ArticleBiophysical journal2021
Conformational Ensembles of Antibodies Determine Their Hydrophobicity.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Article
- Article
- Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0].Living journal of computational molecular science · 2025Article
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- Prospects for the computational humanization of antibodies and nanobodies.Frontiers in immunology · 2024Review
- PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.Journal of chemical information and modeling · 2023Article
- Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.Antibodies (Basel, Switzerland) · 2023Review
- Specific peptide conjugation to a therapeutic antibody leads to enhanced therapeutic potency and thermal stability by reduced Fc dynamics.Scientific reports · 2023Article
- Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics.Molecular pharmaceutics · 2023Article
- Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces.Chemical science · 2023Article
- Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures.Journal of computer-aided molecular design · 2022Article
- Comparison of hydrophobicity scales for predicting biophysical properties of antibodies.Frontiers in molecular biosciences · 2022Article
- Advances and Perspectives in the Use of Carbon Nanotubes in Vaccine Development.International journal of nanomedicine · 2021Review
- Germline-Dependent Antibody Paratope States and Pairing Specific VFrontiers in immunology · 2021Article
- Review
- Review
- Article
- Review
- Article
- Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation propensity of antibodies via precalculated scales for the hydrophobicity or aggregation propensity of single amino acids. However, those scales cannot describe the nonadditive effects of a residue's surrounding on its hydrophobicity. Therefore, they are inherently limited in their ability to describe the impact of subtle differences in molecular structure on the overall hydrophobicity. Here, we introduce a physics-based approach to describe hydrophobicity in terms of the hydration free energy using grid inhomogeneous solvation theory (GIST). We apply this method to assess the effects of starting structures, conformational sampling, and protonation states on the hydrophobicity of antibodies. Our results reveal that high-quality starting structures, i.e., crystal structures, are crucial for the prediction of hydrophobicity and that conformational sampling can compensate errors introduced by the starting structure. On the other hand, sampling of protonation states only leads to good results when combined with high-quality structures, whereas it can even be detrimental otherwise. We conclude by pointing out that a single static homology model may not be adequate for predicting hydrophobicity.
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Registered trials
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