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Ligand and interfacial dynamics in a homodimeric hemoglobin.

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Atomistic simulations reveal intermediate states in dimeric hemoglobin (HbI) dynamics. These findings detail structural changes and water movement during ligand binding transitions.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Dimeric hemoglobin (HbI) from Scapharca inaequivalvis plays a crucial role in oxygen transport.
  • Understanding the dynamic transitions between ligand-bound (R) and ligand-free (T) states is key to elucidating protein function.

Purpose of the Study:

  • To investigate the structural dynamics of HbI in intermediate ligand-binding states.
  • To characterize tertiary structural changes and water dynamics during the R-T transition using atomistic simulations.

Main Methods:

  • Atomistic molecular dynamics simulations were performed on HbI.
  • Simulations covered the microsecond (μs) timescale to capture intermediate states.
  • Analysis focused on tertiary structural changes and water dynamics.

Main Results:

  • Intermediate states were identified between the R and T states of HbI.
  • Key tertiary structural changes include Phe97 side chain rotation, Lys96-heme salt bridge disruption, and Fe-Fe distance alterations.
  • Monomer dynamics were found to be asymmetric on the 100 nanosecond (ns) timescale.
  • Ligand migration pathways were identified between B/G and C/G helices, occurring on the 100 ns timescale.

Conclusions:

  • The observed properties of intermediate states are consistent with experimental data for fully ligand-bound and ligand-free states.
  • The Phe97 side chain rotation occurs on a timescale of 50-100 ns.
  • Asymmetric monomer dynamics and ligand migration pathways provide insights into HbI's functional mechanism.