Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method

2021 ◽  
Author(s):  
Amin Sagar ◽  
Cy M. Jeffries ◽  
Maxim V. Petoukhov ◽  
Dmitri I. Svergun ◽  
Pau Bernadó
Keyword(s):  
Intrinsically Disordered Protein ◽  
Optimization Method ◽  
Scattering Data ◽  
Optimal Parameters ◽  
X Ray ◽  
Conformational Ensembles ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
X Ray Scattering ◽  
Ensemble Optimization

scholarly journals X-ray structure of the PHF core C-terminus: Insight into the folding of the intrinsically disordered protein tau in Alzheimer's disease

FEBS Letters ◽  
2007 ◽  
Vol 581 (30) ◽  
pp. 5872-5878 ◽  
Author(s):  
Jozef Sevcik ◽  
Rostislav Skrabana ◽  
Radovan Dvorsky ◽  
Natalia Csokova ◽  
Khalid Iqbal ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Intrinsically Disordered Protein ◽  
X Ray ◽  
Protein Tau ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
C Terminus ◽  
Insight Into

scholarly journals Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1080 ◽  
Author(s):  
Alexandre G. de Brevern
Keyword(s):  
Intrinsically Disordered Protein ◽  
Sequence Structure ◽  
Structural Alphabet ◽  
X Ray ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
New Ideas ◽  
Local Conformations ◽  
Continuum Of States ◽  
Disease Pathways

Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function theory. Moreover, IDPs are over-represented in major disease pathways and are now often targeted using small molecules for therapeutic purposes. This has had created a complex continuum from order-that encompasses rigid and flexible regions-to disorder regions; the latter being not accessible through classical crystallographic methodologies. In X-ray structures, the notion of order is dictated by access to resolved atom positions, providing rigidity and flexibility information with low and high experimental B-factors, while disorder is associated with the missing (non-resolved) residues. Nonetheless, some rigid regions can be found in disorder regions. Using ensembles of IDPs, their local conformations were analyzed in the light of a structural alphabet. An entropy index derived from this structural alphabet allowed us to propose a continuum of states from rigidity to flexibility and finally disorder. In this study, the analysis was extended to comparing these results to disorder predictions, underlying a limited correlation, and so opening new ideas to characterize and predict disorder.

scholarly journals Improving the global dimensions of intrinsically disordered proteins in Martini 3

2021 ◽  
Author(s):  
F. Emil Thomasen ◽  
Francesco Pesce ◽  
Mette Ahrensback Roesgaard ◽  
Giulio Tesei ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Saxs Data ◽  
X Ray ◽  
Conformational Ensembles ◽  
Intrinsically Disordered ◽  
X Ray Scattering ◽  
Dynamics Simulations

AbstractCoarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of intrinsically disordered proteins (IDPs). Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of IDPs when compared with small angle X-ray scattering (SAXS) data. Increasing the strength of protein-water interactions favors more expanded conformations, improving agreement with SAXS data and alleviating problems with overestimated IDP-IDP interactions.

Conformational Ensembles of an Intrinsically Disordered Protein Consistent with NMR, SAXS, and Single-Molecule FRET

2020 ◽  
Vol 142 (37) ◽  
pp. 15697-15710 ◽  
Author(s):  
Gregory-Neal W. Gomes ◽  
Mickaël Krzeminski ◽  
Ashley Namini ◽  
Erik W. Martin ◽  
Tanja Mittag ◽  
...  
Keyword(s):  
Single Molecule ◽  
Intrinsically Disordered Protein ◽  
Conformational Ensembles ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Single Molecule Fret
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