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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis.

Benjamin S Cowan1,2, David L Beveridge3,4, Kelly M Thayer1,3,4,2

  • 1Department of Computer Science, Wesleyan University, Middletown, Connecticut06457, United States.

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This study uses network analysis to reveal how signals travel through proteins, focusing on the PDZ domain. Findings illuminate residue dynamics and sampled volumes, advancing the understanding of allosteric signaling mechanisms.

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Area of Science:

  • Protein dynamics and biophysics
  • Computational biology and bioinformatics
  • Molecular mechanisms of allosteric regulation

Background:

  • Allosteric signaling is crucial for protein function, but the precise pathways remain under investigation.
  • Electrostatic interactions are increasingly recognized for their role in long-range allosteric communication.
  • Network approaches offer a powerful framework for analyzing complex protein interactions.

Purpose of the Study:

  • To investigate allosteric signaling dynamics in the PDZ domain using a network-based approach.
  • To analyze per-residue dynamics and the influence of effectors and ligands on signal transmission.
  • To introduce a novel metric for quantifying residue sampling in latent space.

Main Methods:

  • Utilized molecular dynamics (MD) simulations of PDZ domain constructs.
  • Constructed residue interaction networks from MD trajectories.
  • Applied heat kernel analysis plotted onto principal component axes.
  • Introduced a new metric to quantify residue volume sampled in latent space.

Main Results:

  • Detailed per-residue allosteric dynamics were elucidated for PDZ constructs.
  • Network analysis revealed key pathways of signal transmission.
  • The novel metric provided quantitative insights into residue mobility and sampling.
  • Heat kernel analysis visualized the propagation of allosteric effects.

Conclusions:

  • Network approaches effectively capture and visualize allosteric signaling dynamics in proteins.
  • Understanding residue-level dynamics is critical for deciphering allosteric mechanisms.
  • This study provides new quantitative tools and insights into the PDZ allosteric system and the broader field.
  • Findings contribute to the fundamental understanding of how proteins transmit signals over long distances.