Technical Approach to Investigate Weak Structures in Disordered Protein Domains

Ensemble model for the LCD of hnRNP A1

The Jeschke (D-CHAB, ETHZ) and Allain (D-BIOL, ETHZ) labs developed an approach to probe whether the conformational ensemble of disorderd protein regions deviate from what would be expected from random coil. Their approach was published in Frontiers in Molecular Biosciences in an article entitled "Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions". 

Function of intrinsically disordered proteins may depend on deviation of their conformational ensemble from that of a random coil. Such deviation may be hard to characterize and quantify, if it is weak. We explored the potential of distance distributions between spin labels, as they can be measured by electron paramagnetic resonance techniques, for aiding such characterization. On the example of the intrinsically disordered N-terminal domain 1-267 of fused in sarcoma (FUS) we examined what such distance distributions can and cannot reveal on the random-coil reference state. On the example of the glycine-rich domain 188-320 of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) we studied whether deviation from a random-coil ensemble can be robustly detected with 19 distance distribution restraints. We discuss limitations imposed by ill-posedness of the conversion of primary data to distance distributions and propose overlap of distance distributions as a fit criterion that can tackle this problem. For testing consistency and size sufficiency of the restraint set, we propose jack-knife resampling. At current desktop computers, our approach is expected to be viable for domains up to 150 residues and for between 10 and 50 distance distribution restraints.

Read the Publication in Frotniers in Molecular Biosciences (Open Access)

Website Allain lab

Abstract, figure and title from Ritsch et al. (2021) Frontiers in Biomolecular Sciences published under a CC BY 4.0 license.