A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein

2019 ◽  
Vol 59 (4) ◽  
pp. 1458-1471 ◽  
Author(s):  
Rafael Ramis ◽  
Joaquín Ortega-Castro ◽  
Rodrigo Casasnovas ◽  
Laura Mariño ◽  
Bartolomé Vilanova ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Intrinsically Disordered Protein ◽  
Coarse Grained ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Coarse Grained Molecular Dynamics

Molecular dynamics simulations of the intrinsically disordered protein amelogenin

2016 ◽  
Vol 35 (8) ◽  
pp. 1813-1823 ◽  
Author(s):  
Alessandra Apicella ◽  
Matteo Marascio ◽  
Vincenzo Colangelo ◽  
Monica Soncini ◽  
Alfonso Gautieri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Intrinsically Disordered Protein ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Dynamics Simulations

scholarly journals Extreme Fuzzy Association of an Intrinsically Disordered Protein with Acidic Membranes

2020 ◽  
Author(s):  
Alan Hicks ◽  
Cristian A. Escobar ◽  
Timothy A. Cross ◽  
Huan-Xiang Zhou
Keyword(s):  
Molecular Dynamics ◽  
Solid State Nmr ◽  
Transmembrane Helix ◽  
Intrinsically Disordered Protein ◽  
Membrane Association ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Disordered Protein ◽  
Membrane Tethering ◽  
Dynamics Simulations

AbstractMany physiological and pathophysiological processes, including Mycobacterium tuberculosis (Mtb) cell division, may involve fuzzy membrane association by proteins via intrinsically disordered regions. The fuzziness is extreme when the conformation and pose of the bound protein and the composition of the proximal lipids are all highly dynamic. Here we tackled the challenge in characterizing the extreme fuzzy membrane association of the disordered, cytoplasmic N-terminal region (NT) of ChiZ, an Mtb divisome protein, by combining solution and solid-state NMR spectroscopy and molecular dynamics simulations. In a typical pose, NT is anchored to acidic membranes by Arg residues in the midsection. Competition for Arg interactions between lipids and acidic residues, all in the first half of NT, makes the second half more prominent in membrane association. This asymmetry is accentuated by membrane tethering of the downstream transmembrane helix. These insights into sequence-interaction relations may serve as a paradigm for understanding fuzzy membrane association.

The regulation mechanism of phosphorylation and mutations in intrinsically disordered protein 4E-BP2

2020 ◽  
Vol 22 (5) ◽  
pp. 2938-2948
Author(s):  
Ke Wang ◽  
Shangbo Ning ◽  
Yue Guo ◽  
Mojie Duan ◽  
Minghui Yang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Intrinsically Disordered Protein ◽  
Regulation Mechanism ◽  
Energy Landscapes ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Free Energy Landscapes

The free energy landscapes of 4E-BP2 and its variants were obtained by replica-exchanged molecular dynamics, which elucidate the regulation mechanism of phosphorylation and mutations on the intrinsically disordered protein.

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