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Protein binding dynamics are state-dependent. Dimethyl sulfoxide (DMSO) unbinding from FKBP protein is slower from the DMSO-bound state, revealing protein memory effects crucial for drug discovery.

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Area of Science:

  • Biochemistry
  • Molecular Dynamics
  • Structural Biology

Background:

  • Protein-ligand interactions are fundamental to biological processes.
  • Understanding small molecule binding dynamics is key for drug development.
  • FK506-binding protein (FKBP) is a rotamase enzyme involved in cellular signaling.

Purpose of the Study:

  • To investigate the unbinding dynamics of dimethyl sulfoxide (DMSO) from FKBP.
  • To explore the influence of protein conformational states on ligand dissociation rates.
  • To develop a novel methodology for simulating protein relaxation without artificial constraints.

Main Methods:

  • Molecular dynamics simulations were employed to study DMSO unbinding from FKBP.
  • A novel method was introduced to relax the protein without constraints, accommodating faster ligand unbinding than protein relaxation.
  • Two distinct FKBP states (apo-relaxed and holo-relaxed) were simulated.

Main Results:

  • DMSO unbinding from the holo-relaxed FKBP state was an order of magnitude longer than from the apo-relaxed state.
  • Protein relaxation time scales influence ligand unbinding rates, indicating a 'protein memory' effect.
  • Multiple binding modes were observed in the apo-relaxed state, while a single dominant mode was found in the holo-relaxed state.

Conclusions:

  • Ligand unbinding rates are dependent on the protein's conformational state and history.
  • The findings challenge the assumption of rigid protein targets in high-throughput docking.
  • Protein memory effects are significant and must be considered in molecular simulations and drug design.