Journal of Molecular Biology, volume 432, issue 10, pages 3309-3325

Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop

Javier A Jaimes ¹

Nicole M. Andre ¹

Joshua S. Chappie ²

Jean Marc M. Millet ³

G. R. Whittaker ⁴

Hide authors affiliations Show authors affiliations: 4 affiliations

Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , NY , 14853 , USA |

Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA. |

Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78350, Jouy-en-Josas, France. |

⁴

Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA. |

Publication type: Journal Article

Publication date: 2020-05-01

Elsevier

Journal: Journal of Molecular Biology

Quartile SCImago

Quartile WOS

Impact factor: 5.6

ISSN: 00222836, 10898638

DOI: 10.1016/j.jmb.2020.04.009

Copy DOI

Molecular Biology

Structural Biology

Abstract

The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) originally arose as part of a major outbreak of respiratory disease centered on Hubei province, China. It is now a global pandemic and is a major public health concern. Taxonomically, SARS-CoV-2 was shown to be a Betacoronavirus (lineage B) closely related to SARS-CoV and SARS-related bat coronaviruses, and it has been reported to share a common receptor with SARS-CoV (ACE-2). Subsequently, betacoronaviruses from pangolins were identified as close relatives to SARS-CoV-2. Here, we perform structural modeling of the SARS-CoV-2 spike glycoprotein. Our data provide support for the similar receptor utilization between SARS-CoV-2 and SARS-CoV, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV and all other coronaviruses in Betacoronavirus lineage B, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains. We suggest this loop confers fusion activation and entry properties more in line with betacoronaviruses in lineages A and C, and be a key component in the evolution of SARS-CoV-2 with this structural loop affecting virus stability and transmission.

By date By citations

Top-30

Citations by journals

	2 4 6 8 10 12 14
Viruses	Viruses, 13, 3.35% Viruses 13 publications, 3.35%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 9, 2.32% International Journal of Molecular Sciences 9 publications, 2.32%
Frontiers in Immunology	Frontiers in Immunology, 8, 2.06% Frontiers in Immunology 8 publications, 2.06%
Scientific Reports	Scientific Reports, 7, 1.8% Scientific Reports 7 publications, 1.8%
PLoS ONE	PLoS ONE, 7, 1.8% PLoS ONE 7 publications, 1.8%
Vaccines	Vaccines, 6, 1.55% Vaccines 6 publications, 1.55%
Cells	Cells, 5, 1.29% Cells 5 publications, 1.29%
F1000Research	F1000Research, 4, 1.03% F1000Research 4 publications, 1.03%
International Journal of Biological Macromolecules	International Journal of Biological Macromolecules, 4, 1.03% International Journal of Biological Macromolecules 4 publications, 1.03%
iScience	iScience, 4, 1.03% iScience 4 publications, 1.03%
Journal of Virology	Journal of Virology, 4, 1.03% Journal of Virology 4 publications, 1.03%
mBio	mBio, 4, 1.03% mBio 4 publications, 1.03%
PeerJ	PeerJ, 3, 0.77% PeerJ 3 publications, 0.77%
mSystems	mSystems, 3, 0.77% mSystems 3 publications, 0.77%
Frontiers in Genetics	Frontiers in Genetics, 3, 0.77% Frontiers in Genetics 3 publications, 0.77%
Nature Communications	Nature Communications, 3, 0.77% Nature Communications 3 publications, 0.77%
Cell Reports	Cell Reports, 3, 0.77% Cell Reports 3 publications, 0.77%
PLoS Pathogens	PLoS Pathogens, 3, 0.77% PLoS Pathogens 3 publications, 0.77%
Journal of Molecular Graphics and Modelling	Journal of Molecular Graphics and Modelling, 3, 0.77% Journal of Molecular Graphics and Modelling 3 publications, 0.77%
Journal of Medical Virology	Journal of Medical Virology, 3, 0.77% Journal of Medical Virology 3 publications, 0.77%
Journal of Physical Chemistry B	Journal of Physical Chemistry B, 3, 0.77% Journal of Physical Chemistry B 3 publications, 0.77%
Emerging Infectious Diseases	Emerging Infectious Diseases, 2, 0.52% Emerging Infectious Diseases 2 publications, 0.52%
Microorganisms	Microorganisms, 2, 0.52% Microorganisms 2 publications, 0.52%
Pathogens	Pathogens, 2, 0.52% Pathogens 2 publications, 0.52%
Biomedicines	Biomedicines, 2, 0.52% Biomedicines 2 publications, 0.52%
Frontiers in Medical Technology	Frontiers in Medical Technology, 2, 0.52% Frontiers in Medical Technology 2 publications, 0.52%
Frontiers in Veterinary Science	Frontiers in Veterinary Science, 2, 0.52% Frontiers in Veterinary Science 2 publications, 0.52%
Frontiers in Cellular and Infection Microbiology	Frontiers in Cellular and Infection Microbiology, 2, 0.52% Frontiers in Cellular and Infection Microbiology 2 publications, 0.52%
Frontiers in Microbiology	Frontiers in Microbiology, 2, 0.52% Frontiers in Microbiology 2 publications, 0.52%
	2 4 6 8 10 12 14

