[GPUGrid] New paper: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p

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[GPUGrid] New paper: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p

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The latest scientific publication obtained with your support and computation is here: Herrera-Nieto, P., Pérez, A. & De Fabritiis, G. Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. Sci Rep 10, 12402 (2020). It investigates an open and difficult problem in biology, namely the structure-function relationship of intrinsically disordered proteins (IDP). IDP proteins are involved in many regulatory processes, and yet are difficult to study both experimentally and computationally. The amount of power provided by GPUGRID volunteers came to the rescue, enabling very extensive sampling of p53, an exemplary IDP involved in oncogenic processes. The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for ∼ 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel 𝛽-sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

Source: http://www.gpugrid.net/forum_thread.php?id=5156
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