Computational design of the sequence and structure of a protein-binding peptide

J Am Chem Soc. 2011 Mar 30;133(12):4190-2. doi: 10.1021/ja110296z. Epub 2011 Mar 9.

Abstract

The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to Gα(i1). An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 Å.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology*
  • Computer Simulation*
  • Crystallography, X-Ray
  • GTP-Binding Protein alpha Subunits, Gi-Go / chemistry*
  • GTP-Binding Protein alpha Subunits, Gi-Go / metabolism
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Conformation

Substances

  • Peptides
  • GTP-Binding Protein alpha Subunits, Gi-Go