Role of electrostatic interactions in PDZ domain ligand recognition

Biochemistry. 2003 Mar 18;42(10):2797-805. doi: 10.1021/bi027061p.

Abstract

PDZ domains are protein-protein interaction modules that normally recognize short C-terminal peptides. The apparent requirement for a ligand with a free terminal carboxylate group has led to the proposal that electrostatic interactions with the terminus play a significant role in recognition. However, this model has been called into question by the more recent finding that PDZ domains can recognize some internal peptide motifs that occur within a specific secondary structure context. Although these motifs bind at the same interface, they lack a terminal charge. Here we have investigated the role of electrostatics in PDZ-mediated recognition in the mouse alpha1-syntrophin PDZ domain by examining the salt dependence of binding to both terminal and internal ligands and the effects of mutating a conserved basic residue previously proposed to play a role in electrostatic recognition. These studies indicate that direct electrostatic interactions with the peptide terminus do not play a significant energetic role in binding. Additional chemical modification studies of the peptide terminus support a model in which steric and hydrogen bonding complementarity play a primary role in recognition specificity. Peptides with a free carboxy terminus, or presented within a specific structural context, can satisfy these requirements.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites / genetics
  • Calcium-Binding Proteins
  • Conserved Sequence / genetics
  • Hydrogen Bonding
  • Ligands
  • Membrane Proteins / chemistry*
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Mice
  • Molecular Sequence Data
  • Muscle Proteins / chemistry*
  • Muscle Proteins / genetics
  • Muscle Proteins / metabolism
  • Mutagenesis, Site-Directed
  • Nerve Tissue Proteins / chemistry
  • Nerve Tissue Proteins / metabolism
  • Osmolar Concentration
  • Peptide Fragments / chemistry
  • Peptide Fragments / genetics
  • Peptide Fragments / metabolism
  • Protein Binding / genetics
  • Protein Interaction Mapping
  • Protein Structure, Tertiary / genetics
  • Sequence Homology, Amino Acid
  • Static Electricity

Substances

  • Calcium-Binding Proteins
  • Ligands
  • Membrane Proteins
  • Muscle Proteins
  • Nerve Tissue Proteins
  • Peptide Fragments
  • postsynaptic density proteins
  • syntrophin alpha1