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Membrane Constriction by Dynamin through GTP-Driven Conformational Changes from Coarse-Grained Molecular Dynamics

Md Iqbal Mahmood1,2, Shintaroh Kubo3, Hiroshi Noguchi4

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Dynamin, a GTPase crucial for membrane fission, undergoes conformational changes during GTP hydrolysis. Simulations reveal these changes indirectly constrict membranes by loosening dynamin rings, advancing our understanding of endocytosis.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Background:

  • Dynamin is a GTPase essential for membrane remodeling and fission during endocytosis.
  • Understanding dynamin's assembly and GTP hydrolysis-induced conformational changes is key to membrane constriction mechanisms.
  • The complexity of dynamin assemblies hinders comprehensive molecular mechanism studies.

Purpose of the Study:

  • To elucidate the chemo-mechanical coupling mechanism of dynamin-mediated membrane constriction.
  • To investigate dynamin's conformational changes on lipid membranes using molecular dynamics simulations.

Main Methods:

  • Coarse-grained molecular dynamics (CG-MD) simulations using the Martini force field.
  • Simulation of dynamin rings on a tubular membrane with controlled length via pressure coupling.
  • Analysis of nucleotide-state-dependent conformational changes.

Main Results:

  • Dynamin ring conformational changes to the GDP state were observed.
  • These changes lead to loosening and expansion of dynamin rings.
  • Indirect membrane constriction in protein-uncoated regions was identified as a consequence.

Conclusions:

  • The study provides insights into the chemo-mechanical coupling of dynamin.
  • Simulations suggest indirect membrane constriction driven by dynamin ring dynamics.
  • This work establishes a foundation for further simulations of dynamin-mediated membrane processes.