Variable Regions of Antibodies and T-Cell Receptors May Not Be Sufficient in Molecular Simulations Investigating Binding

Abstract

Antibodies and T-cell receptors are important proteins of the immune system that share similar structures. Both contain variable and constant regions. Insight into the dynamics of their binding can be provided by computational simulations. For these simulations the constant regions are often removed to save runtime as binding occurs in the variable regions. Here we present the first study to investigate the effect of removing the constant regions from antibodies and T-cell receptors on such simulations. We performed simulations of an antibody/antigen and T-cell receptor/MHC system with and without constant regions using 10 replicas of 100 ns of each of the four setups. We found that simulations without constant regions show significantly different behavior compared to simulations with constant regions. If the constant regions are not included in the simulations alterations in the binding interface hydrogen bonds and even partial unbinding can occur. These results indicate that constant regions should be included in antibody and T-cell receptor simulations for reliable conclusions to be drawn.

Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding

“…Experimentally, we found that the double mutants were produced at a significantly reduced rate in our transient expressions, and that there were compromises in terms of binding ability to Her2, albeit at different magnitudes, despite unmodified variable regions. This further demonstrated that the constant region had clear significant effects on antigen binding, agreeing with other such studies on IgGs [21,22,24,40], in the IgA context. To understand the mechanism underlying our experimental observations, we showed that the allosteric signalling propagated bi-directionally between the two distant regions, from Her2-binding region to the Fc region and vice versa, on the IgA isotypes.…”

VH‐VL interdomain dynamics observed by computer simulations and NMR

“…Understanding the role of the C H 1 and C L domains is crucial in characterizing the antigen‐binding process and has therefore been targeted by various experimental and computational studies . The presence of the constant domains C H 1 and C L in the Fab has been discussed to have stability benefits in terms of interdomain orientation; however, this also might be a consequence of too short timescales considered. NMR experiments directly compared the complexed scFv with a Fab and provide evidence that scFvs bind target proteins identically to Fabs .…”

“…Therefore, various studies only consider the Fv fragment to describe and investigate antigen‐binding. This reduces the system size and thereby decreases the computational time and costs . The Fv fragment is the focal point of recombination and hypermutation events .…”

“…Modifications of the V H ‐V L domain orientation directly change the binding site geometry and have an effect on the specificity of the paratope, the antigen‐binding site, for target antigens . It has been shown that reducing the system to the variable regions might not always be sufficient to characterize the antigen‐binding process with molecular dynamics simulations, because of possible stabilization in the Fab by C H 1‐C L . Still, the characterization of the V H ‐V L domain orientation is crucial in understanding the antigen‐binding process.…”

Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms

“…Such a large conformational change, although remote from the binding site, may be important for binding. Indeed, constant regions have been shown to stabilize antibodyantigen binding, in particular during Molecular Dynamics simulations [30]. Similarly, correct modeling of the constant regions may be necessary in order to improve the accuracy of the scoring functions in docking algorithms.…”