Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status
Abstract
:1. Introduction
2. Results
2.1. P Dimer Quality Control by Peptic Digest and Native MS
2.2. Bimodality of Deuterated Peak Distributions Indicates a Lower Deuterated Protein Subpopulation
2.3. Analysis of Glycan Induced Changes in P Dimers of Different Strains by HDX-MS
2.4. Influence of N373 Deamidation on Dynamics and Glycan Binding of GII.4 P Dimers
2.5. MD Simulations
3. Discussion
3.1. Putative Origin of Bimodal Peak Distributions
3.2. Glycan Binding in Different Strains
3.3. The Role of N373 Deamidation
4. Materials and Methods
4.1. Expression and Purification of P Dimers
4.2. Glycan Structures
4.3. Native MS
4.4. HDX-MS
4.5. Peptide and PTM Identification
4.6. HDX Data Analysis
4.7. Experimental Design and Statistical Rationale
4.8. Structure and Sequence Alignment
4.9. Homology Modeling of GII.4 MI001 P Dimer Structure
4.10. MD Simulations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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P Dimer Dataset | Protected Residues in HDX | Fucose Binding Site 1/2 | Fucose Binding Site 3/4 |
---|---|---|---|
GII.10 Vietnam + 100 mM fucose [14] | 311–336 | - | - |
337–364 | N355 (chain A) R356 (chain A) | E359 (chain A) | |
379–399 | D385 (chain A) | W381 (chain A) | |
442–458 | G451 (chain B) Y452 (chain B) | L449 (chain A) | |
GII.10 Vietnam + 10 mM HBGA B trisaccharide [12] | 336–361 | N355 (chain A) R356 (chain A) | - |
379–428 | D385 (chain A) | - | |
440–458 | G451 (chain B) Y452 (chain B) | - | |
483–496 | - | - | |
GII.17 Kawasaki + 100 mM fucose [13,27] | 269–286 | - | - |
333–353 | T348 (chain A) R349 (chain A) | - | |
434–452 | G443 (chain B) Y444 (chain B) | - | |
- | D378 (chain A) | - | |
GII.17 Kawasaki + 10 mM HBGA B trisaccharide [13] | 333–353 | T348 (chain A) R349 (chain A) | - |
- | G443 (chain B) Y444 (chain B) | - | |
GII.4 MI001 + 100 mM fucose | 283–303 | NA | NA |
434–449 | NA | NA | |
GII.4 MI001 + 10 mM HBGA B trisaccharide | 283–298 | NA | NA |
333–353 | NA | NA | |
434–450 | NA | NA | |
GII.4 Saga + 100 mM fucose / GII.4 Saga + 10 mM HBGA B trisaccharide [15,21] | 283–303 | - | - |
no coverage | D374 (chain A) | - | |
434–449 | G443 (chain B) Y444 (chain B) | - | |
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Dülfer, J.; Yan, H.; Brodmerkel, M.N.; Creutznacher, R.; Mallagaray, A.; Peters, T.; Caleman, C.; Marklund, E.G.; Uetrecht, C. Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status. Molecules 2021, 26, 2125. https://doi.org/10.3390/molecules26082125
Dülfer J, Yan H, Brodmerkel MN, Creutznacher R, Mallagaray A, Peters T, Caleman C, Marklund EG, Uetrecht C. Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status. Molecules. 2021; 26(8):2125. https://doi.org/10.3390/molecules26082125
Chicago/Turabian StyleDülfer, Jasmin, Hao Yan, Maxim N. Brodmerkel, Robert Creutznacher, Alvaro Mallagaray, Thomas Peters, Carl Caleman, Erik G. Marklund, and Charlotte Uetrecht. 2021. "Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status" Molecules 26, no. 8: 2125. https://doi.org/10.3390/molecules26082125