ArticleProtein science : a publication of the Protein Society2019
Experimental evaluation of single-domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability.
Article in Protein science : a publication of the Protein Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 14 citations in OpenAlex.
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Amino Acids Frequency and Interaction Trends: Comprehensive Analysis of Experimentally Validated Viral Antigen-Antibody Complexes.Molecular biotechnology · 2026Article
- Single-Domain Antibodies as Antibody-Drug Conjugates: From Promise to Practice-A Systematic Review.Cancers · 2024Review
- Understanding the Specific Implications of Amino Acids in the Antibody Development.The protein journal · 2024Review
- General Trends of theInternational journal of molecular sciences · 2023Article
- Application Progress of the Single Domain Antibody in Medicine.International journal of molecular sciences · 2023Review
- Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations.Methods in molecular biology (Clifton, N.J.) · 2023Article
- VInternational journal of molecular sciences · 2022Review
- Structural Insights into the Design of Synthetic Nanobody Libraries.Molecules (Basel, Switzerland) · 2022Review
- Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VScientific reports · 2021Article
- Experimental evaluation of single-domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability.Protein science : a publication of the Protein Society · 2019Article
- Isolation of Novel Fully Human Single-Domain Antibodies Targeting GUCY2C from a Heavy-Chain-Only Transgenic Mouse Platform.Technology in cancer research & treatmentArticle
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently Bekker et al. [Bekker G-J et al. Protein Sci. 2019;28:429-438.] described a computational strategy of applying molecular-dynamics simulations to estimate the relative stabilities of single-domain antibodies, and utilized their method to design changes with the aim of increasing the stability of a single-domain antibody with a known crystal structure. The structure from which they generated potentially stabilizing mutations is an anti-cholera toxin single domain antibody selected from a naïve library which has relatively low thermal stability, reflected by a melting point of 48°C. Their work was purely theoretical, so to examine their predictions, we prepared the parental and predicted stabilizing mutant single domain antibodies and examined their thermal stability, ability to refold and affinity. We found that the mutation that improved stability the most (~7°C) was one which changed an amino acid in CDR1 from an asparagine to an aspartic acid. This change unfortunately was also accompanied by a reduction in affinity. Thus, while their modeling did appear to successfully predict stabilizing mutations, introducing mutations in the binding regions is problematic. Of further interest, the mutations selected via their high temperature simulations, did improve refolding, suggesting that they were successful in stabilizing the structure at high temperatures and thereby decrease aggregation. Our result should permit them to reassess and refine their model and may one day lead to a usefulin silico approach to protein stabilization.
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