Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations

Abstract

Antibodies protect organisms from a huge variety of foreign antigens. Antibody diversity originates from both genetic and structural levels. Antigen recognition relies on complementarity between antigen-antibody interfaces. Recent methodological advances in structural biology and the accompanying rapid increase of the number of crystal structures of proteins have enabled atomic-level manipulation of protein structures to effect alterations in function. In this study, we explored the designability of electrostatic complementarity at an antigen-antibody interface on the basis of a crystal structure of the complex. We designed several variants with altered charged residues at the interface and characterized the designed variants by surface plasmon resonance, circular dichroism, differential scanning calorimetry, and molecular dynamics simulations. Both successes and failures of the structure-based design are discussed. The variants that compensate electrostatic interactions can restore the interface complementarity, enabling the cognate antigen-antibody binding. Retrospectively, we also show that these mutational effects could be predicted by the simulations. Our study demonstrates the importance of charged residues on the physical properties of this antigen-antibody interaction and suggests that computational approaches can facilitate design of antibodies that recognize a weakly immunogenic antigen.

The challenges of glycan recognition with natural and artificial receptors

“…58 Modulation of the electrostatic interactions can therefore be used to improve the binding properties of antibodies. 59,60 Furthermore, combination of microarray screening and saturation transfer difference NMR provide key information regarding the role of the amino acid linker, such as serine or threonine, in the binding process. 56 A related approach has also been used to elucidate the effects of multiple O-glycosylation states on antibody recognition.…”

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

“…Next, we explored basic physical chemical aspects that could offer a simple and quick reasoning to understand the above free energy results and eventually be used as descriptors to scan databases of mAbs to filter promising ideal candidates. Although different driven forces can result in protein-protein complexation (Barroso da Silva et al, 2016; Delboni and Barroso da Silva, 2016), pH and charge-charge interactions seems especially important for viral proteins (Poveda-Cuevas et al, 2020;Poveda-Cuevas et al, 2018;Yoshida et al, 2019;Yang et al, 2004;Tan et al, 2005;Lamarre and Talbot, 1989;Jaume et al, 2011). Indeed, the protein net charges numbers (Z) obtained as function of the solution pH show that the SARS-CoV-2 S RDB protein is always slightly more positively charged than SARS-CoV-1 S RDB protein at the same physical chemical environment (Z equals to 5.2 and 5.5, respectively, for them at pH 4.6) − see Table 1.…”

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

“…Although different driven forces can result in protein-protein complexation, 42,43 pH and charge-charge interactions seems especially important for viral proteins. 27,55,[81][82][83][84][85] Indeed, the protein net charges numbers (Z) obtained as function of the solution pH show that the SARS-CoV-2 S RDB protein is always slightly more positively charged than SARS-CoV-1 S RDB protein at the same physical chemical environment (Z equals to 5.2 and 5.5, respectively, for them at pH 4.6) − see table 1. Since all studied fragments of Abs are also positively charged at pH 4.6 (Z equals to 9.1, 4.2, 2.7, 5.8 for 80R, CR3022, m396 and F26G19, respectively), it can be easily seen that the order observed for the binding affinities above in the free energy analyses do follow a simple charge-charge rule for the mAbs with similar surface area (A~10,000 Å 2 ).…”