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Putative staphylococcal enterotoxin possesses two common structural motifs for MHC-II binding
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Abstract
Staphylococcus aureus has become a significant cause of health risks in humankind. Staphylococcal superantigens (SAgs) or enterotoxins are the key virulent factors that can exhibit acute diseases to severe life-threatening conditions. Recent literature reports S. aureus has steadily gained new enterotoxin genes over the past few decades. In spite of current knowledge of the established SAgs, several questions on putative enterotoxins are still remaining unanswered. Keeping that in mind, this study sheds light on a putative enterotoxin SEl26 to characterize its structural and functional properties. In-silico analyses indicate its close relation with the conventional SAgs, especially the zinc-binding SAgs. Additionally, important residues that are vital for the T-cell receptor (TcR) and major histocompatibility complex class II (MHC-II) interaction were predicted and compared with established SAgs. Besides, our biochemical analyses exhibited the binding of this putative enterotoxin with MHC-II, followed by regulating pro-inflammatory and anti-inflammatory cytokines.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581
MEGA11: Molecular Evolutionary Genetics Analysis Version 11
Tamura, K., Stecher, G., & Kumar, S. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab120 · Cited by 22,403
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
Sievers, F., Wilm, A., Dineen, D. G., Gibson, T. J., Karplus, K. J., Li, W., López, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,487
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391
Wiederstein, M., & Sippl, M. J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm290 · Cited by 5,909
Verification of protein structures: Patterns of nonbonded atomic interactions
Colovos, C., & Yeates, T. O. (1993) · Protein Science · doi:10.1002/pro.5560020916 · Cited by 4,618
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
Tian, C., Kasavajhala, K., Belfon, K. A. A., Raguette, L. E., Huang, H., Migues, A. N., Bickel, J. D., Wang, Y., Pincay, J., Wu, Q., et al. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00591 · Cited by 2,672
Paysan‐Lafosse, T., Blum, M., Chuguransky, S., Grego, T., Pinto, B. L., Salazar, G. A., Bileschi, M. L., Bork, P., Bridge, A. J., Colwell, L. J., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac993 · Cited by 2,522
VERIFY3D: assessment of protein models with three-dimensional profiles.
Eisenberg, D., Lüthy, R., & Bowie, J. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)77022-8 · Cited by 2,149
Food Poisoning and Staphylococcus aureus Enterotoxins
Argudín, M. Á., Mendoza, M. C., & Rodicio, M. R. (2010) · Toxins · doi:10.3390/toxins2071751 · Cited by 1,161
Domain enhanced lookup time accelerated BLAST
Boratyn, G. M., Schäffer, A. A., Agarwala, R., Altschul, S. F., Lipman, D. J., & Madden, T. (2012) · Biology Direct · doi:10.1186/1745-6150-7-12 · Cited by 795
Computational Alanine Scanning of Protein-Protein Interfaces
Kortemme, T., Kim, D. E., & Baker, D. A. (2004) · Science s STKE · doi:10.1126/stke.2192004pl2 · Cited by 593
Jardetzky, T. S., Brown, J. H., Gorga, J. C., Stern, L. J., Urban, R. G., Chi, Y., Stauffacher, C. V., Strominger, J. L., & Wiley, D. C. (1994) · Nature · doi:10.1038/368711a0 · Cited by 575
AlphaFill: enriching AlphaFold models with ligands and cofactors
Hekkelman, M. L., de Vries, I., Joosten, R. P., & Perrakis, A. (2023) · Nature Methods · doi:10.1038/s41592-022-01685-y · Cited by 511
The bacterial superantigen and superantigen‐like proteins
Fraser, J. D., & Proft, T. (2008) · Immunological Reviews · doi:10.1111/j.1600-065x.2008.00681.x · Cited by 510
Generalized Born Model with a Simple, Robust Molecular Volume Correction
Mongan, J., Simmerling, C. L., McCammon, J. A., Case, D. A., & Onufriev, A. V. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct600085e · Cited by 443
The Role of Macrophages in Staphylococcus aureus Infection
Pidwill, G. R., Gibson, J. F., Cole, J., Renshaw, S. A., & Foster, S. J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2020.620339 · Cited by 366
THE STRUCTURAL BASIS OF T CELL ACTIVATION BY SUPERANTIGENS
Li, H., Llera, A. S., Malchiodi, E. L., & Mariuzza, R. A. (1999) · Annual Review of Immunology · doi:10.1146/annurev.immunol.17.1.435 · Cited by 324
Superantigens: Bacterial and Viral Proteins that Manipulate the Immune System
Scherer, M. T., Ignatowicz, L., Winslow, G. M., Kappler, J. W., & Marrack, P. (1993) · Annual Review of Cell Biology · doi:10.1146/annurev.cb.09.110193.000533 · Cited by 238
Langley, R. J., Wines, B. D., Willoughby, N., Basu, I., Proft, T., & Fraser, J. D. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.174.5.2926 · Cited by 237
Staphylococcal superantigen-like 5 binds PSGL-1 and inhibits P-selectin–mediated neutrophil rolling
