Protein mechanical unfolding: importance of non-native interactions

Details Protein mechanical unfolding: importance of non-native interactions Protein mechanical unfolding: importance of non-native interactions

2009-12-06

arxiv.org/abs/0912.1080v1

J. Chem. Phys., 131, 215103 (2009)

Biology

Quantitative Biology

Biomolecules

27 pages, 15 figures

Scientific paper

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 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 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.

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