scholarly journals idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments

2018 ◽  
Vol 3 (32) ◽  
pp. 1007
Author(s):  
Jose Borreguero ◽  
Fahima Islam ◽  
Utsab Shrestha ◽  
Loukas Petridis
Keyword(s):  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Angle Scattering

scholarly journals Small-angle scattering and the protein crystallographer: A relationship of ever-increasing interest

2014 ◽  
Vol 36 (1) ◽  
pp. 44-48 ◽  
Author(s):  
David J. Scott
Keyword(s):  
High Resolution ◽  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Structural Information ◽  
Crystallographic Analysis ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Angle Scattering ◽  
Relationship Of

Protein crystallography is one of the great intellectual achievements of the 20th Century, and it continues to open up new vistas of research as scientists are able to visualize in exquisite detail the molecules of Life. It has become increasingly apparent, however, that not all proteins are amenable to crystallographic analysis. These include (but are not confined to) proteins with functional flexible segments, glycoproteins and intrinsically disordered proteins. There are also proteins that, although rigid and folded, refuse to crystallize as an entire full-length construct, and hence high-resolution information has to be pieced together domain by domain. It is into this space that small-angle scattering is increasingly being used as the technique of choice with regard to attainable structural information.

scholarly journals Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Utsab R. Shrestha ◽  
Jeremy C. Smith ◽  
Loukas Petridis
Keyword(s):  
Molecular Dynamics ◽  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Scattering Data ◽  
General Applicability ◽  
Intrinsically Disordered ◽  
Angle Scattering

AbstractMolecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

scholarly journals Small-angle scattering studies of intrinsically disordered proteins and their complexes

2017 ◽  
Vol 42 ◽  
pp. 15-23 ◽  
Author(s):  
Tiago N Cordeiro ◽  
Fátima Herranz-Trillo ◽  
Annika Urbanek ◽  
Alejandro Estaña ◽  
Juan Cortés ◽  
...  
Keyword(s):  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Angle Scattering

scholarly journals Characterizing Intrinsically Disordered Proteins by Small-Angle Neutron Scattering

2011 ◽  
Vol 100 (3) ◽  
pp. 63a
Author(s):  
Christopher B. Stanley ◽  
Laura Grese ◽  
Erica Rowe ◽  
Hugh O'Neill ◽  
Valerie Berthelier
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered
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