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Cosolvent Dimethyl Sulfoxide Influences Protein–Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein–Ligand Encounter
[Image: see text] Protein–ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9813907/ https://www.ncbi.nlm.nih.gov/pubmed/36542811 http://dx.doi.org/10.1021/acs.biochem.2c00507 |
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author | Wernersson, Sven Birgersson, Simon Akke, Mikael |
author_facet | Wernersson, Sven Birgersson, Simon Akke, Mikael |
author_sort | Wernersson, Sven |
collection | PubMed |
description | [Image: see text] Protein–ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts of DMSO following titration of solubilized ligands into aqueous protein samples. Therefore, it is critical to establish whether DMSO influences protein–ligand binding. Here, we address the general and indirect effect of DMSO on protein–ligand binding caused by solvent viscosity, which is strongly dependent on the relative concentrations of DMSO and water. As a model system, we studied the binding of a drug-like ligand to the carbohydrate recognition domain of galectin-3 in the presence of variable amounts of DMSO. We used isothermal titration calorimetry to characterize binding thermodynamics and (15)N NMR relaxation to monitor kinetics. The binding enthalpy is not affected, but we observe a subtle trend of increasingly unfavorable entropy of binding, and consequently decreased affinity, with increasing DMSO concentration. The increasing concentration of DMSO results in a reduced association rate of binding, while the dissociation rate is less affected. The observed association rate is inversely proportional to the viscosity of the DMSO–water mixture, as expected from theory, but significantly reduced from the diffusion-controlled limit. By comparing the viscosity dependence of the observed association rate with that of the theoretical diffusion-controlled association rate, we estimate the success rate of productive complex formation following an initial encounter of proteins and ligands, showing that only one out of several hundred binding “attempts” are successful. |
format | Online Article Text |
id | pubmed-9813907 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-98139072023-01-06 Cosolvent Dimethyl Sulfoxide Influences Protein–Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein–Ligand Encounter Wernersson, Sven Birgersson, Simon Akke, Mikael Biochemistry [Image: see text] Protein–ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts of DMSO following titration of solubilized ligands into aqueous protein samples. Therefore, it is critical to establish whether DMSO influences protein–ligand binding. Here, we address the general and indirect effect of DMSO on protein–ligand binding caused by solvent viscosity, which is strongly dependent on the relative concentrations of DMSO and water. As a model system, we studied the binding of a drug-like ligand to the carbohydrate recognition domain of galectin-3 in the presence of variable amounts of DMSO. We used isothermal titration calorimetry to characterize binding thermodynamics and (15)N NMR relaxation to monitor kinetics. The binding enthalpy is not affected, but we observe a subtle trend of increasingly unfavorable entropy of binding, and consequently decreased affinity, with increasing DMSO concentration. The increasing concentration of DMSO results in a reduced association rate of binding, while the dissociation rate is less affected. The observed association rate is inversely proportional to the viscosity of the DMSO–water mixture, as expected from theory, but significantly reduced from the diffusion-controlled limit. By comparing the viscosity dependence of the observed association rate with that of the theoretical diffusion-controlled association rate, we estimate the success rate of productive complex formation following an initial encounter of proteins and ligands, showing that only one out of several hundred binding “attempts” are successful. American Chemical Society 2022-12-21 2023-01-03 /pmc/articles/PMC9813907/ /pubmed/36542811 http://dx.doi.org/10.1021/acs.biochem.2c00507 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Wernersson, Sven Birgersson, Simon Akke, Mikael Cosolvent Dimethyl Sulfoxide Influences Protein–Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein–Ligand Encounter |
title | Cosolvent Dimethyl
Sulfoxide Influences Protein–Ligand
Binding Kinetics via Solvent Viscosity Effects: Revealing the Success
Rate of Complex Formation Following Diffusive Protein–Ligand
Encounter |
title_full | Cosolvent Dimethyl
Sulfoxide Influences Protein–Ligand
Binding Kinetics via Solvent Viscosity Effects: Revealing the Success
Rate of Complex Formation Following Diffusive Protein–Ligand
Encounter |
title_fullStr | Cosolvent Dimethyl
Sulfoxide Influences Protein–Ligand
Binding Kinetics via Solvent Viscosity Effects: Revealing the Success
Rate of Complex Formation Following Diffusive Protein–Ligand
Encounter |
title_full_unstemmed | Cosolvent Dimethyl
Sulfoxide Influences Protein–Ligand
Binding Kinetics via Solvent Viscosity Effects: Revealing the Success
Rate of Complex Formation Following Diffusive Protein–Ligand
Encounter |
title_short | Cosolvent Dimethyl
Sulfoxide Influences Protein–Ligand
Binding Kinetics via Solvent Viscosity Effects: Revealing the Success
Rate of Complex Formation Following Diffusive Protein–Ligand
Encounter |
title_sort | cosolvent dimethyl
sulfoxide influences protein–ligand
binding kinetics via solvent viscosity effects: revealing the success
rate of complex formation following diffusive protein–ligand
encounter |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9813907/ https://www.ncbi.nlm.nih.gov/pubmed/36542811 http://dx.doi.org/10.1021/acs.biochem.2c00507 |
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