The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of binding. The Structure/Calorimetry of Reported Protein Interactions Online database of published isothermal titration calorimetry studies an...

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Published inJournal of molecular biology Vol. 384; no. 4; pp. 1002 - 1017
Main Authors Olsson, Tjelvar S.G., Williams, Mark A., Pitt, William R., Ladbury, John E.
Format Journal Article
LanguageEnglish
Published England Elsevier Ltd 26.12.2008
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Abstract Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of binding. The Structure/Calorimetry of Reported Protein Interactions Online database of published isothermal titration calorimetry studies and structural information on the interactions between proteins and small-molecule ligands is used here to reveal general thermodynamic properties of protein–ligand interactions and to investigate correlations with changes in solvation. The overwhelming majority of interactions are found to be enthalpically favoured. Synthetic inhibitors and biological ligands form two distinct subpopulations in the data, with the former having greater average affinity due to more favourable entropy changes on binding. The greatest correlation is found between the binding free energy and apolar surface burial upon complex formation. However, the free-energy contribution per unit area buried is only 30–50% of that expected from earlier studies of transfer free energies of small molecules. A simple probability-based estimator for the maximal affinity of a binding site in terms of its apolar surface area is proposed. Polar surface area burial also contributes substantially to affinity but is difficult to express in terms of unit area due to the small variation in the amount of polar surface buried and a tendency for cancellation of its enthalpic and entropic contributions. Conventionally, the contribution of apolar desolvation to affinity is attributed to gain of entropy due to solvent release. Although data presented here are supportive of this notion, because the correlation of entropy change with apolar surface burial is relatively weak, it cannot, on present evidence, be confidently considered to be correct. Further, thermodynamic changes arising from small differences between ligands binding to individual proteins are relatively large and, in general, uncorrelated with changes in solvation, suggesting that trends identified across widely differing proteins are of limited use in explaining or predicting the effects of ligand modifications.
AbstractList Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of binding. The Structure/Calorimetry of Reported Protein Interactions Online database of published isothermal titration calorimetry studies and structural information on the interactions between proteins and small-molecule ligands is used here to reveal general thermodynamic properties of protein–ligand interactions and to investigate correlations with changes in solvation. The overwhelming majority of interactions are found to be enthalpically favoured. Synthetic inhibitors and biological ligands form two distinct subpopulations in the data, with the former having greater average affinity due to more favourable entropy changes on binding. The greatest correlation is found between the binding free energy and apolar surface burial upon complex formation. However, the free-energy contribution per unit area buried is only 30–50% of that expected from earlier studies of transfer free energies of small molecules. A simple probability-based estimator for the maximal affinity of a binding site in terms of its apolar surface area is proposed. Polar surface area burial also contributes substantially to affinity but is difficult to express in terms of unit area due to the small variation in the amount of polar surface buried and a tendency for cancellation of its enthalpic and entropic contributions. Conventionally, the contribution of apolar desolvation to affinity is attributed to gain of entropy due to solvent release. Although data presented here are supportive of this notion, because the correlation of entropy change with apolar surface burial is relatively weak, it cannot, on present evidence, be confidently considered to be correct. Further, thermodynamic changes arising from small differences between ligands binding to individual proteins are relatively large and, in general, uncorrelated with changes in solvation, suggesting that trends identified across widely differing proteins are of limited use in explaining or predicting the effects of ligand modifications.
Author Pitt, William R.
Olsson, Tjelvar S.G.
Williams, Mark A.
Ladbury, John E.
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/18930735$$D View this record in MEDLINE/PubMed
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ISSN 0022-2836
IngestDate Fri Oct 25 22:20:37 EDT 2024
Fri Dec 06 01:42:36 EST 2024
Sat Sep 28 07:47:26 EDT 2024
Fri Feb 23 02:26:31 EST 2024
IsPeerReviewed true
IsScholarly true
Issue 4
Keywords CSA
protein structure
isothermal titration calorimetry
solvent-accessible surface
protein–ligand interaction
thermodynamics
ITC
SCORPIO
SMILES
ASA
PDB
Language English
License https://www.elsevier.com/tdm/userlicense/1.0
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crossref_primary_10_1016_j_jmb_2008_09_073
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  year: 2008
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PublicationTitle Journal of molecular biology
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Snippet Isothermal titration calorimetry is able to provide accurate information on the thermodynamic contributions of enthalpy and entropy changes to free energies of...
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SubjectTerms isothermal titration calorimetry
Ligands
Protein Binding
protein structure
Protein Structure, Quaternary
Proteins - metabolism
protein–ligand interaction
solvent-accessible surface
Thermodynamics
Title The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design
URI https://dx.doi.org/10.1016/j.jmb.2008.09.073
https://www.ncbi.nlm.nih.gov/pubmed/18930735
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