Analyzing and comparing the radius of gyration and hydrodynamic radius in conformational ensembles of intrinsically disordered proteins
Ahmed, M. C.; Crehuet, R.; Lindorff-Larsen, K.
Show abstract
The 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.
Matching journals
The top 1 journal accounts for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
- Free energy perturbation calculations of mutation effects on SARS-CoV-2 RBD::ACE2 binding affinity 95%
- Solution AFM imaging and coarse-grained molecular modeling of yeast condensin structural variation coupled to the ATP hydrolysis cycle 92%
- WASCO: A Wasserstein-based statistical tool to compare conformational ensembles of intrinsically disordered proteins 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.