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Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Leonid Yurkovetskiy1, Xue Wang2, Kristen E Pascal3
1Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
Abstract:
The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.
Insights
The SARS-CoV-2 D614G spike protein variant increased infectiousness by enhancing viral entry into cells. This variant’s structural changes facilitate ACE2 binding and cell fusion without affecting antibody neutralization.
Area of Science:
- Virology
- Structural Biology
- Molecular Biology
Background:
- The SARS-CoV-2 spike (S) protein variant D614G rapidly became globally dominant.
- Understanding the molecular mechanisms driving this variant's spread is crucial.
Purpose of the Study:
- To investigate the functional and structural basis for the increased infectivity of the SARS-CoV-2 D614G spike protein variant.
- To compare the infectivity of D614G with the ancestral strain across various cell types.
Main Methods:
- Infectivity assays on human lung and colon cells, and ACE2-expressing cells.
- Cryo-electron microscopy of the spike protein trimer.
- Biochemical analysis of ACE2 binding affinity.
Main Results:
- The D614G variant exhibited enhanced infectivity across tested cell models, including those expressing mammalian ACE2 orthologs.
- Cryo-EM revealed that D614G alters spike trimer conformation, favoring ACE2 binding and membrane fusion.
- Reduced ACE2 binding affinity was observed due to a faster dissociation rate, yet infectivity increased.
- Antibody neutralization potency against the receptor-binding domain remained unaffected.
Conclusions:
- The D614G mutation enhances SARS-CoV-2 infectivity by promoting a more open spike conformation conducive to ACE2 binding and cell entry.
- Structural and functional adaptations of the D614G spike protein explain its rapid global dissemination.
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