scholarly journals High-resolution structural characterization of Noxa, an intrinsically disordered protein, by microsecond molecular dynamics simulations

2015 ◽  
Vol 11 (7) ◽  
pp. 1850-1856 ◽  
Author(s):  
L. Michel Espinoza-Fonseca ◽  
Ameeta Kelekar
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Molecular Dynamics Simulations ◽  
Intrinsically Disordered Protein ◽  
Atomic Level ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Functional Features ◽  
Dynamics Simulations

Microsecond molecular dynamics simulations reveal structural and functional features of Noxa, an intrinsically disordered protein, at atomic-level resolution.

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

Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau

2015 ◽  
Vol 119 (39) ◽  
pp. 12580-12589 ◽  
Author(s):  
Yann Fichou ◽  
Matthias Heyden ◽  
Giuseppe Zaccai ◽  
Martin Weik ◽  
Douglas J. Tobias
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Intrinsically Disordered Protein ◽  
Protein Tau ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Dynamics Simulations

scholarly journals Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pablo Herrera-Nieto ◽  
Adrià Pérez ◽  
Gianni De Fabritiis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Intrinsically Disordered Proteins ◽  
Dynamical Behavior ◽  
Disordered Proteins ◽  
Partially Ordered ◽  
Intrinsically Disordered ◽  
State Models ◽  
Dynamics Simulations

Abstract 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 $$\sim $$ ∼ 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 $$\beta $$ β -sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

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.

scholarly journals Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

2011 ◽  
Vol 405 (2) ◽  
pp. 570-583 ◽  
Author(s):  
Nikolaos G. Sgourakis ◽  
Myrna Merced-Serrano ◽  
Christos Boutsidis ◽  
Petros Drineas ◽  
Zheming Du ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Atomic Level ◽  
Spectral Algorithms ◽  
Dynamics Simulations

scholarly journals Author Correction: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pablo Herrera-Nieto ◽  
Adrià Pérez ◽  
Gianni De Fabritiis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Partially Ordered ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Dynamics Simulations

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