de Bruyn E, Dorn AE, Zimmermann O, Rossetti G. SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories.
Biology (Basel) 2023;
12:biology12040581. [PMID:
37106781 PMCID:
PMC10135740 DOI:
10.3390/biology12040581]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
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.
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