Journal:Acta Cryst F:S2053230X23006817
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Up to now, studies of Anticalins have mainly provided examples for an induced fit mechanism. Here, we have investigated the crystal structure of Colchicalin, an Anticalin with picomolar affinity and neutralizing activity towards the plant poison colchicine, in its ligand-free state (PDB ID: [[6z6z]]) and compared this with the previously solved structure of its colchicine complex (PDB ID: [[5nkn]]): | Up to now, studies of Anticalins have mainly provided examples for an induced fit mechanism. Here, we have investigated the crystal structure of Colchicalin, an Anticalin with picomolar affinity and neutralizing activity towards the plant poison colchicine, in its ligand-free state (PDB ID: [[6z6z]]) and compared this with the previously solved structure of its colchicine complex (PDB ID: [[5nkn]]): | ||
*<scene name='99/992444/Overallcom/1'>Overall architecture of the previously described Colchicalin Δ4-D6.3 in complex with colchicine</scene> (PDB ID: [[5nkn]]; colchicine is colored in orange). | *<scene name='99/992444/Overallcom/1'>Overall architecture of the previously described Colchicalin Δ4-D6.3 in complex with colchicine</scene> (PDB ID: [[5nkn]]; colchicine is colored in orange). | ||
+ | *<scene name='99/992444/Overallapo/1'>Overall architecture of Colchicalin D6.2 in its apo state</scene> (PDB ID: [[6z6z]]). The marked conformational rearrangement of loop #3 is evident (loops colored magenta and cyan, respectively). | ||
Surprisingly, a superposition of the two Colchicalin structures revealed a largely occluded binding pocket in the unliganded protein. As result of a lid-like movement in particular of the variable loop #3 the side chain of Ile97 at its tip occupies part of the binding site and, thus, would interfere with ligand binding. Conversely, in order to liberate the necessary space for colchicine, a dramatic shift of loop #3 by 11 Å, in combination with a side chain flip of Phe71 on the neighboring loop #2 is required. Consequently, one has to assume that the open conformation of Colchicalin must already exist, even though at a low proportion, in the absence of the ligand to enable its binding, which is then followed by a shift in the equilibrium between the closed and open protein states. Hence, the mechanism of conformational selection appears to adequately describe the mode of ligand binding for this Anticalin. Accordingly, the Colchicalin-colchicine pair provides another example for the analogy between (engineered) lipocalins and antibodies with regard to the mechanism of ligand/antigen recognition. | Surprisingly, a superposition of the two Colchicalin structures revealed a largely occluded binding pocket in the unliganded protein. As result of a lid-like movement in particular of the variable loop #3 the side chain of Ile97 at its tip occupies part of the binding site and, thus, would interfere with ligand binding. Conversely, in order to liberate the necessary space for colchicine, a dramatic shift of loop #3 by 11 Å, in combination with a side chain flip of Phe71 on the neighboring loop #2 is required. Consequently, one has to assume that the open conformation of Colchicalin must already exist, even though at a low proportion, in the absence of the ligand to enable its binding, which is then followed by a shift in the equilibrium between the closed and open protein states. Hence, the mechanism of conformational selection appears to adequately describe the mode of ligand binding for this Anticalin. Accordingly, the Colchicalin-colchicine pair provides another example for the analogy between (engineered) lipocalins and antibodies with regard to the mechanism of ligand/antigen recognition. | ||
Revision as of 15:16, 31 August 2023
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