Protein mechanical unfolding: Importance of non-native interactions.
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.
Kouza
Maksim
M
Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland.
Hu
Chin-Kun
CK
Zung
Hoang
H
Li
Mai Suan
MS
D003198:Computer Simulation; D003285:Contractile Proteins / Q000737:chemistry*; D004023:Dictyostelium / Q000737:chemistry*; D064448:Filamins; D008840:Microfilament Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D015800:Protozoan Proteins / Q000737:chemistry*
D003285:Contractile Proteins; D064448:Filamins; D008840:Microfilament Proteins; D015800:Protozoan Proteins