treatment of cancer and various other diseases [1]
We present three examples with and without prior structural information where affinity maturation/reduced promiscuity leads to a significant rigidification of the complementary determining region (CDR)-H3 loop [29,30,31]
To visualize the decreased flexibility of the matured antibody compared to the naïve antibody a principle component analysis (PCA) of the CDR-H3 loop was performed (Figure S2)
Summary
Antibodies have emerged as essential therapeutic agents in the treatment of cancer and various other diseases [1]. The specificity of an antibody, mainly influenced by the complementary determining region (CDR), plays a key role in antigen recognition and binding processes [4]. A clear characterization of structure and dynamics of an antibody is essential to understand the antigen binding process, the involved conformational changes and the associated biological implications [13]. Protein-protein interactions such as antibody-antigen binding were assumed to follow the “lock and key”(14) mechanism suggesting a rigid complementary paratope and a rigid antigen [15]. This “lock and key” hypothesis has been challenged by the “induced fit”(16) and the “conformational selection”(17) concepts. While the “induced fit” binding paradigm argues for structural rearrangements as response to the binding process, “conformational selection” follows the idea of an ensemble of pre-existing conformational states with varying probabilities from which a binding competent state is selected [17,18,19]
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