Abstract
Physicochemical complementarity is commonly believedto be the driving force for molecular binding. The comple-mentarity for example of electrostatic potentials isregarded as the force that draws the ligand from the sol-vent into the binding site [1]. If this hypothesis is true, thesame ligand should encounter complementarity environ-mental properties in all proteins to which it binds. Wehave used our recently published ligand and bindingpocket matching algorithm [2] to test this commonassumption by searching for property distributions thatare similar for the same ligand bound to different pro-teins.
Highlights
Physicochemical complementarity is commonly believed to be the driving force for molecular binding
Hydrophobic parts of the ligand are often confronted with hydrophobic parts of the protein, giving rise to similar hydrophobicity distributions within different binding pockets binding the same ligand
These results demonstrate that binding sites that bind the same ligand can exhibit a large variation of properties by facing different physicochemical forces within different binding sites
Summary
Physicochemical complementarity is commonly believed to be the driving force for molecular binding. The complementarity for example of electrostatic potentials is regarded as the force that draws the ligand from the solvent into the binding site [1]. If this hypothesis is true, the same ligand should encounter complementarity environmental properties in all proteins to which it binds. We have used our recently published ligand and binding pocket matching algorithm [2] to test this common assumption by searching for property distributions that are similar for the same ligand bound to different proteins
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