ArticleAnalytical chemistry2019
An Integrated Approach for Determining a Protein-Protein Binding Interface in Solution and an Evaluation of Hydrogen-Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models.
Article in Analytical chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Deep-learning structure elucidation from single-mutant deep mutational scanning.Nature communications · 2025Article
- Binding mechanism and distant regulation of histone deacetylase 8 by PCI-34051.Communications biology · 2025Article
- An integrative structural biology approach to identify the binding mode of a nanobody towards the pea ascorbate peroxidase.Computational and structural biotechnology journal · 2025Article
- Evaluating Chemical Footprinting-Induced Perturbation of Protein Higher Order Structure.Analytical chemistry · 2024Article
- Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope inAnalytical chemistry · 2024Article
- Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry.International journal of mass spectrometry · 2024Article
- Toward a MALDI in-source decay (ISD) method for top-down analysis of protein footprinting.European journal of mass spectrometry (Chichester, England) · 2023Article
- Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.Briefings in bioinformatics · 2023Article
- MALDI Peptide Mapping for Fast Analysis in Protein Footprinting.International journal of mass spectrometry · 2023Article
- Workflow for Validating Specific Amino Acid Footprinting Reagents for Protein Higher Order Structure Elucidation.Analytical chemistry · 2023Article
- Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry.Nature communications · 2022Article
- Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction.Nature communications · 2022Article
- Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation.Analytical chemistry · 2022Article
- Protein Structure Prediction with Mass Spectrometry Data.Annual review of physical chemistry · 2022Review
- Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook.Frontiers in immunology · 2022Review
- Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry.Chemical science · 2021Article
- Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens.Diagnostics (Basel, Switzerland) · 2021Review
- Accurate protein structure prediction with hydroxyl radical protein footprinting data.Nature communications · 2021Article
- Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction NetworksJournal of proteome research · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
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8 authors.
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Abstract
We describe an integrated approach of using hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (XL-MS), and molecular docking to characterize the binding interface and to predict the three-dimensional quaternary structure of a protein-protein complex in solution. Interleukin 7 (IL-7) and its α-receptor, IL-7Rα, serving as essential mediators in the immune system, are the model system. HDX kinetics reports widespread protection on IL-7Rα but shows no differential evidence of binding-induced protection or remote conformational change. Cross-linking with reagents that differ in spacer lengths and targeting residues increases the spatial resolution. Using five cross-links as distance restraints for protein-protein docking, we generated a high-confidence model of the IL-7/IL-7Rα complex. Both the predicted binding interface and regions with direct contacts agree well with those in the solid-state structure, as confirmed by previous X-ray crystallography. An additional binding region was revealed to be the C-terminus of helix B of IL-7, highlighting the value of solution-based characterization. To generalize the integrated approach, protein-protein docking was executed with a different number of cross-links. Combining cluster analysis and HDX kinetics adjudication, we found that two intermolecular cross-link-derived restraints are sufficient to generate a high-confidence model with root-mean-square distance (rmsd) value of all alpha carbons below 2.0 Å relative to the crystal structure. The remarkable results of binding-interface determination and quaternary structure prediction highlight the effectiveness and capability of the integrated approach, which will allow more efficient and comprehensive analysis of interprotein interactions with broad applications in the multiple stages of design, implementation, and evaluation for protein therapeutics.
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