Journal Article

FZJ-2023-01833

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

de Bruyn, E. (First author)FZJ* ; Dorn, A.FZJ* ; Zimmermann, O. (Corresponding author)FZJ* ; Rossetti, G. (Corresponding author)FZJ*

2023
MDPI Basel

This record in other databases:    

Please use a persistent id in citations: http://hdl.handle.net/2128/34336  doi:10.3390/biology12040581

Abstract: 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.

---

Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. Computational Biomedicine (IAS-5)
3. Computational Biomedicine (INM-9)

Research Program(s):

1. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)
2. HDS LEE - Helmholtz School for Data Science in Life, Earth and Energy (HDS LEE) (HDS-LEE-20190612) (HDS-LEE-20190612)

Appears in the scientific report 2023

---

Database coverage:
; ; ; ; BIOSIS Previews ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DOAJ Seal ; Ebsco Academic Search ; IF < 5 ; JCR ; PubMed Central ; SCOPUS ; Web of Science Core Collection ; Zoological Record

---