Bestebroer, J., Poppelier, M. J. J. G., Ulfman, L. H., Lenting, P. J., Denis, C. V., van Kessel, K. P. M., van Strijp, J. A. G., & de Haas, C. J. C. (2006) · Blood · doi:10.1182/blood-2006-06-015461 · Cited by 184
Hudson, K., Tiedemann, R. E., Urban, R. G., et al. (1995) · The Journal of Experimental Medicine · doi:10.1084/jem.182.3.711 · Cited by 178
Abrahmsén, L., Dohlsten, M., Segrén, S., Björk, P., Jonsson, E., & Kalland, T. (1995) · The EMBO Journal · doi:10.1002/j.1460-2075.1995.tb07300.x · Cited by 160
P-SHAKE: A quadratically convergent SHAKE in
Gonnet, P. (2006) · Journal of Computational Physics · doi:10.1016/j.jcp.2006.05.032 · Cited by 122
Crystal structure of a superantigen bound to MHC class II displays zinc and peptide dependence
Petersson, K., Håkansson, M., Nilsson, H., et al. (2001) · The EMBO Journal · doi:10.1093/emboj/20.13.3306 · Cited by 121
Tiedemann, R. E., & Fraser, J. D. (1996) · The Journal of Immunology · doi:10.4049/jimmunol.157.9.3958 · Cited by 96
Arcus, V. L., Langley, R. J., Proft, T., Fraser, J. D., & Baker, E. N. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m203914200 · Cited by 83
Sundberg, E. J., Li, Y., & Mariuzza, R. A. (2002) · Current Opinion in Immunology · doi:10.1016/s0952-7915(01)00296-5 · Cited by 82
Petersson, K., Thunnissen, M. M. G. M., Forsberg, G., et al. (2002) · Structure · doi:10.1016/s0969-2126(02)00895-x · Cited by 65
Rödström, K. E. J., Elbing, K., & Lindkvist‐Petersson, K. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1401268 · Cited by 62
Fernández, M. M., Guan, R., Swaminathan, C. P., Malchiodi, E. L., & Mariuzza, R. A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603969200 · Cited by 54
Tuffs, S. W., Goncheva, M. I., Xu, S. X., Craig, H. C., Kasper, K. J., Choi, J., Flannagan, R. S., Kerfoot, S. M., Heinrichs, D. E., & McCormick, J. K. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2115987119 · Cited by 52
Staphylococcal Superantigens Spark Host-Mediated Danger Signals
Krakauer, T., Pradhan, K., & Stiles, B. G. (2016) · Frontiers in Immunology · doi:10.3389/fimmu.2016.00023 · Cited by 48
Isolation of HLA-DR1.(staphylococcal enterotoxin A)2 trimers in solution.
Tiedemann, R. E., Urban, R. G., Strominger, J. L., & Fraser, J. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.26.12156 · Cited by 47
Sundberg, E. J., Andersen, P. S., Schlievert, P. M., Karjalainen, K., & Mariuzza, R. A. (2003) · Structure · doi:10.1016/s0969-2126(03)00187-4 · Cited by 35
The etiology of Kawasaki disease: a superantigen-mediated process
Yeung, R. S. M. (2004) · Progress in Pediatric Cardiology · doi:10.1016/j.ppedcard.2004.08.004 · Cited by 26
Dicks, J. L., Turnbull, J. D., Russell, J. E., Parkhill, J., & Alexander, S. (2021) · Journal of Bacteriology · doi:10.1128/jb.00587-20 · Cited by 26
Two common structural motifs for TCR recognition by staphylococcal enterotoxins
Rödström, K. E. J., Regenthal, P., Bahl, C. D., Ford, A., Baker, D. A., & Lindkvist‐Petersson, K. (2016) · Scientific Reports · doi:10.1038/srep25796 · Cited by 17
Superantigens: Bacterial and Viral Proteins that Manipulate the Immune System
Scherer, M. T. (1993) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.9.1.101 · Cited by 14
Staphylococcal superantigen‐like proteins interact with human MAP kinase signaling protein ERK2
Dutta, D., Mukherjee, D., Mukherjee, I. A., Maiti, T. K., Basak, A., & Das, A. K. (2019) · FEBS Letters · doi:10.1002/1873-3468.13590 · Cited by 8
Self-citationExperimental Arthritis in the Rat Induced by the Superantigen Staphylococcal Enterotoxin A
Gerlach, K., Tomuschat, C., Finke, R., Staege, M. S., Brütting, C., Brandt, J., Jordan, B., Schwesig, R., Rosemeier, A., Delank, K. S., et al. (2017) · Scandinavian Journal of Immunology · doi:10.1111/sji.12530 · Cited by 7
Metadata
- Authors
- Rahman, S., Saha, S., Dasgupta, S. B., & Das, A. K.
- Affiliations
- Indian Institute of Technology Kharagpur (IN)
- Corresponding author
- Das, Amit Kumar
- Venue
- International Journal of Biological Macromolecules
- Publisher
- Elsevier BV
- Published
- 2024-01
- Volume
- 256
- Issue
- Pt 1
- Pages
- 128437
- ISSN
- 0141-8130 (ISSN-L)
- OpenAlex
- W4388997196
- Cited by
- 0
- References
- 43
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- International Journal of Biological Macromolecules (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Funders
- Science and Engineering Research Board (CRG/2020/002622, EMR/2016/002825)
- Indian Institute of Technology Kharagpur
- Topics
- Health Sciences › Medicine › Infectious Diseases › Antimicrobial Resistance in Staphylococcus
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- staphylococcal enterotoxins, staphylococcal superantigens, MHC class II binding, T cell receptor interaction, cytokine regulation, inflammatory cytokines, anti-inflammatory cytokines, protein structural motifs
- MeSH terms
- Amino Acid Sequence, Histocompatibility Antigens Class II, Binding Sites, Enterotoxins, Staphylococcus, Staphylococcus aureus, Superantigens
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