ArticleProceedings of the National Academy of Sciences of the United States of America2022
Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
- Conformational stability and domain-specific structural features of tumor autoantigens regulate autoantibody epitope propensity.Protein science : a publication of the Protein Society · 2026Article
- Construction of Synthetic Probiotic Bacteria for In Situ Delivery of Anti-SARS-CoV-2 Nanobodies.Probiotics and antimicrobial proteins · 2026Article
- Exploring antibody-antigen binding affinity using degree-based topological indices: a graph-theoretical approach.Frontiers in chemistry · 2026Article
- Nanobodies in biomedicine: from molecular characteristics to fabrication and clinical translation.Military Medical Research · 2026Review
- Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.Applied biochemistry and biotechnology · 2025Review
- Sparse networks of conformational fluctuations communicate signals within proteins.bioRxiv : the preprint server for biology · 2025Article
- Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.PLoS computational biology · 2025Article
- Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments.Science advances · 2025Article
- Improving the production and stability of nanobodies.Protein engineering, design & selection : PEDS · 2025Article
- Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions.Nature machine intelligence · 2025Article
- Facilitating and restraining virus infection using cell-attachable soluble viral receptors.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality.Protein science : a publication of the Protein Society · 2024Article
- Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2.Open biology · 2024Article
- Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization.PLoS pathogens · 2023Article
- Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy.Biochemistry · 2023Article
- Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics.FEBS open bio · 2023Article
- Therapeutic applications of nanobodies against SARS-CoV-2 and other viral infections: Current update.International journal of biological macromolecules · 2023Review
- Chemistry towards Biology-Instruct: Snapshot.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
20 authors at 6 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.