A general computational approach for repeat protein design

J Mol Biol. 2015 Jan 30;427(2):563-75. doi: 10.1016/j.jmb.2014.11.005. Epub 2014 Nov 14.

Abstract

Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds.

Keywords: computational design; de novo design; idealized proteins; repeat proteins; thermodynamic stability.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Ankyrins / chemistry
  • Ankyrins / genetics
  • Armadillo Domain Proteins / chemistry
  • Armadillo Domain Proteins / genetics
  • Biocompatible Materials / chemistry
  • Computer Simulation*
  • Crystallography, X-Ray
  • Microfilament Proteins / chemistry
  • Microfilament Proteins / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Protein Conformation
  • Protein Engineering / methods*
  • Proteins / chemistry*
  • Proteins / genetics
  • Sequence Alignment
  • Sequence Analysis, Protein

Substances

  • Ankyrins
  • Armadillo Domain Proteins
  • Biocompatible Materials
  • Microfilament Proteins
  • Proteins
  • leucine-rich repeat proteins

Associated data

  • PDB/4GMR
  • PDB/4GPM
  • PDB/4HB5
  • PDB/4HQD
  • PDB/4HXT
  • PDB/4PQ8
  • PDB/4PSJ