Are Hot-Spots Occluded From Water?

J Biomol Struct Dyn. 2014;32(2):186-97. doi: 10.1080/07391102.2012.758598. Epub 2013 Feb 5.

Abstract

Protein-protein interactions are the basis of many biological processes and are governed by focused regions with high binding affinities, the warm- and hot-spots. It was proposed that these regions are surrounded by areas with higher packing density leading to solvent exclusion around them - "the O-ring theory." This important inference still lacks sufficient demonstration. We have used Molecular Dynamics (MD) simulations to investigate the validity of the O-ring theory in the context of the conformational flexibility of the proteins, which is critical for function, in general, and for interaction with water, in particular. The MD results were analyzed for a variety of solvent-accessible surface area (SASA) features, radial distribution functions (RDFs), protein-water distances, and water residence times. The measurement of the average solvent-accessible surface area features for the warm- and hot-spots and the null-spots, as well as data for corresponding RDFs, identify distinct properties for these two sets of residues. Warm- and hot-spots are found to be occluded from the solvent. However, it has to be borne in mind that water-mediated interactions have significant power to construct an extensive and strongly bonded interface. We observed that warm- and hot-spots tend to form hydrogen bond (H-bond) networks with water molecules that have an occupancy around 90%. This study provides strong evidence in support of the O-ring theory and the results show that hot-spots are indeed protected from the bulk solvent. Nevertheless, the warm- and hot-spots still make water-mediated contacts, which are also important for protein-protein binding.

MeSH terms

  • Binding Sites
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Binding*
  • Protein Conformation
  • Protein Interaction Mapping / methods*
  • Protein Structure, Quaternary
  • Proteins / chemistry*
  • Proteins / metabolism
  • Solvents / chemistry*
  • Water / chemistry*
  • Water / metabolism

Substances

  • Proteins
  • Solvents
  • Water