Antibodies exhibit multiple paratope states influencing VH–VL domain orientations
Monica L. Fernández‐Quintero, Nancy D. Pomarici, Barbara A. Math, Katharina B. Kroell, Franz Waibl, Alexander Bujotzek, Guy Georges, Klaus R. Liedl
Abstract
Abstract In the last decades, antibodies have emerged as one of the most important and successful classes of biopharmaceuticals. The highest variability and diversity of an antibody is concentrated on six hypervariable loops, also known as complementarity determining regions (CDRs) shaping the antigen-binding site, the paratope. Whereas it was assumed that certain sequences can only adopt a limited set of backbone conformations, in this study we present a kinetic classification of several paratope states in solution. Using molecular dynamics simulations in combination with experimental structural information we capture the involved conformational transitions between different canonical clusters and additional dominant solution structures occurring in the micro-to-millisecond timescale. Furthermore, we observe a strong correlation of CDR loop movements. Another important aspect when characterizing different paratope states is the relative V H /V L orientation and the influence of the distinct CDR loop states on the V H /V L interface. Conformational rearrangements of the CDR loops do not only have an effect on the relative V H /V L orientations, but also influence in some cases the elbow-angle dynamics and shift the respective distributions. Thus, our results show that antibodies exist as several interconverting paratope states, each contributing to the antibody’s properties.