Next Article in Journal
Phloroglucinol Derivative Carbomer Hydrogel Accelerates MRSA-Infected Wounds’ Healing
Next Article in Special Issue
Role of the Pangolin in Origin of SARS-CoV-2: An Evolutionary Perspective
Previous Article in Journal
Possible Implications of Bacteriospermia on the Sperm Quality, Oxidative Characteristics, and Seminal Cytokine Network in Normozoospermic Men
Previous Article in Special Issue
Effectiveness of SARS-CoV-2 Vaccines for Short- and Long-Term Immunity: A General Overview for the Pandemic Contrast
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 23
Issue 15
10.3390/ijms23158680
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins

by
Ingrid Guarnetti Prandi
1,
Carla Mavian
2,3,
Emanuela Giombini
4,
Cesare E. M. Gruber
4,
Daniele Pietrucci
1,5,
Stefano Borocci
1,6,
Nabil Abid
7,8,
Andrea R. Beccari
9,
Carmine Talarico
9,* and
Giovanni Chillemi
1,*
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
Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA
3
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
4
Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
5
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies—IBIOM, CNR, 70126 Bari, Italy
6
Institute for Biological Systems—ISB, CNR, Area della Ricerca di Roma 1, SP35d 9, 00010 Montelibretti, Italy
7
Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
8
High Institute of Biotechnology of Monastir, Department of Molecular and Cellular Biology, University of Monastir, Monastir 5000, Tunisia
9
Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2022, 23(15), 8680; https://doi.org/10.3390/ijms23158680
Submission received: 22 June 2022 / Revised: 1 August 2022 / Accepted: 2 August 2022 / Published: 4 August 2022
(This article belongs to the Special Issue Genomic Variation and Epidemiology of SARS-CoV-2)
Browse Figures
Versions Notes

Abstract

The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on the spike (S) glycoprotein, which mediates virus entry into the host cell by binding to the human ACE2 receptor. Herein, we carry out an investigation into the dynamic properties of the S glycoprotein, focusing on the much more transmissible Delta and Omicron variants. Notwithstanding the great number of mutations that have accumulated, particularly in the Omicron S glycoprotein, our data clearly showed the conservation of some structural and dynamic elements, such as the global motion of the receptor binding domain (RBD). However, our studies also revealed structural and dynamic alterations that were concentrated in the aa 627–635 region, on a small region of the receptor binding motif (aa 483–485), and the so-called “fusion-peptide proximal region”. In particular, these last two S regions are known to be involved in the human receptor ACE2 recognition and membrane fusion. Our structural evidence, therefore, is likely involved in the observed different transmissibility of these S mutants. Finally, we highlighted the role of glycans in the increased RBD flexibility of the monomer in the up conformation of Omicron.
Keywords: SARS-CoV-2; COVID-19; spike; variants; molecular dynamics; omicron; delta SARS-CoV-2; COVID-19; spike; variants; molecular dynamics; omicron; delta

Share and Cite

MDPI and ACS Style

Prandi, I.G.; Mavian, C.; Giombini, E.; Gruber, C.E.M.; Pietrucci, D.; Borocci, S.; Abid, N.; Beccari, A.R.; Talarico, C.; Chillemi, G. Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins. Int. J. Mol. Sci. 2022, 23, 8680. https://doi.org/10.3390/ijms23158680

AMA Style

Prandi IG, Mavian C, Giombini E, Gruber CEM, Pietrucci D, Borocci S, Abid N, Beccari AR, Talarico C, Chillemi G. Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins. International Journal of Molecular Sciences. 2022; 23(15):8680. https://doi.org/10.3390/ijms23158680

Chicago/Turabian Style

Prandi, Ingrid Guarnetti, Carla Mavian, Emanuela Giombini, Cesare E. M. Gruber, Daniele Pietrucci, Stefano Borocci, Nabil Abid, Andrea R. Beccari, Carmine Talarico, and Giovanni Chillemi. 2022. "Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins" International Journal of Molecular Sciences 23, no. 15: 8680. https://doi.org/10.3390/ijms23158680

APA Style

Prandi, I. G., Mavian, C., Giombini, E., Gruber, C. E. M., Pietrucci, D., Borocci, S., Abid, N., Beccari, A. R., Talarico, C., & Chillemi, G. (2022). Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins. International Journal of Molecular Sciences, 23(15), 8680. https://doi.org/10.3390/ijms23158680

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop