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Are hot-spots occluded from water?

Irina Sousa Moreira1, Rui Miguel Ramos, Joao Miguel Martins

  • 1a Faculdade de Ciencias do Porto, Department of Chemistry and Biochemistry , University of Porto , Rua do Campo ALegre 687, Porto , Portugal .

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The O-ring theory suggests protein interaction hotspots are shielded from water. Molecular Dynamics simulations confirm hotspots are indeed protected, though water-mediated interactions remain crucial for binding.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Protein-protein interactions are fundamental to biological processes.
  • These interactions are mediated by specific regions with high binding affinity, termed warm- and hot-spots.
  • The O-ring theory posits that these interaction regions are surrounded by densely packed areas, excluding solvent.

Purpose of the Study:

  • To investigate the validity of the O-ring theory using Molecular Dynamics (MD) simulations.
  • To explore the role of protein conformational flexibility and water interactions in supporting the O-ring theory.
  • To analyze the solvent accessibility and water interactions around warm- and hot-spots.

Main Methods:

  • Molecular Dynamics (MD) simulations were employed to study protein flexibility and water interactions.
  • Analysis included solvent-accessible surface area (SASA) features, radial distribution functions (RDFs), protein-water distances, and water residence times.
  • Comparison of SASA and RDF data for warm-, hot-, and null-spots.

Main Results:

  • Warm- and hot-spots exhibit distinct properties compared to null-spots, being occluded from bulk solvent.
  • Despite occlusion, warm- and hot-spots form significant hydrogen bond (H-bond) networks with water (around 90% occupancy).
  • MD simulations provide strong evidence supporting the O-ring theory, showing hotspots are protected but still engage in water-mediated contacts.

Conclusions:

  • The study provides robust evidence supporting the O-ring theory regarding solvent exclusion around protein interaction hotspots.
  • Hotspots are confirmed to be protected from bulk solvent, aligning with the O-ring theory's predictions.
  • Water-mediated interactions at warm- and hot-spots play a significant role in constructing stable protein-protein interfaces and binding.