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Visualizing protein motion in Couette flow by all-atom molecular dynamics.

Erik Walinda1, Daichi Morimoto2, Masahiro Shirakawa2

  • 1Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

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Cellular fluid flow affects biomacromolecules. Molecular dynamics simulations reveal proteins exhibit diffusion and rolling motions, with high shear causing unfolding and aggregation.

Keywords:
Couette flowFluid mechanicsHydrodynamic interactionMolecular dynamicsProtein aggregationRotational diffusionShear flow

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Area of Science:

  • Biophysics
  • Computational Biology
  • Biochemistry

Background:

  • Biomacromolecules function in crowded, viscous cellular environments, unlike dilute in vitro conditions.
  • Cytoplasmic streaming, a form of fluid motion, is common in cells but its impact on biomolecules is understudied.
  • Existing NMR techniques visualize protein aggregation under shear but lack visual detail of protein motion.

Purpose of the Study:

  • To investigate biomacromolecule motion in a shearing flow using molecular dynamics simulations.
  • To elucidate the effects of varying shear stress on protein dynamics, structure, and interactions.
  • To bridge the gap between experimental observations and the visual understanding of shear-induced protein behavior.

Main Methods:

  • Molecular dynamics simulations were employed to model the behavior of three proteins with varying size and shape.
  • A simple shearing flow (Couette flow field) was applied to the simulated system.
  • Analysis focused on protein rotational diffusion, translational motion, structural changes, and inter-molecular interactions.

Main Results:

  • Proteins displayed a combination of random rotational diffusion and shear-flow-induced motion.
  • At low shear stress, random diffusion predominated; at higher stress, a 'rolling motion' along the flow axis emerged.
  • Elevated shear stress induced local and global protein unfolding, and promoted correlated motion, increasing aggregation probability.

Conclusions:

  • Cellular fluid flow significantly influences biomacromolecule dynamics and conformation.
  • Shear stress can induce protein unfolding and enhance intermolecular interactions, potentially leading to aggregation.
  • Integrating computational simulations with in situ shear flow experiments offers a powerful approach to study protein behavior under flow conditions.