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]
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