Abstract
Biological systems rely on the establishment of interactions between biomolecules, which take place in the aqueous environment of the cell. It was already demonstrated that a small set of residues at the interface, Hot-Spots(HS), contributes significantly to the binding free energy. However, these energetic determinants of affinity and specificity are still not fully understood. Moreover, the contribution of water to their HS character is also poorly characterized. In this review, we have focused on the structural data available that support the occlusion of HS from solvent, and therefore the “Oring theory”not only on protein-protein but also on protein-DNA complexes. We also emphasized the use of Solvent Accessible Surface Area (SASA) features in a variety of machine-learning approaches that aim to detect binding HS.
Keywords: Feature-based methods, Hot-spots, O-ring, Solvent accessible surface area, Water, Wet-spots.
Current Topics in Medicinal Chemistry
Title:The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot
Volume: 15 Issue: 20
Author(s): Irina S. Moreira
Affiliation:
Keywords: Feature-based methods, Hot-spots, O-ring, Solvent accessible surface area, Water, Wet-spots.
Abstract: Biological systems rely on the establishment of interactions between biomolecules, which take place in the aqueous environment of the cell. It was already demonstrated that a small set of residues at the interface, Hot-Spots(HS), contributes significantly to the binding free energy. However, these energetic determinants of affinity and specificity are still not fully understood. Moreover, the contribution of water to their HS character is also poorly characterized. In this review, we have focused on the structural data available that support the occlusion of HS from solvent, and therefore the “Oring theory”not only on protein-protein but also on protein-DNA complexes. We also emphasized the use of Solvent Accessible Surface Area (SASA) features in a variety of machine-learning approaches that aim to detect binding HS.
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Cite this article as:
Moreira S. Irina, The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot, Current Topics in Medicinal Chemistry 2015; 15 (20) . https://dx.doi.org/10.2174/1568026615666150519103733
DOI https://dx.doi.org/10.2174/1568026615666150519103733 |
Print ISSN 1568-0266 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4294 |
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