Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with the ff99IDPs Force Field

RSC Advances
Xiang GuoHai-Feng Chen

Abstract

The intrinsically disordered protein c-Myb plays a critical role in cellular proliferation and differentiation. Loss of c-myb function results in embryonic lethality due to failure of fetal hepatic hematopoiesis. The conformation dynamics of the intrinsically disordered c-Myb are still unknown. Here, molecular dynamics (MD) simulations with the intrinsically disordered protein force field ff99IDPs were used to study the conformation dynamics. In comparison with ff99SBildn, ff99IDPs can reproduce more diverse disordered conformers of c-Myb. The predicted secondary chemical shift under ff99IDPs is more close to that of experiment data than that under ff99SBildn. Therefore, ff99IDPs can sample native molten globule, native pre-molten globule and native coil conformers for c-Myb. These results are consistent with those of other intrinsically disordered proteins. Kinetic analysis of MD simulations shows that c-Myb folds via a two-state process and indicates that c-Myb folds in the order of tertiary folding and helical folding. The folding nucleus of KEL plays an essential role in stabilizing the folding state with dynamic correlation networks. The influences of solvent models for TIP3P, TIP4P-EW and TIP5P were also investigated and ...Continue Reading

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Citations

Jun 8, 2018·Chemical Biology & Drug Design·Jianzhong ChenWeiliang Zhu
Dec 21, 2019·Journal of Biomolecular Structure & Dynamics·Jianzhong ChenWeiliang Zhu
Jan 1, 2021·The Journal of Physical Chemistry. B·Srinivasa M GopalLars V Schäfer
Aug 3, 2018·Biochimica Et Biophysica Acta. General Subjects·Bin SunPeter M Kekenes-Huskey
Oct 28, 2019·Journal of Chemical Theory and Computation·Yangpeng ZhangHai-Feng Chen

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Methods Mentioned

BETA
NMR

Software Mentioned

Amber Tools
AMBER12
AMBER
ff99SBildn
PyMOL
Cytoscape3
SPARTA
MMTSB
PMEMD
Kclust

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