Research advances in hydrogen–deuterium exchange mass spectrometry for protein epitope mapping

Sun, Haofeng; Ma, Lulin; Wang, Leyu; Xiao, Peng; Li, Hongmei; Zhou, Min; Song, Da

doi:10.1007/s00216-020-03091-9

Cited by 31 publications

(32 citation statements)

References 116 publications

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“…While HDX-MS can facilitate the understanding of the conformational dynamics of binding, it may give recurrent false positives and the experimental proposal must fulfill an exacting list of requirements to obtain good results (16). Thus, HDX-MS is usually coupled to methods like cryo-EM to marry conformational dynamics with structural insight.…”

Section: Rsc Chemical Biology Accepted Manuscriptmentioning

confidence: 99%

“…There exist several relatively mature technologies available to delineate the sequences, structures, or sequence constraints of epitopes. In fact, several comprehensive reviews of individual methods have been published in this century (9)(10)(11)(12)(13)(14)(15)(16). Table 1 lists common experimental methods for epitope mapping.…”

Section: Introductionmentioning

confidence: 99%

“…Such conformationally sensitive epitopes are typically resolved by structural determination using X-ray crystallography or electron microscopy (EM). Less commonly, hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) 16 or deep mutational scanning 17 can be employed. All methods have their relative strengths and drawbacks, but generally it has been difficult to compare directly between methods as not all are typically performed on the same set of proteins.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

Francino-Urdániz

Whitehead

2021

RSC Chem. Biol.

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Section: Rsc Chemical Biology Accepted Manuscriptmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

Francino-Urdániz

Whitehead

2021

RSC Chem. Biol.

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“…Nevertheless, most antibodies have low K d (nanomolar range), hence the 10 and 30 min timepoints often capture the largest difference in deuterium uptake, to enable epitope identification. [16][17][18][19][20][21][22][23]…”

Section: Screening Workflowmentioning

confidence: 99%

“…[14,15] Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) is an alternative that can characterize both the structural and dynamic aspects of antibody-antigen complexes in-solution. [16][17][18][19][20][21][22][23] It also provides a moderate increase in throughput, while substantially reducing the requirements for purified biological material. Apart from the structural aspect, HDX-MS has also been used to report binding affinities for protein-protein interactions, highlighting the versatility of HDX technology.…”

mentioning

confidence: 99%

Epitope screening using Hydrogen/Deuterium Exchange Mass Spectrometry (HDX‐MS): An accelerated workflow for evaluation of lead monoclonal antibodies

Zhu

Liuni

Chen

et al. 2021

Biotechnology Journal

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Background: Epitope mapping is an increasingly important aspect of biotherapeutic and vaccine development. Recent advances in therapeutic antibody design and production have enabled candidate mAbs to be identified at a rapidly increasing rate, resulting in a significant bottleneck in the characterization of "structural" epitopes, that are challenging to determine using existing high throughput epitope mapping tools. Here, a Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) epitope screening workflow was introduced that is well suited for accelerated characterization of epitopes with a common antigen. Main methods and major results:The method is demonstrated on set of six candidate mAbs targeting Pertactin (PRN). Using this approach, five of the six epitopes were unambiguously determined using two HDX mixing timepoints in 24 h total run time, which is equivalent to the instrument time required to map a single epitope using the conventional workflow. Conclusion:An accelerated HDX-MS epitope screening workflow was developed. The "screening" workflow successfully characterized five (out of six attempted) novel epitopes on the PRN antigen; information that can be used to support vaccine antigenicity assays.

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Multi‐perspectives and challenges in identifying B‐cell epitopes

Kumar,

Bajiya,

Patiyal

et al. 2023

Protein Science

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The identification of B‐cell epitopes in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. Over the past four decades, numerous in silico methods have been developed for predicting B‐cell epitopes. However, existing reviews have only covered specific aspects, such as the progress in predicting conformational or linear B‐cell epitopes. Therefore, in this paper, we have undertaken a systematic approach to provide a comprehensive review covering all aspects associated with the identification of B‐cell epitopes. Firstly, we have covered the experimental techniques developed over the years for identifying linear and conformational epitopes, including the limitations and challenges associated with these techniques. Secondly, we have briefly described the historical perspectives and resources that maintain experimentally validated information on B‐cell epitopes. Thirdly, we have extensively reviewed the computational methods developed for predicting conformational B‐cell epitopes from the structure of the antigen, as well as the methods for predicting conformational epitopes from the sequence. Fourthly, we have systematically reviewed the in silico methods developed in the last four decades for predicting linear or continuous B‐cell epitopes. Finally, we have discussed the overall challenge of identifying continuous or conformational B‐cell epitopes. In this review, we only listed major computational resources; a complete list with the URL is available from the BCinfo website (https://webs.iiitd.edu.in/raghava/bcinfo/ ).This article is protected by copyright. All rights reserved.

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Research advances in hydrogen–deuterium exchange mass spectrometry for protein epitope mapping

Cited by 31 publications

References 116 publications

An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

Epitope screening using Hydrogen/Deuterium Exchange Mass Spectrometry (HDX‐MS): An accelerated workflow for evaluation of lead monoclonal antibodies

Multi‐perspectives and challenges in identifying B‐cell epitopes

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