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Friday, August 08, 2008

How Do Ligands Bind to Proteins?

When glutamine is bound to glutamine-binding protein, the protein is wrapped around the ligand to form a closed binding site that brings more amino acid side chains into contact with the ligand. The unbound protein has a much more open confromation.

The traditional explanations of binding is that the ligand binds to to open form of the protein and causes it to undergo a conformational change creating a closed pocket. The mechanism is called "induced fit." Now, there is evidence that the protein may transiently adopt the closed conformation in the absence of ligand and the ligand binds directly to the closed conformation.

Discount Thoughts reviews a recent paper [Do conformational changes precede or follow binding?]

[Figure credit: Okazaki, K., Takada, S. (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms. Proc. Nat. Acad. Sci. (USA) 105:11182-11187. [DOI: 10.1073/pnas.0802524105]


TheChemistryOfBeer said...

Thanks for the post! I will try to make time to read the paper.

Anonymous said...

A classic chicken and egg dilemma. A pseudo one. It's all about coupled equilibria. Binding a partner shifts equilibrium, simple as that.

Anonymous said...

This was once a favorite subject of mine.

Mari Rose PD said...

Good day! I understand that ligands have electron pairs. Are these electron pairs responsible for the binding of the ligands to biomolelcules like proteins? Or do the ligand & protein just bind according to the traditonal explanation that you mentioned w/o any sharing of electron pairs at all? If so, then the ligand that is binded to the protein still has its electron pairs and are the ones responsible for the binding of a heavy metal ions like Hg, Pb etc to the biomolecule (protein)?