SPEADI

SPEADI characterizes time-resolved local chemical environment dynamics in molecular dynamics (MD) simulations using a Time-Resolved Radial Distribution Function (TRRDF) to quantify dynamic ion-residue interactions around Intrinsically Disordered Proteins (IDPs).

Key Features:

• Time-Resolved Radial Distribution Function (TRRDF): Implements TRRDF to provide time-resolved radial distribution analysis rather than trajectory-averaged RDFs.
• Local chemical environment dynamics: Quantifies temporal changes in local chemical environments around specified residues in MD simulations.
• IDP focus: Targets analysis of Intrinsically Disordered Proteins (IDPs) to capture high structural variability and dynamic interactions.
• Ion distribution characterization: Characterizes dynamic distributions of ions and their interactions with protein residues over time.
• Example systems: Applied to Alpha-Synuclein (AS), Humanin (HN), and selected mutants for ion-residue interaction analysis.
• Implementation: Provided as a Python package for computing TRRDF from MD data.

Scientific Applications:

• IDP interaction analysis: Resolves temporal ion-residue interactions in Intrinsically Disordered Proteins to study their dynamic chemical environments.
• Comparative mutant studies: Enables comparison of ion distributions around wild-type and mutant forms such as AS and HN mutants to assess mutation effects.
• Mechanistic insight into function and misfunction: Provides data to investigate how local ion-residue interactions influence protein structure, function, and potential misfunction.

Methodology:

Computes Time-Resolved Radial Distribution Function (TRRDF) from molecular dynamics (MD) trajectories to obtain time-resolved ion distributions and ion-residue interaction profiles.