Backbone hydration determines the folding signature of amino acid residues

J Am Chem Soc. 2015 Apr 8;137(13):4300-3. doi: 10.1021/jacs.5b00660. Epub 2015 Mar 26.

Abstract

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids*
  • Hydrogen Bonding
  • Molecular Dynamics Simulation
  • Oligopeptides / chemistry*
  • Protein Conformation
  • Protein Folding*
  • Water / chemistry*

Substances

  • Amino Acids
  • Oligopeptides
  • Water