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bioRxiv · 10.1101/2024.12.16.628603

Solution AFM imaging and coarse-grained molecular modeling of yeast condensin structural variation coupled to the ATP hydrolysis cycle

Koide, H.·Kodera, N.·Takada, S.·Terakawa, T.
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Abstract

Condensin is a protein complex that regulates chromatin structural changes during mitosis. It varies the molecular conformation through the ATP hydrolysis cycle and extrudes DNA loops into its ring-like structure as a molecular motor. Condensin contains Smc2 and Smc4, in which a coiled-coil arm tethers the hinge and head domains and dimerizes at the hinge. ATPs bind between the heads, induce their engagement, and are hydrolyzed to promote their disengagement. In the previous study, we performed solution atomic force microscopy (AFM) imaging of yeast condensin holo-complex in the presence of ATP and conducted flexible molecular fitting to the AFM image, obtaining the hinge structure with open conformation. However, it has yet to be clarified how the opening/closing of the hinge is coupled to the ATP hydrolysis cycle. In this study, we performed solution AFM imaging in the presence and absence of varying nucleotides, including AMP-PNP, ATP{gamma}S, and ADP. Furthermore, we conducted coarse-grained molecular dynamics simulations of a Smc2/4 heterodimer and selected the molecular structure that best represented each AFM image. Our results suggested that head engagement upon ATP binding is coupled to hinge opening. Also, the results indicated that the N-terminal region of Brn1, one of the accessory subunits, re-associates to the Smc2 head after ADP release. This study deepens our understanding of the conformational variation of yeast condensin driven by the ATP hydrolysis cycle.

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Koide, H., Kodera, N., Takada, S., Terakawa, T.. 2025-01-03. Solution AFM imaging and coarse-grained molecular modeling of yeast condensin structural variation coupled to the ATP hydrolysis cycle. https://doi.org/10.1101/2024.12.16.628603

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