Infrared Spectroscopy of SARS-CoV-2 Viral Protein: from Receptor Binding Domain to Spike Protein.
ATR‐IR spectroscopy
MultiFOLD
Spike glycoproteins
hydrophobicity
secondary structure
Journal
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
ISSN: 2198-3844
Titre abrégé: Adv Sci (Weinh)
Pays: Germany
ID NLM: 101664569
Informations de publication
Date de publication:
12 Jul 2024
12 Jul 2024
Historique:
revised:
10
04
2024
received:
23
01
2024
medline:
13
7
2024
pubmed:
13
7
2024
entrez:
13
7
2024
Statut:
aheadofprint
Résumé
Spike (S) glycoprotein is the largest structural protein of SARS-CoV-2 virus and the main one involved in anchoring of the host receptor ACE2 through the receptor binding domain (RBD). S protein secondary structure is of great interest for shedding light on various aspects, from functionality to pathogenesis, finally to spectral fingerprint for the design of optical biosensors. In this paper, the secondary structure of SARS-CoV-2 S protein and its constituting components, namely RBD, S1 and S2 regions, are investigated at serological pH by measuring their amide I infrared absorption bands through Attenuated Total Reflection Infrared (ATR-IR) spectroscopy. Experimental data in combination with MultiFOLD predictions, Define Secondary Structure of Proteins (DSSP) web server and Gravy value calculations, provide a comprehensive understanding of RBD, S1, S2, and S proteins in terms of their secondary structure content, conformational order, and interaction with the solvent.
Identifiants
pubmed: 39001588
doi: 10.1002/advs.202400823
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2400823Subventions
Organisme : NATO Science for Peace and Security Program
ID : G5889
Organisme : Next Generation EU (NGEU) PRIN PNRR 2022 MIUR
ID : P2022NMBAJ
Informations de copyright
© 2024 The Authors. Advanced Science published by Wiley‐VCH GmbH.
Références
D. Cucinotta, M. Vanelli, Acta Biomed. 2020, 91, 157.
G. Campi, M. V. Mazziotti, A. Valletta, G. Ravagnan, A. Marcelli, A. Perali, A. Bianconi, Sci. Rep. 2021, 11, 12412.
A. Bianconi, A. Marcelli, G. Campi, A. Perali, Phys. Biol. 2020, 17, 065006.
B. J. Bosch, R. van der Zee, C. A. M. de Haan, P. J. M. Rottier, J. Virol. 2003, 77, 8801.
W. Tai, H. Lei, X. Zhang, J. Pu, D. Voronin, S. Jiang, Y. Zhou, L. Du, Cell Mol. Immunol. 2020, 17, 613.
Q. Wang, Y. Qiu, J. Y. Li, Z. J. Zhou, C. H. Liao, X. Y. Ge, Virol. Sin. 2020, 35, 337.
Q. Wang, Y. Zhang, L. Wu, S. Niu, C. Song, Z. Zhang, G. Lu, C. Qiao, Y. Hu, K. Y. Yuen, Q. Wang, H. Zhou, J. Yan, J. Qi, Cell 2020, 181, 894.
D. Wrapp, N. Wang, K. S. Corbett, J. A. Goldsmith, C. L. Hsieh, O. Abiona, B. S. Graham, J. S. McLellan, Science 2020, 367, 1260.
L. Casalino, Z. Gaieb, J. A. Goldsmith, C. K. Hjorth, A. C. Dommer, A. M. Harbison, C. A. Fogarty, E. P. Barros, B. C. Taylor, J. S. McLellan, E. Fadda, R. E. Amaro, ACS Cent. Sci. 2020, 6, 1722.
Y. Watanabe, Z. T. Berndsen, J. Raghwani, G. E. Seabright, J. D. Allen, O. G. Pybus, J. S. McLellan, I. A. Wilson, T. A. Bowden, A. B. Ward, M. Crispin, Nat. Commun. 2020, 11, 2688.
M. A. Tortorici, A. C. Walls, Y. Lang, C. Wang, Z. Li, D. Koerhuis, G. J. Boons, B. J. Bosch, F. A. Rey, R. J. de Groot, D. Veesler, Nat. Struct. Mol. Biol. 2019, 26, 481.
A. Shajahan, N. T. Supekar, A. S. Gleinich, P. Azadi, Glycobiology 2020, 30, 981.
K. G. Andersen, A. Rambaut, W. I. Lipkin, E. C. Holmes, R. F. Garry, Nat. Med. 2020, 26, 450.
J. Pallesen, N. Wang, K. S. Corbett, D. Wrapp, R. N. Kirchdoerfer, H. L. Turner, C. A. Cottrell, M. M. Becker, L. Wang, W. Shi, W.‐P. Kong, E. L. Andres, A. N. Kettenbach, M. R. Denison, J. D. Chappell, B. S. Graham, A. B. Ward, J. S. McLellan, Proc. Natl. Acad. Sci. 2017, 114, E7348.
A. C. Walls, M. A. Tortorici, B. Frenz, J. Snijder, W. Li, F. A. Rey, F. Di Maio, B. J. Bosch, D. Veesler, Nat. Struct. Mol. Biol. 2016, 23, 899.
B. Imperiali, S. E. O'Connor, Curr. Opin. Chem. Biol. 1999, 3, 643.
E. Lisowska, Cell. Mol. Life Sci. 2002, 59, 445.
Z. Cournia, T. W. Allen, I. Andricioaei, B. Antonny, D. Baum, G. Brannigan, N. V. Buchete, J. T. Deckman, L. Delemotte, C. del Val, R. Friedman, P. Gkeka, H. C. Hege, J. Hénin, M. A. Kasimova, A. Kolocouris, M. L. Klein, S. Khalid, M. J. Lemieux, N. Lindow, M. Roy, J. Selent, M. Tarek, F. Tofoleanu, S. Vanni, S. Urban, D. J. Wales, J. C. Smith, A. N. Bondar, J. Membrane Biol. 2015, 248, 611.
