tetano
Editor, Senior Moderator
Proc Natl Acad Sci U S A
. 2022 Aug 2;119(31):e2205412119.
doi: 10.1073/pnas.2205412119. Epub 2022 Jul 15.
Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes
Halina Mikolajek[SUP] 1 2 [/SUP], Miriam Weckener[SUP] 3 [/SUP], Z Faidon Brotzakis[SUP] 4 [/SUP], Jiandong Huo[SUP] 2 3 5 [/SUP], Evmorfia V Dalietou[SUP] 3 [/SUP], Audrey Le Bas[SUP] 2 3 [/SUP], Pietro Sormanni[SUP] 4 [/SUP], Peter J Harrison[SUP] 1 2 [/SUP], Philip N Ward[SUP] 2 3 [/SUP], Steven Truong[SUP] 4 [/SUP], Lucile Moynie[SUP] 2 3 [/SUP], Daniel K Clare[SUP] 1 [/SUP], Maud Dumoux[SUP] 2 3 [/SUP], Joshua Dormon[SUP] 2 3 [/SUP], Chelsea Norman[SUP] 2 3 [/SUP], Naveed Hussain[SUP] 2 3 5 6 [/SUP], Vinod Vogirala[SUP] 1 [/SUP], Raymond J Owens[SUP] 2 3 5 [/SUP], Michele Vendruscolo[SUP] 4 [/SUP], James H Naismith[SUP] 2 3 5 [/SUP]
Affiliations
Abstract
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.
Keywords: COVID-19; affinity; biophysics; computational tool; electron microscopy.
. 2022 Aug 2;119(31):e2205412119.
doi: 10.1073/pnas.2205412119. Epub 2022 Jul 15.
Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes
Halina Mikolajek[SUP] 1 2 [/SUP], Miriam Weckener[SUP] 3 [/SUP], Z Faidon Brotzakis[SUP] 4 [/SUP], Jiandong Huo[SUP] 2 3 5 [/SUP], Evmorfia V Dalietou[SUP] 3 [/SUP], Audrey Le Bas[SUP] 2 3 [/SUP], Pietro Sormanni[SUP] 4 [/SUP], Peter J Harrison[SUP] 1 2 [/SUP], Philip N Ward[SUP] 2 3 [/SUP], Steven Truong[SUP] 4 [/SUP], Lucile Moynie[SUP] 2 3 [/SUP], Daniel K Clare[SUP] 1 [/SUP], Maud Dumoux[SUP] 2 3 [/SUP], Joshua Dormon[SUP] 2 3 [/SUP], Chelsea Norman[SUP] 2 3 [/SUP], Naveed Hussain[SUP] 2 3 5 6 [/SUP], Vinod Vogirala[SUP] 1 [/SUP], Raymond J Owens[SUP] 2 3 5 [/SUP], Michele Vendruscolo[SUP] 4 [/SUP], James H Naismith[SUP] 2 3 5 [/SUP]
Affiliations
- PMID: 35858383
- DOI: 10.1073/pnas.2205412119
Abstract
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.
Keywords: COVID-19; affinity; biophysics; computational tool; electron microscopy.