HDX-MS: An Analytical Tool to Capture Protein Motion in Action

Narang, Dominic; Lento, Cristina; Wilson, Derek J.

doi:10.3390/biomedicines8070224

Cited by 45 publications

(32 citation statements)

References 75 publications

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“…Peptides encompassing the loop exhibited a multimodal spectrum that reflects conformational ensemble behaviour or intratrimer conformational heterogeneity, with a major lower exchanging population and minor, higher exchanging population in solution (Figure 4, Figure S7). 30,31 We compared this with our simulated systems and observed a similar multimodality in the behaviour of the loop, or in this case, its associated peptide. Solvent accessibility of the simulated peptide reflected a similar pattern of behaviour, with a large population of states with lower solvent accessibility, and rarer occurrences of states with a more accessible peptide surface.…”

mentioning

confidence: 75%

Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein

Zuzic

Samsudin

Shivgan

et al. 2021

Preprint

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The recent global COVID-19 pandemic has prompted a rapid response in terms of vaccine and drug development targeting the viral pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this work, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein, the primary target of vaccine and therapeutics development, based on available structural data and known glycan content. We then used molecular dynamics (MD) simulations to study the system in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets on the S protein surface. We uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in the formation of S protein multimers on the viral surface. A marked multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. Interestingly, the pocket is also the site of the D614G mutation, known to be important for SARS-CoV-2 fitness, and within close proximity to mutations in the novel SARS-CoV-2 strains B.1.1.7 and B.1.1.28, both of which are associated with increased transmissibility and severity of infection. The pocket was present in systems emulating both immature and mature glycosylation states, suggesting its druggability may not be dependent upon the stage of virus maturation. Overall, the predominantly hydrophobic nature of the cryptic pocket, its well conserved surface, and proximity to regions of functional relevance in viral assembly and fitness are all promising indicators of its potential for therapeutic targeting. Our method also successfully recapitulated hydrophobic pockets in the receptor binding domain and N-terminal domain associated with detergent or lipid binding in prior cryo-electron microscopy (cryo-EM) studies. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.

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mentioning

confidence: 75%

Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein

Zuzic

Samsudin

Shivgan

et al. 2021

Preprint

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“…Its rapid turnaround time can be beneficial in urgent public health situations when Ab profiling is necessary for Ab therapeutic development (28). In addition, HDX-MS requires minimal amounts of protein material (ml of the sample at low mM concentrations), which renders it applicable for the characterization of large panels of Ab-Ag complexes (19,29). Furthermore, HDX-MS is unrestricted by the size of the proteins because they are cleaved into peptic peptides prior to deuterium uptake analysis.…”

Section: Hdx-ms Overview: Fundamentals Applications and Advantages As...mentioning

confidence: 99%

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

et al. 2022

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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.

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“…Insights into the allosteric cross-talk between regulatory sites and ligand or protein binding can be further delineated by integrating computational analyses with experimental data from nuclear magnetic resonance (NMR) chemical shift perturbations or hydrogen/deuterium exchange mass spectrometry (HDX-MS). 92,93…”

Section: Braf and Ksr2mentioning

confidence: 99%

Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles

2021

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The bilobal protein kinase-like fold in pseudokinases lack one or more catalytic residues, conserved in canonical protein kinases, and are considered enzymatically deficient. Tertiary structures of pseudokinases reveal that their loops topologically equivalent to activation segments of kinases adopt contracted configurations, which is typically extended in active conformation of kinases. Herein, anisotropic network model based normal mode analysis (NMA) was conducted on 51 active conformation structures of protein kinases and 26 crystal structures of pseudokinases. Our observations indicate that although backbone fluctuation profiles are similar for individual kinase-pseudokinase families, low intensity mean square fluctuations in pseudoactivation segment and other sub-structures impart rigidity to pseudokinases. Analyses of collective motions from functional modes reveal that pseudokinases, compared to active kinases, undergo distinct conformational transitions using the same structural fold. All-atom NMA of protein kinase-pseudokinase pairs from each family, sharing high amino acid sequence identities, yielded distinct community clusters, partitioned by residues exhibiting highly correlated fluctuations. It appears that atomic fluctuations from equivalent activation segments guide community membership and network topologies for respective kinase and pseudokinase. Our findings indicate that such adaptations in backbone and side-chain fluctuations render pseudokinases competent for catalysis-independent roles.

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HDX-MS: An Analytical Tool to Capture Protein Motion in Action

Cited by 45 publications

References 75 publications

Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein

Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein

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

Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles

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