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SLIDE: Quantifying Transmembrane Protein Interface Specificity through Persistence Score and Friction Energy.

Takeshi Sato1

  • 1Kyoto Pharmaceutical University, 5 Misasaginakauchi-cho, Yamashina-ku, Kyoto City , Kyoto 607-8414, Japan.

Journal of Chemical Information and Modeling
|April 20, 2026
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Summary
This summary is machine-generated.

This study introduces SLIDE, a new computational framework to analyze how residue pairs interact and change at protein interfaces over time. It quantifies interface stability and dynamics, revealing specific lipid roles in protein interactions.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Transmembrane protein interfaces are dynamic, with residue contacts constantly forming and breaking.
  • Current methods often measure contact frequency but not the stability or turnover of these residue-pair interactions.

Purpose of the Study:

  • To introduce SLIDE (Stability and Lability Interface Dynamics Evaluator), a novel framework for quantifying residue-pair turnover dynamics in molecular simulations.
  • To differentiate between stable associations and transient interactions at protein interfaces.
  • To analyze the influence of specific lipids on interface dynamics.

Main Methods:

  • Development of the SLIDE framework to analyze molecular dynamics trajectories.
  • Quantification of residue-pair turnover using Persistence Score (Jaccard similarity) and friction energy (E_friction).
  • Lipid-conditioned analysis and Granger causality to assess lipid modulation of interface dynamics.

Main Results:

  • SLIDE quantitatively distinguishes between stable and labile residue-pair interactions at protein interfaces.
  • The Persistence Score and E_friction provide measures of interface stability and rearrangement barriers.
  • Lipid-conditioned analysis revealed specific lipid species' roles in modulating interface dynamics, with Granger causality differentiating active vs. passive roles.
  • Validation on EGFR, Notch, and FGFR3 transmembrane domains confirmed SLIDE's ability to distinguish specific and nonspecific associations.

Conclusions:

  • SLIDE offers a robust method for analyzing the dynamics of residue-pair interactions at protein interfaces.
  • The framework provides insights into the kinetic and thermodynamic properties governing protein-protein interactions in membranes.
  • SLIDE is available as an open-source Python package, facilitating broader application in biophysical and structural biology research.