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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Human phosphofructokinase-1 (PFK1) forms filaments and large-scale assemblies essential for glycolysis spatial organization.
  • The molecular mechanisms driving PFK1 assembly and isoform-specific assembly tendencies are not well understood.

Purpose of the Study:

  • To characterize interactions between PFK1 tetramers using molecular dynamics simulations.
  • To evaluate the accuracy of coarse-grained models in capturing PFK1 assembly dynamics.
  • To propose improvements for coarse-grained models to better represent protein complex interactions.

Main Methods:

  • Combined coarse-grained (Martini, OPEPv7) and all-atom molecular dynamics simulations.
  • Identification of key regions mediating PFK1-PFK1 interactions.
  • Development and testing of enhanced coarse-grained models with additional hydrogen-bonding terms.

Main Results:

  • Identified key regions involved in transient PFK1-PFK1 interactions, including known filament-forming interfaces.
  • Demonstrated that current coarse-grained models lack resolution for specific side-chain interactions critical for filament stability.
  • Showed that enhanced coarse-grained models improve filament stability and accurately reproduce mutation effects.

Conclusions:

  • Current coarse-grained models require refinement to accurately capture specific interactions in protein assemblies like PFK1 filaments.
  • Proposed modifications enhance coarse-grained models, providing a foundation for studying glycolytic enzyme organization.
  • The study offers a strategy to improve coarse-grained modeling of dynamic protein complexes.