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TitleCorrelation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 31, Page e2205412119, Year 2022
Publish dateAug 2, 2022
AuthorsHalina Mikolajek / Miriam Weckener / Z Faidon Brotzakis / Jiandong Huo / Evmorfia V Dalietou / Audrey Le Bas / Pietro Sormanni / Peter J Harrison / Philip N Ward / Steven Truong / Lucile Moynie / Daniel K Clare / Maud Dumoux / Joshua Dormon / Chelsea Norman / Naveed Hussain / Vinod Vogirala / Raymond J Owens / Michele Vendruscolo / James H Naismith /
PubMed AbstractCamelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. ...Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron 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 improved affinity for the spike protein.
External linksProc Natl Acad Sci U S A / PubMed:35858383 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.55 - 4.2 Å
Structure data

EMDB-14531, PDB-7z6v:
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11 nanobody complex
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-14539, PDB-7z7x:
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H6 nanobody complex
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-14543, PDB-7z85:
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-B5 nanobody complex
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-14544, PDB-7z86:
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 1Up2Down conformation
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-14575, PDB-7z9q:
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-14576, PDB-7z9r:
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 2Up1Down conformation
Method: EM (single particle) / Resolution: 4.2 Å

PDB-7z1a:
Nanobody H11 and F2 bound to RBD
Method: X-RAY DIFFRACTION / Resolution: 2.59 Å

PDB-7z1b:
Nanobody H11-A10 and F2 bound to RBD
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-7z1c:
Nanobody H11-B5 and H11-F2 bound to RBD
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7z1d:
Nanobody H11-H6 bound to RBD
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7z1e:
Nanobody H11-H4 Q98R H100E bound to RBD
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-GOL:
GLYCEROL

ChemComp-NO3:
NITRATE ION

Source
  • severe acute respiratory syndrome coronavirus 2
  • lama glama (llama)
  • escherichia virus t4
  • tequatrovirus t4
KeywordsANTIVIRAL PROTEIN / spike / nanobody / high affinity / Complex / Spike glycoprotein / nanobody H11 / nanobody H11-H6 / nanobody H11-B5 / nanobody H11-H4 Q98R H100E / nanobody H11-A10

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