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Literature detail

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.

Tyler N Starr1 Allison J Greaney2,3,4 Sarah K Hilton2,5 Daniel Ellis6,7,8 Katharine H D Crawford2,3,4 Adam S Dingens1 Mary Jane Navarro9 John E Bowen9 M Alejandra Tortorici9 Alexandra C Walls9 Neil P King6,9 David Veesler9 Jesse D Bloom2,3,10
Affiliations 10 institutions
  1. Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  2. Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
  3. Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
  4. Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.
  5. Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  6. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
  7. Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
  8. Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA.
  9. Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  10. Howard Hughes Medical Institute, Seattle, WA 98109, USA. Electronic address: [email protected].
PMID 32841599 2020 Cell eng ppublish
PubMed DOI Browse context

Article

Publication summary

The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and is a major determinant of host range and a dominant target of neutralizing antibodies. Here, we experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity-enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.

ACE2 deep mutational scanning receptor-binding domain SARS-CoV-2 Molecular Docking Simulation Mutation Angiotensin-Converting Enzyme 2 Binding Sites HEK293 Cells Humans Peptidyl-Dipeptidase A Phenotype Protein Binding Protein Folding Saccharomyces cerevisiae Spike Glycoprotein, Coronavirus ACE2 protein, human spike protein, SARS-CoV-2

Structured evidence records

Evidence records

2 total
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.95
Key finding

Deep mutational scanning of the SARS-CoV-2 spike RBD identified amino acid substitutions that enhance ACE2 binding and others that impair folding, indicating molecular adaptation potential in receptor interaction.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

We experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, but a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses.

Genes or proteins
spike glycoprotein; receptor-binding domain; RBD
Receptors
ACE2
Mechanism types
receptor_binding; protein_folding; binding_affinity; host_range
Receptor Usage 1 records
Receptor Usage Extraction confidence 0.95
Key finding

Mutations in the SARS-CoV-2 spike RBD alter its binding affinity to the human ACE2 receptor, with most mutations decreasing ACE2 binding while some enhance affinity.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and we experimentally measure how all amino acid mutations to the RBD affect its affinity for ACE2.

Method
deep mutational scanning; binding assay
Receptors
ACE2