K. Mathieu, W. Javed, S. Vallet, C. Lesterlin, M. P. Candusso, F. Ding, X. N. Xu, C. Ebel, J. M. Jault, C. Orelle, Sci. Rep. 2019, 9, 2654.
A. Barth, Prog. Biophys. Mol. Biol. 2000, 74, 141.
H. Li, R. Lantz, D. Du, Molecules 2019, 24, 186.
V. Ricciardi, M. Portaccio, G. Perna, M. Lasalvia, V. Capozzi, F. P. Cammarata, P. Pisciotta, G. Petringa, I. Delfino, L. Manti, M. Lepore, Appl. Sci. 2021, 11, 540.
A. D'Arco, M. Di Fabrizio, T. Mancini, R. Mosetti, S. Macis, G. Tranfo, G. Della Ventura, A. Marcelli, M. Petrarca, S. Lupi, Int. J. Mol. Sci. 2023, 24, 9550.
N. Mahanta, S. Sharma, L. G. Sharma, L. M. Pandey, U. S. Dixit, Int. J. Biol. Macromol. 2022, 221, 71.
L. Costa, A. C. Esteves, A. Correia, C. Moreirinha, I. Delgadillo, A. Cunha, M. G. P. S. Neves, M. A. F. Faustino, A. Almeida, J. Virol. Methods 2014, 209, 103.
K. Kim, J. Narayanan, A. Sen, S. Chellam, Environ. Sci. Technol. 2021, 55, 13198.
L. J. McGuffin, N. S. Edmunds, A. G. Genc, S. M. A. Alharbi, B. R. Salehe, R. Adiyaman, Nucleic Acids Res. 2023, 51, W274.
F. Piccirilli, F. Tardani, A. D'Arco, G. Birarda, L. Vaccari, S. Sennato, S. Casciardi, S. Lupi, Nanomaterials 2021, 11, 1103.
H. Yang, S. Yang, J. Kong, A. Dong, S. Yu, Nat. Protoc. 2015, 10, 382.
M. Wolpert, P. Hellwig, Spectrochim. Acta, Part A 2006, 64, 987.
J. P. Lomont, J. S. Ostrander, J.‐J. Ho, M. K. Petti, M. T. Zanni, J. Phys. Chem. B 2017, 121, 8935.
S. D. Moran, M. T. Zanni, J. Phys. Chem. Lett. 2014, 5, 1984.
I. Delfino, M. Portaccio, B. Della Ventura, D. G. Mita, M. Lepore, Mater. Sci. Eng.: C 2013, 33, 304.
W. Kabsch, C. Sander, Biopolymers 1983, 22, 2577.
W. G. Touw, C. Baakman, J. Black, T. A. H. Te Beek;, E. Krieger;, R. P. Joosten, G. Vriend, Nucleic Acids Res. 2015, 43, D364.
A. Fersht, Nat. Rev. Mol. Cell Biol. 2008, 9, 650.
J. Kong, S. Yu, Acta Bioch. Bioph. Sin. 2007, 39, 549.
M. Alrosan, T.‐C. Tan, A. M. Easa, S. Gammoh, M. H. Alu'datt, Crit. Rev. Food Sci. Nutr. 2022, 62, 4036.
P. I. Haris, Biochim. Biophys. Acta Biomembr. 2013, 1828, 2265.
F. Greco, A. P. Falanga, M. Terracciano, C. D'Ambrosio, G. Piccialli, G. Oliviero, G. N. Roviello, N. Borbone, Biomolecules 2022, 12, 1071.
J. Zhang, T. Xiao, Y. Cai, B. Chen, Curr. Opin. Virol. 2021, 50, 173.
M. Letko, A. Marzi, V. Munster, Nat. Microbiol. 2020, 5, 562.
F. Vosough, A. Barth, ACS Chem. Neurosci. 2021, 12, 473.
S. Woutersen, P. Hamm, J. Chem. Phys. 2001, 115, 7737.
A. Barth, C. Zscherp, Q. Rev. Biophys. 2002, 35, 369.
C. Lee, M. Cho, J. Phys. Chem. B 2004, 108, 20397.
H. S. Chung, A. Tokmakoff, J. Phys. Chem. B 2006, 110, 2888.
R. J. Jakobsen, F. M. Wasacz, J. W. Brasch, K. B. Smith, Biopolymers 1986, 25, 639.
E. S. Manas, Z. Getahun, W. W. Wright, W. F. DeGrado, J. M. Vanderkooi, J. Am. Chem. Soc. 2000, 122, 9883.
N. S. Myshakina, Z. Ahmed, S. A. Asher, J. Phys. Chem. B 2008, 112, 11873.
X. Zhou, J. Hu, C. Zhang, G. Zhang, Y. Zhang, Proc. Natl. Acad. Sci. U. S. A. 2019, 116, 15930.
J. T. Pelton, L. R. McLean, Anal. Biochem. 2000, 277, 167.
J. De Meutter, E. Goormaghtigh, Eur. Biophys. J. 2021, 50, 641.
V. Mariani, M. Biasini, A. Barbato, T. Schwede, Bioinformatics 2013, 29, 2722.
Y. Zhang, J. Skolnick, Proteins: Struct., Funct., Bioinf. 2004, 57, 702.