The methionine-aromatic motif plays a unique role in stabilizing protein structure

J Biol Chem. 2012 Oct 12;287(42):34979-34991. doi: 10.1074/jbc.M112.374504. Epub 2012 Aug 1.

Abstract

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1-1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins.

MeSH terms

  • Amino Acid Motifs
  • HEK293 Cells
  • Humans
  • Jurkat Cells
  • Lymphotoxin-alpha / chemistry*
  • Lymphotoxin-alpha / genetics
  • Lymphotoxin-alpha / metabolism
  • Methionine / chemistry*
  • Methionine / genetics
  • Methionine / metabolism
  • Mutation
  • Protein Stability
  • Protein Structure, Quaternary
  • Receptors, TNF-Related Apoptosis-Inducing Ligand / chemistry*
  • Receptors, TNF-Related Apoptosis-Inducing Ligand / genetics
  • Receptors, TNF-Related Apoptosis-Inducing Ligand / metabolism
  • Receptors, Tumor Necrosis Factor, Type I / chemistry*
  • Receptors, Tumor Necrosis Factor, Type I / genetics
  • Receptors, Tumor Necrosis Factor, Type I / metabolism
  • TNF-Related Apoptosis-Inducing Ligand / chemistry*
  • TNF-Related Apoptosis-Inducing Ligand / genetics
  • TNF-Related Apoptosis-Inducing Ligand / metabolism

Substances

  • Lymphotoxin-alpha
  • Receptors, TNF-Related Apoptosis-Inducing Ligand
  • Receptors, Tumor Necrosis Factor, Type I
  • TNF-Related Apoptosis-Inducing Ligand
  • TNFSF10 protein, human
  • Tnfrsf1a protein, mouse
  • Methionine