Protein mechanical unfolding: Importance of non-native interactions

J Chem Phys. 2009 Dec 7;131(21):215103. doi: 10.1063/1.3272275.

Abstract

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension DeltaR approximately 22 nm in the force-extension curve is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at DeltaR approximately 2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Contractile Proteins / chemistry*
  • Dictyostelium / chemistry*
  • Filamins
  • Microfilament Proteins / chemistry*
  • Molecular Dynamics Simulation
  • Protein Folding
  • Protein Structure, Tertiary
  • Protozoan Proteins / chemistry*

Substances

  • Contractile Proteins
  • Filamins
  • Microfilament Proteins
  • Protozoan Proteins