TY  - JOUR
AU  - de Bruyn, Emile
AU  - Dorn, Anton
AU  - Zimmermann, Olav
AU  - Rossetti, Giulia
TI  - SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories
JO  - Biology
VL  - 12
IS  - 4
SN  - 2079-7737
CY  - Basel
PB  - MDPI
M1  - FZJ-2023-01833
SP  - 581 -
PY  - 2023
AB  - The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion–residue interactions play an important role in the structures and behaviors of IDPs.
LB  - PUB:(DE-HGF)16
C6  - 37106781
UR  - <Go to ISI:>//WOS:000978909400001
DO  - DOI:10.3390/biology12040581
UR  - https://juser.fz-juelich.de/record/1006780
ER  -