Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook

Abstract

Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.

Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold

“…However, its accuracy and precision can be compromised by insufficient peptide coverage for large complexes or highly glycosylated antigens, or the inability to discriminate between direct binding interface and allosteric conformational change. 32 The Ala mutagenesis technique can provide some answers on the areas of the antigen involved in the interaction, but is far less precise than DMS, which scans the 20 proteinogenic amino acids. In our dataset, we observe that Ala substitutions would not have identified some important positions, such as K151 for mAb B or L310 for mAb A, and of course not A108, which is already an alanine residue.…”

Hydrogen deuterium exchange and other mass spectrometry- based approaches for epitope mapping

“…Utilizing crosslinking distances and contacting residues guided their docking experiment to afford the best scoring complex that recapitulates overall HDX-MS results. We should mention that HDX-MS for docking studies in epitope mapping is not new (Pandit et al, 2012) and is summarized in (Tran et al, 2022) 7 Conclusion and future prospects Meta analysis of >80 papers reviewed (Supplementary Table S1) in the preparation of this article indicates interesting trends for HDX-MS in epitope mapping (Figure 9). 1) Immobilized pepsin columns now enjoy widespread popularity in the field.…”

Recent Advances in NMR Protein Structure Prediction with ROSETTA

“…Previous studies [127][128][129][130][131][132] demonstrated that sophisticated sampling methods (such as MD simulations) are needed to match structures to the experimental HDX data, as well as to better understand the factors influencing the HD exchange. HDX data measured from MS have also been used for computational structure prediction [133] and for protein-protein docking [134,135].…”