Correlation between the binding affinity and the conformational entropy of nanobodies targeting the SARSCoV- 2 spike protein
Creators
- Halina Mikolajek1
- Miriam Weckener2
- Z. Faidon Brotzakis3
- Jiandong Huo4
- Evmorfia V Dalietou5
- Audrey Le Bas5
- Pietro Sormanni3
- Peter J Harrison1
- Philip N Ward4
- Steven Truong3
- Lucile Moynie4
- Daniel Clare1
- Maud Dumoux4
- Josh Dormon4
- Chelsea Norman4
- Naveed Hussain4
- Vinod Vogirala1
- Raymond J Owens4
- Michele Vendruscolo3
- James H Naismith5
- 1. Diamond Light Source, Harwell Campus, Didcot
- 2. The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire, OX11 OQS
- 3. Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW
- 4. PPUK, The Research Complex at Harwell, Harwell Campus, Didcot, Oxfordshire
- 5. The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire
Description
Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from na.ve
libraries for specific targets. However, they often bind too weakly to their targets to be
immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, a
process known as maturation, can deliver useful reagents for different areas of biology and
potentially medicine. Using the receptor binding domain (RBD) of the SARS-CoV-2 spike protein,
we generated closely related nanobodies with micromolar to nanomolar binding affinities. By
analysing the structure-activity relationship using X-ray crystallography, cryo-electron microscopy,
and biophysical methods, we observed that higher conformational entropy losses in the formation
of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we
generated structural ensembles of the different complexes from electron microscopy maps and
correlated the conformational fluctuations with binding affinity. This insight guided the engineering
of a nanobody with high binding affinity for the spike protein.
Notes
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Additional details
Related works
- Is cited by
- Dataset: 10.5281/zenodo.6505382 (DOI)