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Macromolecular diffusion in crowded media beyond the hard-sphere model.

Pablo M Blanco1, Josep Lluís Garcés2, Sergio Madurga1

  • 1Department of Material Science and Physical Chemistry, Barcelona University, 08028 Barcelona, Spain. fmas@ub.edu pmblanco@ub.edu s.madurga@ub.edu and Institute of Theoretical and Computational Chemistry (IQTC), Barcelona University, 08028 Barcelona, Spain.

Soft Matter
|April 6, 2018
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Summary

A new Chain Entanglement Softened Potential (CESP) model improves macromolecular crowding simulations. This model better predicts protein diffusion by accounting for flexibility and entanglement, outperforming hard-core sphere models.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Materials Science

Background:

  • Macromolecular crowding significantly impacts molecular diffusion, a phenomenon not fully captured by simple hard-core sphere models.
  • Understanding diffusion in crowded environments is crucial for biological processes and material design.

Purpose of the Study:

  • To introduce and validate a novel coarse-grained model, the Chain Entanglement Softened Potential (CESP), for simulating diffusion in crowded systems.
  • To account for macromolecular flexibility and chain entanglement, improving upon existing models.

Main Methods:

  • Development of the CESP model featuring a shoulder-shaped interaction potential with a single parameter (Ur) for chain entanglement energy.
  • Implementation of the CESP model within Brownian Dynamics (BD) simulations, incorporating hydrodynamic interactions via Tokuyama mean-field equations.
  • Parametrization of Ur using experimental diffusion data of streptavidin in D50 dextran obstacles.

Main Results:

  • The CESP model demonstrates superior quantitative agreement with experimental long-time diffusion coefficients (Dlong) compared to hard-core sphere models.
  • The model accurately predicts Dlong and the anomalous diffusion exponent (α) for streptavidin diffusion across various dextran obstacle sizes (D10, D400, D700).
  • A new empirical expression was used to derive Dlong, short-time diffusion coefficient (Dshort), and α from BD simulations, capturing the full temporal diffusion evolution.

Conclusions:

  • The CESP model offers a more realistic and predictive approach to simulating diffusion in macromolecularly crowded environments.
  • Accounting for chain entanglement and flexibility is essential for accurate modeling of protein diffusion dynamics.
  • The developed model provides a valuable tool for studying complex biological and material systems.