Citations by publishers

	10 20 30 40 50 60 70
Elsevier	Elsevier, 69, 17.78% Elsevier 69 publications, 17.78%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 64, 16.49% Cold Spring Harbor Laboratory 64 publications, 16.49%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 47, 12.11% Multidisciplinary Digital Publishing Institute (MDPI) 47 publications, 12.11%
Springer Nature	Springer Nature, 38, 9.79% Springer Nature 38 publications, 9.79%
Frontiers Media S.A.	Frontiers Media S.A., 26, 6.7% Frontiers Media S.A. 26 publications, 6.7%
Wiley	Wiley, 20, 5.15% Wiley 20 publications, 5.15%
American Chemical Society (ACS)	American Chemical Society (ACS), 14, 3.61% American Chemical Society (ACS) 14 publications, 3.61%
American Society for Microbiology	American Society for Microbiology, 13, 3.35% American Society for Microbiology 13 publications, 3.35%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 10, 2.58% Public Library of Science (PLoS) 10 publications, 2.58%
Taylor & Francis	Taylor & Francis, 7, 1.8% Taylor & Francis 7 publications, 1.8%
Oxford University Press	Oxford University Press, 7, 1.8% Oxford University Press 7 publications, 1.8%
Bentham Science	Bentham Science, 5, 1.29% Bentham Science 5 publications, 1.29%
F1000 Research	F1000 Research, 4, 1.03% F1000 Research 4 publications, 1.03%
PeerJ	PeerJ, 3, 0.77% PeerJ 3 publications, 0.77%
SAGE	SAGE, 3, 0.77% SAGE 3 publications, 0.77%
Centers for Disease Control and Prevention (CDC)	Centers for Disease Control and Prevention (CDC), 2, 0.52% Centers for Disease Control and Prevention (CDC) 2 publications, 0.52%
Future Medicine	Future Medicine, 2, 0.52% Future Medicine 2 publications, 0.52%
Spandidos Publications	Spandidos Publications, 2, 0.52% Spandidos Publications 2 publications, 0.52%
Wolters Kluwer Health	Wolters Kluwer Health, 2, 0.52% Wolters Kluwer Health 2 publications, 0.52%
World Scientific	World Scientific, 2, 0.52% World Scientific 2 publications, 0.52%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 2, 0.52% American Society for Biochemistry and Molecular Biology 2 publications, 0.52%
IOP Publishing	IOP Publishing, 2, 0.52% IOP Publishing 2 publications, 0.52%
King Saud University	King Saud University, 2, 0.52% King Saud University 2 publications, 0.52%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 2, 0.52% American Association for the Advancement of Science (AAAS) 2 publications, 0.52%
American Society for Clinical Investigation	American Society for Clinical Investigation, 1, 0.26% American Society for Clinical Investigation 1 publication, 0.26%
Canadian Science Publishing	Canadian Science Publishing, 1, 0.26% Canadian Science Publishing 1 publication, 0.26%
European Respiratory Society (ERS)	European Respiratory Society (ERS), 1, 0.26% European Respiratory Society (ERS) 1 publication, 0.26%
IOS Press	IOS Press, 1, 0.26% IOS Press 1 publication, 0.26%
Mary Ann Liebert	Mary Ann Liebert, 1, 0.26% Mary Ann Liebert 1 publication, 0.26%
	10 20 30 40 50 60 70

We do not take into account publications without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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Jaimes J. A. et al. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop // Journal of Molecular Biology. 2020. Vol. 432. No. 10. pp. 3309-3325.

GOST all authors (up to 50) Copy

Jaimes J. A., Andre N. M., Chappie J. S., Millet J. M. M., Whittaker G. R. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop // Journal of Molecular Biology. 2020. Vol. 432. No. 10. pp. 3309-3325.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1016/j.jmb.2020.04.009

UR - https://doi.org/10.1016/j.jmb.2020.04.009

TI - Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop

T2 - Journal of Molecular Biology

AU - Jaimes, Javier A

AU - Andre, Nicole M.

AU - Chappie, Joshua S.

AU - Millet, Jean Marc M.

AU - Whittaker, G. R.

PY - 2020

DA - 2020/05/01 00:00:00

PB - Elsevier

SP - 3309-3325

IS - 10

VL - 432

SN - 0022-2836

SN - 1089-8638

ER -

BibTex |

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BibTex Copy

@article{2020_Jaimes,

author = {Javier A Jaimes and Nicole M. Andre and Joshua S. Chappie and Jean Marc M. Millet and G. R. Whittaker},

title = {Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop},

journal = {Journal of Molecular Biology},

year = {2020},

volume = {432},

publisher = {Elsevier},

month = {may},

url = {https://doi.org/10.1016/j.jmb.2020.04.009},

number = {10},

pages = {3309--3325},

doi = {10.1016/j.jmb.2020.04.009}

}

MLA

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MLA Copy

Jaimes, Javier A., et al. “Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop.” Journal of Molecular Biology, vol. 432, no. 10, May. 2020, pp. 3309-3325. https://doi.org/10.1016/j.jmb.2020.04.009.

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Publisher

Elsevier

Journal

Journal of Molecular Biology

Quartile SCImago

Quartile WOS

Impact factor

5.6

ISSN

00222836 (Print)
10898638 (Electronic)