Volume 132, Number 2, October 2020
|Number of page(s)||5|
|Section||Interdisciplinary Physics and Related Areas of Science and Technology|
|Published online||22 December 2020|
Network of inter-basin traffic in intrinsically disordered PUMA protein
Institute of Physics, Polish Academy of Sciences -Al. Lotników 32/46, 02-668 Warsaw, Poland
Received: 13 July 2020
Accepted: 23 September 2020
The equilibrium dynamics of the intrinsically disordered proteins is thought to consist of transitions between many basins in the free-energy landscape. This picture can be demonstrated by studying networks defined on the discretized plane: conformational end-to-end distances vs. radii of gyration. The bin sizes are defined by the time scale involved in monitoring the molecular dynamics evolution. We investigate the behavior of PUMA protein that is intrinsically disordered when not bound into a complex. We derive its inter-basin kinetic graph with a coarse-grained model and show that its features are qualitatively consistent with the disconnectivity graphs derived previously for this system by using all-atom simulations.
PACS: 87.15.hp – Conformational changes / 87.14.E- – Proteins / 87.15.A- – Theory, modeling, and computer simulation
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