Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain

2018 ◽  
Vol 122 (39) ◽  
pp. 9087-9101 ◽  
Author(s):  
Robert I. Cukier
Keyword(s):  
Markov Chain ◽  
Intrinsically Disordered Protein ◽  
Conformational Ensembles ◽  
Intrinsically Disordered ◽  
Disordered Protein

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

scholarly journals Computing, analyzing and comparing the radius of gyration and hydrodynamic radius in conformational ensembles of intrinsically disordered proteins

2019 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Ramon Crehuet ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Hydrodynamic Radius ◽  
Intrinsically Disordered Proteins ◽  
Intrinsically Disordered Protein ◽  
Disordered Proteins ◽  
Radius Of Gyration ◽  
Conformational Ensemble ◽  
Conformational Ensembles ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Nmr Diffusion

AbstractThe level of compaction of an intrinsically disordered protein may affect both its physical and biological properties, and can be probed via different types of biophysical experiments. Small-angle X-ray scattering (SAXS) probe the radius of gyration (Rg) whereas pulsed-field-gradient nuclear magnetic resonance (NMR) diffusion, fluorescence correlation spectroscopy and dynamic light scattering experiments can be used to determine the hydrodynamic radius (Rh). Here we show how to calculate Rg and Rh from a computationally-generated conformational ensemble of an intrinsically disordered protein. We further describe how to use a Bayesian/Maximum Entropy procedure to integrate data from SAXS and NMR diffusion experiments, so as to derive conformational ensembles in agreement with those experiments.

Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain

2018 ◽  
Author(s):  
Sarah Klass ◽  
Matthew J. Smith ◽  
Tahoe Fiala ◽  
Jessica Lee ◽  
Anthony Omole ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Fusion Proteins ◽  
Organic Molecules ◽  
Intrinsically Disordered Protein ◽  
Protein Domain ◽  
Enzymatic Cleavage ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Self Assembling ◽  
Protein Tag

Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications.

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