ArticleAnalytical chemistry2020
Epitope and Paratope Mapping of PD-1/Nivolumab by Mass Spectrometry-Based Hydrogen-Deuterium Exchange, Cross-linking, and Molecular Docking.
Article in Analytical chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 54 citations in OpenAlex.
- Probing protein-lipid interactions by hydrogen/deuterium exchange-mass spectrometry: advances, challenges and future directions.Chemical science · 2026Review
- Epitope Screening by Hydrogen-Deuterium Exchange Mass Spectrometry for Improved Immunotherapeutic Outcomes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Mass Spectrometry-Driven Epitope Mapping: Application of Diethylpyrocarbonate Covalent Labeling for the Immunotherapeutic Target Programmed Cell Death Protein 1.Journal of the American Society for Mass Spectrometry · 2025Article
- Epitope and Paratope Mapping of a SUMO-Remnant Antibody Using Cross-Linking Mass Spectrometry and Molecular Docking.Journal of proteome research · 2025Article
- Mass Spectrometry-Based Protein Footprinting for Protein Structure Characterization.Accounts of chemical research · 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
- Epitope Mapping of Japanese Encephalitis Virus Neutralizing Antibodies by Native Mass Spectrometry and Hydrogen/Deuterium Exchange.Biomolecules · 2024Article
- Navigating the landscape of PD-1/PD-L1 imaging tracers: from challenges to opportunities.Frontiers in medicine · 2024Review
- Peptide Antibodies: Current Status.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Toward a MALDI in-source decay (ISD) method for top-down analysis of protein footprinting.European journal of mass spectrometry (Chichester, England) · 2023Article
- Hybrid structural modeling of alloantibody binding to human leukocyte antigen with rapid and reproducible cross-linking mass spectrometry.Cell reports methods · 2023Article
- Determination of Protein Monoclonal-Antibody Epitopes by a Combination of Structural Proteomics Methods.Journal of proteome research · 2023Article
- DeepBindPPI: Protein-Protein Binding Site Prediction Using Attention Based Graph Convolutional Network.The protein journal · 2023Article
- MALDI Peptide Mapping for Fast Analysis in Protein Footprinting.International journal of mass spectrometry · 2023Article
- Mechanisms of Action and Limitations of Monoclonal Antibodies and Single Chain Fragment Variable (scFv) in the Treatment of Cancer.Biomedicines · 2023Review
- Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping.Frontiers in analytical science · 2023Article
- Development of a High-Affinity Antibody against the Tumor-Specific and Hyperactive 611-p95HER2 Isoform.Cancers · 2022Article
- Complementary Structural Information for Antibody-Antigen Complexes from Hydrogen-Deuterium Exchange and Covalent Labeling Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2022Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Epitope Mapping with Diethylpyrocarbonate Covalent Labeling-Mass Spectrometry.Analytical chemistry · 2022Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Programmed cell death-1 (PD-1), an antigen co-receptor on cell surfaces, is one of the conspicuous immune checkpoints. Nivolumab, a monoclonal antibody therapeutic approved by the FDA, binds to PD-1 and efficiently blocks its pathways. In this study, an integrated approach was developed to map the epitope/paratope of PD-1/nivolumab. The approach includes hydrogen-deuterium exchange mass spectrometry (HDX-MS) followed by electron-transfer dissociation (ETD), chemical cross-linking, and molecular docking. HDX-ETD offers some binding-site characterization with amino acid resolution. Chemical cross-linking provides complementary information on one additional epitope (i.e., the BC-loop) and a potential paratope at the N-terminus of the heavy chain. Furthermore, cross-linking identifies another loop region (i.e., the C'D-loop) that undergoes a remote conformational change. The distance restraints derived from the cross-links enable building high-confidence models of PD-1/nivolumab, evaluated with respect to a resolved crystal structure. This integrated strategy is an opportunity to characterize comprehensively other antigen-antibody interactions, to enable the understanding of binding mechanisms, and to design future antibody therapeutics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.