Protein structure dynamics by crosslinking mass spectrometry

Chen, Zhuo A.; Rappsilber, Juri

doi:10.1016/j.sbi.2023.102599

Cited by 9 publications

(3 citation statements)

References 64 publications

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“…In a typical cross-linking MS experiment, proteins are cross-linked in solution, digested into peptides using a protease (typically trypsin) and subsequently analysed by LC-MS/MS in data-dependent acquisition mode (Ref. 127 ).…”

Section: Target Protein Identification Techniquesmentioning

confidence: 99%

Trauma diagnostic-related target proteins and their detection techniques

Wei,

Ren,

Yuan

et al. 2024

Expert Rev. Mol. Med.

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Trauma is a significant health issue that not only leads to immediate death in many cases but also causes severe complications, such as sepsis, thrombosis, haemorrhage, acute respiratory distress syndrome and traumatic brain injury, among trauma patients. Target protein identification technology is a vital technique in the field of biomedical research, enabling the study of biomolecular interactions, drug discovery and disease treatment. It plays a crucial role in identifying key protein targets associated with specific diseases or biological processes, facilitating further research, drug design and the development of treatment strategies. The application of target protein technology in biomarker detection enables the timely identification of newly emerging infections and complications in trauma patients, facilitating expeditious medical interventions and leading to reduced post-trauma mortality rates and improved patient prognoses. This review provides an overview of the current applications of target protein identification technology in trauma-related complications and provides a brief overview of the current target protein identification technology, with the aim of reducing post-trauma mortality, improving diagnostic efficiency and prognostic outcomes for patients.

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Section: Target Protein Identification Techniquesmentioning

confidence: 99%

Trauma diagnostic-related target proteins and their detection techniques

Wei,

Ren,

Yuan

et al. 2024

Expert Rev. Mol. Med.

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show abstract

“…However, the majority of the methods require prior assumptions of the structure of the interaction and are very labor intensive, making the methods unsuitable for early-stage Ab screening and selection. The methods used today are X-ray crystallography, Cryo electron microscopy, mutational scanning, hydrogen/ deuterium exchange (HDX-MS) [14][15][16][17], chemical cross-linking (CX-MS) [18][19][20][21][22], and chemical foot-printing [23][24][25][26][27]. All the methods require several sample handlings steps, which might alter the native structure of the protein in question.…”

Section: Introductionmentioning

confidence: 99%

Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls

Larsen,

Kaczmarek,

Palarasah

et al. 2023

Preprint

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Epitope mapping methods using hydroxyl radical protein footprinting (HRPF) are currently hampered by high initial cost and complex experimental setup. Here we set out to present a generally applicable method using Fenton chemistry for mapping of epitopes and paratopes in a standard laboratory setting. Furthermore, the described method illustrates the importance of controls on several levels when performing mass spectrometry-based epitope mapping. In particular, the inclusion of negative antibody controls has not previously been widely utilized in epitope mapping by HRPF analysis. In order to limit the false positives, we further introduced quantification by TMT labelling, thereby allowing for direct comparison between sample conditions and biological triplicates. Lastly, up to six technical replicates were incorporated in the experimental setup in order to achieve increased depth of the final analysis.Both binding and openings of regions on receptor binding domain (RBD) from SARS-CoV-2 Spike Protein, Alpha and Delta variants, were observed. The negative control antibody experiment, combined with the high overlap between biological triplicates, resulted in the exclusion of 40% of the significantly changed regions, including both binding and opening regions. The identified binding region agrees with the literature for neutralizing antibodies towards SARS-CoV-2 Spike Protein.The presented method is an easily implementable technique for the analysis of HRPF in a generic MS-based laboratory. The high reliability of the data was achieved by increasing the number of technical and biological replicates combined with negative antibody controls.

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“…However, the improvements demonstrated in this paper represent a strong move in the right direction toward our goal of understanding how protein complexes are reorganized in response to environmental or genetic cues. Moreover, it seems feasible that the approach presented by Bludau et al could be extended even further and combined with other structural MS approaches such as cross-linking MS. , Such integrated approaches could not only help to improve the resolution of the interrogated protein assemblies but hopefully eventually enable us to better understand how such dynamic changes contribute to the determination of a specific cellular phenotype.…”

mentioning

confidence: 99%

Measuring Changes in Protein Complex Membership at Scale

Stengel

2023

J. Proteome Res.

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Protein structure dynamics by crosslinking mass spectrometry

Cited by 9 publications

References 64 publications

Trauma diagnostic-related target proteins and their detection techniques

Trauma diagnostic-related target proteins and their detection techniques

Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls

Measuring Changes in Protein Complex Membership at Scale

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