Hot Spot Occlusion From Bulk Water: A Comprehensive Study of the Complex Between the Lysozyme HEL and the Antibody FVD1.3

J Phys Chem B. 2007 Mar 15;111(10):2697-706. doi: 10.1021/jp067096p. Epub 2007 Feb 22.

Abstract

Alanine scanning of protein-protein interfaces has shown that there are some residues in the protein-protein interfaces, responsible for most of the binding free energy, which are called hot spots. Hot spots tend to exist in densely packed central clusters, and a hypothesis has been proposed that considers that inaccessibility to the solvent must be a necessary condition to define a residue as a binding hot spot. This O-ring hypothesis is mainly based on the analysis of the accessible surface area (ASA) of 23 static, crystallographic structures of protein complexes. It is known, however, that protein flexibility allows for temporary exposures of buried interfacial groups, and even though the ASA provides a general trend of the propensity for hydration, protein/solvent-specific interactions or hydrogen bonding cannot be considered here. Therefore, a microscopic level, atomistic picture of hot spot solvation is needed to support the O-ring hypothesis. In this study, we began by applying a computational alanine-scanning mutagenesis technique, which reproduces the experimental results and allows for decomposing the binding free energy difference in its different energetic factors. Subsequently, we calculated the radial distribution function and residence times of the water molecules near the hot/warm spots to study the importance of the water environment around those energetically important amino acid residues. This study shows that within a flexible, dynamic protein framework, the warm/hot spot residues are, indeed, kept sheltered from the bulk solvent during the whole simulation, which allows a better interacting microenvironment.

MeSH terms

  • Alanine / chemistry
  • Amino Acids / chemistry*
  • Antibodies / chemistry*
  • Binding Sites
  • Computer Simulation*
  • Hydrogen Bonding
  • Models, Molecular*
  • Muramidase / chemistry*
  • Muramidase / genetics
  • Mutagenesis
  • Protein Binding
  • Water / chemistry*

Substances

  • Amino Acids
  • Antibodies
  • Water
  • hen egg lysozyme
  • Muramidase
  • Alanine