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Volume 22
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10.3390/ijms22115464
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Article

Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein

by
Stefano Borocci
1,2,
Carmen Cerchia
3,
Alessandro Grottesi
4,
Nico Sanna
1,
Ingrid Guarnetti Prandi
5,
Nabil Abid
6,7,
Andrea R. Beccari
8,
Giovanni Chillemi
1,9,* and
Carmine Talarico
8,*
1
Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
2
Institute for Biological Systems, ISB, CNR, Via Salaria, Km 29.500, Monterotondo, 00015 Rome, Italy
3
Department of Pharmacy, University of Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
4
Department HPC, CINECA, Via dei Tizii 6, 00185 Roma, Italy
5
Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 3, 56124 Pisa, Italy
6
Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
7
High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University of Manouba, BP-66, Ariana-Tunis 2020, Tunisia
8
Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy
9
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
*
Authors to whom correspondence should be addressed.
Academic Editor: Igor Rogozin
Int. J. Mol. Sci. 2021, 22(11), 5464; https://doi.org/10.3390/ijms22115464
Received: 3 May 2021 / Revised: 18 May 2021 / Accepted: 20 May 2021 / Published: 22 May 2021
(This article belongs to the Special Issue Exscalate4CoV: Innovative High Performing Computing (HPC) Strategies to Tackle Pandemic Crisis)
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Abstract

The COVID-19 pandemic is caused by SARS-CoV-2. Currently, most of the research efforts towards the development of vaccines and antibodies against SARS-CoV-2 were mainly focused on the spike (S) protein, which mediates virus entry into the host cell by binding to ACE2. As the virus SARS-CoV-2 continues to spread globally, variants have emerged, characterized by multiple mutations of the S glycoprotein. Herein, we employed microsecond-long molecular dynamics simulations to study the impact of the mutations of the S glycoprotein in SARS-CoV-2 Variant of Concern 202012/01 (B.1.1.7), termed the “UK variant”, in comparison with the wild type, with the aim to decipher the structural basis of the reported increased infectivity and virulence. The simulations provided insights on the different dynamics of UK and wild-type S glycoprotein, regarding in particular the Receptor Binding Domain (RBD). In addition, we investigated the role of glycans in modulating the conformational transitions of the RBD. The overall results showed that the UK mutant experiences higher flexibility in the RBD with respect to wild type; this behavior might be correlated with the increased transmission reported for this variant. Our work also adds useful structural information on antigenic “hotspots” and epitopes targeted by neutralizing antibodies. View Full-Text
Keywords: SARS-CoV-2; COVID-19; spike; variants; molecular dynamics SARS-CoV-2; COVID-19; spike; variants; molecular dynamics
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MDPI and ACS Style

Borocci, S.; Cerchia, C.; Grottesi, A.; Sanna, N.; Prandi, I.G.; Abid, N.; Beccari, A.R.; Chillemi, G.; Talarico, C. Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein. Int. J. Mol. Sci. 2021, 22, 5464. https://doi.org/10.3390/ijms22115464

AMA Style

Borocci S, Cerchia C, Grottesi A, Sanna N, Prandi IG, Abid N, Beccari AR, Chillemi G, Talarico C. Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein. International Journal of Molecular Sciences. 2021; 22(11):5464. https://doi.org/10.3390/ijms22115464

Chicago/Turabian Style

Borocci, Stefano, Carmen Cerchia, Alessandro Grottesi, Nico Sanna, Ingrid Guarnetti Prandi, Nabil Abid, Andrea R. Beccari, Giovanni Chillemi, and Carmine Talarico. 2021. "Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein" International Journal of Molecular Sciences 22, no. 11: 5464. https://doi.org/10.3390/ijms22115464

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