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Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example
Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Uppsala University, Sweden; Beijing Institute of Technology, People’s Republic of China; Université de Tours, France; Far Eastern Federal University, Russia.
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Number of Authors: 5
2017 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 95, no 3, 032406Article in journal (Refereed) Published
Abstract [en]

We propose to combine a mean-field approach with all-atom molecular dynamics ( MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques. We argue that a room-temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the C alpha backbone of Myc in a crystallographic heteromer as an initial ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy to describe the C alpha profile with ultrahigh precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground-state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyze the thermal stability of this Glauber attractor using room-temperature molecular dynamics. We identify and scrutinize a particularly stable subset in which the two helical segments of the original multisoliton align in parallel next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal alpha helix, some of which resemble a translating Davydov's Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.

Place, publisher, year, edition, pages
2017. Vol. 95, no 3, 032406
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Physical Sciences Mathematics
Identifiers
URN: urn:nbn:se:su:diva-142674DOI: 10.1103/PhysRevE.95.032406ISI: 000396040800010PubMedID: 28415220OAI: oai:DiVA.org:su-142674DiVA: diva2:1094573
Available from: 2017-05-10 Created: 2017-05-10 Last updated: 2017-05-10Bibliographically approved

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